diff --git a/.gitignore b/.gitignore index 65dca7e9..5e4e63e6 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,17 @@ imports/*.tmp mp-edit.owl hp-edit.owl /obo-grep.pl +src/old +src/ontology/mirror +src/ontology/mirror/* +src/ontology/upheno.obo +src/ontology/upheno.owl +semantic.cache +bin/ +src/ontology/seed.txt +src/ontology/target/ +src/ontology/dosdp-tools.log +src/patterns/imports/seed_sorted.txt +src/ontology/ed_definitions_merged.owl +src/ontology/patterns +.DS_Store diff --git a/src/metadata/README.md b/src/metadata/README.md new file mode 100644 index 00000000..5a76155e --- /dev/null +++ b/src/metadata/README.md @@ -0,0 +1,23 @@ +Metadata files for the OBO Library + + * [upheno.yml](upheno.yml) + * Determines how your purl.obolibrary.org/obo/upheno/ redirects will be handled + * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config + * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config) + * Paste in the contents of [upheno.yml](upheno.yml) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + * [upheno.md](upheno.md) + * Determines how your metadata is shown on OBO Library, OLS and AberOWL + * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology + * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology) + * Paste in the contents of [upheno.md](upheno.md) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + +For more background see: + + * http://obofoundry.org/ + * http://obofoundry.org/faq/how-do-i-edit-metadata.html diff --git a/src/metadata/upheno.md b/src/metadata/upheno.md new file mode 100644 index 00000000..1e7400ee --- /dev/null +++ b/src/metadata/upheno.md @@ -0,0 +1,36 @@ +--- +layout: ontology_detail +id: upheno +title: upheno +jobs: + - id: https://travis-ci.org/obophenotype/upheno + type: travis-ci +build: + checkout: git clone https://github.com/obophenotype/upheno.git + system: git + path: "." +contact: + email: cjmungall@lbl.gov + label: Chris Mungall +description: upheno is an ontology... +domain: stuff +homepage: https://github.com/obophenotype/upheno +products: + - id: upheno.owl + - id: upheno.obo +dependencies: + - id: iao + - id: go + - id: ro + - id: pato + - id: bfo + - id: chebi + - id: cl + - id: uberon +tracker: https://github.com/obophenotype/upheno/issues +license: + url: http://creativecommons.org/licenses/by/3.0/ + label: CC-BY +--- + +Enter a detailed description of your ontology here diff --git a/src/metadata/upheno.yml b/src/metadata/upheno.yml new file mode 100644 index 00000000..4db81ac6 --- /dev/null +++ b/src/metadata/upheno.yml @@ -0,0 +1,27 @@ +# PURL configuration for http://purl.obolibrary.org/obo/upheno + +idspace: UPHENO +base_url: /obo/upheno + +products: +- upheno.owl: https://raw.githubusercontent.com/obophenotype/upheno/master/upheno.owl +- upheno.obo: https://raw.githubusercontent.com/obophenotype/upheno/master/upheno.obo + +term_browser: ontobee +example_terms: +- UPHENO_0000000 + +entries: + +- prefix: /releases/ + replacement: https://raw.githubusercontent.com/obophenotype/upheno/v + +- prefix: /tracker/ + replacement: https://github.com/obophenotype/upheno/issues + +- prefix: /about/ + replacement: http://www.ontobee.org/ontology/UPHENO?iri=http://purl.obolibrary.org/obo/ + +## generic fall-through, serve direct from github by default +- prefix: / + replacement: https://raw.githubusercontent.com/obophenotype/upheno/master/ diff --git a/src/ontology/Dockerfile b/src/ontology/Dockerfile new file mode 100644 index 00000000..661e66df --- /dev/null +++ b/src/ontology/Dockerfile @@ -0,0 +1,3 @@ +FROM cmungall/osk + +CMD make test diff --git a/src/ontology/Makefile b/src/ontology/Makefile new file mode 100644 index 00000000..7e403d8a --- /dev/null +++ b/src/ontology/Makefile @@ -0,0 +1,237 @@ +# ---------------------------------------- +# Makefile for upheno +# Generated using ontology-starter-kit +# ---------------------------------------- +# + +# ---------------------------------------- +# Standard Constants +# ---------------------------------------- +# these can be overwritten on the command line + +OBO=http://purl.obolibrary.org/obo +ONT=upheno +BASE=$(OBO)/$(ONT) +SRC=$(ONT)-edit.owl +RELEASEDIR=../.. +ROBOT= robot +OWLTOOLS= owltools +USECAT= --use-catalog +SPARQLDIR = ../sparql +DOSDP_SCHEMA=http:// # change to PURL when ready. +PATTERN_TESTER=simple_pattern_tester.py +DOSDPT=dosdp-tools +TARGET=target +IMPORTS = iao go ro pato bfo chebi cl uberon + + +# ---------------------------------------- +# Top-level targets +# ---------------------------------------- + +all: patterns all_imports sparql_test $(ONT).owl $(ONT).obo + echo 'Release files created successfully.' +test: sparql_test all +prepare_release: all + cp $(ONT).owl $(ONT).obo $(RELEASEDIR) &&\ + mkdir -p $(RELEASEDIR)/imports &&\ + cp imports/*.owl $(RELEASEDIR)/imports &&\ + cp imports/*.obo $(RELEASEDIR)/imports &&\ + git add $(RELEASEDIR)/imports/*.obo &&\ + git add $(RELEASEDIR)/imports/*.owl &&\ + (test -f subsets/*owl && cp subsets/* $(RELEASEDIR)/subsets && git add $(RELEASEDIR)/subsets/* || echo "no subsets") &&\ + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github" + +# ---------------------------------------- +# Main release targets +# ---------------------------------------- + +# by default we use Elk to perform a reason-relax-reduce chain +# after that we annotate the ontology with the release versionInfo +$(ONT).owl: $(SRC) + $(ROBOT) reason -i $< -r ELK -e none relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ &&\ + echo "$(ONT).owl successfully created." + +$(ONT).obo: $(ONT).owl + $(ROBOT) convert --check false -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ &&\ + echo "$(ONT).obo successfully created." + +# ---------------------------------------- +# Import modules +# ---------------------------------------- +# Most ontologies are modularly constructed using portions of other ontologies +# These live in the imports/ folder +# These can be regenerated with make all_imports + +IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) $(patsubst %, imports/%_import.obo,$(IMPORTS)) $(patsubst %, imports/%_terms.txt,$(IMPORTS)) + +# generate seed with all referenced entities + +ed_definitions_merged.owl: $(SRC) ../patterns/definitions.owl + $(ROBOT) merge -i $(SRC) -i ../patterns/definitions.owl -o $@ + +seed.txt: ed_definitions_merged.owl + $(ROBOT) query -f csv -i $< --query ../sparql/terms.sparql $@ + +# Generate terms.txt for each import. # Assume OBO-style Possibly hacky step? +# Should be able to drop this if robot can just take a big messy list of terms as input. + +imports/%_terms_combined.txt: seed.txt + cat $< imports/$*_terms.txt | sort | uniq > $@ + +# Make this target to regenerate ALL +all_imports: $(IMPORTS_OWL) + +# Use ROBOT, driven entirely by terms lists NOT from source ontology +imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt + $(ROBOT) extract -i $< -T imports/$*_terms_combined.txt --method BOT -O $(BASE)/$@ -o $@ +.PRECIOUS: imports/%_import.owl + +# convert imports to obo. +# this can be useful for spot-checks and diffs. +# we set strict mode to false by default. For discussion see https://github.com/owlcs/owlapi/issues/752 +imports/%_import.obo: imports/%_import.owl + $(ROBOT) convert --check false -i $< -f obo -o $@.tmp && mv $@.tmp $@ + +# clone remote ontology locally, perfoming some excision of relations and annotations +mirror/%.owl: + $(ROBOT) convert -I $(OBO)/$*.owl -o $@ +.PRECIOUS: mirror/%.owl + +# ---------------------------------------- +# Release +# ---------------------------------------- +# copy from staging area (this directory) to top-level +release: $(ONT).owl $(ONT).obo + cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports + +# ---------------------------------------- +# Sparql queries: Q/C +# ---------------------------------------- + +# these live in the ../sparql directory, and have suffix -violation.sparql +# adding the name here will make the violation check live +VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels + +# Only needed until robot supports catalogs + + + +# run all violation checks +VQUERIES = $(foreach V,$(VCHECKS),$(SPARQLDIR)/$V-violation.sparql) +sparql_test: $(SRC) + robot verify --catalog catalog-v001.xml -i $< --queries $(VQUERIES) -O reports/ + +# ---------------------------------------- +# Sparql queries: Reports + # ---------------------------------------- + +REPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms +REPORT_ARGS = $(foreach V,$(REPORTS),-s $(SPARQLDIR)/$V.sparql reports/$V.tsv) +all_reports: $(SRC) + robot query -f tsv -i $< $(REPORT_ARGS) + +# ---------------------------------------- +# Docker (experimental) +# ---------------------------------------- +IM=build-$(ONT) +build-docker: + docker build -t $(ONT) . + +# ---------------------------------------- +# Patterns (experimental) +# ---------------------------------------- + +# Test patterns for schema compliance: + + +# TODO - move declarations like this to top +IMS=$(TARGET)/intermediates + +#PATTERN_IMPORTS = ../patterns/pattern.owl $(patsubst %, ../patterns/imports/%_import.owl,$(IMPORTS)) + + +# Better to make this an intermediate & merge with pattern.owl file having correct iri and import statements - configured by make + + +# ---------------------------------------- +# Main command to generate the pattern ontology and the definitions +# ---------------------------------------- +# The pattern.owl ontology contains the OWL versions of all the patterns currently in the patterns directory +DOSDP_TEMP=$(IMS)/dosdp +DOSDP_TEMP_PATTERN=$(DOSDP_TEMP)/patterns +DOSDP_TEMP_PATTERN_MANUAL=$(DOSDP_TEMP_PATTERN)/manual +DOSDP_TEMP_PATTERN_AUTO=$(DOSDP_TEMP_PATTERN)/auto +DOSDP_TEMP_TERMS=$(DOSDP_TEMP)/terms +DOSDP_TEMP_ONTOLOGIES=$(DOSDP_TEMP)/ontologies + +.PHONY patterns: ../patterns/pattern.owl ../patterns/definitions.owl + +pattern_clean: + rm -r $(DOSDP_TEMP) + +$(DOSDP_TEMP): + mkdir -p $@ + +$(DOSDP_TEMP_PATTERN): + mkdir -p $@ + +$(DOSDP_TEMP_TERMS): + mkdir -p $@ + +$(DOSDP_TEMP_ONTOLOGIES): + mkdir -p $@ + +$(DOSDP_TEMP_PATTERN_MANUAL): $(DOSDP_TEMP_PATTERN) + mkdir -p $@ + +$(DOSDP_TEMP_PATTERN_AUTO): $(DOSDP_TEMP_PATTERN) + mkdir -p $@ + +# ---------------------------------------- +# Build pattern.owl +# ---------------------------------------- +# The pattern.owl ontology contains the OWL versions of all the patterns currently in the patterns directory + +../patterns/pattern.owl: pattern_schema_checks + $(DOSDPT) prototype --obo-prefixes --template=../patterns/dosdp-patterns --outfile=$@ + +pattern_schema_checks: + simple_pattern_tester.py ../patterns/dosdp-patterns/ # 2>&1 | tee $@ + +# ---------------------------------------- +# Build definitions.owl +# ---------------------------------------- +# The following target will create a merged version of all imports indicated as project import dependencies (including the edit file itself), and then extract a module based +# on the entities used in the TSV files +individual_patterns_manual := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_MANUAL)/%.ofn, $(notdir $(wildcard ../patterns/data/manual/*.tsv))) +individual_patterns_auto := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_AUTO)/%.ofn, $(notdir $(wildcard ../patterns/data/auto/*.tsv))) +pattern_term_lists_auto := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_AUTO)/%.txt, $(notdir $(wildcard ../patterns/data/auto/*.tsv))) +pattern_term_lists_manual := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_MANUAL)/%.txt, $(notdir $(wildcard ../patterns/data/manual/*.tsv))) + +../patterns/definitions.owl: $(DOSDP_TEMP_PATTERN_MANUAL) $(individual_patterns_manual) $(individual_patterns_auto) + $(ROBOT) merge $(addprefix -i , $(individual_patterns_manual)) $(addprefix -i , $(individual_patterns_auto)) annotate --ontology-iri $(OBO)/$(ONT)/patterns/definitions.owl -o $@ + +$(DOSDP_TEMP_PATTERN_MANUAL)/%.ofn: ../patterns/data/manual/%.tsv ../patterns/dosdp-patterns/%.yaml $(DOSDP_TEMP_ONTOLOGIES)/all_imports_module.owl $(DOSDP_TEMP_PATTERN_MANUAL) + dosdp-tools generate --infile=$< --template=$(word 2, $^) --ontology=$(word 3, $^) --obo-prefixes=true --outfile=$@ + +$(DOSDP_TEMP_PATTERN_AUTO)/%.ofn: ../patterns/data/auto/%.tsv ../patterns/dosdp-patterns/%.yaml $(DOSDP_TEMP_ONTOLOGIES)/all_imports_module.owl $(DOSDP_TEMP_PATTERN_AUTO) + dosdp-tools generate --infile=$< --template=$(word 2, $^) --ontology=$(word 3, $^) --obo-prefixes=true --outfile=$@ + +$(DOSDP_TEMP_ONTOLOGIES)/all_imports_module.owl: $(DOSDP_TEMP_ONTOLOGIES)/all_pattern_terms.txt $(DOSDP_TEMP_ONTOLOGIES)/all_imports.owl $(DOSDP_TEMP_ONTOLOGIES) + $(ROBOT) extract -i $(word 2, $^) -T $< --method BOT -o $@ + +$(DOSDP_TEMP_ONTOLOGIES)/all_pattern_terms.txt: $(pattern_term_lists_auto) $(pattern_term_lists_manual) $(DOSDP_TEMP_ONTOLOGIES) + cat $^ $(word 2, $^) | sort | uniq >$@ + +$(DOSDP_TEMP_PATTERN_MANUAL)/%.txt: ../patterns/dosdp-patterns/%.yaml ../patterns/data/manual/%.tsv $(DOSDP_TEMP_PATTERN_MANUAL) + dosdp-tools terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@ + +$(DOSDP_TEMP_PATTERN_AUTO)/%.txt: ../patterns/dosdp-patterns/%.yaml ../patterns/data/auto/%.tsv $(DOSDP_TEMP_PATTERN_AUTO) + dosdp-tools terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@ + +imports_all_pattern := $(patsubst %, mirror/%.owl,$(IMPORTS)) + +$(DOSDP_TEMP_ONTOLOGIES)/all_imports.owl: $(imports_all_pattern) + echo 'imports: '$(imports_all_pattern) &&\ + $(ROBOT) merge $(addprefix -i , $^) annotate --ontology-iri $(DOSDP_TEMP_ONTOLOGIES)/all_imports.owl -o $@ diff --git a/src/ontology/README-editors.md b/src/ontology/README-editors.md new file mode 100644 index 00000000..6cec0f5d --- /dev/null +++ b/src/ontology/README-editors.md @@ -0,0 +1,194 @@ +These notes are for the EDITORS of upheno + +This project was created using the [ontology development kit](https://github.com/INCATools/ontology-development-kit). See the site for details. + +For more details on ontology management, please see the [OBO tutorial](https://github.com/jamesaoverton/obo-tutorial) or the [Gene Ontology Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/) + +You may also want to read the [GO ontology editors guide](http://go-ontology.readthedocs.org/) + +## Requirements + + 1. Protege (for editing) + 2. A git client (we assume command line git) + 3. [docker](https://www.docker.com/get-docker) (for managing releases) + +## Editors Version + +Make sure you have an ID range in the [idranges file](upheno-idranges.owl) + +If you do not have one, get one from the maintainer of this repo. + +The editors version is [upheno-edit.owl](upheno-edit.owl) + +** DO NOT EDIT upheno.obo OR upheno.owl in the top level directory ** + +[../../upheno.owl](../../upheno.owl) is the release version + +To edit, open the file in Protege. First make sure you have the repository cloned, see [the GitHub project](https://github.com/obophenotype/upheno) for details. + +You should discuss the git workflow you should use with the maintainer +of this repo, who should document it here. If you are the maintainer, +you can contact the odk developers for assistance. You may want to +copy the flow an existing project, for example GO: [Gene Ontology +Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/). + +In general, it is bad practice to commit changes to master. It is +better to make changes on a branch, and make Pull Requests. + +## ID Ranges + +These are stored in the file + + * [upheno-idranges.owl](upheno-idranges.owl) + +** ONLY USE IDs WITHIN YOUR RANGE!! ** + +If you have only just set up this repository, modify the idranges file + and add yourself or other editors. Note Protege does not read the file +- it is up to you to ensure correct Protege configuration. + + +### Setting ID ranges in Protege + +We aim to put this up on the technical docs for OBO on http://obofoundry.org/ + +For now, consult the [GO Tutorial on configuring Protege](http://go-protege-tutorial.readthedocs.io/en/latest/Entities.html#new-entities) + +## Imports + +All import modules are in the [imports/](imports/) folder. + +There are two ways to include new classes in an import module + + 1. Reference an external ontology class in the edit ontology. In Protege: "add new entity", then paste in the PURL + 2. Add to the imports/foo_terms.txt file + +After doing this, you can run + +`./run.sh make all_imports` + +to regenerate imports. + +Note: the foo_terms.txt file may include 'starter' classes seeded from +the ontology starter kit. It is safe to remove these. + +## Design patterns + +You can automate (class) term generation from design patterns by placing DOSDP +yaml file and tsv files under src/patterns. Any pair of files in this +folder that share a name (apart from the extension) are assumed to be +a DOSDP design pattern and a corresponding tsv specifying terms to +add. + +Design patterns can be used to maintain and generate complete terms +(names, definitions, synonyms etc) or to generate logical axioms +only, with other axioms being maintained in editors file. This can be +specified on a per-term basis in the TSV file. + +Design pattern docs are checked for validity via Travis, but can be +tested locally using + +`./run.sh make patterns` + +In addition to running standard tests, this command generates an owl +file (`src/patterns/pattern.owl`), which demonstrates the relationships +between design patterns. + +(At the time of writing, the following import statements need to be +added to `src/patterns/pattern.owl` for all imports generated in +`src/imports/*_import.owl`. This will be automated in a future release.') + +To compile design patterns to terms run: + +`./run.sh make ../patterns/definitions.owl` + +This generates a file (`src/patterns/definitions.owl`). You then need +to add an import statement to the editor's file to import the +definitions file. + + +## Release Manager notes + +You should only attempt to make a release AFTER the edit version is +committed and pushed, AND the travis build passes. + +These instructions assume you have +[docker](https://www.docker.com/get-docker). This folder has a script +[run.sh](run.sh) that wraps docker commands. + +to release: + +first type + + git branch + +to make sure you are on master + + cd src/ontology + ./build.sh + +If this looks good type: + + ./prepare_release.sh + +This generates derived files such as upheno.owl and upheno.obo and places +them in the top level (../..). + +Note that the versionIRI value automatically will be added, and will +end with YYYY-MM-DD, as per OBO guidelines. + +Commit and push these files. + + git commit -a + +And type a brief description of the release in the editor window + +Finally type: + + git push origin master + +IMMEDIATELY AFTERWARDS (do *not* make further modifications) go here: + + * https://github.com/obophenotype/upheno/releases + * https://github.com/obophenotype/upheno/releases/new + +__IMPORTANT__: The value of the "Tag version" field MUST be + + vYYYY-MM-DD + +The initial lowercase "v" is REQUIRED. The YYYY-MM-DD *must* match +what is in the `owl:versionIRI` of the derived upheno.owl (`data-version` in +upheno.obo). This will be today's date. + +This cannot be changed after the fact, be sure to get this right! + +Release title should be YYYY-MM-DD, optionally followed by a title (e.g. "january release") + +You can also add release notes (this can also be done after the fact). These are in markdown format. +In future we will have better tools for auto-generating release notes. + +Then click "publish release" + +__IMPORTANT__: NO MORE THAN ONE RELEASE PER DAY. + +The PURLs are already configured to pull from github. This means that +BOTH ontology purls and versioned ontology purls will resolve to the +correct ontologies. Try it! + + * http://purl.obolibrary.org/obo/upheno.owl <-- current ontology PURL + * http://purl.obolibrary.org/obo/upheno/releases/YYYY-MM-DD.owl <-- change to the release you just made + +For questions on this contact Chris Mungall or email obo-admin AT obofoundry.org + +# Travis Continuous Integration System + +Check the build status here: [![Build Status](https://travis-ci.org/obophenotype/upheno.svg?branch=master)](https://travis-ci.org/obophenotype/upheno) + +Note: if you have only just created this project you will need to authorize travis for this repo. + + 1. Go to [https://travis-ci.org/profile/obophenotype](https://travis-ci.org/profile/obophenotype) + 2. click the "Sync account" button + 3. Click the tick symbol next to upheno + +Travis builds should now be activated + diff --git a/src/ontology/build.sh b/src/ontology/build.sh new file mode 100755 index 00000000..22add54c --- /dev/null +++ b/src/ontology/build.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make all diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml new file mode 100644 index 00000000..cc4bd794 --- /dev/null +++ b/src/ontology/catalog-v001.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/src/ontology/imports/bfo_import.obo b/src/ontology/imports/bfo_import.obo new file mode 100644 index 00000000..b955ec09 --- /dev/null +++ b/src/ontology/imports/bfo_import.obo @@ -0,0 +1,17 @@ +format-version: 1.2 +ontology: upheno/imports/bfo_import + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl new file mode 100644 index 00000000..53496fb7 --- /dev/null +++ b/src/ontology/imports/bfo_import.owl @@ -0,0 +1,115 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + diff --git a/src/ontology/imports/bfo_terms.txt b/src/ontology/imports/bfo_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/bfo_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/chebi_import.obo b/src/ontology/imports/chebi_import.obo new file mode 100644 index 00000000..96bfa0b7 --- /dev/null +++ b/src/ontology/imports/chebi_import.obo @@ -0,0 +1,19 @@ +format-version: 1.2 +ontology: upheno/imports/chebi_import + +[Term] +id: CHEBI:24431 +name: chemical entity +namespace: chebi_ontology +def: "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances." [] +subset: 3_STAR +synonym: "chemical entity" EXACT [UniProt] + +[Typedef] +id: has_part +name: has part +namespace: chebi_ontology +xref: BFO:0000051 +is_cyclic: false +is_transitive: true + diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl new file mode 100644 index 00000000..16f3db9f --- /dev/null +++ b/src/ontology/imports/chebi_import.owl @@ -0,0 +1,135 @@ + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000051 + chebi_ontology + has_part + false + has_part + has part + + + + + + + + + + + + + A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. + chemical entity + chebi_ontology + CHEBI:24431 + + chemical entity + + + + + chemical entity + UniProt + + + + + + + diff --git a/src/ontology/imports/chebi_terms.txt b/src/ontology/imports/chebi_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/chebi_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/cl_import.obo b/src/ontology/imports/cl_import.obo new file mode 100644 index 00000000..bed6ef3f --- /dev/null +++ b/src/ontology/imports/cl_import.obo @@ -0,0 +1,2758 @@ +format-version: 1.2 +ontology: upheno/imports/cl_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n\n############################\n# Classes\n############################\n\n# Class: (organism subdivision)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (surface structure)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (splanchnopleure)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectComplementOf(ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\n) + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CARO:0000003 +name: anatomical structure +is_a: CARO:0000006 ! material anatomical entity + +[Term] +id: CARO:0000006 +name: material anatomical entity +is_a: BFO:0000040 ! material entity + +[Term] +id: CARO:0000014 +name: cell part +is_a: CARO:0000003 ! anatomical structure + +[Term] +id: CHEBI:24431 +name: chemical entity + +[Term] +id: CL:0000000 +name: cell +namespace: cell +def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah] +comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). +subset: ubprop:upper_level +xref: CALOHA:TS-2035 +xref: FMA:68646 +xref: GO:0005623 +xref: KUPO:0000002 +xref: VHOG:0001533 +xref: WBbt:0004017 +xref: XAO:0003012 +is_a: CARO:0000003 ! anatomical structure +is_a: GO:0005575 ! cellular_component +equivalent_to: GO:0005623 ! cell + +[Term] +id: CL:0000003 +name: native cell +namespace: cell +def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah] +comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). +subset: ubprop:upper_level +synonym: "cell in vivo" NARROW [] +xref: CARO:0000013 +is_a: CL:0000000 ! cell +is_a: GO:0005623 ! cell + +[Term] +id: CL:0000031 +name: neuroblast +namespace: cell +def: "A cell that will develop into a neuron often after a migration phase." [GOC:NV, http://en.wikipedia.org/wiki/Neuroblast] +xref: BTO:0000930 +xref: FBbt:00005146 +xref: FMA:70563 +is_a: CL:0000047 ! neuronal stem cell +is_a: CL:0000055 ! non-terminally differentiated cell + +[Term] +id: CL:0000034 +name: stem cell +namespace: cell +def: "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:tfm, MESH:A11.872] +xref: CALOHA:TS-2086 +xref: FMA:63368 +is_a: CL:0011115 ! precursor cell +intersection_of: CL:0000003 ! native cell +intersection_of: RO:0002215 GO:0017145 ! capable of stem cell division +relationship: RO:0002215 GO:0017145 ! capable of stem cell division +relationship: RO:0002215 GO:0030154 ! capable of cell differentiation + +[Term] +id: CL:0000047 +name: neuronal stem cell +namespace: cell +def: "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors." [GOC:tfm, http://en.wikipedia.org/wiki/Neural_stem_cell, MESH:D058953, PMID:15247488] +synonym: "neural stem cell" EXACT [] +synonym: "NSC" EXACT [] +xref: BTO:0002881 +xref: CALOHA:TS-2360 +xref: FMA:86684 +is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell +is_a: CL:0002319 ! neural cell +intersection_of: CL:0000048 ! multi fate stem cell +intersection_of: BFO:0000050 UBERON:0001017 ! part of central nervous system +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell + +[Term] +id: CL:0000048 +name: multi fate stem cell +namespace: cell +def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add] +synonym: "multi-fate stem cell" EXACT [] +synonym: "multifate stem cell" EXACT [] +synonym: "multipotent cell" EXACT [] +synonym: "multipotent stem cell" EXACT [] +xref: FMA:84789 +is_a: CL:0000034 ! stem cell +is_a: CL:0002371 ! somatic cell +intersection_of: CL:0002371 ! somatic cell +intersection_of: RO:0000053 PATO:0001402 ! bearer of multipotent +intersection_of: RO:0002215 GO:0017145 ! capable of stem cell division +relationship: RO:0000053 PATO:0001402 ! bearer of multipotent +relationship: RO:0002215 GO:0017145 ! capable of stem cell division + +[Term] +id: CL:0000055 +name: non-terminally differentiated cell +namespace: cell +def: "A precursor cell with a limited number of potential fates." [SANBI:mhl] +comment: define using PATO mulit-potent or oligopotent? +synonym: "blast cell" EXACT [] +xref: BTO:0000125 +xref: FMA:84782 +is_a: CL:0011115 ! precursor cell +relationship: RO:0002215 GO:0030154 ! capable of cell differentiation + +[Term] +id: CL:0000066 +name: epithelial cell +namespace: cell +def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [FB:ma, GOC:tfm, MESH:A11.436] +synonym: "epitheliocyte" EXACT [] +xref: BTO:0000414 +xref: CALOHA:TS-2026 +xref: CARO:0000077 +xref: FBbt:00000124 +xref: FMA:66768 +xref: WBbt:0003672 +is_a: CL:0000548 ! animal cell +intersection_of: CL:0000548 ! animal cell +intersection_of: BFO:0000050 UBERON:0000483 ! part of epithelium +relationship: BFO:0000050 UBERON:0000483 ! part of epithelium + +[Term] +id: CL:0000075 +name: columnar/cuboidal epithelial cell +namespace: cell +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell + +[Term] +id: CL:0000082 +name: epithelial cell of lung +namespace: cell +synonym: "lung epithelial cell" EXACT [] +xref: BTO:0004299 +is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: BFO:0000050 UBERON:0002048 ! part of lung +relationship: BFO:0000050 UBERON:0000115 ! part of lung epithelium +relationship: BFO:0000050 UBERON:0002048 ! part of lung + +[Term] +id: CL:0000133 +name: neurectodermal cell +namespace: cell +def: "Ectoderm destined to be nervous tissue." [GOC:tfm, ISBN:068340007X] +synonym: "neurectoderm cell" EXACT [] +is_a: CL:0000221 ! ectodermal cell + +[Term] +id: CL:0000211 +name: electrically active cell +namespace: cell +def: "A cell whose function is determined by the generation or the reception of an electric signal." [FB:ma] +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000221 +name: ectodermal cell +namespace: cell +def: "A cell of the outer of the three germ layers of the embryo." [MESH:A16.254.425.273] +synonym: "ectoderm cell" EXACT [] +xref: FMA:72549 +is_a: CL:0002321 ! embryonic cell +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm + +[Term] +id: CL:0000223 +name: endodermal cell +namespace: cell +def: "A cell of the inner of the three germ layers of the embryo." [MESH:A16.254.425.407] +synonym: "endoderm cell" EXACT [] +xref: FMA:72555 +is_a: CL:0002321 ! embryonic cell +relationship: BFO:0000050 UBERON:0000925 ! part of endoderm + +[Term] +id: CL:0000225 +name: anucleate cell +namespace: cell +def: "A cell that lacks a nucleus." [FB:ma] +synonym: "non-nucleated cell" EXACT [] +xref: FMA:68647 +is_a: CL:0000003 ! native cell +intersection_of: CL:0000003 ! native cell +intersection_of: RO:0000053 PATO:0001405 ! bearer of anucleate +disjoint_from: CL:0002242 ! nucleate cell +relationship: RO:0000053 PATO:0001405 ! bearer of anucleate + +[Term] +id: CL:0000255 +name: eukaryotic cell +namespace: cell +is_a: CL:0000003 ! native cell + +[Term] +id: CL:0000362 +name: epidermal cell +namespace: cell +alt_id: CL:1000396 +def: "An epithelial cell of the integument (the outer layer of an organism)." [Flybase:dsj, MA:ma] +synonym: "cell of epidermis" EXACT [FMA:62411] +synonym: "epithelial cell of skin" NARROW [FMA:62411] +xref: BTO:0001470 +xref: CALOHA:TS-0283 +xref: FMA:62411 +is_a: CL:0002159 ! general ecto-epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: BFO:0000050 UBERON:0007376 ! part of outer epithelium +relationship: BFO:0000050 UBERON:0007376 ! part of outer epithelium + +[Term] +id: CL:0000393 +name: electrically responsive cell +namespace: cell +def: "A cell whose function is determined by its response to an electric signal." [FB:ma] +is_a: CL:0000211 ! electrically active cell + +[Term] +id: CL:0000404 +name: electrically signaling cell +namespace: cell +def: "A cell that initiates an electrical signal and passes that signal to another cell." [FB:ma] +is_a: CL:0000211 ! electrically active cell + +[Term] +id: CL:0000540 +name: neuron +namespace: cell +def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [http://en.wikipedia.org/wiki/Neuron, MESH:A08.663, MESH:D009474] +comment: These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. +synonym: "nerve cell" EXACT [] +xref: BTO:0000938 +xref: CALOHA:TS-0683 +xref: FBbt:00005106 +xref: FMA:54527 +xref: VHOG:0001483 +xref: WBbt:0003679 +is_a: CL:0000000 ! cell +is_a: CL:0000393 ! electrically responsive cell +is_a: CL:0000404 ! electrically signaling cell +is_a: CL:0002319 ! neural cell +relationship: RO:0002202 CL:0000031 ! develops from neuroblast +relationship: RO:0002215 GO:0019226 ! capable of transmission of nerve impulse + +[Term] +id: CL:0000548 +name: animal cell +namespace: cell +subset: ubprop:upper_level +is_a: CL:0000255 ! eukaryotic cell + +[Term] +id: CL:0000710 +name: neurecto-epithelial cell +namespace: cell +def: "Epithelial cells derived from neural plate and neural crest." [GOC:tfm] +comment: The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). +synonym: "neuroepithelial cell" BROAD [] +xref: BTO:0004301 +xref: FMA:70557 +is_a: CL:0000075 ! columnar/cuboidal epithelial cell +is_a: CL:0002077 ! ecto-epithelial cell +intersection_of: CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 CL:0000133 ! develops from neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell + +[Term] +id: CL:0001061 +name: abnormal cell +namespace: cell +def: "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." [GOC:add, GOC:cg, GOC:wdd] +comment: https://github.com/obophenotype/cell-ontology/issues/448 +xref: https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 +is_a: CL:0000000 ! cell +is_a: GO:0005623 ! cell +intersection_of: GO:0005623 ! cell +intersection_of: RO:0000053 PATO:0000460 ! bearer of abnormal +relationship: RO:0000053 PATO:0000460 ! bearer of abnormal +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/elements/1.1/date 2017-01-30T18:53:32Z xsd:dateTime + +[Term] +id: CL:0002076 +name: endo-epithelial cell +namespace: cell +def: "An epithelial cell derived from endoderm." [FMA:69075, GOC:tfm] +xref: FMA:69075 +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell +relationship: RO:0002202 CL:0000223 ! develops from endodermal cell +created_by: tmeehan +creation_date: 2010-06-29T03:38:14Z + +[Term] +id: CL:0002077 +name: ecto-epithelial cell +namespace: cell +def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] +xref: FMA:69074 +is_a: CL:0000066 ! epithelial cell +is_a: CL:0002371 ! somatic cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +created_by: tmeehan +creation_date: 2010-06-29T03:38:22Z + +[Term] +id: CL:0002159 +name: general ecto-epithelial cell +namespace: cell +def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] +xref: FMA:70556 +is_a: CL:0002077 ! ecto-epithelial cell +created_by: tmeehan +creation_date: 2010-08-26T08:31:08Z + +[Term] +id: CL:0002242 +name: nucleate cell +namespace: cell +def: "A cell containing at least one nucleus." [GOC:tfm] +xref: FMA:67513 +is_a: CL:0000003 ! native cell +intersection_of: CL:0000003 ! native cell +intersection_of: BFO:0000051 GO:0005634 ! has part nucleus +relationship: BFO:0000051 GO:0005634 ! has part nucleus +created_by: tmeehan +creation_date: 2010-09-07T03:32:33Z + +[Term] +id: CL:0002251 +name: epithelial cell of alimentary canal +namespace: cell +def: "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." [GOC:tfm, ISBN:0721662544] +is_a: CL:0002076 ! endo-epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: BFO:0000050 UBERON:0001555 ! part of digestive tract +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract +created_by: tmeehan +creation_date: 2010-09-08T09:26:53Z + +[Term] +id: CL:0002319 +name: neural cell +namespace: cell +def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] +xref: CALOHA:TS-2040 +xref: FMA:70333 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 ! somatic cell +intersection_of: CL:0000000 ! cell +intersection_of: BFO:0000050 UBERON:0001016 ! part of nervous system +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system +created_by: tmeehan +creation_date: 2010-09-15T01:34:57Z + +[Term] +id: CL:0002320 +name: connective tissue cell +namespace: cell +alt_id: CL:1000406 +def: "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." [GOC:tfm, ISBN:0618947256] +xref: CALOHA:TS-2096 +xref: FMA:63875 +is_a: CL:0000548 ! animal cell +is_a: CL:0002371 {is_inferred="true"} ! somatic cell +intersection_of: CL:0002371 ! somatic cell +intersection_of: BFO:0000050 UBERON:0002384 ! part of connective tissue +relationship: BFO:0000050 UBERON:0002384 ! part of connective tissue +created_by: tmeehan +creation_date: 2010-09-15T03:01:54Z + +[Term] +id: CL:0002321 +name: embryonic cell +namespace: cell +def: "A cell of the embryo." [FMA:0618947256] +xref: CALOHA:TS-0263 +xref: FMA:82840 +xref: FMA:82841 +xref: WBbt:0007028 +is_a: CL:0000548 ! animal cell +created_by: tmeehan +creation_date: 2010-09-15T03:39:21Z + +[Term] +id: CL:0002368 +name: respiratory epithelial cell +namespace: cell +def: "An endo-epithelial cell of the respiratory tract." [GOC:tfm] +synonym: "airway epithelial cell" EXACT [] +xref: BTO:0004533 +is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell +intersection_of: CL:0002076 ! endo-epithelial cell +intersection_of: BFO:0000050 UBERON:0000065 ! part of respiratory tract +relationship: BFO:0000050 UBERON:0000065 ! part of respiratory tract +created_by: tmeehan +creation_date: 2010-09-23T04:38:49Z + +[Term] +id: CL:0002371 +name: somatic cell +namespace: cell +def: "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." [GOC:tfm, ISBN:0721662544] +subset: ubprop:upper_level +xref: BTO:0001268 +xref: FMA:72300 +xref: WBbt:0008378 +is_a: CL:0000003 ! native cell +created_by: tmeehan +creation_date: 2010-09-24T09:44:42Z + +[Term] +id: CL:0002632 +name: epithelial cell of lower respiratory tract +namespace: cell +is_a: CL:0002368 {is_inferred="true"} ! respiratory epithelial cell +intersection_of: CL:0002368 ! respiratory epithelial cell +intersection_of: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract +relationship: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract +created_by: tmeehan +creation_date: 2011-06-21T12:29:31Z + +[Term] +id: CL:0011115 +name: precursor cell +def: "A cell that, by division or terminal differentiation, can give rise to other cell types." [GOC:dos] +comment: Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. +is_a: CL:0000003 ! native cell +intersection_of: CL:0000003 ! native cell +intersection_of: RO:0002215 GO:0030154 ! capable of cell differentiation +relationship: RO:0002215 GO:0030154 ! capable of cell differentiation + +[Term] +id: CL:2000029 +name: central nervous system neuron +namespace: cell +def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] +is_a: CL:0000540 ! neuron +intersection_of: CL:0000540 ! neuron +intersection_of: BFO:0000050 UBERON:0001017 ! part of central nervous system +relationship: BFO:0000050 UBERON:0001017 ! part of central nervous system +created_by: TermGenie +creation_date: 2014-06-25T01:17:43Z + +[Term] +id: CL:2000032 +name: peripheral nervous system neuron +namespace: cell +def: "Any neuron that is part of a peripheral nervous system." [GOC:TermGenie] +is_a: CL:0000540 ! neuron +intersection_of: CL:0000540 ! neuron +intersection_of: BFO:0000050 UBERON:0000010 ! part of peripheral nervous system +relationship: BFO:0000050 UBERON:0000010 ! part of peripheral nervous system +created_by: TermGenie +creation_date: 2014-06-25T02:28:17Z + +[Term] +id: GO:0003008 +name: system process +is_a: GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0005575 +name: cellular_component + +[Term] +id: GO:0005623 +name: cell +is_a: CARO:0000003 ! anatomical structure +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0005634 +name: nucleus +is_a: GO:0043231 ! intracellular membrane-bounded organelle +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0008150 +name: biological_process + +[Term] +id: GO:0009987 +name: cellular process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0017145 +name: stem cell division +is_a: GO:0051301 ! cell division + +[Term] +id: GO:0019226 +name: transmission of nerve impulse +is_a: GO:0035637 ! multicellular organismal signaling +is_a: GO:0050877 ! nervous system process + +[Term] +id: GO:0023052 +name: signaling +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0030154 +name: cell differentiation +is_a: GO:0048869 ! cellular developmental process + +[Term] +id: GO:0032501 +name: multicellular organismal process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0032502 +name: developmental process +is_a: GO:0008150 ! biological_process + +[Term] +id: GO:0035637 +name: multicellular organismal signaling +is_a: GO:0023052 ! signaling +is_a: GO:0032501 ! multicellular organismal process + +[Term] +id: GO:0043226 +name: organelle +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0043227 +name: membrane-bounded organelle +is_a: GO:0043226 ! organelle + +[Term] +id: GO:0043229 +name: intracellular organelle +is_a: GO:0043226 ! organelle +is_a: GO:0044424 ! intracellular part + +[Term] +id: GO:0043231 +name: intracellular membrane-bounded organelle +is_a: GO:0043227 ! membrane-bounded organelle +is_a: GO:0043229 ! intracellular organelle + +[Term] +id: GO:0044424 +name: intracellular part +is_a: GO:0044464 ! cell part + +[Term] +id: GO:0044464 +name: cell part +is_a: CARO:0000014 ! cell part +is_a: GO:0005575 ! cellular_component + +[Term] +id: GO:0048869 +name: cellular developmental process +is_a: GO:0009987 ! cellular process +is_a: GO:0032502 ! developmental process + +[Term] +id: GO:0050877 +name: nervous system process +is_a: GO:0003008 ! system process + +[Term] +id: GO:0051301 +name: cell division +is_a: GO:0009987 ! cellular process + +[Term] +id: PATO:0000001 +name: quality + +[Term] +id: PATO:0000068 +name: qualitative +is_a: PATO:0000001 ! quality + +[Term] +id: PATO:0000069 +name: deviation(from_normal) +is_a: PATO:0000068 ! qualitative + +[Term] +id: PATO:0000460 +name: abnormal +is_a: PATO:0000069 ! deviation(from_normal) + +[Term] +id: PATO:0001241 +name: physical object quality +is_a: PATO:0000001 ! quality + +[Term] +id: PATO:0001396 +name: cellular quality +is_a: PATO:0001241 ! physical object quality + +[Term] +id: PATO:0001397 +name: cellular potency +is_a: PATO:0001396 ! cellular quality + +[Term] +id: PATO:0001402 +name: multipotent +is_a: PATO:0001397 ! cellular potency + +[Term] +id: PATO:0001404 +name: nucleate quality +is_a: PATO:0001396 ! cellular quality + +[Term] +id: PATO:0001405 +name: anucleate +is_a: PATO:0001404 ! nucleate quality + +[Term] +id: PATO:0002505 +name: nucleated +is_a: PATO:0001404 ! nucleate quality + +[Term] +id: UBERON:0000010 +name: peripheral nervous system +def: "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [] +synonym: "pars peripherica" EXACT [] +synonym: "PNS" BROAD [] +synonym: "systema nervosum periphericum" EXACT [] +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system + +[Term] +id: UBERON:0000025 +name: tube +def: "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." [] +synonym: "anatomical tube" EXACT [] +synonym: "duct" NARROW [] +is_a: UBERON:0004111 ! anatomical conduit +relationship: BFO:0000051 UBERON:0013522 ! has part subdivision of tube + +[Term] +id: UBERON:0000060 +name: anatomical wall +def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [] +synonym: "organ wall" RELATED [] +synonym: "wall" BROAD [] +synonym: "wall of organ" EXACT [] +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000051 UBERON:0004923 ! has part organ component layer + +[Term] +id: UBERON:0000061 +name: anatomical structure +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [] +synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [] +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0000062 +name: organ +def: "Anatomical structure that performs a specific function or group of functions [WP]." [] +synonym: "anatomical unit" RELATED [] +synonym: "body organ" RELATED [] +synonym: "element" RELATED [] +is_a: UBERON:0010000 ! multicellular anatomical structure +disjoint_from: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0000467 ! part of anatomical system + +[Term] +id: UBERON:0000064 +name: organ part +def: "A multicellular structure that is a part of an organ." [] +synonym: "cardinal organ part" EXACT [] +synonym: "regional part of organ" RELATED [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000062 ! part of organ + +[Term] +id: UBERON:0000065 +name: respiratory tract +def: "Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts" [] +is_a: UBERON:0001005 ! respiratory airway +is_a: UBERON:0004119 ! endoderm-derived structure +relationship: RO:0002202 UBERON:0007026 ! develops from presumptive gut +relationship: RO:0002202 UBERON:0008947 ! develops from respiratory primordium + +[Term] +id: UBERON:0000072 +name: proximo-distal subdivision of respiratory tract +def: "An section of a respiratory tract." [] +synonym: "respiratory tract" RELATED [] +synonym: "subdivision of respiratory tract" RELATED [] +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0013522 ! subdivision of tube +intersection_of: UBERON:0013522 ! subdivision of tube +intersection_of: BFO:0000050 UBERON:0000065 ! part of respiratory tract +relationship: BFO:0000050 UBERON:0000065 ! part of respiratory tract + +[Term] +id: UBERON:0000075 +name: subdivision of skeletal system +def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [] +synonym: "skeletal system part" RELATED [] +synonym: "skeletal system subdivision" EXACT [] +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system +relationship: BFO:0000051 UBERON:0004765 ! has part skeletal element + +[Term] +id: UBERON:0000076 +name: external ectoderm +def: "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." [] +synonym: "surface (external) ectoderm" EXACT [] +synonym: "surface ectoderm" EXACT [] +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0000924 ! part of ectoderm + +[Term] +id: UBERON:0000077 +name: mixed endoderm/mesoderm-derived structure +def: "An anatomical structure that develops from the endoderm and the mesoderm." [] +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm + +[Term] +id: UBERON:0000078 +name: mixed ectoderm/mesoderm/endoderm-derived structure +def: "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." [] +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm + +[Term] +id: UBERON:0000114 +name: lung connective tissue +def: "the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin" [] +synonym: "connective tissue of lung" EXACT [] +synonym: "lung interstitial tissue" RELATED [] +synonym: "lung interstitium" RELATED [] +synonym: "pulmonary connective tissue" RELATED [] +synonym: "pulmonary interstitial tissue" RELATED [] +synonym: "pulmonary interstitium" EXACT [] +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003580 ! lower respiratory tract connective tissue +is_a: UBERON:0003837 ! thoracic segment connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: BFO:0000050 UBERON:0002048 ! part of lung +relationship: BFO:0000050 UBERON:0002048 ! part of lung +relationship: RO:0002202 UBERON:0004883 ! develops from lung mesenchyme + +[Term] +id: UBERON:0000115 +name: lung epithelium +def: "The epithelial layer of the lung." [] +synonym: "epithelial tissue of lung" EXACT [] +synonym: "epithelium of lung" EXACT [] +synonym: "lung epithelial tissue" EXACT [] +synonym: "pulmonary epithelium" RELATED [] +is_a: UBERON:0004815 ! lower respiratory tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0002048 ! part of lung +relationship: BFO:0000050 UBERON:0002048 ! part of lung + +[Term] +id: UBERON:0000117 +name: respiratory tube +def: "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea." [] +synonym: "respiratory conducting tube" NARROW [] +synonym: "segment of tracheobronchial tree" EXACT [] +synonym: "segment of tracheobronchial tree" NARROW [] +synonym: "tracheobronchial tree segment" NARROW [] +is_a: UBERON:0000025 ! tube +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: UBERON:0000025 ! tube +intersection_of: BFO:0000050 UBERON:0000065 ! part of respiratory tract +relationship: BFO:0000050 UBERON:0000065 ! part of respiratory tract +relationship: BFO:0000051 UBERON:0000483 ! has part epithelium + +[Term] +id: UBERON:0000118 +name: lung bud +def: "Structure derived from foregut that becomes a lung[GO]." [] +synonym: "gemma pulmonalis" RELATED [] +synonym: "gemma respiratoria" RELATED [] +synonym: "lung bud" RELATED [] +synonym: "primary lung bud" RELATED [] +synonym: "respiratory diverticulum" RELATED [] +is_a: UBERON:0005153 ! epithelial bud +is_a: UBERON:0005911 ! endo-epithelium +relationship: RO:0002202 UBERON:0005597 ! develops from lung primordium +relationship: RO:0002202 UBERON:0008947 ! develops from respiratory primordium + +[Term] +id: UBERON:0000170 +name: pair of lungs +def: "The pair of anatomical structures comprised of a left lung and right lung." [] +synonym: "lungs" EXACT [] +synonym: "lungs pair" EXACT [] +synonym: "pulmones" EXACT [] +synonym: "set of lungs" EXACT [] +is_a: UBERON:0034925 ! anatomical collection +relationship: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract +relationship: BFO:0000051 UBERON:0002167 ! has part right lung +relationship: BFO:0000051 UBERON:0002168 ! has part left lung + +[Term] +id: UBERON:0000171 +name: respiration organ +def: "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [] +synonym: "apparatus respiratorius organ" EXACT [] +synonym: "breathing organ" EXACT [] +synonym: "gas exchange organ" RELATED [] +synonym: "organ of apparatus respiratorius" EXACT [] +synonym: "organ of respiratory system" EXACT [] +synonym: "respiratory organ" EXACT [] +synonym: "respiratory system organ" EXACT [] +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0001004 ! part of respiratory system + +[Term] +id: UBERON:0000307 +name: blastula +def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [] +synonym: "blastosphere" RELATED [] +synonym: "blastula embryo" EXACT [] +is_a: UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo + +[Term] +id: UBERON:0000328 +name: gut wall +def: "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity)." [] +synonym: "digestive tract wall" EXACT [] +synonym: "wall of alimentary tract" RELATED [] +synonym: "wall of digestive tract" EXACT [] +synonym: "wall of gut" EXACT [] +is_a: UBERON:0000060 ! anatomical wall +intersection_of: UBERON:0000060 ! anatomical wall +intersection_of: BFO:0000050 UBERON:0001555 ! part of digestive tract +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0000383 +name: musculature of body +def: "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]." [] +synonym: "muscle system" EXACT [] +synonym: "muscle system of body" EXACT [] +synonym: "muscular system" EXACT [] +synonym: "musculature system" EXACT [] +synonym: "muskelsystem" RELATED [] +synonym: "set of all muscles" EXACT [] +synonym: "set of muscles of body" EXACT [] +synonym: "vertebrate muscular system" EXACT [] +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0002204 ! part of musculoskeletal system +relationship: BFO:0000051 UBERON:0001015 ! has part musculature + +[Term] +id: UBERON:0000464 +name: anatomical space +def: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [] +synonym: "anatomical spaces" RELATED [] +synonym: "lumen" BROAD [] +synonym: "lumen space" EXACT [] +synonym: "space" BROAD [] +is_a: UBERON:0000466 ! immaterial anatomical entity + +[Term] +id: UBERON:0000465 +name: material anatomical entity +def: "Anatomical entity that has mass." [] +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000466 +name: immaterial anatomical entity +def: "Anatomical entity that has no mass." [] +synonym: "immaterial physical anatomical entity" EXACT [] +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000467 +name: anatomical system +def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [] +synonym: "anatomical systems" RELATED [] +synonym: "body system" EXACT [] +synonym: "connected anatomical system" EXACT [] +synonym: "organ system" EXACT [] +synonym: "system" BROAD [] +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism +relationship: BFO:0000051 UBERON:0000062 ! has part organ + +[Term] +id: UBERON:0000468 +name: multicellular organism +def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [] +synonym: "animal" NARROW [] +synonym: "body" RELATED [] +synonym: "Koerper" RELATED [] +synonym: "multi-cellular organism" EXACT [] +synonym: "organism" BROAD [] +synonym: "whole body" RELATED [] +synonym: "whole organism" RELATED [] +is_a: UBERON:0010000 ! multicellular anatomical structure + +[Term] +id: UBERON:0000475 +name: organism subdivision +def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [] +synonym: "anatomic region" EXACT [] +synonym: "body part" RELATED [] +synonym: "body region" RELATED [] +synonym: "cardinal body part" RELATED [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0000476 +name: acellular anatomical structure +def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [] +synonym: "acellular anatomical structures" RELATED [] +is_a: UBERON:0000061 ! anatomical structure +disjoint_from: UBERON:0010000 ! multicellular anatomical structure + +[Term] +id: UBERON:0000477 +name: anatomical cluster +def: "Anatomical group that has its parts adjacent to one another." [] +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000479 +name: tissue +def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [] +synonym: "portion of tissue" EXACT [] +synonym: "simple tissue" NARROW [] +synonym: "tissue portion" EXACT [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0000483 +name: epithelium +def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [] +synonym: "epithelial tissue" EXACT [] +synonym: "portion of epithelium" EXACT [] +is_a: UBERON:0000479 ! tissue +union_of: UBERON:0000486 ! multilaminar epithelium +union_of: UBERON:0000490 ! unilaminar epithelium +relationship: BFO:0000051 UBERON:0005769 ! has part basement membrane of epithelium + +[Term] +id: UBERON:0000485 +name: simple columnar epithelium +def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [] +synonym: "columnar epithelium" BROAD [] +synonym: "columnar epithlium" BROAD [] +synonym: "epithelium simplex columnare" EXACT [] +synonym: "simple columnar epithelia" RELATED [] +synonym: "simple columnar epithelium" EXACT [] +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0012274 ! columnar epithelium + +[Term] +id: UBERON:0000486 +name: multilaminar epithelium +def: "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]" [] +synonym: "laminated epithelium" RELATED [] +synonym: "stratified epithelium" EXACT [] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0000490 +name: unilaminar epithelium +def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [] +synonym: "simple epithelium" EXACT [] +synonym: "unilaminar epithelia" RELATED [] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0000915 +name: thoracic segment of trunk +def: "Subdivision of trunk that lies between the head and the abdomen." [] +synonym: "anterior subdivision of trunk" RELATED [] +synonym: "thorax" EXACT [] +synonym: "upper body" RELATED [] +synonym: "upper trunk" RELATED [] +is_a: UBERON:0009569 ! subdivision of trunk +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: BFO:0000051 UBERON:0014477 ! has part thoracic skeleton + +[Term] +id: UBERON:0000922 +name: embryo +def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [] +synonym: "developing organism" RELATED [] +synonym: "developmental tissue" RELATED [] +synonym: "embryonic organism" EXACT [] +is_a: UBERON:0000468 ! multicellular organism + +[Term] +id: UBERON:0000923 +name: germ layer +def: "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [] +synonym: "embryonic germ layer" RELATED [] +synonym: "embryonic germ layers" RELATED [] +synonym: "embryonic tissue" BROAD [] +synonym: "germinal layer" EXACT [] +synonym: "primary germ layer" NARROW [] +is_a: UBERON:0010316 ! germ layer / neural crest + +[Term] +id: UBERON:0000924 +name: ectoderm +def: "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [] +synonym: "embryonic ectoderm" EXACT [] +is_a: UBERON:0000923 ! germ layer +relationship: RO:0002495 UBERON:0006601 ! immediate transformation of presumptive ectoderm + +[Term] +id: UBERON:0000925 +name: endoderm +def: "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [] +synonym: "entoderm" RELATED [] +is_a: UBERON:0000923 ! germ layer +relationship: RO:0002495 UBERON:0006595 ! immediate transformation of presumptive endoderm + +[Term] +id: UBERON:0000926 +name: mesoderm +def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [] +synonym: "embryonic mesoderm" RELATED [] +synonym: "entire mesoderm" RELATED [] +synonym: "mesodermal mantle" RELATED [] +is_a: UBERON:0000923 ! germ layer +relationship: RO:0002495 UBERON:0006603 ! immediate transformation of presumptive mesoderm + +[Term] +id: UBERON:0000982 +name: skeletal joint +def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [] +synonym: "articular joint" RELATED [] +synonym: "articulation" BROAD [] +synonym: "joint" BROAD [] +synonym: "joints" RELATED [] +is_a: UBERON:0004905 ! articulation +union_of: UBERON:0002217 ! synovial joint +union_of: UBERON:0011134 ! nonsynovial joint + +[Term] +id: UBERON:0001004 +name: respiratory system +def: "Functional system which consists of structures involved in respiration." [] +synonym: "apparatus respiratorius" EXACT [] +synonym: "apparatus respiratorius" RELATED [] +synonym: "Atmungssystem" RELATED [] +synonym: "respiratory system" EXACT [] +synonym: "systema respiratorium" RELATED [] +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001007 ! digestive system +disjoint_from: UBERON:0001009 ! circulatory system +disjoint_from: UBERON:0001016 ! nervous system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002416 ! integumental system + +[Term] +id: UBERON:0001005 +name: respiratory airway +def: "An airway through which respiratory air passes in organisms." [] +synonym: "airway" BROAD [] +synonym: "airways" BROAD [] +is_a: UBERON:0003103 ! compound organ +relationship: BFO:0000050 UBERON:0001004 ! part of respiratory system + +[Term] +id: UBERON:0001007 +name: digestive system +def: "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [] +synonym: "alimentary system" RELATED [] +synonym: "alimentary tract" RELATED [] +synonym: "gastrointestinal system" RELATED [] +synonym: "gut" RELATED [] +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001009 ! circulatory system +disjoint_from: UBERON:0001016 ! nervous system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002416 ! integumental system + +[Term] +id: UBERON:0001009 +name: circulatory system +def: "organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [] +synonym: "systema cardiovasculare" RELATED [] +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001016 ! nervous system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002416 ! integumental system + +[Term] +id: UBERON:0001015 +name: musculature +def: "A subdivision of the muscular system corresponding to a subdisivision of an organism." [] +synonym: "muscle group" EXACT [] +synonym: "muscle system" RELATED [] +synonym: "muscles" RELATED [] +synonym: "muscles set" EXACT [] +synonym: "musculature" EXACT [] +synonym: "musculature system" RELATED [] +synonym: "musculi" EXACT [] +synonym: "set of muscles" EXACT [] +synonym: "set of skeletal muscles" EXACT [] +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0000383 ! part of musculature of body +relationship: BFO:0000051 UBERON:0001630 ! has part muscle organ + +[Term] +id: UBERON:0001016 +name: nervous system +def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [] +synonym: "nerve net" NARROW [] +synonym: "neurological system" EXACT [] +synonym: "systema nervosum" RELATED [] +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002416 ! integumental system +relationship: RO:0002495 UBERON:0016880 ! immediate transformation of future nervous system + +[Term] +id: UBERON:0001017 +name: central nervous system +def: "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord." [] +synonym: "cerebrospinal axis" NARROW [] +synonym: "CNS" EXACT [] +synonym: "neuraxis" RELATED [] +synonym: "systema nervosum centrale" EXACT [] +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0001016 ! part of nervous system +relationship: RO:0002495 UBERON:0016879 ! immediate transformation of future central nervous system + +[Term] +id: UBERON:0001041 +name: foregut +def: "Anterior subdivision of a digestive tract." [] +synonym: "praeenteron" RELATED [] +synonym: "proenteron" RELATED [] +is_a: UBERON:0004921 ! subdivision of digestive tract + +[Term] +id: UBERON:0001048 +name: primordium +def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." [] +synonym: "bud" RELATED [] +synonym: "future organ" RELATED [] +synonym: "placode" RELATED [] +synonym: "primordia" RELATED [] +synonym: "rudiment" RELATED [] +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism + +[Term] +id: UBERON:0001062 +name: anatomical entity +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [] + +[Term] +id: UBERON:0001434 +name: skeletal system +def: "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system." [] +synonym: "set of all bones and joints" NARROW [] +synonym: "skeleton system" EXACT [] +synonym: "Skelettsystem" RELATED [] +is_a: UBERON:0011216 ! organ system subdivision +intersection_of: UBERON:0011216 ! organ system subdivision +intersection_of: BFO:0000051 UBERON:0004288 ! has part skeleton +intersection_of: BFO:0000051 UBERON:0004770 ! has part articular system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002416 ! integumental system +relationship: BFO:0000050 UBERON:0002204 ! part of musculoskeletal system +relationship: BFO:0000051 UBERON:0004288 ! has part skeleton +relationship: BFO:0000051 UBERON:0004770 ! has part articular system + +[Term] +id: UBERON:0001555 +name: digestive tract +def: "A tube extending from the mouth to the anus." [] +synonym: "alimentary canal" NARROW [] +synonym: "alimentary tract" NARROW [] +synonym: "digestive canal" RELATED [] +synonym: "digestive tube" EXACT [] +synonym: "enteric tract" EXACT [] +synonym: "gut" BROAD [] +synonym: "gut tube" RELATED [] +is_a: UBERON:0000025 ! tube +relationship: BFO:0000050 UBERON:0001007 ! part of digestive system +relationship: RO:0002495 UBERON:0007026 ! immediate transformation of presumptive gut + +[Term] +id: UBERON:0001558 +name: lower respiratory tract +def: "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]" [] +is_a: CARO:0000003 ! anatomical structure +is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract +relationship: BFO:0000051 UBERON:0000170 ! has part pair of lungs + +[Term] +id: UBERON:0001630 +name: muscle organ +def: "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]." [] +synonym: "muscle" BROAD [] +is_a: CARO:0000003 ! anatomical structure +is_a: UBERON:0000062 ! organ +is_a: UBERON:0005090 ! muscle structure +relationship: BFO:0000050 UBERON:0001015 ! part of musculature +relationship: BFO:0000051 UBERON:0002385 ! has part muscle tissue + +[Term] +id: UBERON:0002048 +name: lung +def: "Respiration organ that develops as an oupocketing of the esophagus." [] +synonym: "pulmo" EXACT [] +is_a: UBERON:0000171 ! respiration organ +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0005178 ! thoracic cavity element +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0000170 ! part of pair of lungs +relationship: RO:0002202 UBERON:0000118 ! develops from lung bud + +[Term] +id: UBERON:0002050 +name: embryonic structure +def: "Anatomical structure that is part of an embryo." [] +synonym: "developing embryonic structure" EXACT [] +synonym: "developing structure" RELATED [] +synonym: "embryonale Struktur" RELATED [] +synonym: "embryonic anatomical structure" EXACT [] +synonym: "embryonic structures" RELATED [] +is_a: UBERON:0005423 ! developing anatomical structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000050 UBERON:0000922 ! part of embryo + +[Term] +id: UBERON:0002090 +name: postcranial axial skeleton +def: "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]." [] +synonym: "axial skeleton" BROAD [] +synonym: "post-cranial axial skeleton" EXACT [] +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0005944 ! part of axial skeleton plus cranial skeleton +relationship: BFO:0000050 UBERON:0011138 ! part of postcranial axial skeletal system + +[Term] +id: UBERON:0002100 +name: trunk +def: "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." [] +synonym: "Rumpf" RELATED [] +synonym: "thoracolumbar region" EXACT [] +synonym: "torso" EXACT [] +synonym: "trunk region" EXACT [] +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: BFO:0000050 UBERON:0013702 ! part of body proper + +[Term] +id: UBERON:0002167 +name: right lung +def: "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]" [] +is_a: UBERON:0002048 ! lung +relationship: BFO:0000050 UBERON:0000170 ! part of pair of lungs + +[Term] +id: UBERON:0002168 +name: left lung +def: "Lung which consists of the left upper lobe and left lower lobe.[FMA]" [] +is_a: UBERON:0002048 ! lung +relationship: BFO:0000050 UBERON:0000170 ! part of pair of lungs + +[Term] +id: UBERON:0002204 +name: musculoskeletal system +def: "Anatomical system that consists of the muscular and skeletal systems." [] +synonym: "musculo-skeletal system" EXACT [] +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0002416 ! integumental system +relationship: BFO:0000051 UBERON:0000383 ! has part musculature of body +relationship: BFO:0000051 UBERON:0001434 ! has part skeletal system + +[Term] +id: UBERON:0002217 +name: synovial joint +def: "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]" [] +synonym: "articulatio synoviale" EXACT [] +synonym: "diarthrodial joints" RELATED [] +synonym: "diarthroses" EXACT [] +synonym: "diarthrosis" EXACT [] +synonym: "diarthrosis joint" EXACT [] +is_a: UBERON:0000982 ! skeletal joint +disjoint_from: UBERON:0011134 ! nonsynovial joint + +[Term] +id: UBERON:0002329 +name: somite +def: "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm." [] +synonym: "epimere" RELATED [] +synonym: "epimere mesoderm" RELATED [] +synonym: "epithelial somite" RELATED [] +synonym: "mesodermal cluster" BROAD [] +synonym: "somites" RELATED [] +synonym: "somitic mesoderm" RELATED [] +synonym: "somitus" RELATED [] +is_a: UBERON:0005423 ! developing anatomical structure +is_a: UBERON:0007503 ! epithelial vesicle +relationship: RO:0002202 UBERON:0003059 ! develops from presomitic mesoderm + +[Term] +id: UBERON:0002384 +name: connective tissue +def: "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [] +synonym: "Bindegewebe" RELATED [] +synonym: "portion of connective tissue" EXACT [] +synonym: "textus connectivus" EXACT [] +is_a: UBERON:0000479 ! tissue + +[Term] +id: UBERON:0002385 +name: muscle tissue +def: "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." [] +synonym: "muscular tissue" EXACT [] +synonym: "portion of muscle tissue" EXACT [] +synonym: "textus muscularis" EXACT [] +is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: BFO:0000050 UBERON:0001015 ! part of musculature + +[Term] +id: UBERON:0002416 +name: integumental system +def: "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle." [] +synonym: "body surface" RELATED [] +synonym: "dermal system" RELATED [] +synonym: "external covering of organism" RELATED [] +synonym: "integumentary system" EXACT [] +synonym: "integumentum commune" RELATED [] +synonym: "organism surface" RELATED [] +synonym: "surface" RELATED [] +is_a: UBERON:0000467 ! anatomical system +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism +relationship: BFO:0000051 UBERON:0007376 ! has part outer epithelium + +[Term] +id: UBERON:0002532 +name: epiblast (generic) +def: "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]" [] +synonym: "blastocyst" RELATED [] +synonym: "ectoblast" RELATED [] +synonym: "epiblast" EXACT [] +synonym: "epiblastus" RELATED [] +synonym: "primitive ectoderm" RELATED [] +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0003059 +name: presomitic mesoderm +def: "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." [] +synonym: "presumptive somite mesoderm" RELATED [] +synonym: "PSM" RELATED [] +synonym: "segmental plate" EXACT [] +synonym: "somitogenic mesoderm" RELATED [] +synonym: "somitomeric mesoderm" RELATED [] +synonym: "unsegmented mesenchyme" RELATED [] +synonym: "unsegmented paraxial mesoderm" EXACT [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0003077 ! part of paraxial mesoderm +relationship: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate + +[Term] +id: UBERON:0003077 +name: paraxial mesoderm +def: "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]" [] +synonym: "mesoderma paraxiale" RELATED [] +synonym: "paraxial mesenchyme" EXACT [] +synonym: "somitic mesoderm" EXACT [] +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 ! dense mesenchyme tissue +is_a: UBERON:0015212 ! lateral structure +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: RO:0002495 UBERON:0007285 ! immediate transformation of presumptive paraxial mesoderm + +[Term] +id: UBERON:0003081 +name: lateral plate mesoderm +def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [] +synonym: "lateral mesoderm" EXACT [] +synonym: "lateral plate" RELATED [] +synonym: "lateral plate mesenchyme" RELATED [] +synonym: "LPM" EXACT [] +synonym: "mesoderma laminae lateralis" RELATED [] +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 ! dense mesenchyme tissue +relationship: BFO:0000050 UBERON:0000926 ! part of mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm + +[Term] +id: UBERON:0003089 +name: sclerotome +def: "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [] +synonym: "sclerotomes" EXACT [] +synonym: "sclerotomus" RELATED [] +is_a: UBERON:0005856 ! developing mesenchymal condensation +is_a: UBERON:0007530 ! migrating mesenchyme population +relationship: RO:0002202 UBERON:0002329 ! develops from somite + +[Term] +id: UBERON:0003102 +name: surface structure +def: "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism." [] +synonym: "anatomical surface feature" EXACT [] +synonym: "surface feature" RELATED [] +synonym: "surface region" RELATED [] +synonym: "surface structures" RELATED [] +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0003103 +name: compound organ +def: "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [] +synonym: "organ" RELATED [] +is_a: UBERON:0000062 ! organ + +[Term] +id: UBERON:0003104 +name: mesenchyme +def: "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]." [] +synonym: "mesenchyma" RELATED [] +synonym: "mesenchymal tissue" EXACT [] +synonym: "mesenchyme tissue" EXACT [] +synonym: "portion of mesenchymal tissue" EXACT [] +synonym: "portion of mesenchyme tissue" EXACT [] +is_a: UBERON:0000479 ! tissue + +[Term] +id: UBERON:0003258 +name: endoderm of foregut +def: "An endoderm that is part of a foregut [Automatically generated definition]." [] +synonym: "foregut endoderm" EXACT [] +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0015833 ! foregut epithelium +intersection_of: UBERON:0000490 ! unilaminar epithelium +intersection_of: BFO:0000050 UBERON:0001041 ! part of foregut +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm + +[Term] +id: UBERON:0003364 +name: epithelium of right lung +def: "An epithelium that is part of a right lung [Automatically generated definition]." [] +synonym: "epithelial tissue of right lung" EXACT [] +synonym: "right lung epithelial tissue" EXACT [] +synonym: "right lung epithelium" EXACT [] +is_a: UBERON:0000115 ! lung epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0002167 ! part of right lung +relationship: BFO:0000050 UBERON:0002167 ! part of right lung + +[Term] +id: UBERON:0003365 +name: epithelium of left lung +def: "An epithelium that is part of a left lung [Automatically generated definition]." [] +synonym: "epithelial tissue of left lung" EXACT [] +synonym: "left lung epithelial tissue" EXACT [] +synonym: "left lung epithelium" EXACT [] +is_a: UBERON:0000115 ! lung epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0002168 ! part of left lung +relationship: BFO:0000050 UBERON:0002168 ! part of left lung + +[Term] +id: UBERON:0003570 +name: respiratory system connective tissue +def: "A portion of connective tissue that is part of a respiratory system [Automatically generated definition]." [] +synonym: "apparatus respiratorius connective tissue" EXACT [] +synonym: "apparatus respiratorius portion of connective tissue" EXACT [] +synonym: "apparatus respiratorius textus connectivus" EXACT [] +synonym: "connective tissue of apparatus respiratorius" EXACT [] +synonym: "connective tissue of respiratory system" EXACT [] +synonym: "portion of connective tissue of apparatus respiratorius" EXACT [] +synonym: "portion of connective tissue of respiratory system" EXACT [] +synonym: "respiratory system portion of connective tissue" EXACT [] +synonym: "respiratory system textus connectivus" EXACT [] +synonym: "textus connectivus of apparatus respiratorius" EXACT [] +synonym: "textus connectivus of respiratory system" EXACT [] +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: BFO:0000050 UBERON:0001004 ! part of respiratory system +relationship: BFO:0000050 UBERON:0001004 ! part of respiratory system + +[Term] +id: UBERON:0003580 +name: lower respiratory tract connective tissue +def: "A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]." [] +synonym: "connective tissue of lower respiratory tract" EXACT [] +synonym: "lower respiratory tract portion of connective tissue" EXACT [] +synonym: "lower respiratory tract textus connectivus" EXACT [] +synonym: "portion of connective tissue of lower respiratory tract" EXACT [] +synonym: "textus connectivus of lower respiratory tract" EXACT [] +is_a: UBERON:0003570 ! respiratory system connective tissue +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract +relationship: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract + +[Term] +id: UBERON:0003586 +name: trunk connective tissue +def: "A portion of connective tissue that is part of a trunk [Automatically generated definition]." [] +synonym: "connective tissue of torso" EXACT [] +synonym: "connective tissue of trunk" EXACT [] +synonym: "portion of connective tissue of torso" EXACT [] +synonym: "portion of connective tissue of trunk" EXACT [] +synonym: "textus connectivus of torso" EXACT [] +synonym: "textus connectivus of trunk" EXACT [] +synonym: "torso connective tissue" EXACT [] +synonym: "torso portion of connective tissue" EXACT [] +synonym: "torso textus connectivus" EXACT [] +synonym: "trunk portion of connective tissue" EXACT [] +synonym: "trunk textus connectivus" EXACT [] +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0003831 +name: respiratory system muscle +def: "Any muscle organ that is part of a respiratory system [Automatically generated definition]." [] +synonym: "apparatus respiratorius muscle organ" EXACT [] +synonym: "muscle organ of apparatus respiratorius" EXACT [] +synonym: "muscle organ of respiratory system" EXACT [] +synonym: "respiratory system muscle organ" EXACT [] +is_a: UBERON:0001630 ! muscle organ +intersection_of: UBERON:0001630 ! muscle organ +intersection_of: BFO:0000050 UBERON:0001004 ! part of respiratory system +relationship: BFO:0000050 UBERON:0001004 ! part of respiratory system + +[Term] +id: UBERON:0003837 +name: thoracic segment connective tissue +def: "A portion of connective tissue that is part of a thorax [Automatically generated definition]." [] +synonym: "connective tissue of thorax" EXACT [] +synonym: "portion of connective tissue of thorax" EXACT [] +synonym: "textus connectivus of thorax" EXACT [] +synonym: "thorax connective tissue" EXACT [] +synonym: "thorax portion of connective tissue" EXACT [] +synonym: "thorax textus connectivus" EXACT [] +synonym: "upper body connective tissue" RELATED [] +is_a: UBERON:0003586 ! trunk connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk +relationship: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk + +[Term] +id: UBERON:0003914 +name: epithelial tube +def: "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [] +synonym: "epithelial or endothelial tube" EXACT [] +is_a: UBERON:0000025 ! tube +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0003929 +name: digestive tract epithelium +def: "An epithelium that lines the lumen of the digestive tract." [] +synonym: "alimentary tract epithelium" RELATED [] +synonym: "digestive tract epithelial tissue" EXACT [] +synonym: "epithelial tissue of digestive tract" EXACT [] +synonym: "epithelial tissue of gut" EXACT [] +synonym: "epithelium of digestive tract" EXACT [] +synonym: "epithelium of gut" EXACT [] +synonym: "gastrodermis" EXACT [] +synonym: "gut epithelial tissue" EXACT [] +synonym: "gut epithelium" EXACT [] +is_a: UBERON:0000483 ! epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0001555 ! part of digestive tract +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0004111 +name: anatomical conduit +def: "Any tube, opening or passage that connects two distinct anatomical spaces." [] +synonym: "foramen" NARROW [] +synonym: "foramina" NARROW [] +synonym: "opening" RELATED [] +synonym: "ostia" RELATED [] +synonym: "ostium" RELATED [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000051 UBERON:0013686 ! has part anatomical conduit space + +[Term] +id: UBERON:0004119 +name: endoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the endoderm." [] +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +relationship: RO:0002202 UBERON:0000925 ! develops from endoderm + +[Term] +id: UBERON:0004120 +name: mesoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the mesoderm." [] +synonym: "mesodermal derivative" EXACT [] +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm + +[Term] +id: UBERON:0004121 +name: ectoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the ectoderm." [] +synonym: "ectodermal deriviative" EXACT [] +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm + +[Term] +id: UBERON:0004185 +name: endodermal part of digestive tract +def: "A portions of the gut that is derived from endoderm." [] +synonym: "endodermal gut" EXACT [] +synonym: "gut endoderm" EXACT [] +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004921 ! subdivision of digestive tract +intersection_of: UBERON:0004921 ! subdivision of digestive tract +intersection_of: BFO:0000050 UBERON:0001555 ! part of digestive tract +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm + +[Term] +id: UBERON:0004253 +name: skin muscle +def: "Any muscle organ that is part of a skin of body [Automatically generated definition]." [] +synonym: "integumental system muscle" EXACT [] +synonym: "muscle of integumental system" EXACT [] +synonym: "muscle organ of skin" EXACT [] +synonym: "skin muscle organ" EXACT [] +is_a: UBERON:0001630 ! muscle organ +intersection_of: UBERON:0001630 ! muscle organ +intersection_of: BFO:0000050 UBERON:0002416 ! part of integumental system +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0004288 +name: skeleton +def: "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." [] +synonym: "set of all bones" EXACT [] +synonym: "set of bones of body" EXACT [] +is_a: UBERON:0034925 ! anatomical collection +disjoint_from: UBERON:0004770 ! articular system +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system +relationship: BFO:0000051 UBERON:0004765 ! has part skeletal element + +[Term] +id: UBERON:0004464 +name: musculature of thorax +def: "Any collection of muscles that is part of a thorax [Automatically generated definition]." [] +synonym: "muscle group of thorax" EXACT [] +synonym: "muscles of thorax" EXACT [] +synonym: "musculi thoracis" EXACT [] +synonym: "set of muscles of thorax" EXACT [] +synonym: "thoracic musculature" EXACT [] +is_a: UBERON:0004479 ! musculature of trunk +intersection_of: UBERON:0001015 ! musculature +intersection_of: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk +relationship: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk + +[Term] +id: UBERON:0004479 +name: musculature of trunk +def: "Any collection of muscles that is part of a trunk [Automatically generated definition]." [] +synonym: "muscle group of trunk" EXACT [] +synonym: "muscular system of trunk" RELATED [] +synonym: "set of muscles of trunk" EXACT [] +is_a: UBERON:0001015 ! musculature +intersection_of: UBERON:0001015 ! musculature +intersection_of: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0004765 +name: skeletal element +def: "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." [] +is_a: UBERON:0000062 ! organ +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system + +[Term] +id: UBERON:0004770 +name: articular system +def: "Anatomical system that consists of all the joints of the body." [] +synonym: "joint system" EXACT [] +synonym: "set of all joints" RELATED [] +synonym: "set of all joints of body" EXACT [] +synonym: "set of joints of body" RELATED [] +is_a: UBERON:0034925 ! anatomical collection +relationship: BFO:0000050 UBERON:0001434 ! part of skeletal system +relationship: BFO:0000051 UBERON:0000982 ! has part skeletal joint + +[Term] +id: UBERON:0004802 +name: respiratory tract epithelium +def: "the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi" [] +synonym: "airway epithelium" RELATED [] +synonym: "epithelial tissue of respiratory tract" EXACT [] +synonym: "epithelium of respiratory tract" EXACT [] +synonym: "respiratory epithelium" RELATED [] +synonym: "respiratory tract epithelial tissue" EXACT [] +is_a: UBERON:0004807 ! respiratory system epithelium +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0010499 ! pseudostratified ciliated columnar epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0000065 ! part of respiratory tract +relationship: BFO:0000050 UBERON:0000072 ! part of proximo-distal subdivision of respiratory tract + +[Term] +id: UBERON:0004807 +name: respiratory system epithelium +def: "An epithelium that is part of a respiratory system [Automatically generated definition]." [] +synonym: "apparatus respiratorius epithelial tissue" EXACT [] +synonym: "apparatus respiratorius epithelium" EXACT [] +synonym: "epithelial tissue of apparatus respiratorius" EXACT [] +synonym: "epithelial tissue of respiratory system" EXACT [] +synonym: "epithelium of apparatus respiratorius" EXACT [] +synonym: "epithelium of respiratory system" EXACT [] +synonym: "respiratory system epithelial tissue" EXACT [] +is_a: UBERON:0000483 ! epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0001004 ! part of respiratory system +relationship: BFO:0000050 UBERON:0001004 ! part of respiratory system + +[Term] +id: UBERON:0004815 +name: lower respiratory tract epithelium +def: "An epithelium that is part of a lower respiratory tract [Automatically generated definition]." [] +synonym: "epithelial tissue of lower respiratory tract" EXACT [] +synonym: "epithelium of lower respiratory tract" EXACT [] +synonym: "lower respiratory tract epithelial tissue" EXACT [] +is_a: UBERON:0004802 ! respiratory tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract +relationship: BFO:0000050 UBERON:0001558 ! part of lower respiratory tract + +[Term] +id: UBERON:0004873 +name: splanchnopleure +def: "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]." [] +synonym: "ventral splanchnic mesoderm" RELATED [] +is_a: UBERON:0002050 ! embryonic structure +relationship: BFO:0000050 UBERON:0003081 ! part of lateral plate mesoderm + +[Term] +id: UBERON:0004883 +name: lung mesenchyme +def: "The mass of tissue made up of mesenchymal cells in the lung." [] +synonym: "lung-associated mesenchyme" EXACT [] +synonym: "mesenchyme of lung" EXACT [] +synonym: "pulmonary mesenchyme" EXACT [] +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003104 ! mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: BFO:0000050 UBERON:0002048 ! part of lung +relationship: BFO:0000050 UBERON:0002048 ! part of lung +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm + +[Term] +id: UBERON:0004905 +name: articulation +def: "Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [] +synonym: "joint" NARROW [] +is_a: UBERON:0034921 ! multi organ part structure +relationship: BFO:0000050 UBERON:0004770 ! part of articular system + +[Term] +id: UBERON:0004906 +name: ectodermal part of digestive tract +def: "A portion of the gut that is derived from ectoderm." [] +synonym: "ectodermal gut" EXACT [] +synonym: "gut ectoderm" EXACT [] +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0004921 ! subdivision of digestive tract +intersection_of: UBERON:0004921 ! subdivision of digestive tract +intersection_of: BFO:0000050 UBERON:0001555 ! part of digestive tract +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm + +[Term] +id: UBERON:0004921 +name: subdivision of digestive tract +def: "A proximal-distal subdivision of the digestive tract." [] +synonym: "alimentary system subdivision" RELATED [] +synonym: "intestinal tract" RELATED [] +synonym: "segment of intestinal tract" RELATED [] +synonym: "subdivision of alimentary system" RELATED [] +is_a: UBERON:0013522 ! subdivision of tube +relationship: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0004923 +name: organ component layer +def: "A part of a wall of an organ that forms a layer." [] +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000060 ! part of anatomical wall + +[Term] +id: UBERON:0005090 +name: muscle structure +def: "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." [] +synonym: "muscle" RELATED [] +synonym: "muscle element" RELATED [] +synonym: "musculus" EXACT [] +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0005153 +name: epithelial bud +def: "A bud is a protrusion that forms from an epithelial sheet by localized folding." [] +is_a: UBERON:0005157 ! epithelial fold + +[Term] +id: UBERON:0005157 +name: epithelial fold +def: "An epithelial sheet bent on a linear axis." [] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0005177 +name: trunk region element +def: "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." [] +synonym: "trunk organ" EXACT [] +is_a: UBERON:0000062 ! organ +intersection_of: UBERON:0000062 ! organ +intersection_of: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0005178 +name: thoracic cavity element +def: "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." [] +synonym: "thoracic cavity organ" EXACT [] +is_a: UBERON:0005181 ! thoracic segment organ + +[Term] +id: UBERON:0005181 +name: thoracic segment organ +def: "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." [] +synonym: "upper body organ" RELATED [] +is_a: UBERON:0005177 ! trunk region element +intersection_of: UBERON:0000062 ! organ +intersection_of: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk +relationship: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk + +[Term] +id: UBERON:0005256 +name: trunk mesenchyme +def: "Mesenchyme that is part of a developing trunk." [] +synonym: "trunk and cervical mesenchyme" RELATED [] +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0005291 ! embryonic tissue +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: BFO:0000050 UBERON:0000922 ! part of embryo +intersection_of: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0009142 ! part of entire embryonic mesenchyme + +[Term] +id: UBERON:0005291 +name: embryonic tissue +def: "A portion of tissue that is part of an embryo." [] +synonym: "developing tissue" RELATED [] +synonym: "portion of embryonic tissue" EXACT [] +is_a: UBERON:0000479 ! tissue +intersection_of: UBERON:0000479 ! tissue +intersection_of: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000050 UBERON:0002050 ! part of embryonic structure + +[Term] +id: UBERON:0005423 +name: developing anatomical structure +synonym: "developing structure" RELATED [] +synonym: "developmental structure" RELATED [] +synonym: "developmental tissue" RELATED [] +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0005597 +name: lung primordium +def: "A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum." [] +synonym: "lateral diverticula" RELATED [] +synonym: "lung diverticulum" RELATED [] +synonym: "lung endoderm" RELATED [] +is_a: UBERON:0001048 ! primordium +relationship: BFO:0000050 UBERON:0008947 ! part of respiratory primordium +relationship: RO:0002202 UBERON:0001041 ! develops from foregut + +[Term] +id: UBERON:0005598 +name: trunk somite +def: "A somite that is part of a trunk." [] +is_a: UBERON:0002329 ! somite +intersection_of: UBERON:0002329 ! somite +intersection_of: BFO:0000050 UBERON:0002100 ! part of trunk +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0005764 +name: acellular membrane +def: "A acellular anatomical structure that is the bounding layer of a anatomical structure." [] +is_a: UBERON:0000476 ! acellular anatomical structure +relationship: BFO:0000050 UBERON:0000061 ! part of anatomical structure + +[Term] +id: UBERON:0005769 +name: basement membrane of epithelium +def: "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina." [] +synonym: "basement membrane" RELATED [] +synonym: "basement membrane of connective tissue" EXACT [] +synonym: "membrana basalis" EXACT [] +is_a: UBERON:0005764 ! acellular membrane +relationship: BFO:0000050 UBERON:0000483 ! part of epithelium + +[Term] +id: UBERON:0005856 +name: developing mesenchymal condensation +def: "A delimited region of dense mesenchyme within looser mesenchyme." [] +synonym: "mesenchyme condensation" EXACT [] +is_a: UBERON:0007524 ! dense mesenchyme tissue +is_a: UBERON:0011585 ! cell condensation + +[Term] +id: UBERON:0005911 +name: endo-epithelium +def: "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]" [] +synonym: "endoderm-derived epithelium" EXACT [] +synonym: "endoepithelium" EXACT [] +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: UBERON:0000483 ! epithelium +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm + +[Term] +id: UBERON:0005944 +name: axial skeleton plus cranial skeleton +def: "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]." [] +synonym: "skeleton axiale" RELATED [] +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0011137 ! part of axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome + +[Term] +id: UBERON:0006595 +name: presumptive endoderm +def: "Presumptive structure of the blastula that will develop into endoderm." [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0006598 +name: presumptive structure +def: "Portion of embryonic tissue determined by fate mapping to become a structure." [] +synonym: "future structure" EXACT [] +synonym: "presumptive structures" EXACT [] +is_a: UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0006601 +name: presumptive ectoderm +def: "Presumptive structure of the blastula that will develop into ectoderm." [] +synonym: "presumptive epidermis" RELATED [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0006603 +name: presumptive mesoderm +def: "Presumptive structure of the blastula that will develop into mesoderm." [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0007010 +name: cleaving embryo +def: "Organism at the cleavage stage." [] +is_a: UBERON:0000922 ! embryo + +[Term] +id: UBERON:0007026 +name: presumptive gut +synonym: "embryonic digestive tube" RELATED [] +synonym: "future digestive tract" EXACT [] +synonym: "future digestive tube" EXACT [] +synonym: "future gut" EXACT [] +synonym: "primitive gut" EXACT [] +synonym: "primordial digestive tube" RELATED [] +synonym: "primordial gut" RELATED [] +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0007282 +name: presumptive segmental plate +def: "A presumptive structure that has the potential to develop into a presomitic mesoderm." [] +synonym: "presumptive segmental plates" RELATED [] +is_a: UBERON:0006598 ! presumptive structure +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm + +[Term] +id: UBERON:0007285 +name: presumptive paraxial mesoderm +def: "The part of the blastula that has the potential to develop into a paraxial mesoderm." [] +synonym: "future paraxial mesenchyme" EXACT [] +synonym: "future paraxial mesoderm" EXACT [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0000307 ! part of blastula + +[Term] +id: UBERON:0007376 +name: outer epithelium +def: "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]." [] +synonym: "epidermis" EXACT [] +synonym: "epidermis (sensu Metazoa)" EXACT [] +synonym: "hypoderm" RELATED [] +synonym: "hypodermis" RELATED [] +synonym: "outer epidermal layer" EXACT [] +synonym: "outer epithelial layer" EXACT [] +is_a: UBERON:0003102 ! surface structure +is_a: UBERON:0010371 ! ecto-epithelium +relationship: BFO:0000050 UBERON:0000468 ! part of multicellular organism +relationship: RO:0002202 UBERON:0007383 ! develops from enveloping layer of ectoderm + +[Term] +id: UBERON:0007383 +name: enveloping layer of ectoderm +def: "Outermost layer of cells surrounding the embryo." [] +synonym: "enveloping layer" EXACT [] +synonym: "EVL" EXACT [] +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: RO:0002202 UBERON:0000076 ! develops from external ectoderm + +[Term] +id: UBERON:0007499 +name: epithelial sac +def: "An epithelial tube that is open at one end only." [] +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0009856 ! sac + +[Term] +id: UBERON:0007503 +name: epithelial vesicle +def: "A closed epithelium with a lumen." [] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0007524 +name: dense mesenchyme tissue +def: "Mesenchyme with little extracellular matrix." [] +is_a: UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0007530 +name: migrating mesenchyme population +def: "Mesenchymal cells that are migrating." [] +is_a: UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0007592 +name: ciliated columnar epithelium +def: "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]" [] +is_a: UBERON:0000485 ! simple columnar epithelium +is_a: UBERON:0007601 ! ciliated epithelium + +[Term] +id: UBERON:0007601 +name: ciliated epithelium +def: "Epithelium bearing vibratile cilia on the free surface." [] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0007690 +name: early pharyngeal endoderm +def: "." [] +synonym: "early pharyngeal arch endoderm" EXACT [] +synonym: "pharyngeal arch endoderm" RELATED [] +synonym: "pharyngeal endoderm" RELATED [] +synonym: "pharyngeal region endoderm" RELATED [] +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0003258 ! endoderm of foregut +is_a: UBERON:0005291 ! embryonic tissue +relationship: BFO:0000050 UBERON:0009722 ! part of entire pharyngeal arch endoderm +relationship: RO:0002202 UBERON:0000925 ! develops from endoderm + +[Term] +id: UBERON:0008814 +name: pharyngeal arch system +def: "A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]." [] +synonym: "embryonic pharyngeal complex" EXACT [] +synonym: "pharyngeal apparatus" EXACT [] +synonym: "pharyngeal arch complex" RELATED [] +synonym: "pharyngeal arch region" RELATED [] +synonym: "pharyngeal arches and clefts" RELATED [] +synonym: "pharyngeal complex" RELATED [] +synonym: "pharyngeal system" EXACT [] +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000050 UBERON:0009145 ! part of pharyngeal region of foregut + +[Term] +id: UBERON:0008947 +name: respiratory primordium +is_a: UBERON:0001048 ! primordium +relationship: BFO:0000050 UBERON:0003258 ! part of endoderm of foregut + +[Term] +id: UBERON:0009142 +name: entire embryonic mesenchyme +def: "Sum total of mesenchyme in the embryo." [] +is_a: UBERON:0000477 ! anatomical cluster +relationship: BFO:0000050 UBERON:0000922 ! part of embryo +relationship: BFO:0000051 UBERON:0003104 ! has part mesenchyme + +[Term] +id: UBERON:0009145 +name: pharyngeal region of foregut +synonym: "pharyngeal region" EXACT [] +is_a: UBERON:0005423 ! developing anatomical structure +relationship: BFO:0000050 UBERON:0001041 ! part of foregut + +[Term] +id: UBERON:0009569 +name: subdivision of trunk +synonym: "region of trunk" EXACT [] +synonym: "trunk subdivision" EXACT [] +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0002100 ! part of trunk + +[Term] +id: UBERON:0009602 +name: left lung associated mesenchyme +def: "Mesenchyme that is part of a developing left lung." [] +synonym: "left lung mesenchyme" EXACT [] +is_a: UBERON:0004883 ! lung mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: BFO:0000050 UBERON:0002168 ! part of left lung +relationship: BFO:0000050 UBERON:0002168 ! part of left lung + +[Term] +id: UBERON:0009603 +name: right lung associated mesenchyme +def: "Mesenchyme that is part of a developing right lung." [] +synonym: "right lung mesenchyme" EXACT [] +is_a: UBERON:0004883 ! lung mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: BFO:0000050 UBERON:0002167 ! part of right lung +relationship: BFO:0000050 UBERON:0002167 ! part of right lung + +[Term] +id: UBERON:0009618 +name: trunk paraxial mesoderm +synonym: "trunk and cervical paraxial mesenchyme" EXACT [] +synonym: "trunk paraxial mesenchyme" RELATED [] +is_a: UBERON:0005256 ! trunk mesenchyme +relationship: BFO:0000050 UBERON:0003077 ! part of paraxial mesoderm +relationship: BFO:0000050 UBERON:0005256 ! part of trunk mesenchyme + +[Term] +id: UBERON:0009722 +name: entire pharyngeal arch endoderm +synonym: "pharyngeal arch endoderm" RELATED [] +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0015833 ! foregut epithelium +relationship: BFO:0000050 UBERON:0003929 ! part of digestive tract epithelium +relationship: BFO:0000050 UBERON:0008814 ! part of pharyngeal arch system +relationship: RO:0002202 UBERON:0000925 ! develops from endoderm + +[Term] +id: UBERON:0009854 +name: digestive tract diverticulum +def: "Branch or outpocketing of the digestive tract." [] +synonym: "diverticulum of gut" RELATED [] +synonym: "intestinal pouch" RELATED [] +is_a: UBERON:0004921 ! subdivision of digestive tract +is_a: UBERON:0009856 ! sac +intersection_of: UBERON:0009856 ! sac +intersection_of: BFO:0000050 UBERON:0001555 ! part of digestive tract + +[Term] +id: UBERON:0009856 +name: sac +synonym: "diverticulum" RELATED [] +synonym: "pouch" EXACT [] +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +def: "An anatomical structure that has more than one cell as a part." [] +synonym: "multicellular structure" EXACT [] +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0010316 +name: germ layer / neural crest +is_a: UBERON:0000479 ! tissue +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) + +[Term] +id: UBERON:0010371 +name: ecto-epithelium +def: "Epithelium composed of cells that develops from the ectoderm[FMA,modified]." [] +synonym: "ectoderm-derived epithelium" EXACT [] +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000483 ! epithelium +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm + +[Term] +id: UBERON:0010378 +name: mesenchyme from splanchnopleure +def: "Mesenchyme that develops_from a splanchnopleure." [] +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 ! dense mesenchyme tissue +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: BFO:0000050 UBERON:0000922 ! part of embryo +intersection_of: RO:0002202 UBERON:0004873 ! develops from splanchnopleure +relationship: BFO:0000050 UBERON:0009142 ! part of entire embryonic mesenchyme +relationship: RO:0002202 UBERON:0004873 ! develops from splanchnopleure + +[Term] +id: UBERON:0010498 +name: pseudostratified columnar epithelium +def: "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels." [] +is_a: UBERON:0000485 ! simple columnar epithelium + +[Term] +id: UBERON:0010499 +name: pseudostratified ciliated columnar epithelium +def: "Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile." [] +synonym: "epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)" EXACT [] +is_a: UBERON:0007592 ! ciliated columnar epithelium +is_a: UBERON:0010498 ! pseudostratified columnar epithelium + +[Term] +id: UBERON:0010912 +name: subdivision of skeleton +def: "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." [] +synonym: "skeletal subdivision" EXACT [] +synonym: "subdivision of skeleton (in vivo)" RELATED [] +is_a: UBERON:0011216 ! organ system subdivision +relationship: BFO:0000050 UBERON:0000075 ! part of subdivision of skeletal system +relationship: BFO:0000050 UBERON:0004288 ! part of skeleton + +[Term] +id: UBERON:0011134 +name: nonsynovial joint +def: "Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis." [] +synonym: "solid joint" EXACT [] +is_a: UBERON:0000982 ! skeletal joint + +[Term] +id: UBERON:0011137 +name: axial skeletal system +def: "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." [] +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: BFO:0000051 UBERON:0000982 ! has part skeletal joint +relationship: BFO:0000051 UBERON:0005944 ! has part axial skeleton plus cranial skeleton + +[Term] +id: UBERON:0011138 +name: postcranial axial skeletal system +def: "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints." [] +synonym: "axial skeletal system" BROAD [] +synonym: "post-cranial axial skeletal system" EXACT [] +is_a: UBERON:0000075 ! subdivision of skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome + +[Term] +id: UBERON:0011216 +name: organ system subdivision +def: "A subdivision of an anatomical system." [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000050 UBERON:0000467 ! part of anatomical system + +[Term] +id: UBERON:0011585 +name: cell condensation +def: "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [] +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0011676 +name: subdivision of organism along main body axis +def: "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column." [] +synonym: "axial subdivision of organism" EXACT [] +synonym: "body segment" RELATED [] +synonym: "main body segment" RELATED [] +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0013701 ! part of main body axis + +[Term] +id: UBERON:0012274 +name: columnar epithelium +def: "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]" [] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0012275 +name: meso-epithelium +def: "Epithelium that derives from the mesoderm. [Automatically generated definition]." [] +synonym: "mesoderm-derived epithelium" EXACT [] +synonym: "mesoepithelium" EXACT [] +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000483 ! epithelium +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm + +[Term] +id: UBERON:0013522 +name: subdivision of tube +is_a: UBERON:0000064 ! organ part +relationship: BFO:0000050 UBERON:0000025 ! part of tube +relationship: BFO:0000051 UBERON:0000060 ! has part anatomical wall +relationship: BFO:0000051 UBERON:0000464 ! has part anatomical space + +[Term] +id: UBERON:0013686 +name: anatomical conduit space +def: "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]." [] +synonym: "foramen space" NARROW [] +is_a: UBERON:0000464 ! anatomical space +relationship: BFO:0000050 UBERON:0004111 ! part of anatomical conduit + +[Term] +id: UBERON:0013701 +name: main body axis +def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [] +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0013702 +name: body proper +def: "The region of the organism associated with the visceral organs." [] +synonym: "body" RELATED [] +synonym: "whole body" RELATED [] +is_a: UBERON:0000475 ! organism subdivision +relationship: BFO:0000050 UBERON:0013701 ! part of main body axis + +[Term] +id: UBERON:0013754 +name: integumentary system layer +def: "A organ component layer that is part of a integumental system." [] +synonym: "layer of skin" NARROW [] +synonym: "skin layer" NARROW [] +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: BFO:0000050 UBERON:0002416 ! part of integumental system +relationship: BFO:0000050 UBERON:0002416 ! part of integumental system + +[Term] +id: UBERON:0013765 +name: digestive system element +def: "Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements." [] +synonym: "digestive organ" EXACT [] +synonym: "digestive system organ" EXACT [] +is_a: UBERON:0000062 ! organ +intersection_of: UBERON:0000062 ! organ +intersection_of: BFO:0000050 UBERON:0001007 ! part of digestive system +relationship: BFO:0000050 UBERON:0001007 ! part of digestive system + +[Term] +id: UBERON:0014477 +name: thoracic skeleton +def: "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum." [] +synonym: "skeleton of thorax" EXACT [] +synonym: "thoracic part of axial skeleton" EXACT [] +synonym: "thoracic skeleton" EXACT [] +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: BFO:0000050 UBERON:0000915 ! part of thoracic segment of trunk +relationship: BFO:0000050 UBERON:0002090 ! part of postcranial axial skeleton + +[Term] +id: UBERON:0015212 +name: lateral structure +def: "Any structure that is placed on one side of the left-right axis of a bilaterian." [] +is_a: UBERON:0000061 ! anatomical structure +relationship: BFO:0000050 UBERON:0000465 ! part of material anatomical entity + +[Term] +id: UBERON:0015329 +name: respiratory system basement membrane +def: "A basement membrane of epithelium that is part of a respiratory system." [] +is_a: UBERON:0005769 ! basement membrane of epithelium +intersection_of: UBERON:0005769 ! basement membrane of epithelium +intersection_of: BFO:0000050 UBERON:0001004 ! part of respiratory system +relationship: BFO:0000050 UBERON:0003570 ! part of respiratory system connective tissue + +[Term] +id: UBERON:0015833 +name: foregut epithelium +def: "A epithelium that is part of a foregut." [] +is_a: UBERON:0003929 ! digestive tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: BFO:0000050 UBERON:0001041 ! part of foregut +relationship: BFO:0000050 UBERON:0001041 ! part of foregut + +[Term] +id: UBERON:0016879 +name: future central nervous system +def: "Primordium that develops into the central nervous system" [] +synonym: "future CNS" EXACT [] +synonym: "presumptive central nervous system" EXACT [] +is_a: UBERON:0006598 ! presumptive structure +relationship: BFO:0000050 UBERON:0016880 ! part of future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm + +[Term] +id: UBERON:0016880 +name: future nervous system +def: "Primordium that develops into the nervous system" [] +synonym: "presumptive nervous system" EXACT [] +is_a: UBERON:0006598 ! presumptive structure + +[Term] +id: UBERON:0034921 +name: multi organ part structure +def: "An multicellular anatomical structure that has subparts of multiple organs as a part." [] +synonym: "anatomical cluster" RELATED [] +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: BFO:0000051 UBERON:0000064 ! has part organ part + +[Term] +id: UBERON:0034925 +name: anatomical collection +def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [] +is_a: UBERON:0000465 ! material anatomical entity +relationship: BFO:0000051 UBERON:0000061 ! has part anatomical structure + +[Term] +id: UBERON:0036072 +name: respiratory primordium epithelium +is_a: UBERON:0004185 ! endodermal part of digestive tract +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0007499 ! epithelial sac +is_a: UBERON:0009854 ! digestive tract diverticulum +is_a: UBERON:0015833 ! foregut epithelium +intersection_of: UBERON:0007499 ! epithelial sac +intersection_of: BFO:0000050 UBERON:0008947 ! part of respiratory primordium +relationship: BFO:0000050 UBERON:0008947 ! part of respiratory primordium +relationship: RO:0002202 UBERON:0007690 ! develops from early pharyngeal endoderm + +[Term] +id: UBERON:0036073 +name: respiratory primordium mesenchyme +synonym: "respiratory primordium associated mesenchyme" EXACT [] +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003104 ! mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: BFO:0000050 UBERON:0008947 ! part of respiratory primordium +relationship: BFO:0000050 UBERON:0008947 ! part of respiratory primordium +relationship: RO:0002202 UBERON:0004873 ! develops from splanchnopleure + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +is_a: RO:0002314 ! inheres in part of +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002202 +name: develops from +name: develops_from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 RO:0002202 +is_transitive: true +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002203 +name: develops into +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: CARO:0000003 ! anatomical structure +range: CARO:0000003 ! anatomical structure +holds_over_chain: BFO:0000051 RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +holds_over_chain: RO:0002203 BFO:0000050 +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002258 +name: developmentally preceded by +def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] +is_a: RO:0002324 ! developmentally related to +inverse_of: RO:0002286 ! developmentally succeeded by + +[Typedef] +id: RO:0002286 +name: developmentally succeeded by +def: "Inverse of developmentally preceded by" [] +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002314 +name: inheres in part of +def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] +holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] + +[Typedef] +id: RO:0002324 +name: developmentally related to +def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] + +[Typedef] +id: RO:0002328 +name: functionally related to + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002384 +name: has developmental potential involving +def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] +is_a: RO:0002324 ! developmentally related to + +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002388 +name: has potential to directly develop into +def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] +is_a: RO:0002387 ! has potential to develop into + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +is_a: RO:0002609 ! related via dependence to + +[Typedef] +id: RO:0002495 +name: immediate transformation of +synonym: "direct_transformation_of" EXACT [] +synonym: "immediately transforms from" EXACT [] + +[Typedef] +id: RO:0002500 +name: causal agent in +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! has causal agent + +[Typedef] +id: RO:0002502 +name: depends on + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +holds_over_chain: BFO:0000051 RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002608 +name: has causal agent +def: "Inverse of 'causal agent in'" [] +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002609 +name: related via dependence to +def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] + diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl new file mode 100644 index 00000000..4ec09508 --- /dev/null +++ b/src/ontology/imports/cl_import.owl @@ -0,0 +1,6231 @@ + + + + + + + + + + + + + + + definition + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a core relation that holds between a part and its whole + part of + part of + + + + + + + + + + a core relation that holds between a whole and its part + has part + has part + + + + + + + + + + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + inheres in + + + + + + + + + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + bearer of + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + overlaps + + + + + + + + + true + + + + + + + + + + + + + + + + + + + + + x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y + develops from + develops_from + + + + + + + + + + + + develops into + + + + + + + + + + + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + capable of part of + + + + + + + + + true + + + + + + + + + + + + + + + + x has developmental contribution from y iff x has some part z such that z develops from y + has developmental contribution from + + + + + + + + + + + + + + developmentally contributes to + + + + + + + + + + Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p + developmentally preceded by + + + + + + + + + Inverse of developmentally preceded by + developmentally succeeded by + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + inheres in part of + + + + + + + + + true + + + + + + + + A mereological relationship or a topological relationship + mereotopologically related to + + + + + + + + A relationship that holds between entities participating in some developmental process (GO:0032502) + developmentally related to + + + + + + + + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + part of structure that is capable of + + + + + + + + + true + + + + + + + + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). + has developmental potential involving + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + has potential to developmentally contribute to + + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + has potential to develop into + + + + + + + + + x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y + has potential to directly develop into + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + causally related to + + + + + + + + direct_transformation_of + immediately transforms from + immediate transformation of + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + causal agent in + + + + + + + + depends on + + + + + + + + + + + + + + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + causal relation between material entity and a process + + + + + + + + + Inverse of 'causal agent in' + has causal agent + + + + + + + + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + related via dependence to + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + anatomical structure + + + + + + + + + material anatomical entity + + + + + + + + + cell part + + + + + + + + chemical entity + + + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CALOHA:TS-2035 + FMA:68646 + GO:0005623 + KUPO:0000002 + VHOG:0001533 + WBbt:0004017 + XAO:0003012 + cell + + The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). + cell + cell + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CARO:mah + + + + + + + + + + A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + CARO:0000013 + cell in vivo + cell + + To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). + native cell + + + + + A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). + CARO:mah + + + + + + + + + + A cell that will develop into a neuron often after a migration phase. + BTO:0000930 + FBbt:00005146 + FMA:70563 + cell + neuroblast + + + + + A cell that will develop into a neuron often after a migration phase. + GOC:NV + http://en.wikipedia.org/wiki/Neuroblast + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. + CALOHA:TS-2086 + FMA:63368 + cell + stem cell + + + + + A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. + GOC:tfm + MESH:A11.872 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. + BTO:0002881 + CALOHA:TS-2360 + FMA:86684 + NSC + neural stem cell + cell + neuronal stem cell + + + + + + true + + + + + Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. + GOC:tfm + MESH:D058953 + PMID:15247488 + http://en.wikipedia.org/wiki/Neural_stem_cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A stem cell that can give rise to multiple lineages of cells. + FMA:84789 + multi-fate stem cell + multifate stem cell + multipotent cell + multipotent stem cell + cell + multi fate stem cell + + + + + A stem cell that can give rise to multiple lineages of cells. + GOC:add + + + + + + + + + + + + + + + A precursor cell with a limited number of potential fates. + BTO:0000125 + FMA:84782 + blast cell + cell + define using PATO mulit-potent or oligopotent? + non-terminally differentiated cell + + + + + A precursor cell with a limited number of potential fates. + SANBI:mhl + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. + BTO:0000414 + CALOHA:TS-2026 + CARO:0000077 + FBbt:00000124 + FMA:66768 + WBbt:0003672 + epitheliocyte + cell + epithelial cell + + + + + A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. + FB:ma + GOC:tfm + MESH:A11.436 + + + + + + + + + + cell + columnar/cuboidal epithelial cell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BTO:0004299 + lung epithelial cell + cell + epithelial cell of lung + + + + + + + + + Ectoderm destined to be nervous tissue. + neurectoderm cell + cell + neurectodermal cell + + + + + Ectoderm destined to be nervous tissue. + GOC:tfm + ISBN:068340007X + + + + + + + + + A cell whose function is determined by the generation or the reception of an electric signal. + cell + electrically active cell + + + + + A cell whose function is determined by the generation or the reception of an electric signal. + FB:ma + + + + + + + + + + + + + + + A cell of the outer of the three germ layers of the embryo. + FMA:72549 + ectoderm cell + cell + ectodermal cell + + + + + A cell of the outer of the three germ layers of the embryo. + MESH:A16.254.425.273 + + + + + + + + + + + + + + + A cell of the inner of the three germ layers of the embryo. + FMA:72555 + endoderm cell + cell + endodermal cell + + + + + A cell of the inner of the three germ layers of the embryo. + MESH:A16.254.425.407 + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that lacks a nucleus. + FMA:68647 + non-nucleated cell + cell + anucleate cell + + + + + A cell that lacks a nucleus. + FB:ma + + + + + + + + + cell + eukaryotic cell + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelial cell of the integument (the outer layer of an organism). + CL:1000396 + BTO:0001470 + CALOHA:TS-0283 + FMA:62411 + cell of epidermis + epithelial cell of skin + cell + epidermal cell + + + + + An epithelial cell of the integument (the outer layer of an organism). + Flybase:dsj + MA:ma + + + + + cell of epidermis + FMA:62411 + + + + + epithelial cell of skin + FMA:62411 + + + + + + + + + A cell whose function is determined by its response to an electric signal. + cell + electrically responsive cell + + + + + A cell whose function is determined by its response to an electric signal. + FB:ma + + + + + + + + + A cell that initiates an electrical signal and passes that signal to another cell. + cell + electrically signaling cell + + + + + A cell that initiates an electrical signal and passes that signal to another cell. + FB:ma + + + + + + + + + + + + + + + + + + + + + + + + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + BTO:0000938 + CALOHA:TS-0683 + FBbt:00005106 + FMA:54527 + VHOG:0001483 + WBbt:0003679 + nerve cell + cell + These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. + neuron + neuron + + + + + The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. + MESH:A08.663 + MESH:D009474 + http://en.wikipedia.org/wiki/Neuron + + + + + + + + + cell + + animal cell + + + + + + + + + + + + + + + + + + + + + + + + + + + Epithelial cells derived from neural plate and neural crest. + neuroepithelial cell + BTO:0004301 + FMA:70557 + cell + The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). + neurecto-epithelial cell + + + + + Epithelial cells derived from neural plate and neural crest. + GOC:tfm + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. + + 2017-01-30T18:53:32Z + https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913 + cell + https://github.com/obophenotype/cell-ontology/issues/448 + abnormal cell + + + + + A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. + GOC:add + GOC:cg + GOC:wdd + + + + + + + + + + + + + + + + An epithelial cell derived from endoderm. + tmeehan + 2010-06-29T03:38:14Z + FMA:69075 + cell + endo-epithelial cell + + + + + An epithelial cell derived from endoderm. + FMA:69075 + GOC:tfm + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelial cell derived from ectoderm. + tmeehan + 2010-06-29T03:38:22Z + FMA:69074 + cell + ecto-epithelial cell + + + + + An epithelial cell derived from ectoderm. + FMA:69074 + GOC:tfm + + + + + + + + + Epithelial cells derived from general body ectoderm and ectoderm placodes. + tmeehan + 2010-08-26T08:31:08Z + FMA:70556 + cell + general ecto-epithelial cell + + + + + Epithelial cells derived from general body ectoderm and ectoderm placodes. + GOC:tfm + + + + + + + + + + + + + + + + + + + + + + + + + + A cell containing at least one nucleus. + tmeehan + 2010-09-07T03:32:33Z + FMA:67513 + cell + nucleate cell + + + + + A cell containing at least one nucleus. + GOC:tfm + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. + tmeehan + 2010-09-08T09:26:53Z + cell + epithelial cell of alimentary canal + + + + + An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. + GOC:tfm + ISBN:0721662544 + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that is part of the nervous system. + tmeehan + 2010-09-15T01:34:57Z + CALOHA:TS-2040 + FMA:70333 + cell + neural cell + + + + + A cell that is part of the nervous system. + GOC:tfm + ISBN:0618947256 + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. + tmeehan + 2010-09-15T03:01:54Z + CL:1000406 + CALOHA:TS-2096 + FMA:63875 + cell + connective tissue cell + + + + + + true + + + + + A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. + GOC:tfm + ISBN:0618947256 + + + + + + + + + A cell of the embryo. + tmeehan + 2010-09-15T03:39:21Z + CALOHA:TS-0263 + FMA:82840 + FMA:82841 + WBbt:0007028 + cell + embryonic cell + + + + + A cell of the embryo. + FMA:0618947256 + + + + + + + + + + + + + + + + + + + + + + + + + + An endo-epithelial cell of the respiratory tract. + tmeehan + 2010-09-23T04:38:49Z + BTO:0004533 + airway epithelial cell + cell + respiratory epithelial cell + + + + + + true + + + + + An endo-epithelial cell of the respiratory tract. + GOC:tfm + + + + + + + + + A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). + tmeehan + 2010-09-24T09:44:42Z + BTO:0001268 + FMA:72300 + WBbt:0008378 + cell + + somatic cell + + + + + A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). + GOC:tfm + ISBN:0721662544 + + + + + + + + + + + + + + + + + + + + + + + + + + tmeehan + 2011-06-21T12:29:31Z + cell + epithelial cell of lower respiratory tract + + + + + + true + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. + precursor cell + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. + GOC:dos + + + + + + + + + + + + + + + + + + + + + + + + + + Any neuron that is part of a central nervous system. + TermGenie + 2014-06-25T01:17:43Z + cell + CL:2000029 + central nervous system neuron + + + + + Any neuron that is part of a central nervous system. + GOC:TermGenie + + + + + + + + + + + + + + + + + + + + + + + + + + Any neuron that is part of a peripheral nervous system. + TermGenie + 2014-06-25T02:28:17Z + cell + CL:2000032 + peripheral nervous system neuron + + + + + Any neuron that is part of a peripheral nervous system. + GOC:TermGenie + + + + + + + + + system process + + + + + + + + cellular_component + + + + + + + + + + cell + + + + + + + + + + nucleus + nucleus + + + + + + + + biological_process + + + + + + + + + cellular process + + + + + + + + + stem cell division + + + + + + + + + + transmission of nerve impulse + + + + + + + + + signaling + + + + + + + + + cell differentiation + + + + + + + + + multicellular organismal process + + + + + + + + + developmental process + + + + + + + + + + multicellular organismal signaling + + + + + + + + + organelle + + + + + + + + + membrane-bounded organelle + + + + + + + + + + intracellular organelle + + + + + + + + + + intracellular membrane-bounded organelle + + + + + + + + + intracellular part + + + + + + + + + + cell part + cell part + + + + + + + + + + cellular developmental process + + + + + + + + + nervous system process + + + + + + + + + cell division + + + + + + + + quality + + + + + + + + + qualitative + + + + + + + + + deviation(from_normal) + + + + + + + + + abnormal + abnormal + + + + + + + + + physical object quality + + + + + + + + + cellular quality + + + + + + + + + cellular potency + + + + + + + + + multipotent + + + + + + + + + nucleate quality + + + + + + + + + anucleate + + + + + + + + + nucleated + + + + + + + + + + + + + + + A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. + PNS + pars peripherica + systema nervosum periphericum + peripheral nervous system + + + + + + + + + + + + + + + Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. + anatomical tube + duct + tube + + + + + + + + + + + + + + + Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. + wall + wall of organ + organ wall + anatomical wall + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + biological structure + connected biological structure + anatomical structure + + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + anatomical unit + body organ + element + organ + + + + + + + + + + + + + + + A multicellular structure that is a part of an organ. + cardinal organ part + regional part of organ + organ part + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts + respiratory tract + + + + + + + + + + + + + + + + + + + + + + + + + + + An section of a respiratory tract. + respiratory tract + subdivision of respiratory tract + proximo-distal subdivision of respiratory tract + + + + + + + + + + + + + + + + + + + + + Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. + skeletal system subdivision + skeletal system part + subdivision of skeletal system + + + + + + + + + + + + + + + + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. + surface (external) ectoderm + surface ectoderm + external ectoderm + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the endoderm and the mesoderm. + mixed endoderm/mesoderm-derived structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the ectoderm, mesoderm and endoderm. + mixed ectoderm/mesoderm/endoderm-derived structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin + connective tissue of lung + pulmonary interstitium + lung interstitial tissue + lung interstitium + pulmonary connective tissue + pulmonary interstitial tissue + lung connective tissue + + + + + + + + + + + + + + + + + + + + + + + + + + The epithelial layer of the lung. + epithelial tissue of lung + epithelium of lung + lung epithelial tissue + pulmonary epithelium + lung epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. + segment of tracheobronchial tree + respiratory conducting tube + segment of tracheobronchial tree + tracheobronchial tree segment + respiratory tube + + + + + + + + + + + + + + + + + + + + + + Structure derived from foregut that becomes a lung[GO]. + gemma pulmonalis + gemma respiratoria + lung bud + primary lung bud + respiratory diverticulum + lung bud + + + + + + + + + + + + + + + + + + + + + + + + + + + The pair of anatomical structures comprised of a left lung and right lung. + lungs + lungs pair + pulmones + set of lungs + pair of lungs + + + + + + + + + + + + + + + Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. + apparatus respiratorius organ + breathing organ + organ of apparatus respiratorius + organ of respiratory system + respiratory organ + respiratory system organ + gas exchange organ + respiration organ + + + + + + + + + + + + + + + Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + blastula embryo + blastosphere + blastula + + + + + + + + + + + + + + + + + + + + + + + + + + The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). + digestive tract wall + wall of digestive tract + wall of gut + wall of alimentary tract + gut wall + + + + + + + + + + + + + + + + + + + + + The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. + muscle system + muscle system of body + muscular system + musculature system + set of all muscles + set of muscles of body + vertebrate muscular system + muskelsystem + musculature of body + + + + + + + + + Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. + lumen + space + lumen space + anatomical spaces + anatomical space + + + + + + + + + Anatomical entity that has mass. + material anatomical entity + + + + + + + + + Anatomical entity that has no mass. + immaterial physical anatomical entity + immaterial anatomical entity + + + + + + + + + + + + + + + + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + system + body system + connected anatomical system + organ system + anatomical systems + anatomical system + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + organism + multi-cellular organism + animal + Koerper + body + whole body + whole organism + multicellular organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + anatomic region + body part + body region + cardinal body part + organism subdivision + + + + + + + + + + Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. + acellular anatomical structures + acellular anatomical structure + + + + + + + + + Anatomical group that has its parts adjacent to one another. + anatomical cluster + + + + + + + + + + + + + + + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + portion of tissue + tissue portion + simple tissue + tissue + + + + + + + + + + + + + + + + + + + + + + + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. + epithelial tissue + portion of epithelium + epithelium + + + + + + + + + + Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] + columnar epithelium + columnar epithlium + epithelium simplex columnare + simple columnar epithelium + simple columnar epithelia + simple columnar epithelium + + + + + + + + + Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] + stratified epithelium + laminated epithelium + multilaminar epithelium + + + + + + + + + Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] + simple epithelium + unilaminar epithelia + unilaminar epithelium + + + + + + + + + + + + + + + + Subdivision of trunk that lies between the head and the abdomen. + thorax + anterior subdivision of trunk + upper body + upper trunk + thoracic segment of trunk + + + + + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + embryonic organism + developing organism + developmental tissue + embryo + + + + + + + + + A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. + embryonic tissue + germinal layer + primary germ layer + embryonic germ layer + embryonic germ layers + germ layer + + + + + + + + + + + + + + + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. + embryonic ectoderm + ectoderm + + + + + + + + + + + + + + + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. + entoderm + endoderm + + + + + + + + + + + + + + + The middle germ layer of the embryo, between the endoderm and ectoderm. + embryonic mesoderm + entire mesoderm + mesodermal mantle + mesoderm + + + + + + + + + + + + + + + + + Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. + articulation + joint + articular joint + joints + skeletal joint + + + + + + + + + + + + + + + Functional system which consists of structures involved in respiration. + apparatus respiratorius + respiratory system + Atmungssystem + apparatus respiratorius + systema respiratorium + respiratory system + + + + + + + + + + + + + + + An airway through which respiratory air passes in organisms. + airway + airways + respiratory airway + + + + + + + + + + + + + + Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. + alimentary system + alimentary tract + gastrointestinal system + gut + digestive system + + + + + + + + + + + + + organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. + systema cardiovasculare + circulatory system + + + + + + + + + + + + + + + + + + + + + A subdivision of the muscular system corresponding to a subdisivision of an organism. + muscle group + muscles set + musculature + musculi + set of muscles + set of skeletal muscles + muscle system + muscles + musculature system + musculature + + + + + + + + + + + + + + + + + + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. + neurological system + nerve net + systema nervosum + nervous system + + + + + + + + + + + + + + + + + + + + + + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. + CNS + systema nervosum centrale + cerebrospinal axis + neuraxis + central nervous system + + + + + + + + + Anterior subdivision of a digestive tract. + praeenteron + proenteron + foregut + + + + + + + + + + + + + + + Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. + bud + future organ + placode + primordia + rudiment + primordium + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + skeleton system + set of all bones and joints + Skelettsystem + skeletal system + + + + + + + + + + + + + + + + + + + + + A tube extending from the mouth to the anus. + gut + digestive tube + enteric tract + alimentary canal + alimentary tract + digestive canal + gut tube + digestive tract + + + + + + + + + + + + + + + + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] + lower respiratory tract + + + + + + + + + + + + + + + + + + + + + + + Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. + muscle + muscle organ + + + + + + + + + + + + + + + + + + + + + + + + Respiration organ that develops as an oupocketing of the esophagus. + pulmo + lung + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of an embryo. + developing embryonic structure + embryonic anatomical structure + developing structure + embryonale Struktur + embryonic structures + embryonic structure + + + + + + + + + + + + + + + + + + + + + The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. + axial skeleton + post-cranial axial skeleton + postcranial axial skeleton + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + thoracolumbar region + torso + trunk region + Rumpf + trunk + + + + + + + + + + + + + + + Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] + right lung + + + + + + + + + + + + + + + Lung which consists of the left upper lobe and left lower lobe.[FMA] + left lung + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of the muscular and skeletal systems. + musculo-skeletal system + musculoskeletal system + + + + + + + + + + Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] + articulatio synoviale + diarthroses + diarthrosis + diarthrosis joint + diarthrodial joints + synovial joint + + + + + + + + + + + + + + + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. + mesodermal cluster + epimere + epimere mesoderm + epithelial somite + somites + somitic mesoderm + somitus + somite + + + + + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + portion of connective tissue + textus connectivus + Bindegewebe + connective tissue + + + + + + + + + + + + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + muscular tissue + portion of muscle tissue + textus muscularis + muscle tissue + + + + + + + + + + + + + + + + + + + + + Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. + integumentary system + body surface + dermal system + external covering of organism + integumentum commune + organism surface + surface + integumental system + + + + + + + + + In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] + epiblast + blastocyst + ectoblast + epiblastus + primitive ectoderm + epiblast (generic) + + + + + + + + + + + + + + + + + + + + + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. + segmental plate + unsegmented paraxial mesoderm + PSM + presumptive somite mesoderm + somitogenic mesoderm + somitomeric mesoderm + unsegmented mesenchyme + presomitic mesoderm + + + + + + + + + + + + + + + + + + + + + + + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] + paraxial mesenchyme + somitic mesoderm + mesoderma paraxiale + paraxial mesoderm + + + + + + + + + + + + + + + + + + + + + + + + Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. + LPM + lateral mesoderm + lateral plate + lateral plate mesenchyme + mesoderma laminae lateralis + lateral plate mesoderm + + + + + + + + + + + + + + + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. + sclerotomes + sclerotomus + sclerotome + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + anatomical surface feature + surface feature + surface region + surface structures + surface structure + + + + + + + + + Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. + organ + compound organ + + + + + + + + + Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. + mesenchymal tissue + mesenchyme tissue + portion of mesenchymal tissue + portion of mesenchyme tissue + mesenchyma + mesenchyme + + + + + + + + + + + + + + + + + + + + + + + + + + An endoderm that is part of a foregut [Automatically generated definition]. + foregut endoderm + endoderm of foregut + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a right lung [Automatically generated definition]. + epithelial tissue of right lung + right lung epithelial tissue + right lung epithelium + epithelium of right lung + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a left lung [Automatically generated definition]. + epithelial tissue of left lung + left lung epithelial tissue + left lung epithelium + epithelium of left lung + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. + apparatus respiratorius connective tissue + apparatus respiratorius portion of connective tissue + apparatus respiratorius textus connectivus + connective tissue of apparatus respiratorius + connective tissue of respiratory system + portion of connective tissue of apparatus respiratorius + portion of connective tissue of respiratory system + respiratory system portion of connective tissue + respiratory system textus connectivus + textus connectivus of apparatus respiratorius + textus connectivus of respiratory system + respiratory system connective tissue + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. + connective tissue of lower respiratory tract + lower respiratory tract portion of connective tissue + lower respiratory tract textus connectivus + portion of connective tissue of lower respiratory tract + textus connectivus of lower respiratory tract + lower respiratory tract connective tissue + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a trunk [Automatically generated definition]. + connective tissue of torso + connective tissue of trunk + portion of connective tissue of torso + portion of connective tissue of trunk + textus connectivus of torso + textus connectivus of trunk + torso connective tissue + torso portion of connective tissue + torso textus connectivus + trunk portion of connective tissue + trunk textus connectivus + trunk connective tissue + + + + + + + + + + + + + + + + + + + + + + + + + + Any muscle organ that is part of a respiratory system [Automatically generated definition]. + apparatus respiratorius muscle organ + muscle organ of apparatus respiratorius + muscle organ of respiratory system + respiratory system muscle organ + respiratory system muscle + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a thorax [Automatically generated definition]. + connective tissue of thorax + portion of connective tissue of thorax + textus connectivus of thorax + thorax connective tissue + thorax portion of connective tissue + thorax textus connectivus + upper body connective tissue + thoracic segment connective tissue + + + + + + + + + + Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. + epithelial or endothelial tube + epithelial tube + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that lines the lumen of the digestive tract. + digestive tract epithelial tissue + epithelial tissue of digestive tract + epithelial tissue of gut + epithelium of digestive tract + epithelium of gut + gastrodermis + gut epithelial tissue + gut epithelium + alimentary tract epithelium + digestive tract epithelium + + + + + + + + + + + + + + + Any tube, opening or passage that connects two distinct anatomical spaces. + foramen + foramina + opening + ostia + ostium + anatomical conduit + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the endoderm. + endoderm-derived structure + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the mesoderm. + mesodermal derivative + mesoderm-derived structure + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the ectoderm. + ectodermal deriviative + ectoderm-derived structure + + + + + + + + + + + + + + + + + + + + + + + + + A portions of the gut that is derived from endoderm. + endodermal gut + gut endoderm + endodermal part of digestive tract + + + + + + + + + + + + + + + + + + + + + + + + + + Any muscle organ that is part of a skin of body [Automatically generated definition]. + integumental system muscle + muscle of integumental system + muscle organ of skin + skin muscle organ + skin muscle + + + + + + + + + + + + + + + + + + + + + + Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. + set of all bones + set of bones of body + skeleton + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a thorax [Automatically generated definition]. + muscle group of thorax + muscles of thorax + musculi thoracis + set of muscles of thorax + thoracic musculature + musculature of thorax + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a trunk [Automatically generated definition]. + muscle group of trunk + set of muscles of trunk + muscular system of trunk + musculature of trunk + + + + + + + + + + + + + + + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. + skeletal element + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of all the joints of the body. + joint system + set of all joints of body + set of all joints + set of joints of body + articular system + + + + + + + + + + + + + + + + + + + + + + + + + + + + the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi + epithelial tissue of respiratory tract + epithelium of respiratory tract + respiratory tract epithelial tissue + airway epithelium + respiratory epithelium + respiratory tract epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a respiratory system [Automatically generated definition]. + apparatus respiratorius epithelial tissue + apparatus respiratorius epithelium + epithelial tissue of apparatus respiratorius + epithelial tissue of respiratory system + epithelium of apparatus respiratorius + epithelium of respiratory system + respiratory system epithelial tissue + respiratory system epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a lower respiratory tract [Automatically generated definition]. + epithelial tissue of lower respiratory tract + epithelium of lower respiratory tract + lower respiratory tract epithelial tissue + lower respiratory tract epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. + ventral splanchnic mesoderm + splanchnopleure + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The mass of tissue made up of mesenchymal cells in the lung. + lung-associated mesenchyme + mesenchyme of lung + pulmonary mesenchyme + lung mesenchyme + + + + + + + + + + + + + + + Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. + joint + articulation + + + + + + + + + + + + + + + + + + + + + + + + + A portion of the gut that is derived from ectoderm. + ectodermal gut + gut ectoderm + ectodermal part of digestive tract + + + + + + + + + + + + + + + A proximal-distal subdivision of the digestive tract. + alimentary system subdivision + intestinal tract + segment of intestinal tract + subdivision of alimentary system + subdivision of digestive tract + + + + + + + + + + + + + + + A part of a wall of an organ that forms a layer. + organ component layer + + + + + + + + + Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. + musculus + muscle + muscle element + muscle structure + + + + + + + + + A bud is a protrusion that forms from an epithelial sheet by localized folding. + epithelial bud + + + + + + + + + An epithelial sheet bent on a linear axis. + epithelial fold + + + + + + + + + + + + + + + + + + + + + + + + + + An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. + trunk organ + trunk region element + + + + + + + + + An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + thoracic cavity organ + thoracic cavity element + + + + + + + + + + + + + + + + + + + + + + + + + + An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. + upper body organ + thoracic segment organ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing trunk. + trunk and cervical mesenchyme + trunk mesenchyme + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of tissue that is part of an embryo. + portion of embryonic tissue + developing tissue + embryonic tissue + + + + + + + + + developing structure + developmental structure + developmental tissue + developing anatomical structure + + + + + + + + + + + + + + + + + + + + + A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. + lateral diverticula + lung diverticulum + lung endoderm + lung primordium + + + + + + + + + + + + + + + + + + + + + + + + + + A somite that is part of a trunk. + trunk somite + + + + + + + + + + + + + + + A acellular anatomical structure that is the bounding layer of a anatomical structure. + acellular membrane + + + + + + + + + + + + + + + An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. + basement membrane of connective tissue + membrana basalis + basement membrane + basement membrane of epithelium + + + + + + + + + + A delimited region of dense mesenchyme within looser mesenchyme. + mesenchyme condensation + developing mesenchymal condensation + + + + + + + + + + + + + + + + + + + + + Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] + endoderm-derived epithelium + endoepithelium + endo-epithelium + + + + + + + + + + + + + + + + + + + + + Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. + skeleton axiale + axial skeleton plus cranial skeleton + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into endoderm. + presumptive endoderm + + + + + + + + + Portion of embryonic tissue determined by fate mapping to become a structure. + future structure + presumptive structures + presumptive structure + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into ectoderm. + presumptive epidermis + presumptive ectoderm + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into mesoderm. + presumptive mesoderm + + + + + + + + + Organism at the cleavage stage. + cleaving embryo + + + + + + + + + future digestive tract + future digestive tube + future gut + primitive gut + embryonic digestive tube + primordial digestive tube + primordial gut + presumptive gut + + + + + + + + + + + + + + + A presumptive structure that has the potential to develop into a presomitic mesoderm. + presumptive segmental plates + presumptive segmental plate + + + + + + + + + + + + + + + The part of the blastula that has the potential to develop into a paraxial mesoderm. + future paraxial mesenchyme + future paraxial mesoderm + presumptive paraxial mesoderm + + + + + + + + + + + + + + + + + + + + + + The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. + epidermis + epidermis (sensu Metazoa) + outer epidermal layer + outer epithelial layer + hypoderm + hypodermis + outer epithelium + + + + + + + + + + + + + + + + + + + + + + + Outermost layer of cells surrounding the embryo. + EVL + enveloping layer + enveloping layer of ectoderm + + + + + + + + + + An epithelial tube that is open at one end only. + epithelial sac + + + + + + + + + A closed epithelium with a lumen. + epithelial vesicle + + + + + + + + + Mesenchyme with little extracellular matrix. + dense mesenchyme tissue + + + + + + + + + Mesenchymal cells that are migrating. + migrating mesenchyme population + + + + + + + + + + Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] + ciliated columnar epithelium + + + + + + + + + Epithelium bearing vibratile cilia on the free surface. + ciliated epithelium + + + + + + + + + + + + + + + + + + + + + + + . + early pharyngeal arch endoderm + pharyngeal arch endoderm + pharyngeal endoderm + pharyngeal region endoderm + early pharyngeal endoderm + + + + + + + + + + + + + + + + + + + + + A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. + embryonic pharyngeal complex + pharyngeal apparatus + pharyngeal system + pharyngeal arch complex + pharyngeal arch region + pharyngeal arches and clefts + pharyngeal complex + pharyngeal arch system + + + + + + + + + + + + + + + respiratory primordium + + + + + + + + + + + + + + + + + + + + + Sum total of mesenchyme in the embryo. + entire embryonic mesenchyme + + + + + + + + + + + + + + + pharyngeal region + pharyngeal region of foregut + + + + + + + + + + + + + + + region of trunk + trunk subdivision + subdivision of trunk + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing left lung. + left lung mesenchyme + left lung associated mesenchyme + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing right lung. + right lung mesenchyme + right lung associated mesenchyme + + + + + + + + + + + + + + + + + + + + + trunk and cervical paraxial mesenchyme + trunk paraxial mesenchyme + trunk paraxial mesoderm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + pharyngeal arch endoderm + entire pharyngeal arch endoderm + + + + + + + + + + + + + + + + + + + + + Branch or outpocketing of the digestive tract. + diverticulum of gut + intestinal pouch + digestive tract diverticulum + + + + + + + + + pouch + diverticulum + sac + + + + + + + + + An anatomical structure that has more than one cell as a part. + multicellular structure + multicellular anatomical structure + + + + + + + + + + + + + + + + + germ layer / neural crest + + + + + + + + + + + + + + + + + + + + + Epithelium composed of cells that develops from the ectoderm[FMA,modified]. + ectoderm-derived epithelium + ecto-epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a splanchnopleure. + mesenchyme from splanchnopleure + + + + + + + + + A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. + pseudostratified columnar epithelium + + + + + + + + + + Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. + epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) + pseudostratified ciliated columnar epithelium + + + + + + + + + + + + + + + + + + + + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. + skeletal subdivision + subdivision of skeleton (in vivo) + subdivision of skeleton + + + + + + + + + Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. + solid joint + nonsynovial joint + + + + + + + + + + + + + + + + + + + + + Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. + axial skeletal system + + + + + + + + + + + + + + + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. + axial skeletal system + post-cranial axial skeletal system + postcranial axial skeletal system + + + + + + + + + + + + + + + A subdivision of an anatomical system. + organ system subdivision + + + + + + + + + Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). + cell condensation + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + axial subdivision of organism + body segment + main body segment + subdivision of organism along main body axis + + + + + + + + + An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] + columnar epithelium + + + + + + + + + + + + + + + + + + + + + Epithelium that derives from the mesoderm. [Automatically generated definition]. + mesoderm-derived epithelium + mesoepithelium + meso-epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + + subdivision of tube + + + + + + + + + + + + + + + An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. + foramen space + anatomical conduit space + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + main body axis + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + body + whole body + body proper + + + + + + + + + + + + + + + + + + + + + + + + + + A organ component layer that is part of a integumental system. + layer of skin + skin layer + integumentary system layer + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. + digestive organ + digestive system organ + digestive system element + + + + + + + + + + + + + + + + + + + + + Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. + skeleton of thorax + thoracic part of axial skeleton + thoracic skeleton + thoracic skeleton + + + + + + + + + + + + + + + Any structure that is placed on one side of the left-right axis of a bilaterian. + lateral structure + + + + + + + + + + + + + + + + + + + + + + + + + + A basement membrane of epithelium that is part of a respiratory system. + respiratory system basement membrane + + + + + + + + + + + + + + + + + + + + + + + + + + A epithelium that is part of a foregut. + foregut epithelium + + + + + + + + + + + + + + + + + + + + + Primordium that develops into the central nervous system + future CNS + presumptive central nervous system + future central nervous system + + + + + + + + + Primordium that develops into the nervous system + presumptive nervous system + future nervous system + + + + + + + + + + + + + + + An multicellular anatomical structure that has subparts of multiple organs as a part. + anatomical cluster + multi organ part structure + + + + + + + + + + + + + + + A collection of anatomical structures that are alike in terms of their morphology or developmental origin. + anatomical collection + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + respiratory primordium epithelium + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + respiratory primordium associated mesenchyme + respiratory primordium mesenchyme + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/cl_terms.txt b/src/ontology/imports/cl_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/cl_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/go_import.obo b/src/ontology/imports/go_import.obo new file mode 100644 index 00000000..f391695c --- /dev/null +++ b/src/ontology/imports/go_import.obo @@ -0,0 +1,44 @@ +format-version: 1.2 +ontology: upheno/imports/go_import + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +created_by: janelomax +creation_date: 2012-09-19T15:05:24Z + +[Typedef] +id: has_part +name: has_part +namespace: external +xref: BFO:0000051 +is_transitive: true + +[Typedef] +id: part_of +name: part of +namespace: external +xref: BFO:0000050 +is_transitive: true +inverse_of: has_part ! has_part + diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl new file mode 100644 index 00000000..bda46997 --- /dev/null +++ b/src/ontology/imports/go_import.owl @@ -0,0 +1,184 @@ + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + external + part_of + part_of + part of + + + + + + + + + BFO:0000051 + external + has_part + has_part + has_part + + + + + + + + + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + janelomax + 2012-09-19T15:05:24Z + GO:0000004 + GO:0007582 + GO:0044699 + Wikipedia:Biological_process + biological process + physiological process + biological_process + single organism process + single-organism process + GO:0008150 + + + + + + + + + + Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. + biological_process + + + + + A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + GOC:pdt + + + + + + + diff --git a/src/ontology/imports/go_terms.txt b/src/ontology/imports/go_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/go_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/iao_import.obo b/src/ontology/imports/iao_import.obo new file mode 100644 index 00000000..9ef2449a --- /dev/null +++ b/src/ontology/imports/iao_import.obo @@ -0,0 +1,218 @@ +format-version: 1.2 +ontology: upheno/imports/iao_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\n############################\n# Object Properties\n############################\n\n# Object Property: (part of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (has part)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (inheres in)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n# Object Property: (bearer of)\n\nEquivalentObjectProperties( ObjectInverseOf())\n\n\n############################\n# Classes\n############################\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: ()\n\nEquivalentClasses( ObjectOneOf())\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) + +[Term] +id: BFO:0000001 +name: entity +property_value: BFO:0000179 "entity" xsd:string +property_value: BFO:0000180 "Entity" xsd:string +property_value: IAO:0000112 "Julius Caesar" xsd:string +property_value: IAO:0000112 "the Second World War" xsd:string +property_value: IAO:0000112 "Verdi’s Requiem" xsd:string +property_value: IAO:0000112 "your body mass index" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} +property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +is_a: BFO:0000001 ! entity +property_value: BFO:0000179 "continuant" xsd:string +property_value: BFO:0000180 "Continuant" xsd:string +property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string +property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} +property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} +property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} +property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} +property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000031 ! generically dependent continuant +property_value: BFO:0000179 "sdc" xsd:string +property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string +property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string +property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string +property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string +property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string +property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string +property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string +property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string +property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string +property_value: IAO:0000112 "the role of being a doctor" xsd:string +property_value: IAO:0000112 "the shape of this hole." xsd:string +property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string +property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} +property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000031 +name: generically dependent continuant +def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] +def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +is_a: BFO:0000002 ! continuant +property_value: BFO:0000179 "gdc" xsd:string +property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string +property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string +property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string +property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string +property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: IAO:0000027 +name: data item +def: "a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements." [] +is_a: IAO:0000030 ! information content entity +property_value: IAO:0000111 "data item" xsd:string +property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string +property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string +property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string +property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string +property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string +property_value: IAO:0000118 "data" xsd:string + +[Term] +id: IAO:0000030 +name: information content entity +def: "A generically dependent continuant that is about some thing." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: IAO:0000136 BFO:0000001 ! is about entity +property_value: IAO:0000111 "information content entity" xsd:string +property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string +property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string +property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string +property_value: IAO:0000119 "OBI_0000142" xsd:string + +[Term] +id: IAO:0000078 +name: curation status specification +def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "curation status specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string +property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 "OBI_0000266" xsd:string + +[Term] +id: IAO:0000102 +name: data about an ontology part +def: "data about an ontology part is a data item about a part of an ontology, for example a term" [] +is_a: IAO:0000027 ! data item +property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string + +[Term] +id: IAO:0000225 +name: obsolescence reason specification +def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000111 "obsolescence reason specification" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string +property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string +property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string + +[Term] +id: IAO:0000409 +name: denotator type +def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] +is_a: IAO:0000102 ! data about an ontology part +property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string +property_value: IAO:0000117 "Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string + +[Term] +id: Subset +is_a: IAO:0000102 ! data about an ontology part + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + +[Typedef] +id: IAO:0000136 +name: is about +def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] +property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string +property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string +property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string +domain: IAO:0000030 ! information content entity + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl new file mode 100644 index 00000000..8747f744 --- /dev/null +++ b/src/ontology/imports/iao_import.owl @@ -0,0 +1,875 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + This document is about information artifacts and their representations + + is_about is a (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + is about + + + + + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + + + entity + Entity + Julius Caesar + Verdi’s Requiem + the Second World War + your body mass index + BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + entity + + + + + Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf + + per discussion with Barry Smith + + + + + + An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) + + + + + + + + + + continuant + Continuant + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + continuant + + + + + if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) + + + + + + if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] + + + + + + (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] + + + + + + (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] + + + + + + (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] + + + + + + Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants + + + + + + A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) + + + + + + if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) + + + + + + + + + + + sdc + SpecificallyDependentContinuant + Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key + of one-sided specifically dependent continuants: the mass of this tomato + of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. + the disposition of this fish to decay + the function of this heart: to pump blood + the mutual dependence of proton donors and acceptors in chemical reactions [79 + the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction + the pink color of a medium rare piece of grilled filet mignon at its center + the role of being a doctor + the shape of this hole. + the smell of this portion of mozzarella + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + specifically dependent continuant + + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + + + + + Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. + + per discussion with Barry Smith + + + + + (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] + + + + + + + + + + gdc + GenericallyDependentContinuant + The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. + the pdf file on your laptop, the pdf file that is a copy thereof on my laptop + the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. + A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + generically dependent continuant + + + + + b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) + + + + + + (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] + + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + data item + + + + + + + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + information content entity + + + + + + + + + + + + + + + + + + + + + + + + curation status specification + + The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) + PERSON:Bill Bug + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + OBI_0000266 + curation status specification + + + + + + + + + data about an ontology part is a data item about a part of an ontology, for example a term + Person:Alan Ruttenberg + data about an ontology part + + + + + + + + + + + + + + + + + + + + obsolescence reason specification + + The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. + The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + obsolescence reason specification + + + + + + + + + + + + + + + + + + The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. + A denotator type indicates how a term should be interpreted from an ontological perspective. + Alan Ruttenberg + Barry Smith, Werner Ceusters + denotator type + + + + + + + + + + + + + + + + + + + + + + + + + + + + + example to be eventually removed + + + + + + + + + The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job + Person:Alan Ruttenberg + failed exploratory term + + + + + + + + + Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. + metadata complete + + + + + + + + + term created to ease viewing/sort terms for development purpose, and will not be included in a release + organizational term + + + + + + + + + Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." + ready for release + + + + + + + + + Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. + metadata incomplete + + + + + + + + + Nothing done yet beyond assigning a unique class ID and proposing a preferred term. + uncurated + + + + + + + + + All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. + pending final vetting + + + + + + + + + Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. + PERSON: Alan Ruttenberg + PERSON: Melanie Courtot + core + + + + + + + + + placeholder removed + + + + + + + + + An editor note should explain what were the merged terms and the reason for the merge. + terms merged + + + + + + + + + This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. + term imported + + + + + + + + + This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. + term split + + + + + + + + + This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. + We expect to be able to mine these new reasons and add instances as required. + other + true + + + + + + + + + Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. + Alan Ruttenberg + A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf + universal + + + + + + + + + A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal + "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. + Alan Ruttenberg + defined class + + + + + + + + + A named class expression is a logical expression that is given a name. The name can be used in place of the expression. + named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions + Alan Ruttenberg + named class expression + + + + + + + + + Terms with this status should eventually replaced with a term from another ontology. + Alan Ruttenberg + group:OBI + to be replaced with external ontology term + + + + + + + + + A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. + Alan Ruttenberg + group:OBI + requires discussion + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/iao_terms.txt b/src/ontology/imports/iao_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/iao_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/pato_import.obo b/src/ontology/imports/pato_import.obo new file mode 100644 index 00000000..6c0fad49 --- /dev/null +++ b/src/ontology/imports/pato_import.obo @@ -0,0 +1,56 @@ +format-version: 1.2 +ontology: upheno/imports/pato_import + +[Term] +id: PATO:0000001 +name: quality +namespace: quality +alt_id: PATO:0000072 +def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] +synonym: "trait" EXACT [] + +[Term] +id: PATO:0000068 +name: qualitative +namespace: quality +comment: TODO: define this or obsolete it and move children somewhere else. +is_a: PATO:0000001 ! quality + +[Term] +id: PATO:0000069 +name: deviation(from_normal) +namespace: quality +def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0000068 ! qualitative + +[Term] +id: PATO:0000460 +name: abnormal +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's deviation from normal or average." [PATOC:GVG] +subset: abnormal_slim +subset: mpath_slim +subset: value_slim +synonym: "aberrant" RELATED [] +synonym: "atypia" RELATED [] +synonym: "atypical" RELATED [] +synonym: "defective" RELATED [] +is_a: PATO:0000069 ! deviation(from_normal) +property_value: RO:0002604 PATO:0000461 + +[Typedef] +id: has_part +name: has_part +namespace: quality +def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] +comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. +xref: BFO:0000051 + +[Typedef] +id: part_of +name: part_of +namespace: quality +xref: BFO:0000050 +is_transitive: true + diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl new file mode 100644 index 00000000..05773d25 --- /dev/null +++ b/src/ontology/imports/pato_import.owl @@ -0,0 +1,223 @@ + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + quality + part_of + part_of + part_of + + + + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + BFO:0000051 + quality + has_part + has_part + We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. + has_part + + + + + Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. + PATOC:CJM + + + + + + + + + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATO:0000072 + trait + quality + PATO:0000001 + quality + + + + + A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities + PATOC:GVG + + + + + + + + + quality + PATO:0000068 + TODO: define this or obsolete it and move children somewhere else. + qualitative + + + + + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + quality + PATO:0000069 + + deviation(from_normal) + + + + + A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. + PATOC:GVG + + + + + + + + + A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. + + quality + aberrant + atypia + atypical + defective + PATO:0000460 + + + + abnormal + + + + + A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. + PATOC:GVG + + + + + + + diff --git a/src/ontology/imports/pato_terms.txt b/src/ontology/imports/pato_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/pato_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/ro_import.obo b/src/ontology/imports/ro_import.obo new file mode 100644 index 00000000..c3bafed8 --- /dev/null +++ b/src/ontology/imports/ro_import.obo @@ -0,0 +1,1054 @@ +format-version: 1.2 +ontology: upheno/imports/ro_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: (enabled by)\n\nSubObjectPropertyOf( ObjectInverseOf())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (continuant)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: (occurrent)\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\"^^xsd:string) Annotation(rdfs:label \"involved in BP\"^^xsd:string) Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From ligand activity to has_ligand\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to \\\"... -> overlaps\\\"\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"From has_ligand to ligand activity\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant + +[Term] +id: CARO:0000003 +name: anatomical structure +is_a: CARO:0000006 ! material anatomical entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CARO:0000006 +name: material anatomical entity +is_a: BFO:0000040 ! material entity +property_value: IAO:0000412 http://purl.obolibrary.org/obo/caro.owl + +[Term] +id: CL:0000000 +name: cell +is_a: CARO:0000003 ! anatomical structure +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl + +[Term] +id: CL:0000540 +name: neuron +is_a: CL:0000000 ! cell +property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl + +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string + +[Term] +id: GO:0004872 +name: receptor activity + +[Term] +id: GO:0008150 +name: biological_process +is_a: BFO:0000015 ! process + +[Term] +id: PATO:0000001 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string + +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +is_a: RO:0002131 ! overlaps +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true +is_a: RO:0002131 ! overlaps + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000062 +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +holds_over_chain: BFO:0000050 BFO:0000063 +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000050 BFO:0000066 +inverse_of: BFO:0000067 ! contains process +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: RO:0000052 +name: inheres in +def: "a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "inheres in" xsd:string +property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string +property_value: IAO:0000112 "this red color inheres in this apple" xsd:string +property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string +property_value: IAO:0000118 "inheres_in" xsd:string +property_value: RO:0001900 RO:0001901 +is_a: RO:0002314 ! inheres in part of +inverse_of: RO:0000053 ! bearer of + +[Typedef] +id: RO:0000053 +name: bearer of +def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] +property_value: IAO:0000111 "bearer of" xsd:string +property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string +property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string +property_value: IAO:0000118 "bearer_of" xsd:string +property_value: IAO:0000118 "is bearer of" xsd:string +property_value: RO:0001900 RO:0001901 +range: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: BFO:0000051 RO:0000057 + +[Typedef] +id: RO:0002013 +name: has regulatory component activity +def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] +is_a: RO:0002017 ! has component activity +is_a: RO:0002334 ! regulated by +created_by: dos +creation_date: 2017-05-24T09:30:46Z + +[Typedef] +id: RO:0002014 +name: has negative regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002335 ! negatively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:01Z + +[Typedef] +id: RO:0002015 +name: has positive regulatory component activity +def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] +comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. +is_a: RO:0002013 ! has regulatory component activity +is_a: RO:0002336 ! positively regulated by +created_by: dos +creation_date: 2017-05-24T09:31:17Z + +[Typedef] +id: RO:0002017 +name: has component activity +comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. +is_a: RO:0002018 ! has component process +created_by: dos +creation_date: 2017-05-24T09:44:33Z + +[Typedef] +id: RO:0002018 +name: has component process +def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +is_a: RO:0002180 ! has component +created_by: dos +creation_date: 2017-05-24T09:49:21Z + +[Typedef] +id: RO:0002019 +name: has ligand +def: "A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function." [] +domain: GO:0004872 ! receptor activity +is_a: RO:0002233 ! has input +created_by: dos +creation_date: 2017-07-19T17:30:36Z + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002025 +name: has effector activity +def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] +comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. +is_functional: true +is_a: RO:0002017 ! has component activity +is_a: RO:0002211 ! regulates +created_by: dos +creation_date: 2017-09-22T14:14:36Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: RO:0001900 RO:0001901 +holds_over_chain: BFO:0000050 BFO:0000050 +holds_over_chain: BFO:0000051 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +holds_over_chain: BFO:0000051 RO:0002131 +is_a: RO:0002323 ! mereotopologically related to +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002180 +name: has component +def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string +property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency +is_a: BFO:0000051 ! has part + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of +expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process +expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] + +[Typedef] +id: RO:0002217 +name: actively participates in +def: "x actively participates in y if and only if x participates in y and x realizes some active role" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "agent in" xsd:string +is_a: RO:0000056 ! participates in +inverse_of: RO:0002218 ! has active participant + +[Typedef] +id: RO:0002218 +name: has active participant +def: "x has participant y if and only if x realizes some active role that inheres in y" [] +subset: ro-eco +property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has agent" xsd:string +is_a: RO:0000057 ! has participant + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000040 ! material entity +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/elements/1.1/creator "cjm" xsd:string +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002314 +name: inheres in part of +def: "q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w." [] +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of inheres in part of" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: RO:0001900 RO:0001901 +holds_over_chain: RO:0000052 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} +is_a: RO:0002502 ! depends on +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by +transitive_over: BFO:0000051 ! has part +transitive_over: RO:0002017 ! has component activity + +[Typedef] +id: RO:0002328 +name: functionally related to +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: seeAlso Involved:in +holds_over_chain: RO:0002327 BFO:0000050 +is_a: RO:0002217 ! actively participates in +is_a: RO:0002431 ! involved in or involved in regulation of +transitive_over: BFO:0000050 ! part of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +is_a: RO:0002609 ! related via dependence to + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002448 +name: activity directly regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002449 +name: activity directly negatively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "inhibits" xsd:string +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002450 +name: activity directly positively regulates activity of +def: "Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "activates" xsd:string +is_a: RO:0002448 ! activity directly regulates activity of + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002502 +name: depends on +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: seeAlso BFO:0000169 + +[Typedef] +id: RO:0002506 +name: causal relation between material entities +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (material entity to material entity)" xsd:string +is_a: RO:0002506 ! causal relation between material entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002566 +name: causally influences +def: "Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (material entity to material entity)" xsd:string +is_a: RO:0002506 ! causal relation between material entities + +[Typedef] +id: RO:0002573 +name: has modifier +def: "A relation that holds between an attribute or a qualifier and another attribute." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 +property_value: IAO:0000232 "This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the \"modifiers\" are." xsd:string +domain: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +holds_over_chain: BFO:0000051 RO:0002215 +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002609 +name: related via dependence to +def: "A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes." [] +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +holds_over_chain: RO:0002327 BFO:0000051 +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl new file mode 100644 index 00000000..4722e545 --- /dev/null +++ b/src/ontology/imports/ro_import.owl @@ -0,0 +1,2919 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + definition + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL + is a defining property chain axiom + + + + + + + + If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. + is a defining property chain axiom where second argument is reflexive + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + is part of + my brain is part of my body (continuant parthood, two material entities) + my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) + this day is part of this year (occurrent parthood) + a core relation that holds between a part and its whole + Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. + part_of + + part of + + + http://www.obofoundry.org/ro/#OBO_REL:part_of + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + has part + + + + + + + + + + + + + + + + + preceded by + x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. + is preceded by + preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by + + preceded by + + + + + + + + + + + + + + + + precedes + x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + + precedes + + + + + + + + + + + + + + + + + + + occurs in + b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + occurs_in + unfolds in + unfolds_in + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant + + occurs in + + + + + + + + site of + [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t + Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + + contains process + + + + + + + + + + inheres in + this fragility inheres in this vase + this red color inheres in this apple + a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence + A dependent inheres in its bearer at all times for which the dependent exists. + inheres_in + + inheres in + + + + + + + + + bearer of + this apple is bearer of this red color + this vase is bearer of this fragility + a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence + A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. + bearer_of + is bearer of + + bearer of + + + + + + + + + + + participates in + this blood clot participates in this blood coagulation + this input material (or this output material) participates in this process + this investigator participates in this investigation + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates_in + participates in + + + + + + + + + + + + + + has participant + this blood coagulation has participant this blood clot + this investigation has participant this investigator + this process has participant this input material (or this output material) + a relation between a process and a continuant, in which the continuant is somehow involved in the process + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant + has participant + + + + + + + + + + A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. + dos + 2017-05-24T09:30:46Z + has regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. + dos + 2017-05-24T09:31:01Z + By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. + has negative regulatory component activity + + + + + + + + + + A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. + dos + 2017-05-24T09:31:17Z + By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. + has positive regulatory component activity + + + + + + + + + dos + 2017-05-24T09:44:33Z + A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. + has component activity + + + + + + + + + w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + dos + 2017-05-24T09:49:21Z + has component process + + + + + + + + + + A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function. + dos + 2017-07-19T17:30:36Z + has ligand + + + + + + + + + + dos + 2017-09-17T13:52:24Z + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + directly regulated by + + + + + Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + GOC:dos + + + + + + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + dos + 2017-09-17T13:52:38Z + directly negatively regulated by + + + + + Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. + GOC:dos + + + + + + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + dos + 2017-09-17T13:52:47Z + directly positively regulated by + + + + + Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. + GOC:dos + + + + + + + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + dos + 2017-09-22T14:14:36Z + This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. + has effector activity + + + + + A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. + GOC:dos + + + + + + + + + + David Osumi-Sutherland + + X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) + ends after + + + + + + + + + + David Osumi-Sutherland + starts_at_end_of + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + immediately preceded by + + + + + + + + + David Osumi-Sutherland + ends_at_start_of + meets + + + X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) + immediately precedes + + + + + + + + + + + + + + + + + + + + + + x overlaps y if and only if there exists some z such that x has part z and z part of y + http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + + overlaps + + + + + + + + + true + + + + + + + + + + w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. + The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. + For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. + + + has component + + + + + + + + + + + + + + + + + + + process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. + We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit + Chris Mungall + David Hill + Tanya Berardini + + GO + Regulation precludes parthood; the regulatory process may not be within the regulated process. + regulates (processual) + false + regulates + + + + + + + + + + + Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + negatively regulates (process to process) + + negatively regulates + + + + + + + + + + + + + + + + Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. + Chris Mungall + + positively regulates (process to process) + + positively regulates + + + + + + + + + + + mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) + osteoclast SubClassOf 'capable of' some 'bone resorption' + A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. + Chris Mungall + has function realized in + + + For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". + RO_0000053 some (RO_0000054 only ?Y) + + capable of + + + + + + + + + + + + + + c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. + Chris Mungall + has function in + RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) + capable of part of + + + + + + + + + true + + + + + + + + + + x actively participates in y if and only if x participates in y and x realizes some active role + Chris Mungall + agent in + actively participates in + + + + + + + + + 'heart development' has active participant some Shh protein + + x has participant y if and only if x realizes some active role that inheres in y + This may be obsoleted and replaced by the original 'has agent' relation + Chris Mungall + has agent + + has active participant + + + + + + + + + + + Chris Mungall + + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. + https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 + + A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. + temporally related to + + + + + + + + + + + + + p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. + Chris Mungall + consumes + + has input + + + + + + + + + + + + + A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. + c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of + + + + + + + + + + + + + + A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. + c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. + affects + acts upstream of or within + + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y + causally upstream of, positive effect + + + + + + + + + + + cjm + holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y + causally upstream of, negative effect + + + + + + + + + + + + + + + + + q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. + Because part_of is transitive, inheres in is a sub-relation of inheres in part of + Chris Mungall + + + inheres in part of + + + + + + + + + true + + + + + + + + A mereological relationship or a topological relationship + Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships + + mereotopologically related to + + + + + + + + + + + + + + + + + + a particular instances of akt-2 enables some instance of protein kinase activity + Chris Mungall + catalyzes + executes + has + is catalyzing + is executing + This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. + This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables + + + + + + + + Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function + functionally related to + + + + + + + + + + + + + this relation holds between c and p when c is part of some c', and c' is capable of p. + Chris Mungall + false + part of structure that is capable of + + + + + + + + + true + + + + + + + + + + + + + + + + + + c involved_in p if and only if c enables some process p', and p' is part of p + Chris Mungall + actively involved in + enables part of + involved in + + + + + + + + + + + + + + + inverse of enables + Chris Mungall + enabled by + + + + + + + + + + + + inverse of regulates + Chris Mungall + regulated by (processual) + + regulated by + + + + + + + + + inverse of negatively regulates + Chris Mungall + + negatively regulated by + + + + + + + + + inverse of positively regulates + Chris Mungall + + positively regulated by + + + + + + + + + + inverse of has input + Chris Mungall + + + input of + + + + + + + + + + + + inverse of upstream of + Chris Mungall + causally downstream of + + + + + + + + + + + + Chris Mungall + immediately causally downstream of + + + + + + + + + + This relation groups causal relations between material entities and causal relations between processes + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. + +To define causal relations in an activity-flow type network, we make use of 3 primitives: + + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative + +The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. + +For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. + +For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. + +Each of these 3 primitives can be composed to yield a cross-product of different relation types. + Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causally related to + + + + + + + + + + + + p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain + Chris Mungall + causally upstream of + + + + + + + + + + + p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. + Chris Mungall + + immediately causally upstream of + + + + + + + + + + + p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. + We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 + Chris Mungall + influences (processual) + affects + causally upstream of or within + + + + + + + + + + inverse of causally upstream of or within + Chris Mungall + + + causally downstream of or within + + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' regulates some p + Chris Mungall + involved in regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' positively regulates some p + Chris Mungall + + involved in positive regulation of + + + + + + + + + + + + + + + + + c involved in regulation of p if c is involved in some p' and p' negatively regulates some p + Chris Mungall + + involved in negative regulation of + + + + + + + + + + + c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p + Chris Mungall + involved in or reguates + involved in or involved in regulation of + + + + + + + + + + + + + + A protein that enables activity in a cytosol. + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + Chris Mungall + executes activity in + enables activity in + + is active in + + + + + + + + + true + + + + + c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. + GOC:cjm + GOC:dos + + + + + + + + + + + A relationship that holds between two entities in which the processes executed by the two entities are causally connected. + Considering relabeling as 'pairwise interacts with' + This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. + Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. + in pairwise interaction with + + interacts with + http://purl.obolibrary.org/obo/MI_0914 + https://github.com/oborel/obo-relations/wiki/InteractionRelations + + + + + + + + + + An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. + Chris Mungall + binds + molecularly binds with + molecularly interacts with + + http://purl.obolibrary.org/obo/MI_0915 + + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. + Chris Mungall + molecularly controls + activity directly regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. + Chris Mungall + inhibits + molecularly decreases activity of + activity directly negatively regulates activity of + + + + + + + + + + + + + + Holds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. + Chris Mungall + activates + molecularly increases activity of + activity directly positively regulates activity of + + + + + + + + + + + + + + p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. + Chris Mungall + + has part that occurs in + + + + + + + + + true + + + + + + + + + + A relationship between a material entity and a process where the material entity has some causal role that influences the process + + causal agent in process + + + + + + + + + + + p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between processes + + + + + + + + Chris Mungall + depends on + + + + + + + + + + + + The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch + Chris Mungall + + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + causal relation between material entities + + + + + + + + + + Chris Mungall + + causally influenced by (material entity to material entity) + causally influenced by + + + + + + + + + + + + + + + + + + + Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b + Chris Mungall + + causally influences (material entity to material entity) + causally influences + + + + + + + + + A relation that holds between an attribute or a qualifier and another attribute. + Chris Mungall + + This relation is intended to be used in combination with PATO, to be able to refine PATO quality classes using modifiers such as 'abnormal' and 'normal'. It has yet to be formally aligned into an ontological framework; it's not clear what the ontological status of the "modifiers" are. + + has modifier + + + + + + + + + + Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. + Chris Mungall + + directly regulates (processual) + + directly regulates + + + + + + + + + + + + + + gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' + s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p + Chris Mungall + has part structure that is capable of + + + + + + + + + + + A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + Chris Mungall + + causal relation between material entity and a process + + + + + + + + + + + + + pyrethroid -> growth + Holds between c and p if and only if c is capable of some activity a, and a regulates p. + + capable of regulating + + + + + + + + + + + + + Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. + + capable of negatively regulating + + + + + + + + + + + + + renin -> arteriolar smooth muscle contraction + Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. + + capable of positively regulating + + + + + + + + + Inverse of 'causal agent in process' + + process has causal agent + + + + + + + + A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. + related via dependence to + + + + + + + + + + Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. + + directly positively regulates (process to process) + + directly positively regulates + + + + + + + + + + Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. + + directly negatively regulates (process to process) + + directly negatively regulates + + + + + + + + + + + + + Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. + cjm + 2018-01-25T23:20:13Z + enables subfunction + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:30Z + acts upstream of or within, positive effect + + + + + + + + + + + + + + + cjm + 2018-01-26T23:49:51Z + acts upstream of or within, negative effect + + + + + + + + + + + + + + c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive + + cjm + 2018-01-26T23:53:14Z + acts upstream of, positive effect + + + + + + + + + + + + + + + c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative + + cjm + 2018-01-26T23:53:22Z + acts upstream of, negative effect + + + + + + + + + + + cjm + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + + + + + + + + + + cjm + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + + + + + + + + + + + + + + + + + + + + An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant + + + + + + + + + + + + + + An entity that has temporal parts and that happens, unfolds or develops through time. + occurrent + + + + + + + + + + A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + independent continuant + + + + + + + + + An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + process + + + + + + + + + A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + specifically dependent continuant + + + + + + + + + An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity + + + + + + + + + + anatomical structure + + + + + + + + + + material anatomical entity + + + + + + + + + + cell + + + + + + + + + + neuron + + + + + + + + + molecular process + molecular_function + + + + + + + + receptor activity + + + + + + + + + biological_process + + + + + + + + + + + + + + + quality (PATO) + quality + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z + infer input from direct reg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' + enabling an MF enables its parts + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + true + GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' + involved in BP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From ligand activity to has_ligand + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. + inferring direct reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct neg reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + inferring direct positive reg edge from input to regulatory subfunction + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From has_ligand to ligand activity + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + effector input is compound function input + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Input of effector is input of its parent MF + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly regulates X, its parent MF directly regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly positively regulates X, its parent MF directly positively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + if effector directly negatively regulates X, its parent MF directly negatively regulates X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/ro_terms.txt b/src/ontology/imports/ro_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/ro_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/imports/uberon_import.obo b/src/ontology/imports/uberon_import.obo new file mode 100644 index 00000000..5231a880 --- /dev/null +++ b/src/ontology/imports/uberon_import.obo @@ -0,0 +1,14679 @@ +format-version: 1.2 +ontology: upheno/imports/uberon_import +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (mouth)\n\nSubClassOf(Annotation( \"exceptions in some taxa\"^^xsd:string) ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (organism subdivision)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (hindbrain)\n\nSubClassOf(Annotation( \"modified-source-relation\"^^xsd:string) Annotation( \"ABA\"^^xsd:string) ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (midbrain-hindbrain boundary)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (surface structure)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (splanchnopleure)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (buccopharyngeal membrane)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n# Class: (mouth-foregut junction)\n\nEquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\nSubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))\n\n\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nEquivalentClasses(ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\nDisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))\n) + +[Term] +id: UBERON:0000000 +name: processual entity +namespace: uberon +def: "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." [span:ProcessualEntity] +subset: upper_level +disjoint_from: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000009 +name: submucosa +namespace: uberon +def: "A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]." [http://en.wikipedia.org/wiki/Submucosa] +subset: pheno_slim +subset: uberon_slim +synonym: "organ submucosa" EXACT [FMA:85391] +synonym: "region of submucosa" EXACT [FMA:85392] +synonym: "submucosa of organ" EXACT [FMA:85391] +synonym: "submucosa of region of organ" EXACT [FMA:85392] +synonym: "submucous layer" RELATED [BTO:0002107] +synonym: "tela submucosa" RELATED [BTO:0002107] +synonym: "tunica submucosa" RELATED [] +xref: BTO:0002107 +xref: FMA:85391 +xref: FMA:85392 +xref: http://en.wikipedia.org/wiki/Submucosa +xref: http://linkedlifedata.com/resource/umls/id/C0225344 +xref: http://www.snomedbrowser.com/Codes/Details/68439008 +xref: NCIT:C13167 +xref: UMLS:C0225344 {source="ncithesaurus:Submucosa"} +is_a: UBERON:0004923 ! organ component layer +relationship: composed_primarily_of UBERON:0002384 ! connective tissue +relationship: immediately_deep_to UBERON:0000344 ! mucosa +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png +property_value: UBPROP:0000007 "submucosal" xsd:string + +[Term] +id: UBERON:0000010 +name: peripheral nervous system +namespace: uberon +def: "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [GO:0007422] +subset: cumbo +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "pars peripherica" EXACT LATIN [FMA:9903, FMA:TA, http://en.wikipedia.org/wiki/Peripheral_nervous_system] +synonym: "PNS" BROAD ABBREVIATION [] +synonym: "systema nervosum periphericum" EXACT LATIN [FMA:9903, FMA:TA, http://en.wikipedia.org/wiki/Peripheral_nervous_system] +xref: AAO:0000429 +xref: BAMS:PNS +xref: BILA:0000081 +xref: birnlex:1111 +xref: BTO:0001028 +xref: CALOHA:TS-0808 +xref: EFO:0000891 +xref: EHDAA2:0001445 +xref: EHDAA:2893 +xref: EMAPA:16665 +xref: EV:0100335 +xref: FBbt:00005098 +xref: FMA:9903 +xref: GAID:715 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3232 +xref: http://en.wikipedia.org/wiki/Peripheral_nervous_system +xref: http://linkedlifedata.com/resource/umls/id/C0206417 +xref: http://linkedlifedata.com/resource/umls/id/C1305921 +xref: http://www.snomedbrowser.com/Codes/Details/362292005 +xref: MA:0000218 +xref: MAT:0000338 +xref: MESH:D017933 +xref: MIAA:0000338 +xref: NCIT:C12465 +xref: TAO:0000142 +xref: UMLS:C0206417 {source="NIFSTD:birnlex_1111"} +xref: UMLS:C0206417 {source="ncithesaurus:Peripheral_Nervous_System"} +xref: UMLS:C1305921 {source="NIFSTD:birnlex_1111"} +xref: VHOG:0000399 +xref: XAO:0000178 +xref: ZFA:0000142 +is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision +relationship: part_of UBERON:0001016 ! nervous system +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png +property_value: UBPROP:0000001 "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000142", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000429", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)" xsd:string {source="Cumbo:terms"} +property_value: UBPROP:0000003 "(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000399", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)"} + +[Term] +id: UBERON:0000014 +name: zone of skin +namespace: uberon +def: "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." [http://en.wikipedia.org/wiki/Skin, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "portion of skin" EXACT [] +synonym: "region of skin" EXACT [] +synonym: "skin" EXACT [MA:0000151] +synonym: "skin region" EXACT [] +synonym: "skin zone" EXACT [] +xref: EHDAA2:0001844 +xref: EHDAA:6530 +xref: EMAPA:17525 +xref: EV:0100152 +xref: FMA:86166 +xref: GAID:933 +xref: http://en.wikipedia.org/wiki/Skin +xref: http://www.snomedbrowser.com/Codes/Details/20795001 +xref: MA:0000151 +xref: MAT:0000284 +xref: MESH:D012867 +xref: MIAA:0000284 +xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA +xref: VHOG:0000860 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0034944 {source="FMA"} ! zone of organ +relationship: has_part UBERON:0001003 ! skin epidermis +relationship: has_part UBERON:0002067 ! dermis +relationship: part_of UBERON:0002097 ! skin of body +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg +property_value: IAO:0000232 "Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee" xsd:string +property_value: UBPROP:0000003 "(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000860", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)"} +property_value: UBPROP:0000012 "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive" xsd:string + +[Term] +id: UBERON:0000015 +name: non-material anatomical boundary +namespace: uberon +def: "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." [CARO:0000010] +comment: Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. +subset: upper_level +synonym: "anatomical boundary" EXACT [CARO:0000010] +xref: AEO:0000192 +xref: CARO:0000010 +xref: FMA:50705 +is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity + +[Term] +id: UBERON:0000025 +name: tube +namespace: uberon +def: "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." [http://orcid.org/0000-0002-6601-2165] +synonym: "anatomical tube" EXACT [] +synonym: "duct" NARROW [] +xref: galen:Tube +is_a: UBERON:0004111 ! anatomical conduit +relationship: has_part UBERON:0013522 ! subdivision of tube +property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string +property_value: UBPROP:0000007 "tubular" xsd:string + +[Term] +id: UBERON:0000033 +name: head +namespace: uberon +def: "The head is the anterior-most division of the body [GO]." [GO:0060322, http://en.wikipedia.org/wiki/Head] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "adult head" NARROW [] +synonym: "cephalic area" RELATED [SPD:0000016] +synonym: "head (volume)" EXACT [FMA:7154] +xref: AAO:0010335 +xref: AEO:0000106 +xref: BILA:0000115 +xref: birnlex:1230 +xref: BTO:0000282 +xref: CALOHA:TS-0436 +xref: EFO:0000964 +xref: EHDAA2:0003106 +xref: EMAPA:31858 +xref: FBbt:00000004 +xref: FMA:7154 +xref: GAID:61 +xref: galen:Head +xref: HAO:0000397 +xref: http://en.wikipedia.org/wiki/Head +xref: http://linkedlifedata.com/resource/umls/id/C0018670 +xref: http://www.snomedbrowser.com/Codes/Details/302548004 +xref: MA:0000023 +xref: MAT:0000294 +xref: MESH:D006257 +xref: MIAA:0000294 +xref: NCIT:C12419 +xref: OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg +xref: OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA +xref: SPD:0000016 +xref: TAO:0001114 +xref: TGMA:0000002 +xref: UMLS:C0018670 {source="ncithesaurus:Head"} +xref: UMLS:C0018670 {source="NIFSTD:birnlex_1230"} +xref: VHOG:0001644 +xref: WBbt:0005739 +xref: XAO:0003024 +xref: ZFA:0001114 +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: part_of UBERON:0007811 ! craniocervical region +property_value: UBPROP:0000001 "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001644", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82"} + +[Term] +id: UBERON:0000042 +name: serous membrane +namespace: uberon +def: "multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." [http://en.wikipedia.org/wiki/Serous_membrane, https://github.com/obophenotype/uberon/issues/86] +subset: uberon_slim +subset: vertebrate_core +synonym: "serosa" RELATED [http://en.wikipedia.org/wiki/Serous_membrane] +synonym: "tunica serosa" EXACT LATIN [FMA:9581] +synonym: "wall of serous sac" EXACT [FMA:9581] +xref: FMA:9581 +xref: GAID:19 +xref: http://linkedlifedata.com/resource/umls/id/C0036760 +xref: http://www.snomedbrowser.com/Codes/Details/362878009 +xref: MESH:D012704 +xref: NCIT:C13169 +xref: Serous:membrane +xref: TAO:0005425 +xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} +xref: ZFA:0005425 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: has_part UBERON:0001136 ! mesothelium +relationship: has_part UBERON:0002384 ! connective tissue +relationship: part_of UBERON:0000060 ! anatomical wall +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: UBPROP:0000001 "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="Serous:membrane"} +property_value: UBPROP:0000001 "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string {source="Serous:membrane"} +property_value: UBPROP:0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0000055 +name: vessel +namespace: uberon +def: "A tubular structure that contains, conveys body fluid, such as blood or lymph." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +subset: pheno_slim +is_a: UBERON:0004111 ! anatomical conduit +relationship: channel_for UBERON:0006314 ! bodily fluid + +[Term] +id: UBERON:0000058 +name: duct +namespace: uberon +def: "A tubular structure that transports secreted or excreted substances." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm#ducts] +subset: grouping_class +synonym: "anatomical duct" EXACT [] +synonym: "ducts" RELATED PLURAL [XAO:0004000] +synonym: "exocrine duct" NARROW [] +synonym: "exocrine gland duct" NARROW [] +xref: AAO:0011123 +xref: Duct:(anatomy) +xref: FBbt:00100314 +xref: FMA:30320 +xref: galen:Duct +xref: http://linkedlifedata.com/resource/umls/id/C0687028 +xref: http://www.snomedbrowser.com/Codes/Details/91726008 +xref: NCIT:C12948 +xref: TAO:0005171 +xref: UMLS:C0687028 {source="ncithesaurus:Duct"} +xref: XAO:0004000 +xref: ZFA:0005171 +is_a: UBERON:0000063 ! organ subunit +relationship: conduit_for UBERON:0000463 ! organism substance +relationship: has_part UBERON:0034969 ! epithelial layer of duct +property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} +property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string + +[Term] +id: UBERON:0000060 +name: anatomical wall +namespace: uberon +alt_id: UBERON:0009915 +def: "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." [FMA:82482] +subset: upper_level +synonym: "organ wall" RELATED [FMA:82482] +synonym: "wall" BROAD [] +synonym: "wall of organ" EXACT [FMA:82482] +xref: EMAPA:25036 +xref: FMA:82482 +xref: galen:Wall +is_a: UBERON:0000064 ! organ part +relationship: adjacent_to UBERON:0002553 ! anatomical cavity +relationship: has_part UBERON:0004923 ! organ component layer +property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0000061 +name: anatomical structure +namespace: uberon +def: "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." [CARO:0000003] +subset: upper_level +synonym: "biological structure" EXACT [] +synonym: "connected biological structure" EXACT [CARO:0000003] +xref: AAO:0010825 +xref: AEO:0000003 +xref: BILA:0000003 +xref: CARO:0000003 +xref: EHDAA2:0003003 +xref: EMAPA:0 +xref: FBbt:00007001 +xref: FMA:305751 +xref: FMA:67135 +xref: GAID:781 +xref: HAO:0000003 +xref: http://dbpedia.org/ontology/AnatomicalStructure +xref: http://www.snomedbrowser.com/Codes/Details/362889002 +xref: MA:0003000 +xref: MESH:D000825 +xref: TAO:0000037 +xref: TGMA:0001823 +xref: VHOG:0001759 +xref: XAO:0003000 +xref: ZFA:0000037 +is_a: UBERON:0000465 ! material anatomical entity +relationship: existence_ends_during_or_before UBERON:0000071 ! death stage +relationship: existence_starts_during_or_after UBERON:0000106 ! zygote stage + +[Term] +id: UBERON:0000062 +name: organ +namespace: uberon +def: "Anatomical structure that performs a specific function or group of functions [WP]." [http://en.wikipedia.org/wiki/Organ_(anatomy)] +subset: upper_level +synonym: "anatomical unit" RELATED [] +synonym: "body organ" RELATED [] +synonym: "element" RELATED [http://orcid.org/0000-0002-6601-2165] +xref: birnlex:4 +xref: CARO:0020004 +xref: EFO:0000634 +xref: EMAPA:35949 +xref: ENVO:01000162 +xref: FMA:67498 +xref: http://linkedlifedata.com/resource/umls/id/C0178784 +xref: http://www.snomedbrowser.com/Codes/Details/272625005 +xref: MA:0003001 +xref: NCIT:C13018 +xref: OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA +xref: OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA +xref: Organ:(anatomy) +xref: UMLS:C0178784 {source="ncithesaurus:Organ"} +xref: WBbt:0003760 +is_a: UBERON:0010000 ! multicellular anatomical structure +disjoint_from: UBERON:0034921 ! multi organ part structure +relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage +relationship: has_boundary UBERON:0006984 ! anatomical surface +relationship: part_of UBERON:0000467 ! anatomical system +property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} +property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string + +[Term] +id: UBERON:0000063 +name: organ subunit +namespace: uberon +def: "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "organ region with fixed fiat boundary" RELATED [FMA:86140] +synonym: "organ segment" RELATED [FMA:86140] +synonym: "segment of organ" RELATED [FMA:86140] +xref: FMA:86140 +is_a: UBERON:0000064 ! organ part +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string +property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} +property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} + +[Term] +id: UBERON:0000064 +name: organ part +namespace: uberon +def: "A multicellular structure that is a part of an organ." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: non_informative +subset: upper_level +synonym: "cardinal organ part" EXACT [FMA:82472] +synonym: "regional part of organ" RELATED [NIFSTD:birnlex_16] +xref: AAO:0011124 +xref: birnlex:16 +xref: EFO:0000635 +xref: FMA:82472 +xref: http://www.snomedbrowser.com/Codes/Details/113343008 +xref: http://www.snomedbrowser.com/Codes/Details/91717005 +is_a: UBERON:0010000 ! multicellular anatomical structure +relationship: part_of UBERON:0000062 ! organ +property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string + +[Term] +id: UBERON:0000065 +name: respiratory tract +namespace: uberon +def: "Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts" [https://orcid.org/0000-0002-6601-2165] +xref: EHDAA2:0001606 +xref: EHDAA:1568 +xref: EHDAA:2219 +xref: EMAPA:16737 +xref: FMA:265130 +xref: http://www.snomedbrowser.com/Codes/Details/361110005 +xref: OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA +xref: VHOG:0000393 +is_a: UBERON:0001005 ! respiratory airway +is_a: UBERON:0004119 ! endoderm-derived structure +relationship: develops_from UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut +relationship: develops_from UBERON:0008947 ! respiratory primordium + +[Term] +id: UBERON:0000066 +name: fully formed stage +namespace: uberon +def: "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "adult stage" BROAD [] +synonym: "fully formed animal stage" EXACT [] +synonym: "juvenile-adult stage" EXACT [] +xref: BilaDO:0000004 +xref: BTO:0001043 +xref: EFO:0001272 +xref: FBdv:00005369 +xref: WBls:0000041 +xref: XtroDO:0000084 +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000092 ! post-embryonic stage +relationship: preceded_by UBERON:0000111 ! organogenesis stage +relationship: precedes UBERON:0000071 ! death stage +property_value: seeAlso https://github.com/obophenotype/uberon/issues/566 + +[Term] +id: UBERON:0000068 +name: embryo stage +namespace: uberon +def: "A life cycle stage that starts with fertilization and ends with the fully formed embryo." [http://orcid.org/0000-0002-6601-2165] +synonym: "embryogenesis" RELATED [] +synonym: "embryonic stage" EXACT [] +xref: BilaDO:0000002 +xref: EV:0300001 +xref: FBdv:00005289 +xref: FMA:72652 +xref: HsapDv:0000002 +xref: http://www.snomedbrowser.com/Codes/Details/296280003 +xref: MmusDv:0000002 +xref: OGES:000000 +xref: OGES:000022 +xref: WBls:0000003 +xref: WBls:0000092 +xref: WBls:0000102 +xref: XAO:1000012 +is_a: UBERON:0000105 ! life cycle stage +disjoint_from: UBERON:0000092 ! post-embryonic stage +relationship: precedes UBERON:0000066 ! fully formed stage +relationship: precedes UBERON:0000092 ! post-embryonic stage + +[Term] +id: UBERON:0000071 +name: death stage +namespace: uberon +def: "End of the life of an organism." [XAO:0000437] +synonym: "death" RELATED [] +xref: XAO:0000437 +xref: XtroDO:0000085 +is_a: UBERON:0000105 ! life cycle stage +relationship: ends UBERON:0000104 ! life cycle +property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} + +[Term] +id: UBERON:0000072 +name: proximo-distal subdivision of respiratory tract +namespace: uberon +def: "An section of a respiratory tract." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "respiratory tract" RELATED [MA:0000434] +synonym: "subdivision of respiratory tract" RELATED [] +xref: EMAPA:16737 +xref: FMA:45660 +xref: MA:0000434 +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0013522 ! subdivision of tube +intersection_of: UBERON:0013522 ! subdivision of tube +intersection_of: part_of UBERON:0000065 ! respiratory tract +relationship: part_of UBERON:0000065 ! respiratory tract +property_value: UBPROP:0000012 "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0000073 +name: regional part of nervous system +namespace: uberon +def: "Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS." [NIFSTD:birnlex_1157] +subset: non_informative +subset: upper_level +synonym: "part of nervous system" EXACT [NIFSTD:birnlex_1157] +xref: birnlex:1157 +xref: http://linkedlifedata.com/resource/umls/id/C1518256 +xref: http://www.snomedbrowser.com/Codes/Details/25087005 +xref: NCIT:C13040 +xref: UMLS:C1518256 {source="ncithesaurus:Nervous_System_Part"} +is_a: UBERON:0000481 ! multi-tissue structure +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001016 ! nervous system +relationship: part_of UBERON:0001016 ! nervous system +created_by: Melissa Haendel +creation_date: 2009-06-18T09:00:04Z + +[Term] +id: UBERON:0000075 +name: subdivision of skeletal system +namespace: uberon +alt_id: UBERON:0010322 +def: "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: non_informative +synonym: "skeletal system part" RELATED [] +synonym: "skeletal system subdivision" EXACT [FMA:85544] +xref: FMA:85544 +xref: galen:ComplexSkeletalStructure +xref: http://linkedlifedata.com/resource/umls/id/C1519343 +xref: http://www.snomedbrowser.com/Codes/Details/118966000 +xref: NCIT:C34076 +xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} +is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision +relationship: composed_primarily_of UBERON:0004765 ! skeletal element +relationship: part_of UBERON:0001434 ! skeletal system + +[Term] +id: UBERON:0000076 +name: external ectoderm +namespace: uberon +def: "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." [MGI:anna, MP:0012532] +subset: pheno_slim +synonym: "surface (external) ectoderm" EXACT [] +synonym: "surface ectoderm" EXACT [MP:0012532] +xref: EHDAA2:0001968 +xref: EHDAA:1494 +xref: EHDAA:350 +xref: EHDAA:4784 +xref: EHDAA:4790 +xref: EHDAA:4796 +xref: EHDAA:7860 +xref: EMAPA:16096 +xref: External:ectoderm +xref: FMA:87656 +xref: http://linkedlifedata.com/resource/umls/id/C1515087 +xref: NCIT:C34309 +xref: UMLS:C1515087 {source="ncithesaurus:Surface_Ectoderm"} +is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0005291 ! embryonic tissue +relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png +property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string +property_value: UBPROP:0000011 "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" xsd:string + +[Term] +id: UBERON:0000077 +name: mixed endoderm/mesoderm-derived structure +namespace: uberon +def: "An anatomical structure that develops from the endoderm and the mesoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: develops_from UBERON:0000925 ! endoderm +intersection_of: develops_from UBERON:0000926 ! mesoderm +property_value: IAO:0000232 "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" xsd:string + +[Term] +id: UBERON:0000078 +name: mixed ectoderm/mesoderm/endoderm-derived structure +namespace: uberon +def: "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: develops_from UBERON:0000924 ! ectoderm +intersection_of: develops_from UBERON:0000925 ! endoderm +intersection_of: develops_from UBERON:0000926 ! mesoderm +property_value: IAO:0000232 "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" xsd:string + +[Term] +id: UBERON:0000092 +name: post-embryonic stage +namespace: uberon +def: "stage succeeding embryo, including mature structure" [https://orcid.org/0000-0002-6601-2165] +synonym: "post-hatching stage" NARROW [] +synonym: "postembryonic" RELATED [] +synonym: "postembryonic stage" EXACT [] +xref: BilaDO:0000003 +xref: OGES:000010 +xref: OGES:000014 +xref: OGES:000024 +xref: WBls:0000022 +xref: WBls:0000093 +xref: WBls:0000103 +is_a: UBERON:0000105 ! life cycle stage +relationship: preceded_by UBERON:0000068 ! embryo stage +property_value: seeAlso https://github.com/obophenotype/uberon/issues/344 +property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string + +[Term] +id: UBERON:0000094 +name: membrane organ +namespace: uberon +def: "Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]" [FMA:7145] +synonym: "membrane" BROAD [] +synonym: "membrane of organ" EXACT [] +xref: FMA:7145 +is_a: UBERON:0000062 ! organ +relationship: composed_primarily_of UBERON:0011823 {source="FMA-def"} ! dense connective tissue +created_by: cjm +creation_date: 2009-07-30T05:19:13Z + +[Term] +id: UBERON:0000102 +name: lung vasculature +namespace: uberon +def: "The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]." [GOC:GO] +subset: pheno_slim +synonym: "lung vascular network" EXACT [OBOL:automatic] +synonym: "pulmonary vasculature" EXACT [FMA:73750] +synonym: "vascular network of lung" EXACT [OBOL:automatic] +synonym: "vasculature of lung" EXACT [OBOL:automatic] +xref: FMA:73750 +is_a: UBERON:0002201 ! vasculature of trunk +is_a: UBERON:0006876 ! vasculature of organ +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0002048 ! lung +relationship: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0000104 +name: life cycle +namespace: uberon +def: "An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism." [https://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "entire life cycle" EXACT [] +synonym: "entire lifespan" EXACT [] +synonym: "life" EXACT [] +synonym: "lifespan" EXACT [] +xref: FBdv:00000000 +xref: HsapDv:0000001 +xref: MmusDv:0000001 +xref: ncithesaurus:Life +xref: OGES:000011 +is_a: UBERON:0000000 ! processual entity +relationship: ends_with UBERON:0000071 ! death stage +relationship: has_part UBERON:0000105 ! life cycle stage +relationship: starts_with UBERON:0000106 ! zygote stage +property_value: seeAlso https://github.com/obophenotype/uberon/issues/532 + +[Term] +id: UBERON:0000105 +name: life cycle stage +namespace: uberon +def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: upper_level +synonym: "developmental stage" NARROW [] +synonym: "stage" NARROW [] +xref: BILS:0000105 +xref: EFO:0000399 +xref: FBdv:00007012 +xref: FMA:24120 +xref: HsapDv:0000000 +xref: MmusDv:0000000 +xref: ncithesaurus:Developmental_Stage +xref: OlatDv:0000010 +xref: PdumDv:0000090 +xref: WBls:0000002 +xref: XAO:1000000 +xref: ZFS:0000000 +xref: ZFS:0100000 +is_a: UBERON:0000000 ! processual entity +relationship: part_of UBERON:0000104 ! life cycle +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string +property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string + +[Term] +id: UBERON:0000106 +name: zygote stage +namespace: uberon +def: "A stage at which the organism is a single cell produced by means of sexual reproduction." [http://en.wikipedia.org/wiki/Zygote] +subset: efo_slim +synonym: "1-cell stage" EXACT [] +synonym: "fertilized egg stage" EXACT [BTO:0000854] +synonym: "fertilized egg stage" RELATED [] +synonym: "one cell stage" EXACT [] +synonym: "one-cell stage" RELATED [VHOG:0000745] +synonym: "zygote" RELATED [VHOG:0000745] +synonym: "zygotum" RELATED LATIN [http://en.wikipedia.org/wiki/Zygote] +xref: BilaDO:0000005 +xref: BILS:0000106 +xref: EFO:0001322 +xref: EHDAA:27 +xref: FBdv:00005288 +xref: HsapDv:0000001 +xref: http://en.wikipedia.org/wiki/Zygote +xref: NCIT:C12601 +xref: PdumDv:0000100 +xref: VHOG:0000745 +xref: XAO:1000001 +xref: ZFS:0000001 +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: starts UBERON:0000104 ! life cycle +property_value: seeAlso EMAPA:16033 +property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107"} + +[Term] +id: UBERON:0000107 +name: cleavage stage +namespace: uberon +def: "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula." [GO:0040016, http://en.wikipedia.org/wiki/Cleavage_(embryo)] +subset: efo_slim +xref: BilaDO:0000006 +xref: BILS:0000107 +xref: Cleavage:(embryo) +xref: EFO:0001290 +xref: FBdv:00000054 +xref: MESH:A16.254.270 +xref: MmusDv:0000004 +xref: OGES:000015 +xref: OGES:000020 +xref: PdumDv:0000200 +xref: XAO:1000004 +xref: ZFS:0000046 +is_a: UBERON:0000105 ! life cycle stage +relationship: immediately_preceded_by UBERON:0000106 ! zygote stage +relationship: part_of UBERON:0000068 ! embryo stage + +[Term] +id: UBERON:0000108 +name: blastula stage +namespace: uberon +def: "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [http://en.wikipedia.org/wiki/Blastula] +subset: efo_slim +xref: BilaDO:0000007 +xref: BILS:0000108 +xref: EFO:0001282 +xref: HsapDv:0000006 +xref: http://en.wikipedia.org/wiki/Blastula +xref: MmusDv:0000007 +xref: OGES:000003 +xref: OGES:000016 +xref: OGES:000021 +xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg +xref: WBls:0000005 +xref: XAO:1000003 +xref: ZFS:0000045 +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: preceded_by UBERON:0000107 ! cleavage stage +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string + +[Term] +id: UBERON:0000109 +name: gastrula stage +namespace: uberon +def: "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." [GO:0007369] +subset: efo_slim +synonym: "blastocystis trilaminaris stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastocyst stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastoderm stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar disk stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar germ stage" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar stage" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: BilaDO:0000008 +xref: BILS:0000109 +xref: EFO:0001296 +xref: FBdv:00005317 +xref: HsapDv:0000010 +xref: MmusDv:0000013 +xref: OGES:000004 +xref: OGES:000019 +xref: WBls:0000010 +xref: XAO:1000005 +xref: ZFS:0000047 +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage + +[Term] +id: UBERON:0000110 +name: neurula stage +namespace: uberon +def: "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GO:0001841] +xref: BilaDO:0000009 +xref: BILS:0000110 +xref: HsapDv:0000012 +xref: MmusDv:0000017 +xref: XAO:1000006 +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: preceded_by UBERON:0000109 ! gastrula stage +property_value: seeAlso https://github.com/obophenotype/uberon/issues/343 + +[Term] +id: UBERON:0000111 +name: organogenesis stage +namespace: uberon +def: "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." [http://en.wikipedia.org/wiki/Organogenesis] +synonym: "segmentation stage" RELATED [] +xref: BilaDO:0000010 +xref: BILS:0000111 +xref: HsapDv:0000015 +xref: http://en.wikipedia.org/wiki/Organogenesis +xref: MmusDv:0000018 +xref: OGES:000005 +xref: OGES:000032 +is_a: UBERON:0000105 ! life cycle stage +relationship: part_of UBERON:0000068 ! embryo stage +relationship: preceded_by UBERON:0000110 ! neurula stage +property_value: seeAlso https://github.com/obophenotype/uberon/issues/533 + +[Term] +id: UBERON:0000114 +name: lung connective tissue +namespace: uberon +def: "the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin" [http://www.ncbi.nlm.nih.gov/pubmed/14635660, ISBN:0-683-40008-8, MGI:anna, MP:0002276] +subset: pheno_slim +synonym: "connective tissue of lung" EXACT [OBOL:automatic] +synonym: "lung interstitial tissue" RELATED [MA:0001782] +synonym: "lung interstitium" RELATED [] +synonym: "pulmonary connective tissue" RELATED [EMAPA:35521] +synonym: "pulmonary interstitial tissue" RELATED [] +synonym: "pulmonary interstitium" EXACT [FMA:27533] +xref: EMAPA:35521 +xref: FMA:27533 +xref: http://www.snomedbrowser.com/Codes/Details/201609008 +xref: MA:0001782 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003580 ! lower respiratory tract connective tissue +is_a: UBERON:0003837 ! thoracic segment connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0002048 ! lung +relationship: contributes_to_morphology_of UBERON:0002048 ! lung +relationship: develops_from UBERON:0004883 ! lung mesenchyme +relationship: part_of UBERON:0002048 ! lung +relationship: transformation_of UBERON:0004883 ! lung mesenchyme +property_value: UBPROP:0000009 "it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces" xsd:string + +[Term] +id: UBERON:0000115 +name: lung epithelium +namespace: uberon +def: "The epithelial layer of the lung." [MP:0006382] +subset: pheno_slim +synonym: "epithelial tissue of lung" EXACT [OBOL:automatic] +synonym: "epithelium of lung" EXACT [OBOL:automatic] +synonym: "lung epithelial tissue" EXACT [OBOL:automatic] +synonym: "pulmonary epithelium" RELATED [BTO:0001653] +xref: BTO:0001653 +xref: EMAPA:32860 +xref: MA:0001783 +is_a: UBERON:0004815 ! lower respiratory tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0002048 ! lung +relationship: contributes_to_morphology_of UBERON:0002048 ! lung +relationship: develops_from UBERON:0001041 ! foregut +relationship: part_of UBERON:0002048 ! lung +property_value: UBPROP:0000008 "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[doi:10.1242/dev.115469]" xsd:string + +[Term] +id: UBERON:0000117 +name: respiratory tube +namespace: uberon +def: "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea." [GO:0030323, http://orcid.org/0000-0002-6601-2165] +synonym: "airway" RELATED [] +synonym: "respiratory conducting tube" NARROW [MP:0004391] +synonym: "segment of tracheobronchial tree" EXACT [FMA:12224] +synonym: "segment of tracheobronchial tree" NARROW [FMA:12224] +synonym: "tracheobronchial tree segment" NARROW [FMA:12224] +xref: EMAPA:37946 {source="MA:th"} +xref: FMA:12224 +is_a: UBERON:0000025 ! tube +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: UBERON:0000025 ! tube +intersection_of: part_of UBERON:0000065 ! respiratory tract +relationship: has_part UBERON:0000483 ! epithelium +relationship: part_of UBERON:0000065 ! respiratory tract +property_value: UBPROP:0000012 "in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)" xsd:string {external_ontology="GO"} + +[Term] +id: UBERON:0000118 +name: lung bud +namespace: uberon +def: "Structure derived from foregut that becomes a lung[GO]." [GO:0060431, http://en.wikipedia.org/wiki/Respiratory_bud] +subset: pheno_slim +synonym: "gemma pulmonalis" RELATED LATIN [http://en.wikipedia.org/wiki/Lung_buds] +synonym: "gemma respiratoria" RELATED LATIN [http://en.wikipedia.org/wiki/Lung_buds] +synonym: "lung bud" RELATED PLURAL [] +synonym: "primary lung bud" RELATED [GO:0060572] +synonym: "respiratory diverticulum" RELATED [http://en.wikipedia.org/wiki/Lung_buds] +xref: BTO:0001643 +xref: EHDAA2:0004089 +xref: http://linkedlifedata.com/resource/umls/id/C1514420 +xref: http://linkedlifedata.com/resource/umls/id/C1514897 +xref: http://www.snomedbrowser.com/Codes/Details/361427007 +xref: NCIT:C34260 +xref: NCIT:C34282 +xref: Respiratory:bud +xref: UMLS:C1514420 {source="ncithesaurus:Primary_Bronchial_Bud"} +xref: UMLS:C1514897 {source="ncithesaurus:Respiratory_Diverticulum"} +is_a: UBERON:0005153 {source="GO:0060441"} ! epithelial bud +is_a: UBERON:0005911 ! endo-epithelium +relationship: adjacent_to UBERON:0004872 ! splanchnic layer of lateral plate mesoderm +relationship: develops_from UBERON:0005597 ! lung primordium +relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png +property_value: IAO:0000116 "clarify successors - include bronchi?" xsd:string + +[Term] +id: UBERON:0000153 +name: anterior region of body +namespace: uberon +is_a: UBERON:0000475 ! organism subdivision +disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body +relationship: anterior_to UBERON:0000154 ! posterior region of body + +[Term] +id: UBERON:0000154 +name: posterior region of body +namespace: uberon +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0000161 +name: orifice +namespace: uberon +def: "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]." [FMA:3724] +synonym: "anatomical orifice" EXACT [FMA:3724] +synonym: "anatomical ostium" BROAD [FMA:3724] +synonym: "hilum" NARROW [] +synonym: "ostium" BROAD [] +xref: FMA:3724 +xref: http://www.snomedbrowser.com/Codes/Details/91837002 +is_a: UBERON:0004111 ! anatomical conduit +property_value: UBPROP:0000012 "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0000165 +name: mouth +namespace: uberon +def: "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." [http://en.wikipedia.org/wiki/Mouth, https://github.com/obophenotype/uberon/wiki/The-digestive-tract] +subset: efo_slim +subset: major_organ +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "adult mouth" NARROW [] +synonym: "cavital oralis" RELATED LATIN [http://en.wikipedia.org/wiki/Mouth] +synonym: "cavitas oris" RELATED [BTO:0001090] +synonym: "cavum oris" RELATED [BTO:0001090] +synonym: "mouth cavity" RELATED [BTO:0001090] +synonym: "oral region" RELATED [EHDAA2:0001326] +synonym: "oral vestibule" RELATED [BTO:0001090] +synonym: "regio oralis" EXACT LATIN [FMA:49184, FMA:TA] +synonym: "regio oralis" EXACT [BTO:0004698] +synonym: "rima oris" RELATED [BTO:0001090] +synonym: "stoma" RELATED [] +synonym: "stomatodaeum" RELATED [VHOG:0000812] +synonym: "trophic apparatus" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "vestibule of mouth" RELATED [BTO:0001090] +synonym: "vestibulum oris" RELATED [BTO:0001090] +xref: AAO:0010355 +xref: BTO:0001090 +xref: BTO:0004698 +xref: CALOHA:TS-1315 +xref: EFO:0000825 +xref: EHDAA2:0001326 +xref: EHDAA:542 +xref: EMAPA:16262 +xref: FBbt:00003126 +xref: FMA:49184 +xref: GAID:75 +xref: galen:Mouth +xref: http://en.wikipedia.org/wiki/Mouth +xref: http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg +xref: http://www.snomedbrowser.com/Codes/Details/21082005 +xref: MA:0000341 +xref: MA:0002474 +xref: MAT:0000038 +xref: MESH:D009055 +xref: MIAA:0000038 +xref: OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA +xref: TADS:0000040 +xref: TAO:0000547 +xref: TAO:0000590 +xref: TGMA:0000131 +xref: VHOG:0000280 +xref: VHOG:0000812 +xref: XAO:0003029 +xref: ZFA:0000547 +xref: ZFA:0000590 +is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract +intersection_of: UBERON:0004921 ! subdivision of digestive tract +intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract +relationship: develops_from UBERON:0035804 ! future mouth +relationship: part_of UBERON:0000033 ! head +relationship: proximalmost_part_of UBERON:0001555 ! digestive tract +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg +property_value: seeAlso https://github.com/obophenotype/uberon/issues/661 +property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)"} +property_value: UBPROP:0000007 "oral" xsd:string +property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string +property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0000166 +name: oral opening +namespace: uberon +def: "The orifice that connects the mouth to the exterior of the body." [https://github.com/obophenotype/uberon/wiki/The-digestive-tract] +subset: uberon_slim +subset: vertebrate_core +synonym: "mouth" RELATED INCONSISTENT [] +synonym: "oral fissure" EXACT [FMA:59806] +synonym: "oral orifice" EXACT [FMA:59806] +synonym: "oral part of face" RELATED [] +xref: FMA:59806 +is_a: UBERON:0000161 {source="FMA"} ! orifice +relationship: part_of UBERON:0000165 ! mouth +property_value: UBPROP:0000003 "(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000280", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)"} + +[Term] +id: UBERON:0000167 +name: oral cavity +namespace: uberon +def: "Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)" [https://github.com/obophenotype/uberon/wiki/The-digestive-tract, https://orcid.org/0000-0002-6601-2165, ISBN10:0073040584] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "bucca" RELATED [] +synonym: "buccal cavity" EXACT [FMA:20292, ISBN10:0073040584] +synonym: "cavity of mouth" EXACT [] +xref: AAO:0000053 +xref: AAO:0000960 +xref: BSA:0000107 +xref: CALOHA:TS-1315 +xref: EFO:0001975 +xref: EHDAA2:0001324 +xref: EHDAA:6970 +xref: EMAPA:17411 +xref: EMAPA:18399 +xref: EV:0100057 +xref: FMA:20292 +xref: HAO:0000669 +xref: http://linkedlifedata.com/resource/umls/id/C0226896 +xref: http://www.snomedbrowser.com/Codes/Details/181220002 +xref: NCIT:C12421 +xref: TAO:0001027 +xref: TGMA:0000102 +xref: UMLS:C0226896 {source="ncithesaurus:Oral_Cavity"} +xref: VHOG:0000188 +xref: WBbt:0005255 +xref: XAO:0000126 +xref: ZFA:0001027 +is_a: UBERON:0002553 ! anatomical cavity +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0000165 ! mouth +relationship: contributes_to_morphology_of UBERON:0000165 ! mouth +relationship: luminal_space_of UBERON:0000165 ! mouth +relationship: part_of UBERON:0000165 ! mouth +property_value: UBPROP:0000001 "Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000960", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000001 "The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/oral+cavity"} +property_value: UBPROP:0000003 "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32"} + +[Term] +id: UBERON:0000170 +name: pair of lungs +namespace: uberon +def: "The pair of anatomical structures comprised of a left lung and right lung." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "lungs" EXACT [] +synonym: "lungs pair" EXACT [] +synonym: "pulmones" EXACT LATIN [FMA:68877, FMA:TA] +synonym: "set of lungs" EXACT [] +xref: FMA:68877 +xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA +is_a: UBERON:0034925 ! anatomical collection +intersection_of: UBERON:0034925 ! anatomical collection +intersection_of: has_member UBERON:0002167 ! right lung +intersection_of: has_member UBERON:0002168 ! left lung +relationship: has_member UBERON:0002167 ! right lung +relationship: has_member UBERON:0002167 {minCardinality="1", maxCardinality="1"} ! right lung +relationship: has_member UBERON:0002168 ! left lung +relationship: has_member UBERON:0002168 {minCardinality="1", maxCardinality="1"} ! left lung +relationship: located_in UBERON:0002224 ! thoracic cavity +relationship: part_of UBERON:0001558 {source="FMA-abduced"} ! lower respiratory tract + +[Term] +id: UBERON:0000171 +name: respiration organ +namespace: uberon +def: "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." [GO:0007585] +subset: functional_classification +subset: organ_slim +synonym: "apparatus respiratorius organ" EXACT [OBOL:automatic] +synonym: "breathing organ" EXACT [] +synonym: "gas exchange organ" RELATED [] +synonym: "organ of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "organ of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory organ" EXACT [] +synonym: "respiratory system organ" EXACT [OBOL:automatic] +xref: EMAPA:17607 +xref: http://www.snomedbrowser.com/Codes/Details/272626006 +xref: SPD:0000428 +xref: TGMA:0001247 +is_a: UBERON:0000062 ! organ +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0000178 +name: blood +namespace: uberon +def: "A fluid that is composed of blood plasma and erythrocytes." [FMA:9670, http://en.wikipedia.org/wiki/Blood, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/9] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "portion of blood" EXACT [] +synonym: "vertebrate blood" EXACT [] +synonym: "whole blood" RELATED [BTO:0000089] +xref: AAO:0000046 +xref: BTO:0000089 +xref: CALOHA:TS-0079 +xref: EFO:0000296 +xref: EHDAA2:0000176 +xref: EHDAA:418 +xref: EMAPA:16332 +xref: ENVO:02000027 +xref: EV:0100047 +xref: FMA:9670 +xref: GAID:965 +xref: galen:Blood +xref: http://en.wikipedia.org/wiki/Blood +xref: http://linkedlifedata.com/resource/umls/id/C0005767 +xref: MA:0000059 +xref: MESH:D001769 +xref: MIAA:0000315 +xref: NCIT:C12434 +xref: OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA +xref: TAO:0000007 +xref: UMLS:C0005767 {source="ncithesaurus:Blood"} +xref: VHOG:0000224 +xref: XAO:0000124 +xref: ZFA:0000007 +is_a: UBERON:0000179 ! haemolymphatic fluid +relationship: develops_from UBERON:0006596 ! presumptive blood +relationship: has_part UBERON:0001969 ! blood plasma +relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood +relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature +relationship: part_of UBERON:0002390 ! hematopoietic system +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/tmeehan +property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string +property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} +property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) "} + +[Term] +id: UBERON:0000179 +name: haemolymphatic fluid +namespace: uberon +def: "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." [http://orcid.org/0000-0002-6601-2165] +synonym: "blood or blood analog" RELATED [] +synonym: "circulating fluid" RELATED [] +xref: CARO:0000081 +is_a: UBERON:0006314 ! bodily fluid +intersection_of: UBERON:0000463 ! organism substance +intersection_of: part_of UBERON:0002193 ! hemolymphoid system +relationship: part_of UBERON:0002193 ! hemolymphoid system +created_by: cjm +creation_date: 2009-04-08T04:38:19Z + +[Term] +id: UBERON:0000307 +name: blastula +namespace: uberon +alt_id: UBERON:0007011 +def: "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." [http://en.wikipedia.org/wiki/Blastula] +subset: inconsistent_with_fma +synonym: "blastosphere" RELATED [http://en.wikipedia.org/wiki/Blastula] +synonym: "blastula embryo" EXACT [BILA:0000059] +xref: BILA:0000059 +xref: BTO:0000128 +xref: GAID:1294 +xref: http://en.wikipedia.org/wiki/Blastula +xref: MESH:A16.254.270.274 +xref: OGEM:000006 +xref: OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg +is_a: UBERON:0000922 ! embryo +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage +relationship: develops_from UBERON:0007010 ! cleaving embryo +relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string + +[Term] +id: UBERON:0000328 +name: gut wall +namespace: uberon +def: "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity)." [http://orcid.org/0000-0002-6601-2165] +synonym: "digestive tract wall" EXACT [] +synonym: "wall of alimentary tract" RELATED [] +synonym: "wall of digestive tract" EXACT [] +synonym: "wall of gut" EXACT [FMA:45653] +xref: BTO:0000547 +xref: FMA:45653 +is_a: UBERON:0000060 ! anatomical wall +intersection_of: UBERON:0000060 ! anatomical wall +intersection_of: part_of UBERON:0001555 ! digestive tract +relationship: part_of UBERON:0001555 ! digestive tract +property_value: IAO:0000232 "We model the digestive tract as consisting of two parts: the wall and the lumen." xsd:string + +[Term] +id: UBERON:0000344 +name: mucosa +namespace: uberon +def: "A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]" [http://en.wikipedia.org/wiki/Mucous_membrane] +subset: pheno_slim +synonym: "mucosa of organ" EXACT [FMA:85355] +synonym: "mucosa of organ part" EXACT [FMA:85358] +synonym: "mucosal region" EXACT [FMA:85358] +synonym: "mucous membrane" EXACT [FMA:85355] +synonym: "organ mucosa" EXACT [FMA:85355] +synonym: "region of mucosa" RELATED [FMA:85358] +synonym: "tunica mucosa" RELATED LATIN [http://en.wikipedia.org/wiki/Mucous_membrane] +synonym: "tunica mucosa" RELATED [BTO:0000886] +xref: AEO:0000199 +xref: BTO:0000886 +xref: CALOHA:TS-2031 +xref: EHDAA2_RETIRED:0003234 +xref: EV:0100382 +xref: FMA:85355 +xref: FMA:85358 +xref: GAID:297 +xref: galen:Mucosa +xref: http://linkedlifedata.com/resource/umls/id/C0026724 +xref: http://www.snomedbrowser.com/Codes/Details/361693009 +xref: MESH:D009092 +xref: Mucous:membrane +xref: NCIT:C13166 +xref: OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA +xref: UMLS:C0026724 {source="ncithesaurus:Mucosa"} +is_a: UBERON:0004923 ! organ component layer +relationship: has_part UBERON:0000483 ! epithelium +relationship: has_part UBERON:0002384 ! connective tissue +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png +property_value: UBPROP:0000007 "mucosal" xsd:string +property_value: UBPROP:0000012 "FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0000355 +name: pharyngeal mucosa +namespace: uberon +alt_id: UBERON:0003344 +def: "A mucosa that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] +synonym: "mucosa of organ of pharynx" EXACT [OBOL:automatic] +synonym: "mucosa of pharynx" EXACT [OBOL:automatic] +synonym: "mucous membrane of pharynx" EXACT [OBOL:automatic] +synonym: "mucous membrane of pharynx" EXACT [FMA:55031] +synonym: "mucous membrane of the pharynx" RELATED [BTO:0001047] +synonym: "organ mucosa of pharynx" EXACT [OBOL:automatic] +synonym: "pharynx mucosa" EXACT [OBOL:automatic] +synonym: "pharynx mucosa of organ" EXACT [OBOL:automatic] +synonym: "pharynx mucous membrane" EXACT [OBOL:automatic] +synonym: "pharynx organ mucosa" EXACT [OBOL:automatic] +synonym: "tunica mucosa pharyngea" EXACT LATIN [FMA:55031, FMA:TA] +synonym: "tunica mucosa pharyngis" EXACT [] +xref: BTO:0001047 +xref: EMAPA:26957 +xref: FMA:55031 +xref: http://www.snomedbrowser.com/Codes/Details/362121003 +xref: MA:0003143 +is_a: UBERON:0004785 ! respiratory system mucosa +intersection_of: UBERON:0000344 ! mucosa +intersection_of: part_of UBERON:0001042 ! chordate pharynx +relationship: part_of UBERON:0001042 ! chordate pharynx + +[Term] +id: UBERON:0000379 +name: tracheal mucosa +namespace: uberon +def: "A mucosa that is part of a respiratory airway." [OBOL:automatic] +synonym: "mucosa of organ of trachea" EXACT [OBOL:automatic] +synonym: "mucosa of organ of windpipe" EXACT [OBOL:automatic] +synonym: "mucosa of trachea" EXACT [OBOL:automatic] +synonym: "mucosa of windpipe" EXACT [OBOL:automatic] +synonym: "mucous membrane of trachea" EXACT [FMA:7471] +synonym: "mucous membrane of trachea" EXACT [OBOL:automatic] +synonym: "mucous membrane of windpipe" EXACT [OBOL:automatic] +synonym: "organ mucosa of trachea" EXACT [OBOL:automatic] +synonym: "organ mucosa of windpipe" EXACT [OBOL:automatic] +synonym: "trachea mucosa" EXACT [OBOL:automatic] +synonym: "trachea mucosa of organ" EXACT [OBOL:automatic] +synonym: "trachea mucous membrane" EXACT [OBOL:automatic] +synonym: "trachea organ mucosa" EXACT [OBOL:automatic] +synonym: "tracheal mucous membrane" EXACT [FMA:7471] +synonym: "tunica mucosa (tracheae)" EXACT [FMA:7471] +synonym: "tunica mucosa tracheae" EXACT LATIN [FMA:7471, FMA:TA] +synonym: "windpipe mucosa" EXACT [OBOL:automatic] +synonym: "windpipe mucosa of organ" EXACT [OBOL:automatic] +synonym: "windpipe mucous membrane" EXACT [OBOL:automatic] +synonym: "windpipe organ mucosa" EXACT [OBOL:automatic] +xref: BTO:0001390 +xref: FMA:7471 +xref: http://www.snomedbrowser.com/Codes/Details/660006 +is_a: UBERON:0004785 ! respiratory system mucosa +intersection_of: UBERON:0000344 ! mucosa +intersection_of: part_of UBERON:0001005 ! respiratory airway +relationship: part_of UBERON:0001005 ! respiratory airway + +[Term] +id: UBERON:0000383 +name: musculature of body +namespace: uberon +def: "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]." [VSAO:0000033] +subset: efo_slim +subset: pheno_slim +synonym: "muscle system" EXACT [] +synonym: "muscle system of body" EXACT [] +synonym: "muscular system" EXACT [FMA:72954] +synonym: "musculature system" EXACT [BILA:0000088] +synonym: "muskelsystem" RELATED [BTO:0001485] +synonym: "set of all muscles" EXACT [FMA:72954] +synonym: "set of muscles of body" EXACT [FMA:72954] +synonym: "vertebrate muscular system" EXACT [BTO:0001369] +xref: AAO:0000307 +xref: BILA:0000088 +xref: BTO:0001369 +xref: BTO:0001485 +xref: EFO:0000801 +xref: EMAPA:35578 +xref: FBbt:00005069 +xref: FMA:72954 +xref: MA:0002888 +xref: MAT:0000025 +xref: MIAA:0000025 +xref: VSAO:0000033 +xref: XAO:0004042 +is_a: UBERON:0011216 ! organ system subdivision +intersection_of: UBERON:0011216 ! organ system subdivision +intersection_of: composed_primarily_of UBERON:0001015 ! musculature +relationship: composed_primarily_of UBERON:0001015 ! musculature +relationship: part_of UBERON:0002204 ! musculoskeletal system +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} +property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0000409 +name: serous gland +namespace: uberon +def: "A gland in which the principal secretory cells are serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] +subset: organ_slim +subset: pheno_slim +xref: BTO:0001837 +xref: EMAPA:37950 {source="MA:th"} +xref: FMA:62889 +xref: Serous:gland +is_a: UBERON:0002365 ! exocrine gland +relationship: has_part UBERON:0013232 ! serous acinus +relationship: produces UBERON:0007794 ! secretion of serous gland +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png +property_value: UBPROP:0000001 "glands that secrete watery albuminous material that often contains enzymes[MP:0008052]." xsd:string {source="MP:0008052"} + +[Term] +id: UBERON:0000415 +name: artery wall +namespace: uberon +def: "An anatomical wall that is part of an artery [Automatically generated definition]." [OBOL:automatic] +synonym: "arterial wall" EXACT [FMA:14155] +synonym: "wall of artery" EXACT [FMA:14155] +xref: BTO:0002009 +xref: FMA:14155 +xref: galen:ArterialWall +is_a: UBERON:0035965 ! wall of blood vessel +intersection_of: UBERON:0000060 ! anatomical wall +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0001637 ! artery + +[Term] +id: UBERON:0000456 +name: secretion of exocrine gland +namespace: uberon +alt_id: UBERON:0006540 +def: "A portion of organism substance that is produced by exocrine glands." [http://orcid.org/0000-0002-6601-2165] +synonym: "bodily secretion" EXACT [MESH:D012634] +synonym: "exocrine gland fluid" RELATED [] +synonym: "exocrine gland fluid or secretion" RELATED [] +synonym: "exocrine gland fluid/secretion" EXACT [MA:0002504] +synonym: "exocrine gland secretion" RELATED [] +synonym: "external secretion" RELATED [BTO:0002977] +synonym: "secreted substance" EXACT [] +synonym: "secretion" BROAD [FMA:9675] +xref: AEO:0001005 +xref: BTO:0002977 +xref: BTO:0002979 +xref: EMAPA:36535 +xref: FMA:9675 +xref: galen:Secretion +xref: http://linkedlifedata.com/resource/umls/id/C1516992 +xref: MA:0002504 +xref: MESH:D012634 +xref: NCIT:C34062 +xref: UMLS:C1516992 {source="ncithesaurus:Exocrine_Gland_Fluid_or_Secretion"} +is_a: UBERON:0000463 ! organism substance +intersection_of: UBERON:0000463 ! organism substance +intersection_of: produced_by UBERON:0002365 ! exocrine gland +relationship: produced_by UBERON:0002365 ! exocrine gland +property_value: UBPROP:0000012 "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions" xsd:string {external_ontology="BTO"} + +[Term] +id: UBERON:0000463 +name: organism substance +namespace: uberon +def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [http://orcid.org/0000-0001-9114-8737] +subset: pheno_slim +subset: upper_level +synonym: "body fluid or substance" EXACT [MA:0002450] +synonym: "body substance" EXACT [FMA:9669] +synonym: "organism substance" EXACT [CARO:0000004] +synonym: "portion of body substance" EXACT [FMA:9669] +synonym: "portion of organism substance" EXACT [ZFA:0001487] +xref: AAO:0010839 +xref: AEO:0000004 +xref: BILA:0000004 +xref: CALOHA:TS-2101 +xref: CARO:0000004 +xref: EHDAA2:0003004 +xref: EMAPA:35178 +xref: FBbt:00007019 +xref: FMA:9669 +xref: galen:BodySubstance +xref: HAO:0000004 +xref: MA:0002450 +xref: NCIT:C13236 +xref: SPD:0000008 +xref: TAO:0001487 +xref: TGMA:0001824 +xref: VHOG:0001726 +xref: XAO:0004001 +xref: ZFA:0001487 +is_a: UBERON:0000465 ! material anatomical entity +relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism + +[Term] +id: UBERON:0000464 +name: anatomical space +namespace: uberon +def: "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "anatomical spaces" RELATED PLURAL [ZFA:0001643] +synonym: "lumen" BROAD [] +synonym: "lumen space" EXACT [] +synonym: "space" BROAD [] +xref: AAO:0010110 +xref: AEO:0000005 +xref: BILA:0000005 +xref: CARO:0000005 +xref: EHDAA2:0003005 +xref: FBbt:00007017 +xref: FMA:5897 +xref: HAO:0000005 +xref: http://linkedlifedata.com/resource/umls/id/C0524461 +xref: NCIT:C94478 +xref: TAO:0001668 +xref: TGMA:0001825 +xref: UMLS:C0524461 {source="ncithesaurus:Lumen_Space"} +xref: VHOG:0001728 +xref: XAO:0003190 +xref: ZFA:0001643 +is_a: UBERON:0000466 ! immaterial anatomical entity +relationship: surrounded_by UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0000465 +name: material anatomical entity +namespace: uberon +def: "Anatomical entity that has mass." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +xref: AAO:0010264 +xref: AEO:0000006 +xref: BILA:0000006 +xref: CARO:0000006 +xref: EHDAA2:0003006 +xref: FBbt:00007016 +xref: FMA:67165 +xref: HAO:0000006 +xref: TAO:0001836 +xref: TGMA:0001826 +xref: VHOG:0001721 +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000466 +name: immaterial anatomical entity +namespace: uberon +def: "Anatomical entity that has no mass." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "immaterial physical anatomical entity" EXACT [FMA:67112] +xref: AAO:0010265 +xref: AEO:0000007 +xref: BILA:0000007 +xref: CARO:0000007 +xref: EHDAA2:0003007 +xref: FBbt:00007015 +xref: FMA:67112 +xref: HAO:0000007 +xref: TAO:0001835 +xref: TGMA:0001827 +xref: VHOG:0001727 +is_a: UBERON:0001062 ! anatomical entity + +[Term] +id: UBERON:0000467 +name: anatomical system +namespace: uberon +def: "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." [CARO:0000011] +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "anatomical systems" RELATED PLURAL [ZFA:0001439] +synonym: "body system" EXACT [NIFSTD:birnlex_14] +synonym: "connected anatomical system" EXACT [CARO:0000011] +synonym: "organ system" EXACT [] +synonym: "system" BROAD [GO:0048731] +xref: AAO:0000007 +xref: AEO:0000011 +xref: BILA:0000011 +xref: birnlex:14 +xref: BSA:0000049 +xref: CALOHA:TS-2088 +xref: CARO:0000011 +xref: EHDAA2:0003011 +xref: EHDAA:392 +xref: EMAPA:16103 +xref: EV:0100000 +xref: FBbt:00004856 +xref: FMA:7149 +xref: galen:AnatomicalSystem +xref: HAO:0000011 +xref: http://linkedlifedata.com/resource/umls/id/C0460002 +xref: http://www.snomedbrowser.com/Codes/Details/278195005 +xref: MA:0000003 +xref: NCIT:C12919 +xref: OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ +xref: Organ:system +xref: TAO:0001439 +xref: TGMA:0001831 +xref: UMLS:C0460002 {source="ncithesaurus:Organ_System"} +xref: VHOG:0001725 +xref: WBbt:0005746 +xref: WBbt:0005763 +xref: XAO:0003002 +xref: ZFA:0001439 +is_a: UBERON:0000061 ! anatomical structure +relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage +relationship: has_part UBERON:0000062 ! organ +relationship: part_of UBERON:0000468 ! multicellular organism +property_value: seeAlso EHDAA2:0001330 + +[Term] +id: UBERON:0000468 +name: multicellular organism +namespace: uberon +def: "Anatomical structure that is an individual member of a species and consists of more than one cell." [CARO:0000012, http://en.wikipedia.org/wiki/Multi-cellular_organism, http://orcid.org/0000-0001-9114-8737] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "animal" NARROW [BTO:0000042] +synonym: "body" RELATED [AEO:0000103, FMA:256135, http://uri.neuinfo.org/nif/nifstd/birnlex_18, NCIT:C13041] +synonym: "Koerper" RELATED [BTO:0001489] +synonym: "multi-cellular organism" EXACT [CARO:0000012] +synonym: "organism" BROAD [FBbt:00000001, VHOG:0000671, WBbt:0007833] +synonym: "whole body" RELATED [BTO:0001489] +synonym: "whole organism" RELATED [FBbt:00000001] +xref: AAO:0010026 +xref: AEO:0000191 +xref: BILA:0000012 +xref: birnlex:18 +xref: BSA:0000038 +xref: BTO:0000042 +xref: CARO:0000012 +xref: EFO:0002906 +xref: EHDAA2:0003103 +xref: EHDAA2:0003191 +xref: EHDAA:1 +xref: EMAPA:25765 +xref: EV:0100016 +xref: FBbt:00000001 +xref: FMA:256135 +xref: galen:Organism +xref: HAO:0000012 +xref: http://www.snomedbrowser.com/Codes/Details/243928005 +xref: Multi-cellular:organism +xref: NCIT:C13041 +xref: ncithesaurus:Whole_Organism +xref: TADS:0000001 +xref: TAO:0001094 +xref: TGMA:0001832 +xref: VHOG:0000671 +xref: WBbt:0007833 +xref: XAO:0003004 +xref: ZFA:0001094 +is_a: UBERON:0010000 ! multicellular anatomical structure +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: UBPROP:0000007 "organismal" xsd:string + +[Term] +id: UBERON:0000475 +name: organism subdivision +namespace: uberon +def: "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." [CARO:0000032, CARO:DOS, http://orcid.org/0000-0001-9114-8737] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "anatomic region" EXACT [MA:0002433] +synonym: "body part" RELATED [] +synonym: "body region" RELATED [FMA:7153] +synonym: "cardinal body part" RELATED [FMA:7153] +xref: AAO:0010053 +xref: AEO:0000032 +xref: BILA:0000032 +xref: birnlex:7 +xref: Body:part +xref: CALOHA:TS-2084 +xref: CARO:0000032 +xref: EFO:0000808 +xref: EHDAA2:0003032 +xref: EMAPA:36031 +xref: FBbt:00007009 +xref: FMA:7153 +xref: galen:BodyPart +xref: HAO:0000032 +xref: http://linkedlifedata.com/resource/umls/id/C0229962 +xref: MA:0002433 +xref: MAT:0000293 +xref: MESH:D001829 +xref: MIAA:0000293 +xref: NCIT:C32221 +xref: OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA +xref: TAO:0001308 +xref: TGMA:0001840 +xref: UMLS:C0229962 {source="ncithesaurus:Body_Part"} +xref: VHOG:0001758 +xref: XAO:0003013 +xref: ZFA:0001308 +is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure +relationship: part_of UBERON:0000468 ! multicellular organism +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string + +[Term] +id: UBERON:0000476 +name: acellular anatomical structure +namespace: uberon +def: "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." [http://orcid.org/0000-0001-9114-8737] +subset: vertebrate_core +synonym: "acellular anatomical structures" RELATED PLURAL [ZFA:0000382] +xref: AAO:0010268 +xref: AEO:0000040 +xref: BILA:0000040 +xref: CARO:0000040 +xref: EHDAA2:0003040 +xref: FBbt:00007013 +xref: FMA:63863 +xref: HAO:0000040 +xref: TAO:0000382 +xref: TGMA:0001841 +xref: XAO:0003162 +xref: ZFA:0000382 +is_a: UBERON:0000061 ! anatomical structure +disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure + +[Term] +id: UBERON:0000477 +name: anatomical cluster +namespace: uberon +def: "Anatomical group that has its parts adjacent to one another." [http://orcid.org/0000-0001-9114-8737] +subset: upper_level +xref: AAO:0010009 +xref: AEO:0000041 +xref: BILA:0000041 +xref: CARO:0000041 +xref: EHDAA2:0003041 +xref: FBbt:00007277 +xref: FMA:49443 +xref: HAO:0000041 +xref: TADS:0000605 +xref: TAO:0001478 +xref: TGMA:0001842 +xref: VHOG:0001737 +xref: XAO:0003160 +xref: ZFA:0001478 +is_a: UBERON:0001062 ! anatomical entity +property_value: IAO:0000116 "Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]" xsd:string + +[Term] +id: UBERON:0000478 +name: extraembryonic structure +namespace: uberon +def: "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." [CARO:DOS, http://orcid.org/0000-0001-9114-8737, https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279] +comment: see also conceptus extraembryonic component in EHDAA2. +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "extra-embryonic structure" EXACT [] +synonym: "extraembryonic structures" RELATED PLURAL [ZFA:0000020] +synonym: "extraembryonic tissue" RELATED [] +xref: AAO:0010020 +xref: AEO:0000042 +xref: BILA:0000042 +xref: CALOHA:TS-2119 +xref: CARO:0000042 +xref: EHDAA2:0003042 +xref: EHDAA:46 +xref: FBbt:00005835 +xref: FMA:85537 +xref: HAO:0000042 +xref: http://linkedlifedata.com/resource/umls/id/C1282438 +xref: http://www.snomedbrowser.com/Codes/Details/314908006 +xref: NCIT:C34055 +xref: TAO:0000020 +xref: TGMA:0001843 +xref: UMLS:C1282438 {source="ncithesaurus:Extraembryonic_Structure"} +xref: VHOG:0000292 +xref: XAO:0004005 +xref: ZFA:0000020 +is_a: UBERON:0005423 ! developing anatomical structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: part_of UBERON:0016887 ! entire extraembryonic component +relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage +relationship: part_of UBERON:0016887 ! entire extraembryonic component + +[Term] +id: UBERON:0000479 +name: tissue +namespace: uberon +def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [CARO:0000043] +subset: pheno_slim +subset: upper_level +synonym: "portion of tissue" EXACT [CARO:0000043] +synonym: "simple tissue" NARROW [AEO:0000043] +synonym: "tissue portion" EXACT [] +xref: AAO:0000607 +xref: AAO:0010054 +xref: AEO:0000043 +xref: BILA:0000043 +xref: birnlex:19 +xref: CALOHA:TS-2090 +xref: CARO:0000043 +xref: EHDAA2:0003043 +xref: EMAPA:35868 +xref: FBbt:00007003 +xref: FMA:9637 +xref: galen:Tissue +xref: HAO:0000043 +xref: http://linkedlifedata.com/resource/umls/id/C0040300 +xref: MA:0003002 +xref: MESH:D014024 +xref: NCIT:C12801 +xref: TAO:0001477 +xref: TGMA:0001844 +xref: UMLS:C0040300 {source="ncithesaurus:Tissue"} +xref: VHOG:0001757 +xref: WBbt:0005729 +xref: XAO:0003040 +xref: ZFA:0001477 +is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure +relationship: part_of UBERON:0000468 ! multicellular organism +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string + +[Term] +id: UBERON:0000481 +name: multi-tissue structure +namespace: uberon +def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [CARO:0000055, http://orcid.org/0000-0001-9114-8737] +subset: upper_level +synonym: "multi-tissue structures" RELATED PLURAL [ZFA:0001488] +xref: AAO:0010048 +xref: AEO:0000055 +xref: BILA:0000055 +xref: CARO:0000055 +xref: EHDAA2:0003055 +xref: FBbt:00007010 +xref: HAO:0000055 +xref: TAO:0001488 +xref: TGMA:0001847 +xref: VHOG:0001762 +xref: XAO:0003037 +xref: ZFA:0001488 +is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure +relationship: has_part UBERON:0000479 ! tissue + +[Term] +id: UBERON:0000483 +name: epithelium +namespace: uberon +def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [http://en.wikipedia.org/wiki/Epithelium, http://orcid.org/0000-0001-9114-8737] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "epithelial tissue" EXACT [] +synonym: "portion of epithelium" EXACT [FMA:9639] +xref: AAO:0000144 +xref: AAO:0010055 +xref: AEO:0000066 +xref: BILA:0000066 +xref: BTO:0000416 +xref: CALOHA:TS-0288 +xref: CARO:0000066 +xref: EHDAA2:0003066 +xref: EMAPA:32738 +xref: FBbt:00007005 +xref: FMA:9639 +xref: GAID:402 +xref: HAO:0000066 +xref: http://en.wikipedia.org/wiki/Epithelium +xref: http://linkedlifedata.com/resource/umls/id/C0014609 +xref: http://www.snomedbrowser.com/Codes/Details/31610004 +xref: MA:0003060 +xref: MESH:D004848 +xref: NCIT:C12710 +xref: TAO:0001486 +xref: UMLS:C0014609 {source="ncithesaurus:Epithelium"} +xref: VHOG:0000387 +xref: XAO:0003045 +xref: ZFA:0001486 +is_a: UBERON:0000479 ! tissue +union_of: UBERON:0000486 ! multilaminar epithelium +union_of: UBERON:0000490 ! unilaminar epithelium +relationship: has_part UBERON:0005769 ! basement membrane of epithelium +property_value: depicted:by Tkanka:nablonkowa.png +property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59"} +property_value: UBPROP:0000007 "epithelial" xsd:string + +[Term] +id: UBERON:0000485 +name: simple columnar epithelium +namespace: uberon +def: "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Simple_columnar_epithelium, http://orcid.org/0000-0001-9114-8737] +subset: uberon_slim +subset: vertebrate_core +synonym: "columnar epithelium" BROAD [EHDAA2:0003068] +synonym: "columnar epithlium" BROAD [AEO:0000068] +synonym: "epithelium simplex columnare" EXACT [] +synonym: "simple columnar epithelia" RELATED PLURAL [ZFA:0001496] +synonym: "simple columnar epithelium" EXACT [] +xref: AAO:0010063 +xref: AEO:0000068 +xref: BILA:0000068 +xref: CARO:0000068 +xref: EHDAA2_RETIRED:0003068 +xref: FBbt:00007027 +xref: FMA:45567 +xref: HAO:0000068 +xref: http://en.wikipedia.org/wiki/Simple_columnar_epithelium +xref: http://linkedlifedata.com/resource/umls/id/C0836135 +xref: http://www.snomedbrowser.com/Codes/Details/32210007 +xref: NCIT:C33552 +xref: TAO:0001496 +xref: UMLS:C0836135 {source="ncithesaurus:Simple_Columnar_Epithelium"} +xref: XAO:0004008 +xref: ZFA:0001496 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0012274 ! columnar epithelium +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png + +[Term] +id: UBERON:0000486 +name: multilaminar epithelium +namespace: uberon +def: "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Stratified_epithelium, http://orcid.org/0000-0001-9114-8737] +subset: uberon_slim +subset: vertebrate_core +synonym: "laminated epithelium" RELATED [BTO:0002074] +synonym: "stratified epithelium" EXACT [] +xref: AAO:0010059 +xref: AEO:0000069 +xref: BILA:0000069 +xref: BTO:0002074 +xref: CARO:0000069 +xref: EHDAA2:0003069 +xref: FMA:45562 +xref: HAO:0000069 +xref: http://linkedlifedata.com/resource/umls/id/C0682575 +xref: http://www.snomedbrowser.com/Codes/Details/309044005 +xref: NCIT:C33622 +xref: Stratified:epithelium +xref: TAO:0001494 +xref: UMLS:C0682575 {source="ncithesaurus:Stratified_Epithelium"} +xref: XAO:0004006 +xref: ZFA:0001494 +is_a: UBERON:0000483 ! epithelium +property_value: UBPROP:0000001 "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="http://orcid.org/0000-0001-9114-8737", source="FMA:45562"} + +[Term] +id: UBERON:0000487 +name: simple squamous epithelium +namespace: uberon +def: "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]" [FMA:45565, http://en.wikipedia.org/wiki/Simple_squamous_epithelium, http://orcid.org/0000-0001-9114-8737] +subset: uberon_slim +subset: vertebrate_core +synonym: "epithelium simplex squamosum" EXACT [] +synonym: "simple squamous epithelia" RELATED PLURAL [ZFA:0001498] +xref: AAO:0010066 +xref: AEO:0000070 +xref: BILA:0000070 +xref: BTO:0002073 +xref: CARO:0000070 +xref: EHDAA2:0003070 +xref: FMA:45565 +xref: HAO:0000070 +xref: http://en.wikipedia.org/wiki/Simple_squamous_epithelium +xref: http://linkedlifedata.com/resource/umls/id/C0836133 +xref: NCIT:C13178 +xref: TAO:0001498 +xref: UMLS:C0836133 {source="ncithesaurus:Simple_Squamous_Epithelium"} +xref: XAO:0004010 +xref: ZFA:0001498 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0006914 ! squamous epithelium +property_value: depicted:by Illu:epithelium.jpg +property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="http://orcid.org/0000-0001-9114-8737", source="FMA:45565"} + +[Term] +id: UBERON:0000489 +name: cavitated compound organ +namespace: uberon +def: "Compound organ that contains one or more macroscopic anatomical spaces." [http://orcid.org/0000-0001-9114-8737] +subset: organ_slim +subset: upper_level +synonym: "cavitated compound organs" RELATED PLURAL [ZFA:0001490] +synonym: "cavitated organ" EXACT [FMA:55671] +xref: AAO:0010016 +xref: AEO:0000072 +xref: BILA:0000072 +xref: CARO:0000072 +xref: EHDAA2:0003072 +xref: FMA:55671 +xref: HAO:0000072 +xref: TAO:0001490 +xref: TGMA:0001857 +xref: VHOG:0001730 +xref: XAO:0003165 +xref: ZFA:0001490 +is_a: UBERON:0003103 ! compound organ +intersection_of: UBERON:0003103 ! compound organ +intersection_of: has_part UBERON:0002553 ! anatomical cavity +relationship: has_part UBERON:0002553 ! anatomical cavity +property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string + +[Term] +id: UBERON:0000490 +name: unilaminar epithelium +namespace: uberon +def: "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]" [FMA:45561, http://orcid.org/0000-0001-9114-8737] +subset: vertebrate_core +synonym: "simple epithelium" EXACT [FMA:45561] +synonym: "unilaminar epithelia" RELATED PLURAL [ZFA:0001495] +xref: AAO:0010062 +xref: AEO:0000073 +xref: BILA:0000073 +xref: BTO:0002073 +xref: CARO:0000073 +xref: EHDAA2:0003073 +xref: FMA:45561 +xref: HAO:0000073 +xref: http://linkedlifedata.com/resource/umls/id/C0682574 +xref: http://www.snomedbrowser.com/Codes/Details/309043004 +xref: NCIT:C33554 +xref: TAO:0001495 +xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} +xref: XAO:0004007 +xref: ZFA:0001495 +is_a: UBERON:0000483 ! epithelium +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string +property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="http://orcid.org/0000-0001-9114-8737", source="FMA:45561"} + +[Term] +id: UBERON:0000915 +name: thoracic segment of trunk +namespace: uberon +def: "Subdivision of trunk that lies between the head and the abdomen." [http://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "anterior subdivision of trunk" RELATED [] +synonym: "thorax" EXACT [MA:0000022] +synonym: "upper body" RELATED [] +synonym: "upper trunk" RELATED [FMA:259209] +xref: EMAPA:35862 +xref: FMA:259209 +xref: http://en.wikipedia.org/wiki/Thorax +xref: http://www.snomedbrowser.com/Codes/Details/302551006 +xref: MA:0000022 +is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk +is_a: UBERON:0011676 ! subdivision of organism along main body axis +intersection_of: UBERON:0011676 ! subdivision of organism along main body axis +intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton +relationship: has_skeleton UBERON:0014477 ! thoracic skeleton +property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string + +[Term] +id: UBERON:0000922 +name: embryo +namespace: uberon +def: "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." [BTO:0000379, FB:FBrf0039741, FB:FBrf0041814, GO:0009790, http://en.wikipedia.org/wiki/Embryo] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "developing organism" RELATED [BILA:0000056] +synonym: "developmental tissue" RELATED [] +synonym: "embryonic organism" EXACT [BILA:0000056] +xref: AAO:0011035 +xref: AEO:0000169 +xref: BILA:0000056 +xref: BSA:0000039 +xref: BTO:0000379 +xref: CALOHA:TS-0229 +xref: Category:Embryonic\:organism +xref: EFO:0001367 +xref: EHDAA2:0000002 +xref: EHDAA2_RETIRED:0003236 +xref: EHDAA:38 +xref: EMAPA:16039 +xref: FBbt:00000052 +xref: FMA:69068 +xref: GAID:963 +xref: http://en.wikipedia.org/wiki/Embryo +xref: http://linkedlifedata.com/resource/umls/id/C0013935 +xref: http://www.snomedbrowser.com/Codes/Details/57991002 +xref: MAT:0000226 +xref: MESH:D004622 +xref: MIAA:0000019 +xref: NCIT:C28147 +xref: OGEM:000001 +xref: OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA +xref: UMLS:C0013935 {source="ncithesaurus:Embryo"} +xref: VHOG:0001766 +xref: XAO:0000113 +xref: ZFA:0000103 +is_a: UBERON:0000468 ! multicellular organism +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: existence_ends_with UBERON:0000068 ! embryo stage +intersection_of: existence_starts_with UBERON:0000068 ! embryo stage +relationship: existence_ends_with UBERON:0000068 ! embryo stage +relationship: existence_starts_with UBERON:0000068 ! embryo stage +property_value: depicted:by Wrinkledfrog:embryos.jpg +property_value: seeAlso https://github.com/obophenotype/uberon/issues/503 +property_value: UBPROP:0000007 "embryonic" xsd:string +property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} + +[Term] +id: UBERON:0000923 +name: germ layer +namespace: uberon +def: "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." [http://en.wikipedia.org/wiki/Germ_layer, https://github.com/obophenotype/uberon/issues/203] +comment: Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic germ layer" RELATED [] +synonym: "embryonic germ layers" RELATED [] +synonym: "embryonic tissue" BROAD [FMA:69069] +synonym: "germinal layer" EXACT [ncithesaurus:Germinal_Layer] +synonym: "primary germ layer" NARROW [GO:0001704, ZFA:0001122] +xref: AAO:0000480 +xref: BILA:0000035 +xref: BTO:0000556 +xref: EMAPA:36033 +xref: FBbt:00000110 +xref: FMA:69069 +xref: GAID:1303 +xref: Germ:layer +xref: http://linkedlifedata.com/resource/umls/id/C0920502 +xref: http://linkedlifedata.com/resource/umls/id/C1708239 +xref: MESH:A16.254.425 +xref: NCIT:C12950 +xref: NCIT:C54105 +xref: TAO:0001122 +xref: UMLS:C0920502 {source="ncithesaurus:Embryonic_Tissue"} +xref: UMLS:C1708239 {source="ncithesaurus:Germinal_Layer"} +xref: VHOG:0001223 +xref: XAO:0003011 +xref: ZFA:0001122 +is_a: UBERON:0010316 ! germ layer / neural crest +property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722"} + +[Term] +id: UBERON:0000924 +name: ectoderm +namespace: uberon +def: "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." [http://en.wikipedia.org/wiki/Ectoderm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic ectoderm" EXACT [VHOG:0000153] +xref: AAO:0000137 +xref: BILA:0000036 +xref: BTO:0000315 +xref: CALOHA:TS-0216 +xref: EFO:0000414 +xref: EHDAA2:0000428 +xref: EMAPA:16069 +xref: EV:0100003 +xref: FBbt:00000111 +xref: FMA:69070 +xref: GAID:1304 +xref: http://en.wikipedia.org/wiki/Ectoderm +xref: http://linkedlifedata.com/resource/umls/id/C0013574 +xref: http://www.snomedbrowser.com/Codes/Details/362851007 +xref: MAT:0000155 +xref: MAT:0000173 +xref: MESH:A16.254.425.273 +xref: MIAA:0000173 +xref: NCIT:C12703 +xref: TAO:0000016 +xref: UMLS:C0013574 {source="ncithesaurus:Ectoderm"} +xref: VHOG:0000153 +xref: XAO:0000001 +xref: ZFA:0000016 +is_a: UBERON:0000923 ! germ layer +relationship: develops_from UBERON:0006601 ! presumptive ectoderm +relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png +property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722"} +property_value: UBPROP:0000007 "ectodermal" xsd:string + +[Term] +id: UBERON:0000925 +name: endoderm +namespace: uberon +def: "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." [http://en.wikipedia.org/wiki/Endoderm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "entoderm" RELATED DEPRECATED [http://dx.doi.org/10.5962/bhl.title.1013] +xref: AAO:0000139 +xref: BILA:0000038 +xref: BTO:0000800 +xref: CALOHA:TS-0273 +xref: EFO:0002545 +xref: EHDAA2:0000436 +xref: EMAPA:16062 +xref: EV:0100005 +xref: FBbt:00000125 +xref: FMA:69071 +xref: GAID:1305 +xref: http://en.wikipedia.org/wiki/Endoderm +xref: http://linkedlifedata.com/resource/umls/id/C0014144 +xref: http://www.snomedbrowser.com/Codes/Details/362855003 +xref: MAT:0000175 +xref: MESH:A16.254.425.407 +xref: MIAA:0000175 +xref: NCIT:C12706 +xref: TAO:0000017 +xref: UMLS:C0014144 {source="ncithesaurus:Endoderm"} +xref: VHOG:0000154 +xref: XAO:0000090 +xref: ZFA:0000017 +is_a: UBERON:0000923 ! germ layer +relationship: develops_from UBERON:0006595 ! presumptive endoderm +relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png +property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722"} +property_value: UBPROP:0000007 "endodermal" xsd:string + +[Term] +id: UBERON:0000926 +name: mesoderm +namespace: uberon +alt_id: UBERON:0003263 +def: "The middle germ layer of the embryo, between the endoderm and ectoderm." [http://en.wikipedia.org/wiki/Mesoderm] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic mesoderm" RELATED [VHOG:0000152] +synonym: "entire mesoderm" RELATED [http://www.snomedbrowser.com/Codes/Details/362854004, https://orcid.org/0000-0002-6601-2165] +synonym: "mesodermal mantle" RELATED [] +xref: AAO:0000304 +xref: BILA:0000037 +xref: BTO:0000839 +xref: CALOHA:TS-0623 +xref: EFO:0001981 +xref: EHDAA2:0001128 +xref: EHDAA:124 +xref: EHDAA:160 +xref: EHDAA:183 +xref: EMAPA:16083 +xref: EV:0100006 +xref: FBbt:00000126 +xref: FMA:69072 +xref: GAID:522 +xref: http://en.wikipedia.org/wiki/Mesoderm +xref: http://linkedlifedata.com/resource/umls/id/C0025485 +xref: http://www.snomedbrowser.com/Codes/Details/362854004 +xref: MAT:0000174 +xref: MESH:A16.254.425.660 +xref: MIAA:0000174 +xref: NCIT:C12750 +xref: TAO:0000041 +xref: UMLS:C0025485 {source="ncithesaurus:Mesoderm"} +xref: VHOG:0000152 +xref: XAO:0000050 +xref: ZFA:0000041 +is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +relationship: develops_from UBERON:0006603 ! presumptive mesoderm +relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png +property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722"} +property_value: UBPROP:0000007 "mesodermal" xsd:string +property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} + +[Term] +id: UBERON:0000930 +name: stomodeum +namespace: uberon +def: "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity." [http://en.wikipedia.org/wiki/Stomodeum, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/326] +subset: grouping_class +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mouth pit" RELATED [EMAPA:16263] +synonym: "mouth primordium" EXACT [XAO:0000269] +synonym: "oral ectoderm" RELATED [ZFA:0001290\,ZFIN\:ZDB-PUB-100726-23] +synonym: "oral pit" RELATED [EMAPA:16263] +synonym: "primitive oral cavity" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "stomatodeum" EXACT [http://en.wikipedia.org/wiki/Stomodeum] +synonym: "stomodaeum" EXACT [] +synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] +xref: BTO:0004224 +xref: EHDAA2:0001929 +xref: EMAPA:16263 +xref: FBbt:00000439 +xref: FMA:295846 +xref: http://en.wikipedia.org/wiki/Stomodeum +xref: http://linkedlifedata.com/resource/umls/id/C1514977 +xref: NCIT:C34306 +xref: TAO:0001290 +xref: TGMA:0000135 +xref: UMLS:C1514977 {source="ncithesaurus:Stomodeum"} +xref: XAO:0000269 +xref: ZFA:0001290 +is_a: UBERON:0013522 ! subdivision of tube +relationship: part_of UBERON:0000924 ! ectoderm +relationship: part_of UBERON:0035804 ! future mouth +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string +property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} +property_value: UBPROP:0000007 "stomodeal" xsd:string +property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string + +[Term] +id: UBERON:0000948 +name: heart +namespace: uberon +def: "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [http://en.wikipedia.org/wiki/Heart, http://orcid.org/0000-0002-6601-2165] +comment: Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706 +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "branchial heart" NARROW SENSU [] +synonym: "cardium" RELATED [EMAPA:16105] +synonym: "chambered heart" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "Herz@de" RELATED [BTO:0000562] +synonym: "vertebrate heart" EXACT [] +xref: AAO:0010210 +xref: BILA:0000020 +xref: BTO:0000562 +xref: CALOHA:TS-0445 +xref: EFO:0000815 +xref: EHDAA2:0000738 +xref: EHDAA:420 +xref: EMAPA:16105 +xref: EV:0100018 +xref: FMA:7088 +xref: GAID:174 +xref: galen:Heart +xref: http://en.wikipedia.org/wiki/Heart +xref: http://linkedlifedata.com/resource/umls/id/C0018787 +xref: http://www.snomedbrowser.com/Codes/Details/302509004 +xref: MA:0000072 +xref: MAT:0000036 +xref: MESH:D006321 +xref: MIAA:0000036 +xref: NCIT:C12727 +xref: OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA +xref: TAO:0000114 +xref: UMLS:C0018787 {source="ncithesaurus:Heart"} +xref: VHOG:0000276 +xref: XAO:0000064 +xref: ZFA:0000114 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005181 ! thoracic segment organ +is_a: UBERON:0007100 ! primary circulatory organ +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0007100 ! primary circulatory organ +intersection_of: has_part UBERON:0004151 ! cardiac chamber +relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system +relationship: develops_from UBERON:0004141 ! heart tube +relationship: has_part UBERON:0004151 ! cardiac chamber +relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium +property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} +property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481"} +property_value: UBPROP:0000007 "cardiac" xsd:string + +[Term] +id: UBERON:0000955 +name: brain +namespace: uberon +def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [http://en.wikipedia.org/wiki/Brain, https://github.com/obophenotype/uberon/issues/300] +subset: cumbo +subset: efo_slim +subset: major_organ +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "encephalon" RELATED [BTO:0000142] +synonym: "suprasegmental levels of nervous system" RELATED [NeuroNames:21] +synonym: "suprasegmental structures" RELATED [NeuroNames:21] +synonym: "synganglion" RELATED [] +synonym: "the brain" RELATED [NeuroNames:21] +xref: AAO:0010478 +xref: ABA:Brain +xref: BAMS:Br +xref: BAMS:Brain +xref: BILA:0000135 +xref: birnlex:796 +xref: BTO:0000142 +xref: CALOHA:TS-0095 +xref: DHBA:10155 +xref: EFO:0000302 +xref: EHDAA2:0000183 +xref: EHDAA:2641 +xref: EHDAA:6485 +xref: EMAPA:16894 +xref: EV:0100164 +xref: FBbt:00005095 +xref: FMA:50801 +xref: GAID:571 +xref: galen:Brain +xref: HBA:4005 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 {source="NIFSTD:birnlex_796"} +xref: http://en.wikipedia.org/wiki/Brain +xref: http://linkedlifedata.com/resource/umls/id/C0006104 +xref: http://linkedlifedata.com/resource/umls/id/C1269537 +xref: http://www.snomedbrowser.com/Codes/Details/258335003 +xref: MA:0000168 +xref: MAT:0000098 +xref: MBA:8 +xref: MBA:997 +xref: MESH:D001921 +xref: MIAA:0000098 +xref: NCIT:C12439 +xref: OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA +xref: PBA:3999 +xref: TAO:0000008 +xref: UMLS:C0006104 {source="ncithesaurus:Brain"} +xref: UMLS:C0006104 {source="NIFSTD:birnlex_796"} +xref: UMLS:C1269537 {source="NIFSTD:birnlex_796"} +xref: VHOG:0000157 +xref: XAO:0000010 +xref: ZFA:0000008 +is_a: UBERON:0000062 {source="GO"} ! organ +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system +relationship: develops_from UBERON:0006238 ! future brain +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain +relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism +relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string +property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="Cumbo:terms"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165"} + +[Term] +id: UBERON:0000974 +name: neck +namespace: uberon +def: "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "collum" RELATED LATIN [http://en.wikipedia.org/wiki/Neck] +synonym: "neck (volume)" RELATED [FMA:7155] +xref: AEO:0000108 +xref: BTO:0000420 +xref: CALOHA:TS-2045 +xref: EFO:0000967 +xref: EHDAA2:0003108 +xref: EMAPA:35587 +xref: FMA:7155 +xref: GAID:86 +xref: galen:Neck +xref: http://en.wikipedia.org/wiki/Neck +xref: http://linkedlifedata.com/resource/umls/id/C0027530 +xref: http://www.snomedbrowser.com/Codes/Details/302550007 +xref: MA:0000024 +xref: MAT:0000297 +xref: MESH:D009333 +xref: MIAA:0000297 +xref: NCIT:C13063 +xref: OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA +xref: UMLS:C0027530 {source="ncithesaurus:Neck"} +is_a: UBERON:0000475 ! organism subdivision +relationship: anteriorly_connected_to UBERON:0000033 ! head +relationship: part_of UBERON:0007811 ! craniocervical region +relationship: posteriorly_connected_to UBERON:0002100 ! trunk +property_value: depicted:by Female:neck.jpg +property_value: IAO:0000232 "true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck." xsd:string +property_value: RO:0002174 NCBITaxon:32443 {source="ISBN:9780674021839"} +property_value: UBPROP:0000007 "cervical" xsd:string + +[Term] +id: UBERON:0000982 +name: skeletal joint +namespace: uberon +def: "Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, http://en.wikipedia.org/wiki/Joint, VSAO:0000101] +subset: efo_slim +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "articular joint" RELATED [BTO:0001686] +synonym: "articulation" BROAD [VSAO:0000101] +synonym: "joint" BROAD [FMA:7490, VSAO:0000101] +synonym: "joints" RELATED PLURAL [ZFA:0001596] +xref: AEO:0000182 +xref: BTO:0001686 +xref: CALOHA:TS-2023 +xref: EFO:0000948 +xref: EMAPA:35456 +xref: FMA:7490 +xref: GAID:102 +xref: galen:Joint +xref: http://en.wikipedia.org/wiki/Joint +xref: http://linkedlifedata.com/resource/umls/id/C0022417 +xref: http://www.snomedbrowser.com/Codes/Details/302536002 +xref: MA:0000319 +xref: MAT:0000188 +xref: MESH:D007596 +xref: MIAA:0000188 +xref: NCIT:C13044 +xref: OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA +xref: RETIRED_EHDAA2:0003182 +xref: TAO:0000367 +xref: UMLS:C0022417 {source="ncithesaurus:Joint"} +xref: VHOG:0001276 +xref: VSAO:0000101 +xref: XAO:0000171 +xref: ZFA:0001596 +is_a: UBERON:0004905 ! articulation +union_of: UBERON:0002217 ! synovial joint +union_of: UBERON:0011134 ! nonsynovial joint +relationship: connects UBERON:0004765 ! skeletal element +relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system +property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} +property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} + +[Term] +id: UBERON:0001003 +name: skin epidermis +namespace: uberon +def: "The outer epithelial layer of the skin that is superficial to the dermis." [http://orcid.org/0000-0002-6601-2165, ISBN10:0073040584] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "epidermis" BROAD [] +synonym: "skin" BROAD [] +synonym: "vertebrate epidermis" EXACT [] +xref: AAO:0000143 +xref: BTO:0000404 +xref: CALOHA:TS-0283 +xref: EFO:0000954 +xref: EMAPA:17528 +xref: Epidermis:(skin) +xref: EV:0100153 +xref: FMA:70596 +xref: GAID:932 +xref: http://linkedlifedata.com/resource/umls/id/C0014520 +xref: http://www.snomedbrowser.com/Codes/Details/361694003 +xref: MA:0000153 +xref: MAT:0000154 +xref: MESH:D004817 +xref: MIAA:0000154 +xref: NCIT:C12708 +xref: TAO:0000105 +xref: UMLS:C0014520 {source="ncithesaurus:Epidermis"} +xref: VHOG:0000077 +xref: XAO:0000028 +xref: ZFA:0000105 +is_a: UBERON:0007376 ! outer epithelium +is_a: UBERON:3000961 ! external integument structure +intersection_of: UBERON:0007376 ! outer epithelium +intersection_of: part_of UBERON:0002097 ! skin of body +relationship: adjacent_to UBERON:0002067 ! dermis +relationship: developmentally_replaces UBERON:0003055 ! periderm +relationship: part_of UBERON:0002097 ! skin of body +property_value: UBPROP:0000001 "A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000105", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000002 "relationship loss: subclass external integument structures (AAO:0000961)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO"} +property_value: UBPROP:0000003 "(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000077", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72"} +property_value: UBPROP:0000007 "epidermal" xsd:string +property_value: UBPROP:0000008 "Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes)." xsd:string + +[Term] +id: UBERON:0001004 +name: respiratory system +namespace: uberon +def: "Functional system which consists of structures involved in respiration." [http://en.wikipedia.org/wiki/Respiratory_system, http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: functional_classification +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "apparatus respiratorius" EXACT [] +synonym: "apparatus respiratorius" RELATED [BTO:0000203] +synonym: "Atmungssystem" RELATED [BTO:0000203] +synonym: "respiratory system" EXACT [] +synonym: "systema respiratorium" RELATED LATIN [http://en.wikipedia.org/wiki/Respiratory_system] +xref: AAO:0000541 +xref: BTO:0000203 +xref: CALOHA:TS-1319 +xref: EFO:0000804 +xref: EHDAA2:0001604 +xref: EHDAA:2203 +xref: EMAPA:16727 +xref: EV:0100036 +xref: FMA:7158 +xref: GAID:78 +xref: http://linkedlifedata.com/resource/umls/id/C0035237 +xref: http://www.snomedbrowser.com/Codes/Details/278197002 +xref: MA:0000327 +xref: MAT:0000030 +xref: MESH:D012137 +xref: MIAA:0000030 +xref: NCIT:C12779 +xref: OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA +xref: Respiratory:system +xref: TAO:0000272 +xref: UMLS:C0035237 {source="ncithesaurus:Respiratory_System"} +xref: VHOG:0000202 +xref: XAO:0000117 +xref: ZFA:0000272 +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001007 ! digestive system +disjoint_from: UBERON:0001009 ! circulatory system +disjoint_from: UBERON:0001016 ! nervous system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002330 ! exocrine system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg +property_value: UBPROP:0000001 "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000541", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000202", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23"} + +[Term] +id: UBERON:0001005 +name: respiratory airway +namespace: uberon +def: "An airway through which respiratory air passes in organisms." [http://en.wikipedia.org/wiki/Trachea] +subset: grouping_class +subset: uberon_slim +synonym: "airway" BROAD [http://orcid.org/0000-0002-6601-2165] +synonym: "airways" BROAD PLURAL [http://orcid.org/0000-0002-6601-2165] +xref: FMA:265130 +xref: http://en.wikipedia.org/wiki/Trachea +xref: http://www.snomedbrowser.com/Codes/Details/361380005 +is_a: UBERON:0003103 ! compound organ +is_a: UBERON:0004111 ! anatomical conduit +relationship: channel_for UBERON:0034874 ! air in respiratory system +relationship: part_of UBERON:0001004 ! respiratory system +property_value: IAO:0000232 "This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends" xsd:string + +[Term] +id: UBERON:0001007 +name: digestive system +namespace: uberon +def: "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." [FB:gg, http://en.wikipedia.org/wiki/Digestive_system, NLM:alimentary+system] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "alimentary system" RELATED [] +synonym: "alimentary tract" RELATED [] +synonym: "gastrointestinal system" RELATED [] +synonym: "gut" RELATED [] +xref: AAO:0000129 +xref: BILA:0000082 +xref: BTO:0000058 +xref: CALOHA:TS-1293 +xref: Digestive:system +xref: EFO:0000793 +xref: EV:0100056 +xref: FBbt:00005055 +xref: FMA:7152 +xref: GAID:278 +xref: galen:DigestiveSystem +xref: http://www.snomedbrowser.com/Codes/Details/278859004 +xref: MA:0002431 +xref: MAT:0000018 +xref: MESH:D004064 +xref: MIAA:0000018 +xref: ncithesaurus:Digestive_System +xref: TADS:0000170 +xref: TAO:0000339 +xref: WBbt:0005748 +xref: XAO:0000125 +xref: ZFA:0000339 +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001009 ! circulatory system +disjoint_from: UBERON:0001016 ! nervous system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002330 ! exocrine system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000007 "digestive" xsd:string +property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0001009 +name: circulatory system +namespace: uberon +def: "organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." [http://en.wikipedia.org/wiki/Circulatory_system] +subset: uberon_slim +synonym: "systema cardiovasculare" RELATED LATIN [http://en.wikipedia.org/wiki/Circulatory_system] +xref: AAO:0000959 +xref: CALOHA:TS-2103 +xref: Circulatory:system +xref: FBbt:00005057 +xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA +xref: VHOG:0001248 +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001016 ! nervous system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002330 ! exocrine system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg +property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string +property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} +property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493"} + +[Term] +id: UBERON:0001013 +name: adipose tissue +namespace: uberon +def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue" [http://en.wikipedia.org/wiki/Adipose_tissue, http://orcid.org/0000-0002-6601-2165, MESH:A10.165.114, MGI:cwg, MP:0000003] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "adipose" RELATED [BTO:0001487] +synonym: "bodyfat" RELATED [BTO:0001487] +synonym: "fat" EXACT [MA:0000009] +synonym: "fat tissue" EXACT [] +synonym: "fatty depot" RELATED [] +synonym: "fatty tissue" EXACT [] +xref: AAO:0000001 +xref: Adipose:tissue +xref: AEO:000020 +xref: BTO:0001487 +xref: CALOHA:TS-0013 +xref: EFO:0000790 +xref: EHDAA2:0003120 +xref: EMAPA:35112 +xref: EV:0100381 +xref: FMA:20110 +xref: GAID:920 +xref: galen:FattyTissue +xref: http://linkedlifedata.com/resource/umls/id/C0001527 +xref: http://www.snomedbrowser.com/Codes/Details/55603005 +xref: MA:0000009 +xref: MAT:0000015 +xref: MESH:D000273 +xref: MIAA:0000015 +xref: NCIT:C12472 +xref: OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA +xref: TAO:0002134 +xref: UMLS:C0001527 {source="ncithesaurus:Adipose_Tissue"} +xref: VHOG:0001284 +xref: XAO:0003049 +xref: ZFA:0005345 +is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue +disjoint_from: UBERON:0003714 ! neural tissue +property_value: UBPROP:0000001 "Connective tissue in which fat is stored.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002134", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000002 "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO"} +property_value: UBPROP:0000003 "Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001284", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)"} +property_value: UBPROP:0000007 "adipose" xsd:string +property_value: UBPROP:0000008 "In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen." xsd:string +property_value: UBPROP:0000012 "in FMA this is dense irregular connective tissue" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0001015 +name: musculature +namespace: uberon +def: "A subdivision of the muscular system corresponding to a subdisivision of an organism." [http://en.wikipedia.org/wiki/Muscular_system, https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "muscle group" EXACT [] +synonym: "muscle system" RELATED [] +synonym: "muscles" RELATED [] +synonym: "muscles set" EXACT [] +synonym: "musculature" EXACT [] +synonym: "musculature system" RELATED [] +synonym: "musculi" EXACT LATIN [FMA:32558, FMA:TA] +synonym: "set of muscles" EXACT [FMA:32558] +synonym: "set of skeletal muscles" EXACT [MA:0000165] +xref: AAO:0011066 +xref: BTO:0000887 +xref: EFO:0001949 +xref: EMAPA:32715 +xref: EMAPA:35577 +xref: FMA:32558 +xref: http://linkedlifedata.com/resource/umls/id/C0026845 +xref: MA:0000165 +xref: Muscular:system +xref: NCIT:C13056 +xref: OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA +xref: TAO:0000548 +xref: UMLS:C0026845 {source="ncithesaurus:Muscle"} +xref: VSAO:0005038 +xref: WBbt:0005737 +xref: ZFA:0000548 +is_a: UBERON:0011216 ! organ system subdivision +relationship: composed_primarily_of UBERON:0001630 ! muscle organ +relationship: part_of UBERON:0000383 ! musculature of body +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png +property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0001016 +name: nervous system +namespace: uberon +def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [http://en.wikipedia.org/wiki/Nervous_system, http://uri.neuinfo.org/nif/nifstd/birnlex_844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, ZFIN:curator] +subset: cumbo +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "nerve net" NARROW [http://en.wikipedia.org/wiki/Nerve_net] +synonym: "neurological system" EXACT [GO:0050877] +synonym: "systema nervosum" RELATED LATIN [http://en.wikipedia.org/wiki/Nervous_system] +xref: AAO:0000324 +xref: BILA:0000079 +xref: birnlex:844 +xref: BTO:0001484 +xref: CALOHA:TS-1313 +xref: EFO:0000802 +xref: EHDAA2:0001246 +xref: EHDAA:826 +xref: EMAPA:16469 +xref: EV:0100162 +xref: FBbt:00005093 +xref: FMA:7157 +xref: GAID:466 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3236 +xref: http://linkedlifedata.com/resource/umls/id/C0027763 +xref: http://www.snomedbrowser.com/Codes/Details/278196006 +xref: MA:0000016 +xref: MAT:0000026 +xref: MESH:D009420 +xref: MIAA:0000026 +xref: NCIT:C12755 +xref: Nervous:system +xref: OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA +xref: TAO:0000396 +xref: UMLS:C0027763 {source="ncithesaurus:Nervous_System"} +xref: VHOG:0000402 +xref: WBbt:0005735 +xref: XAO:0000177 +xref: ZFA:0000396 +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0001434 ! skeletal system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002330 ! exocrine system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: develops_from UBERON:0016880 ! future nervous system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png +property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117"} +property_value: UBPROP:0000007 "nervous" xsd:string +property_value: UBPROP:0000007 "neural" xsd:string + +[Term] +id: UBERON:0001017 +name: central nervous system +namespace: uberon +def: "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord." [GO:0021551, http://www.frontiersinzoology.com/content/7/1/29, https://sourceforge.net/p/geneontology/ontology-requests/11422/] +subset: cumbo +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cerebrospinal axis" NARROW [FMA:55675] +synonym: "CNS" EXACT ABBREVIATION [] +synonym: "neuraxis" RELATED [FMA:55675] +synonym: "systema nervosum centrale" EXACT LATIN [FMA:55675, FMA:TA] +xref: AAO:0000090 +xref: BAMS:CNS +xref: BILA:0000080 +xref: birnlex:1099 +xref: BTO:0000227 +xref: CALOHA:TS-0150 +xref: EFO:0000908 +xref: EHDAA2:0000225 +xref: EHDAA:828 +xref: EMAPA:16470 +xref: EMAPA:16754 +xref: EV:0100163 +xref: FBbt:00005094 +xref: FMA:55675 +xref: GAID:570 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=854 +xref: http://en.wikipedia.org/wiki/Central_nervous_system +xref: http://linkedlifedata.com/resource/umls/id/C0927232 +xref: http://www.snomedbrowser.com/Codes/Details/278199004 +xref: MA:0000167 +xref: MAT:0000457 +xref: MESH:D002490 +xref: NCIT:C12438 +xref: OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA +xref: TAO:0000012 +xref: UMLS:C0927232 {source="ncithesaurus:Central_Nervous_System"} +xref: UMLS:C0927232 {source="NIFSTD:birnlex_1099"} +xref: VHOG:0000293 +xref: XAO:0000215 +xref: ZFA:0000012 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision +relationship: develops_from UBERON:0016879 ! future central nervous system +relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system +relationship: part_of UBERON:0001016 ! nervous system +property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="NIFSTD:birnlex_1099"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)"} + +[Term] +id: UBERON:0001041 +name: foregut +namespace: uberon +def: "Anterior subdivision of a digestive tract." [http://orcid.org/0000-0002-6601-2165] +subset: developmental_classification +subset: pheno_slim +subset: uberon_slim +synonym: "praeenteron" RELATED LATIN [http://en.wikipedia.org/wiki/Foregut] +synonym: "proenteron" RELATED LATIN [http://en.wikipedia.org/wiki/Foregut] +xref: AAO:0011042 +xref: BILA:0000085 +xref: BTO:0000507 +xref: EHDAA2:0000557 +xref: EHDAA:520 +xref: EMAPA:16548 +xref: FBbt:00005379 +xref: FMA:45616 +xref: http://en.wikipedia.org/wiki/Foregut +xref: http://linkedlifedata.com/resource/umls/id/C0231051 +xref: http://www.snomedbrowser.com/Codes/Details/361409009 +xref: MA:0001526 +xref: NCIT:C34180 +xref: TGMA:0001014 +xref: UMLS:C0231051 {source="ncithesaurus:Foregut"} +xref: VHOG:0000285 +xref: XAO:0000232 +is_a: UBERON:0004921 ! subdivision of digestive tract +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string +property_value: UBPROP:0000001 "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." xsd:string {source="MP:0000474"} +property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000285", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11"} + +[Term] +id: UBERON:0001042 +name: chordate pharynx +namespace: uberon +def: "A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]." [http://www.feedexp.org] +comment: Consider generalizing to deuterostome pharynx +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "pharynx" BROAD SENSU [FMA:46688] +xref: AAO:0000967 +xref: BTO:0001049 +xref: CALOHA:TS-0785 +xref: EFO:0000836 +xref: EHDAA2:0001458 +xref: EHDAA:2947 +xref: EMAPA:16706 +xref: EV:0100065 +xref: FMA:46688 +xref: GAID:155 +xref: galen:Pharynx +xref: http://en.wikipedia.org/wiki/Pharynx +xref: http://linkedlifedata.com/resource/umls/id/C0031354 +xref: http://www.snomedbrowser.com/Codes/Details/181211006 +xref: MA:0000432 +xref: MESH:A03.867 +xref: NCIT:C12425 +xref: OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA +xref: TAO:0000056 +xref: UMLS:C0031354 {source="ncithesaurus:Pharynx"} +xref: VHOG:0000462 +xref: XAO:0003227 +xref: ZFA:0000056 +is_a: UBERON:0006562 ! pharynx +relationship: develops_from UBERON:0009145 {source="EHDAA2"} ! pharyngeal region of foregut +relationship: part_of UBERON:0001004 ! respiratory system +property_value: UBPROP:0000001 "A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]." xsd:string {source="MESH:A03.867"} +property_value: UBPROP:0000001 "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000001 "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000056", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} +property_value: UBPROP:0000001 "The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="http://bgee.unil.ch/"} +property_value: UBPROP:0000002 "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} +property_value: UBPROP:0000002 "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} +property_value: UBPROP:0000003 "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503"} +property_value: UBPROP:0000012 "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0001048 +name: primordium +namespace: uberon +def: "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." [BTO:0001886, FB:DJS, FB:FBrf0089570, http://flybase.org/reports/FBrf0178740.html] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "bud" RELATED [] +synonym: "future organ" RELATED [] +synonym: "placode" RELATED [FBbt:00005495] +synonym: "primordia" RELATED PLURAL [XAO:0003043] +synonym: "rudiment" RELATED [] +xref: AEO:0000171 +xref: BTO:0001886 +xref: EFO:0001652 +xref: EHDAA2:0003171 +xref: FBbt:00005495 +xref: FMA:86589 +xref: http://en.wikipedia.org/wiki/Primordium +xref: http://linkedlifedata.com/resource/umls/id/C0678727 +xref: MAT:0000482 +xref: NCIT:C34275 +xref: UMLS:C0678727 {source="ncithesaurus:Primordium"} +xref: XAO:0003043 +is_a: UBERON:0005423 {source="EHDAA2"} ! developing anatomical structure +relationship: part_of UBERON:0000468 ! multicellular organism + +[Term] +id: UBERON:0001049 +name: neural tube +namespace: uberon +def: "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]." [http://en.wikipedia.org/wiki/Neural_tube] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "neural primordium" RELATED [] +synonym: "presumptive central nervous system" RELATED [] +synonym: "tubus neuralis" RELATED LATIN [http://en.wikipedia.org/wiki/Neural_tube] +xref: AAO:0010617 +xref: BTO:0001057 +xref: CALOHA:TS-2371 +xref: DHBA:10154 +xref: EHDAA2:0001254 +xref: EHDAA:2869 +xref: EHDAA:908 +xref: EMAPA:16164 +xref: EMAPA:16757 +xref: FMA:293882 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1365 +xref: http://linkedlifedata.com/resource/umls/id/C0231024 +xref: http://www.snomedbrowser.com/Codes/Details/362852000 +xref: MAT:0000069 +xref: MIAA:0000069 +xref: NCIT:C34226 +xref: Neural:tube +xref: TAO:0001135 +xref: UMLS:C0231024 {source="ncithesaurus:Neural_Tube"} +xref: VHOG:0000307 +xref: XAO:0003204 +xref: ZFA:0001135 +is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0016879 ! future central nervous system +relationship: develops_from UBERON:0005068 ! neural rod +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png +property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} +property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} +property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} + +[Term] +id: UBERON:0001062 +name: anatomical entity +namespace: uberon +def: "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." [FMA:62955, http://orcid.org/0000-0001-9114-8737] +subset: upper_level +xref: AAO:0010841 +xref: AEO:0000000 +xref: BILA:0000000 +xref: birnlex:6 +xref: CARO:0000000 +xref: EHDAA2:0002229 +xref: FBbt:10000000 +xref: FBbt_root:00000000 +xref: FMA:62955 +xref: HAO:0000000 +xref: http://linkedlifedata.com/resource/umls/id/C1515976 +xref: MA:0000001 +xref: NCIT:C12219 +xref: TAO:0100000 +xref: TGMA:0001822 +xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance"} +xref: WBbt:0000100 +xref: XAO:0000000 +xref: ZFA:0100000 + +[Term] +id: UBERON:0001068 +name: skin of back +namespace: uberon +def: "A zone of skin that is part of a back [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "back skin" EXACT [] +synonym: "back zone of skin" EXACT [OBOL:automatic] +synonym: "skin, dorsal region" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "zone of skin of back" EXACT [OBOL:automatic] +xref: EMAPA:36392 +xref: FMA:10462 +xref: FMA:22985 +xref: http://www.snomedbrowser.com/Codes/Details/181492002 +xref: MA:0000498 +is_a: UBERON:0001085 {source="MA"} ! skin of trunk +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0001137 ! dorsum +relationship: part_of UBERON:0011270 {source="MA"} ! dorsal trunk +property_value: IAO:0000116 "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string + +[Term] +id: UBERON:0001071 +name: superficial cervical artery +namespace: uberon +def: "It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery." [http://en.wikipedia.org/wiki/Superficial_part_of_transverse_cervical_artery] +comment: The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] +subset: uberon_slim +synonym: "superficial branch of transverse cervical artery" EXACT [http://en.wikipedia.org/wiki/Superficial_part_of_transverse_cervical_artery] +xref: EMAPA:37117 {source="MA:th"} +xref: FMA:10665 +xref: http://en.wikipedia.org/wiki/Superficial_part_of_transverse_cervical_artery +xref: http://linkedlifedata.com/resource/umls/id/C0226271 +xref: http://www.snomedbrowser.com/Codes/Details/161746006 +xref: MA:0002052 +xref: NCIT:C53005 +xref: UMLS:C0226271 {source="ncithesaurus:Superficial_Cervical_Artery"} +is_a: UBERON:0012320 ! cervical artery +intersection_of: UBERON:0012320 ! cervical artery +intersection_of: part_of UBERON:0035549 ! vasculature of integument +relationship: part_of UBERON:0035549 ! vasculature of integument + +[Term] +id: UBERON:0001084 +name: skin of head +namespace: uberon +def: "A zone of skin that is part of a head [Automatically generated definition]." [OBOL:automatic] +synonym: "adult head zone of skin" EXACT [OBOL:automatic] +synonym: "head skin" EXACT [] +synonym: "head zone of skin" EXACT [OBOL:automatic] +synonym: "zone of skin of adult head" EXACT [OBOL:automatic] +synonym: "zone of skin of head" EXACT [OBOL:automatic] +xref: FMA:12166 +xref: FMA:24756 +xref: http://linkedlifedata.com/resource/umls/id/C0205029 +xref: http://www.snomedbrowser.com/Codes/Details/181484006 +xref: MA:0000582 +xref: NCIT:C52757 +xref: UMLS:C0205029 {source="ncithesaurus:Head_Skin"} +is_a: UBERON:0012180 ! head or neck skin +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0000033 ! head +property_value: IAO:0000116 "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string + +[Term] +id: UBERON:0001085 +name: skin of trunk +namespace: uberon +def: "A zone of skin that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +synonym: "torso zone of skin" EXACT [OBOL:automatic] +synonym: "trunk skin" EXACT [] +synonym: "trunk zone of skin" EXACT [OBOL:automatic] +synonym: "zone of skin of torso" EXACT [OBOL:automatic] +synonym: "zone of skin of trunk" EXACT [OBOL:automatic] +xref: EMAPA:37278 {source="MA:th"} +xref: FMA:12167 +xref: FMA:23093 +xref: http://linkedlifedata.com/resource/umls/id/C0205031 +xref: http://www.snomedbrowser.com/Codes/Details/181489001 +xref: MA:0000517 +xref: NCIT:C12295 +xref: UMLS:C0205031 {source="ncithesaurus:Skin_of_the_Trunk"} +is_a: UBERON:0000014 ! zone of skin +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk +property_value: IAO:0000116 "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string + +[Term] +id: UBERON:0001090 +name: synovial fluid +namespace: uberon +def: "Joint fluid is a transudate of plasma that is actively secreted by synovial cells." [https://www.ncbi.nlm.nih.gov/books/NBK274/] +subset: uberon_slim +subset: vertebrate_core +synonym: "joint fluid" EXACT [https://www.ncbi.nlm.nih.gov/books/NBK274/] +xref: BTO:0001339 +xref: CALOHA:TS-0996 +xref: ENVO:02000039 +xref: FMA:12277 +xref: GAID:265 +xref: galen:SynovialFluid +xref: http://linkedlifedata.com/resource/umls/id/C0039097 +xref: MA:0002544 +xref: MESH:D013582 +xref: NCIT:C33718 +xref: Synovial:fluid +xref: TAO:0005154 +xref: UMLS:C0039097 {source="ncithesaurus:Synovial_Fluid"} +xref: ZFA:0005154 +is_a: UBERON:0007779 ! transudate +is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland +relationship: located_in UBERON:0007617 ! synovial cavity of joint +property_value: UBPROP:0000001 "Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005154", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000009 "It provides nutrients and lubrication for articular cartilage" xsd:string +property_value: UBPROP:0000010 "The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma" xsd:string + +[Term] +id: UBERON:0001135 +name: smooth muscle tissue +namespace: uberon +def: "Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]." [GO:0006939, http://en.wikipedia.org/wiki/Smooth_muscle_tissue] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "involuntary muscle" EXACT [] +synonym: "non-striated muscle" EXACT [] +synonym: "smooth muscle" EXACT [] +synonym: "textus muscularis levis; textus muscularis nonstriatus" RELATED LATIN [http://en.wikipedia.org/wiki/Smooth_muscle_tissue] +synonym: "textus muscularis nonstriatus" EXACT LATIN [FMA:14070, FMA:TA] +synonym: "visceral muscle" NARROW SENSU [] +synonym: "visceral muscle tissue" NARROW SENSU [] +xref: AAO:0010244 +xref: AEO:0000141 +xref: BTO:0001260 +xref: CALOHA:TS-0943 +xref: EFO:0000889 +xref: EHDAA2:0003141 +xref: EMAPA:32717 +xref: EV:0100378 +xref: FBbt:00003525 +xref: FMA:14070 +xref: GAID:167 +xref: galen:SmoothMuscle +xref: galen:SmoothMuscleTissue +xref: http://en.wikipedia.org/wiki/Smooth_muscle_tissue +xref: http://linkedlifedata.com/resource/umls/id/C1267092 +xref: MA:0000166 +xref: MAT:0000303 +xref: MESH:D009130 +xref: MIAA:0000303 +xref: NCIT:C12437 +xref: OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA +xref: TAO:0005274 +xref: UMLS:C1267092 {source="ncithesaurus:Smooth_Muscle_Tissue"} +xref: VHOG:0001246 +xref: WBbt:0005781 +xref: XAO:0000175 +xref: ZFA:0005274 +is_a: UBERON:0002385 ! muscle tissue +property_value: depicted:by Glatte:Muskelzellen.jpg +property_value: UBPROP:0000001 "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} +property_value: UBPROP:0000003 "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001246", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)"} +property_value: UBPROP:0000013 "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." xsd:string + +[Term] +id: UBERON:0001136 +name: mesothelium +namespace: uberon +def: "Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri)." [FMA:14074, http://en.wikipedia.org/wiki/Mesothelium] +subset: uberon_slim +xref: AEO:0000111 +xref: BTO:0002422 +xref: CALOHA:TS-1183 +xref: EHDAA2_RETIRED:0003111 +xref: EHDAA:2331 +xref: EHDAA:2349 +xref: EHDAA:295 +xref: EHDAA:6073 +xref: EHDAA:640 +xref: EHDAA:646 +xref: EMAPA:32856 +xref: FMA:14074 +xref: http://en.wikipedia.org/wiki/Mesothelium +xref: http://linkedlifedata.com/resource/umls/id/C0086610 +xref: http://www.snomedbrowser.com/Codes/Details/361918002 +xref: MA:0000565 +xref: NCIT:C33105 +xref: UMLS:C0086610 {source="ncithesaurus:Mesothelium"} +is_a: UBERON:0000487 ! simple squamous epithelium +is_a: UBERON:0012275 ! meso-epithelium +intersection_of: UBERON:0000487 ! simple squamous epithelium +intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: part_of UBERON:0000042 ! serous membrane +relationship: part_of UBERON:0000042 ! serous membrane +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg + +[Term] +id: UBERON:0001137 +name: dorsum +namespace: uberon +def: "A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.." [BSPO:0000063, http://en.wikipedia.org/wiki/Dorsum_(anatomy), UBERONREF:0000006] +subset: efo_slim +subset: uberon_slim +synonym: "back" EXACT [FMA:14181] +synonym: "back of body proper" EXACT [FMA:14181] +synonym: "dorsal part of organism" EXACT [] +xref: BTO:0001713 +xref: CALOHA:TS-2223 +xref: Dorsum:(anatomy) +xref: EFO:0001405 +xref: FMA:14181 +xref: GAID:30 +xref: galen:Back +xref: http://linkedlifedata.com/resource/umls/id/C0004600 +xref: http://www.snomedbrowser.com/Codes/Details/123961009 +xref: MESH:A01.176 +xref: NCIT:C13062 +xref: OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA +xref: UMLS:C0004600 {source="ncithesaurus:Back"} +is_a: UBERON:0000475 ! organism subdivision +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG +property_value: UBPROP:0000007 "dorsal" xsd:string +property_value: UBPROP:0000008 "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" xsd:string + +[Term] +id: UBERON:0001417 +name: skin of neck +namespace: uberon +def: "A zone of skin that is part of a neck [Automatically generated definition]." [OBOL:automatic] +synonym: "neck (volume) zone of skin" EXACT [OBOL:automatic] +synonym: "neck skin" EXACT [] +synonym: "neck zone of skin" EXACT [OBOL:automatic] +synonym: "zone of skin of neck" EXACT [OBOL:automatic] +synonym: "zone of skin of neck (volume)" EXACT [OBOL:automatic] +xref: EMAPA:37277 {source="MA:th"} +xref: FMA:23021 +xref: FMA:23022 +xref: http://linkedlifedata.com/resource/umls/id/C0205030 +xref: http://www.snomedbrowser.com/Codes/Details/361705004 +xref: MA:0000590 +xref: NCIT:C52756 +xref: UMLS:C0205030 {source="ncithesaurus:Neck_Skin"} +is_a: UBERON:0012180 ! head or neck skin +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0000974 ! neck +relationship: part_of UBERON:0000974 ! neck + +[Term] +id: UBERON:0001418 +name: skin of thorax +namespace: uberon +def: "A zone of skin that is part of a thorax [Automatically generated definition]." [OBOL:automatic] +synonym: "thoracic skin" EXACT [] +synonym: "thorax skin" EXACT [] +synonym: "thorax zone of skin" EXACT [OBOL:automatic] +synonym: "upper body skin" RELATED [] +synonym: "zone of skin of thorax" EXACT [OBOL:automatic] +xref: EMAPA:37765 {source="MA:th"} +xref: FMA:23028 +xref: FMA:23029 +xref: http://www.snomedbrowser.com/Codes/Details/281723000 +xref: MA:0000564 +is_a: UBERON:0001085 ! skin of trunk +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0000915 ! thoracic segment of trunk + +[Term] +id: UBERON:0001434 +name: skeletal system +namespace: uberon +def: "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, VSAO:0000027] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "set of all bones and joints" NARROW SENSU [] +synonym: "skeleton system" EXACT [] +synonym: "Skelettsystem" RELATED [BTO:0001486] +xref: AAO:0000566 +xref: BTO:0001486 +xref: CALOHA:TS-1320 +xref: EFO:0000806 +xref: EHDAA2:0003168 +xref: EMAPA:35773 +xref: FMA:23881 +xref: http://linkedlifedata.com/resource/umls/id/C0037253 +xref: MA:0000018 +xref: NCIT:C12788 +xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA +xref: TAO:0000434 +xref: UMLS:C0037253 {source="ncithesaurus:Skeletal_System"} +xref: VHOG:0001254 +xref: VSAO:0000027 +xref: XAO:0003060 +xref: ZFA:0000434 +is_a: UBERON:0011216 ! organ system subdivision +intersection_of: UBERON:0011216 ! organ system subdivision +intersection_of: has_part UBERON:0004288 ! skeleton +intersection_of: has_part UBERON:0004770 ! articular system +disjoint_from: UBERON:0002204 ! musculoskeletal system +disjoint_from: UBERON:0002330 ! exocrine system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: has_part UBERON:0004288 ! skeleton +relationship: has_part UBERON:0004770 ! articular system +relationship: part_of UBERON:0002204 ! musculoskeletal system +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/The-skeletal-system xsd:anyURI +property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} +property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)"} +property_value: UBPROP:0000007 "skeletal" xsd:string +property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} + +[Term] +id: UBERON:0001444 +name: subdivision of head +namespace: uberon +subset: non_informative +synonym: "head region" RELATED [] +synonym: "head subdivision" EXACT [] +synonym: "region of head" RELATED [] +xref: FMA:24218 +xref: http://www.snomedbrowser.com/Codes/Details/123852005 +xref: XAO:0000040 +is_a: UBERON:0000475 ! organism subdivision +relationship: part_of UBERON:0000033 ! head + +[Term] +id: UBERON:0001456 +name: face +namespace: uberon +def: "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc)." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +synonym: "facia/facies" RELATED LATIN [http://en.wikipedia.org/wiki/Face] +synonym: "visage" RELATED [BTO:0003369] +xref: BTO:0003369 +xref: CALOHA:TS-2216 +xref: EMAPA:32763 +xref: FMA:24728 +xref: GAID:64 +xref: galen:Face +xref: HAO:0000316 +xref: http://en.wikipedia.org/wiki/Face +xref: http://linkedlifedata.com/resource/umls/id/C0015450 +xref: http://www.snomedbrowser.com/Codes/Details/302549007 +xref: MA:0002473 +xref: MESH:D005145 +xref: NCIT:C13071 +xref: OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA +xref: UMLS:C0015450 {source="ncithesaurus:Face"} +is_a: UBERON:0001444 ! subdivision of head +relationship: contributes_to_morphology_of UBERON:0000033 ! head +relationship: has_part UBERON:0000165 ! mouth +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg +property_value: UBPROP:0000001 "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." xsd:string {source="FMA:24728"} +property_value: UBPROP:0000001 "The area that extends from the median ocellus to the oral foramen[HAO]." xsd:string {source="http://api.hymao.org/api/ref/67791", source="HAO:0000316", taxon="NCBITaxon:7399"} +property_value: UBPROP:0000007 "facial" xsd:string +property_value: UBPROP:0000011 "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" xsd:string {source="vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf"} + +[Term] +id: UBERON:0001458 +name: skin of lip +namespace: uberon +def: "A zone of skin that is part of a lip [Automatically generated definition]." [OBOL:automatic] +synonym: "lip skin" EXACT [] +synonym: "lip zone of skin" EXACT [OBOL:automatic] +synonym: "skin of lips" RELATED PLURAL [] +synonym: "zone of skin of lip" EXACT [OBOL:automatic] +xref: EMAPA:37643 {source="MA:th"} +xref: FMA:24764 +xref: http://linkedlifedata.com/resource/umls/id/C0222101 +xref: http://www.snomedbrowser.com/Codes/Details/244092005 +xref: MA:0001579 +xref: NCIT:C12291 +xref: UMLS:C0222101 {source="ncithesaurus:Skin_of_the_Lip"} +is_a: UBERON:0001084 ! skin of head +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0001833 ! lip +relationship: part_of UBERON:0001833 ! lip + +[Term] +id: UBERON:0001484 +name: articular capsule +namespace: uberon +def: "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." [http://en.wikipedia.org/wiki/Articular_capsule] +subset: organ_slim +subset: uberon_slim +synonym: "capsula articularis" EXACT LATIN [FMA:34836, FMA:TA] +synonym: "capsulae articulares" RELATED LATIN [http://en.wikipedia.org/wiki/Articular_capsule] +synonym: "fibrous capsule of joint" EXACT [] +synonym: "joint capsule" EXACT [] +synonym: "joint fibrous capsule" EXACT [] +xref: Articular:capsule +xref: EMAPA:37621 {source="MA:th"} +xref: FMA:34836 +xref: GAID:263 +xref: galen:JointCapsule +xref: http://linkedlifedata.com/resource/umls/id/C0206207 +xref: http://www.snomedbrowser.com/Codes/Details/182238002 +xref: MA:0001519 +xref: MESH:D017746 +xref: NCIT:C32259 +xref: NCIT:C84388 +xref: UMLS:C0206207 {source="ncithesaurus:Joint_Capsule"} +is_a: UBERON:0000094 ! membrane organ +intersection_of: UBERON:0000094 ! membrane organ +intersection_of: has_part UBERON:0007616 ! layer of synovial tissue +intersection_of: surrounds UBERON:0002217 ! synovial joint +relationship: has_part UBERON:0007616 ! layer of synovial tissue +relationship: surrounds UBERON:0002217 ! synovial joint +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png +property_value: UBPROP:0000012 "check ncita" xsd:string {external_ontology="ncit"} + +[Term] +id: UBERON:0001555 +name: digestive tract +namespace: uberon +def: "A tube extending from the mouth to the anus." [http://en.wikipedia.org/wiki/Talk\:Human_gastrointestinal_tract, http://sourceforge.net/tracker/?func=detail&atid=440764&aid=2991587&group_id=36855] +subset: uberon_slim +subset: vertebrate_core +synonym: "alimentary canal" NARROW [] +synonym: "alimentary tract" NARROW [] +synonym: "digestive canal" RELATED [BTO:0000058] +synonym: "digestive tube" EXACT [] +synonym: "enteric tract" EXACT [ZFA:0000112] +synonym: "gut" BROAD [] +synonym: "gut tube" RELATED [] +xref: AAO:0010023 +xref: BILA:0000083 +xref: BTO:0000511 +xref: BTO:0000545 +xref: EHDAA2:0000726 +xref: EHDAA:518 +xref: EMAPA:16247 +xref: FBbt:00003125 +xref: FMA:45615 +xref: galen:AlimentaryTract +xref: http://linkedlifedata.com/resource/umls/id/C0017189 +xref: MA:0000917 +xref: NCIT:C34082 +xref: OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA +xref: TAO:0000112 +xref: TGMA:0001819 +xref: UMLS:C0017189 {source="ncithesaurus:Gastrointestinal_Tract"} +xref: VHOG:0000309 +xref: WBbt:0005743 +xref: ZFA:0000112 +is_a: UBERON:0000025 ! tube +relationship: connects UBERON:0000165 ! mouth +relationship: develops_from UBERON:0007026 ! presumptive gut +relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut +relationship: part_of UBERON:0001007 ! digestive system +property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11"} +property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} +property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} +property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string + +[Term] +id: UBERON:0001558 +name: lower respiratory tract +namespace: uberon +def: "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]" [http://en.wikipedia.org/wiki/Lower_respiratory_tract, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +synonym: "lower respiratory system" EXACT [] +xref: EHDAA2:0001036 +xref: EMAPA:16738 +xref: FMA:45662 +xref: http://en.wikipedia.org/wiki/Lower_respiratory_tract +xref: http://www.snomedbrowser.com/Codes/Details/281488008 +xref: MA:0000435 +xref: OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g +xref: VHOG:0000382 +is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract +relationship: has_part UBERON:0000170 ! pair of lungs +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg + +[Term] +id: UBERON:0001586 +name: internal jugular vein +namespace: uberon +def: "One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]." [http://en.wikipedia.org/wiki/Internal_jugular_vein] +subset: uberon_slim +synonym: "internal jugular" EXACT [EHDAA2:0000877] +synonym: "internal jugular venous tree" EXACT [] +synonym: "vena jugularis interna" RELATED LATIN [http://en.wikipedia.org/wiki/Internal_jugular_vein] +xref: AAO:0010236 +xref: EHDAA2:0000877 +xref: EHDAA:5407 +xref: EMAPA:17620 +xref: FMA:4724 +xref: galen:InternalJugularVein +xref: http://en.wikipedia.org/wiki/Internal_jugular_vein +xref: http://linkedlifedata.com/resource/umls/id/C0226550 +xref: http://www.snomedbrowser.com/Codes/Details/181372005 +xref: MA:0002157 +xref: NCIT:C32849 +xref: OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA +xref: RETIRED_EHDAA2:0000878 +xref: UMLS:C0226550 {source="ncithesaurus:Internal_Jugular_Vein"} +xref: XAO:0000382 +is_a: UBERON:0004711 ! jugular vein +relationship: drains UBERON:0000955 ! brain +relationship: drains UBERON:0001456 ! face +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png +property_value: UBPROP:0000001 "Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010236", ontology="AAO", source="AAO:BJB"} + +[Term] +id: UBERON:0001630 +name: muscle organ +namespace: uberon +def: "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]." [GO:0007517] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "muscle" BROAD [ZFA:0005145] +xref: AAO:0011066 +xref: EMAPA:32715 +xref: EMAPA:37474 {source="MA:th"} +xref: EV:0100146 +xref: FMA:5022 +xref: GAID:131 +xref: galen:Muscle +xref: http://www.snomedbrowser.com/Codes/Details/71616004 +xref: MA:0000015 +xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA +xref: TAO:0005145 +xref: VHOG:0001245 +xref: XAO:0000172 +xref: ZFA:0005145 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0005090 ! muscle structure +intersection_of: UBERON:0000062 ! organ +intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue +relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +relationship: part_of UBERON:0001015 ! musculature +property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75"} +property_value: UBPROP:0000007 "muscular" xsd:string + +[Term] +id: UBERON:0001637 +name: artery +namespace: uberon +def: "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." [AEO:JB] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arterial subtree" EXACT [] +synonym: "arterial system" RELATED [] +synonym: "arterial tree organ part" EXACT [] +synonym: "arterial vessel" RELATED [] +synonym: "arteries" EXACT PLURAL [TAO:0000005] +xref: AAO:0010211 +xref: AEO:0000208 +xref: BTO:0000573 +xref: CALOHA:TS-0054 +xref: EFO:0000814 +xref: EHDAA2:0000143 +xref: EHDAA2:0003253 +xref: EMAPA:35147 +xref: EV:0100026 +xref: FMA:50720 +xref: GAID:468 +xref: galen:Artery +xref: http://en.wikipedia.org/wiki/Artery +xref: http://linkedlifedata.com/resource/umls/id/C0003842 +xref: http://www.snomedbrowser.com/Codes/Details/362877004 +xref: MA:0000064 +xref: MAT:0000034 +xref: MESH:D001158 +xref: MIAA:0000034 +xref: NCIT:C12372 +xref: OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA +xref: TAO:0000005 +xref: UMLS:C0003842 {source="ncithesaurus:Artery"} +xref: VHOG:0001251 +xref: XAO:0000114 +xref: ZFA:0000005 +is_a: UBERON:0003509 ! arterial blood vessel +relationship: channels_from UBERON:0000948 ! heart +property_value: IAO:0000116 "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string +property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010211", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001251", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)"} +property_value: UBPROP:0000007 "arterial" xsd:string +property_value: UBPROP:0000202 FMA:63812 + +[Term] +id: UBERON:0001638 +name: vein +namespace: uberon +def: "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [http://en.wikipedia.org/wiki/Vein] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "vascular element" RELATED [EMAPA:th] +synonym: "vena" RELATED LATIN [http://en.wikipedia.org/wiki/Vein] +synonym: "venae" RELATED PLURAL [VHOG:0001743] +synonym: "venous subtree" BROAD [] +synonym: "venous tree organ part" EXACT [] +synonym: "venous vessel" BROAD [] +xref: AAO:0010212 +xref: AEO:0000209 +xref: BTO:0000234 +xref: CALOHA:TS-1108 +xref: EFO:0000816 +xref: EHDAA2:0003254 +xref: EMAPA:35906 +xref: EV:0100031 +xref: FMA:50723 +xref: GAID:492 +xref: galen:Vein +xref: http://en.wikipedia.org/wiki/Vein +xref: http://linkedlifedata.com/resource/umls/id/C0042449 +xref: http://www.snomedbrowser.com/Codes/Details/181367001 +xref: MA:0000067 +xref: MAT:0000037 +xref: MESH:D014680 +xref: MIAA:0000037 +xref: NCIT:C12814 +xref: OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA +xref: TAO:0000082 +xref: UMLS:C0042449 {source="ncithesaurus:Vein"} +xref: VHOG:0001743 +xref: XAO:0000115 +xref: ZFA:0000082 +is_a: UBERON:0003920 ! venous blood vessel +intersection_of: UBERON:0003920 ! venous blood vessel +intersection_of: channel_for UBERON:0013756 ! venous blood +relationship: channel_for UBERON:0013756 ! venous blood +relationship: channels_from UBERON:0001982 ! capillary +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg +property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string +property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010212", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001743", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)"} +property_value: UBPROP:0000007 "venous" xsd:string +property_value: UBPROP:0000202 FMA:63814 + +[Term] +id: UBERON:0001651 +name: right pulmonary artery +namespace: uberon +def: "The pulmonary artery that supplies the right lung." [UBERON:cjm] +subset: uberon_slim +synonym: "arteria pulmonalis dextra" RELATED LATIN [http://en.wikipedia.org/wiki/Right_pulmonary_artery] +synonym: "right main pulmonary artery" EXACT [] +synonym: "right pulmonary arterial tree" EXACT [] +xref: EMAPA:37378 {source="MA:th"} +xref: FMA:50872 +xref: galen:RightPulmonaryArtery +xref: http://en.wikipedia.org/wiki/Right_pulmonary_artery +xref: http://linkedlifedata.com/resource/umls/id/C0923924 +xref: http://www.snomedbrowser.com/Codes/Details/244235003 +xref: MA:0002500 +xref: NCIT:C33489 +xref: UMLS:C0923924 {source="ncithesaurus:Right_Pulmonary_Artery"} +is_a: UBERON:0001637 ! artery +intersection_of: UBERON:0001637 ! artery +intersection_of: supplies UBERON:0002167 ! right lung +relationship: supplies UBERON:0002167 ! right lung +property_value: depicted:by Alveoli:diagram.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png +property_value: IAO:0000116 "TODO - add class 'pulmonary artery tree organ'" xsd:string + +[Term] +id: UBERON:0001652 +name: left pulmonary artery +namespace: uberon +def: "The pulmonary artery that supplies the left lung." [UBERON:cjm] +subset: uberon_slim +synonym: "arteria pulmonalis sinistra" RELATED LATIN [http://en.wikipedia.org/wiki/Left_pulmonary_artery] +synonym: "left main pulmonary artery" EXACT [] +synonym: "left pulmonary arterial tree" EXACT [] +xref: EMAPA:37097 {source="MA:th"} +xref: FMA:50873 +xref: galen:LeftPulmonaryArtery +xref: http://en.wikipedia.org/wiki/Left_pulmonary_artery +xref: http://linkedlifedata.com/resource/umls/id/C0923925 +xref: http://www.snomedbrowser.com/Codes/Details/244234004 +xref: MA:0002032 +xref: NCIT:C32971 +xref: UMLS:C0923925 {source="ncithesaurus:Left_Pulmonary_Artery"} +is_a: UBERON:0001637 ! artery +intersection_of: UBERON:0001637 ! artery +intersection_of: supplies UBERON:0002168 ! left lung +relationship: supplies UBERON:0002168 ! left lung +property_value: depicted:by Alveoli:diagram.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png +property_value: IAO:0000116 "TODO - add class 'pulmonary artery tree organ'" xsd:string + +[Term] +id: UBERON:0001653 +name: facial vein +namespace: uberon +def: "The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]." [http://en.wikipedia.org/wiki/Facial_vein] +subset: uberon_slim +synonym: "anterior facial vein" RELATED INCONSISTENT [http://en.wikipedia.org/wiki/Facial_vein] +synonym: "face vein" EXACT [OBOL:automatic] +synonym: "vein of face" EXACT [OBOL:automatic] +synonym: "vena facialis anterior" RELATED LATIN [http://en.wikipedia.org/wiki/Facial_vein] +xref: AAO:0010513 +xref: EMAPA:19220 +xref: Facial:vein +xref: FMA:50874 +xref: http://linkedlifedata.com/resource/umls/id/C0226532 +xref: http://www.snomedbrowser.com/Codes/Details/181374006 +xref: MA:0002115 +xref: NCIT:C32579 +xref: OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA +xref: UMLS:C0226532 {source="ncithesaurus:Facial_Vein"} +is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0003502 ! neck blood vessel +is_a: UBERON:0009141 ! craniocervical region vein +relationship: part_of UBERON:0001456 ! face +relationship: part_of UBERON:0001586 ! internal jugular vein +relationship: tributary_of UBERON:0001586 {source="FMA"} ! internal jugular vein +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png +property_value: UBPROP:0000001 "Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010513", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000012 "MA and NCITA also has 'anterior facial vein'" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0001731 +name: cavity of pharynx +namespace: uberon +def: "A anatomical space that is enclosed by a pharynx." [OBOL:automatic] +synonym: "cavitas pharyngealis" RELATED LATIN [] +synonym: "cavitas pharyngis" RELATED [BTO:0002097] +synonym: "lumen of pharynx" EXACT [] +synonym: "pharyngeal cavity" EXACT [] +xref: AAO:0010435 +xref: BSA:0000113 +xref: BTO:0002097 +xref: EMAPA:18381 +xref: FMA:54935 +xref: http://www.snomedbrowser.com/Codes/Details/180543003 +xref: XAO:0000105 +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0006562 ! pharynx +relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut +relationship: luminal_space_of UBERON:0006562 ! pharynx +relationship: part_of UBERON:0006562 ! pharynx +property_value: UBPROP:0000008 "See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship" xsd:string +property_value: UBPROP:0000011 "TOODO check" xsd:string + +[Term] +id: UBERON:0001833 +name: lip +namespace: uberon +def: "One of the two fleshy folds which surround the opening of the mouth." [http://en.wikipedia.org/wiki/Lip, http://www.medterms.com/script/main/art.asp?articlekey=9458] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "labia oris" RELATED LATIN [http://en.wikipedia.org/wiki/Lip] +synonym: "lips" RELATED [] +xref: BTO:0001647 +xref: CALOHA:TS-0558 +xref: EMAPA:32839 +xref: FMA:59816 +xref: GAID:76 +xref: galen:Lip +xref: http://en.wikipedia.org/wiki/Lip +xref: http://linkedlifedata.com/resource/umls/id/C0023759 +xref: http://www.snomedbrowser.com/Codes/Details/181221003 +xref: MA:0000343 +xref: MESH:D008046 +xref: NCIT:C12220 +xref: OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA +xref: TAO:0007006 +xref: UBERON:0001833 +xref: UMLS:C0023759 {source="ncithesaurus:Lip"} +xref: VHOG:0000677 +xref: ZFA:0007006 +is_a: UBERON:0003102 {source="ZFA"} ! surface structure +relationship: contributes_to_morphology_of UBERON:0000165 ! mouth +relationship: part_of UBERON:0000165 {source="BTO", source="FMA-implicit", source="VHOG", source="ZFA"} ! mouth +relationship: surrounds UBERON:0000166 {source="cjm"} ! oral opening +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg +property_value: UBPROP:0000001 "Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007006", ontology="TAO", source="http://purl.obolibrary.org/obo/uberon/http/:www.medterms.com/script/main/art.asp?articlekey=9458", source="ZFIN:curator"} +property_value: UBPROP:0000007 "labial" xsd:string + +[Term] +id: UBERON:0001891 +name: midbrain +namespace: uberon +def: "The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." [GO:0030901] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "MB" BROAD ABBREVIATION [http://uri.neuinfo.org/nif/nifstd/birnlex_1667, NIFSTD:NeuroNames_abbrevSource] +synonym: "mesencephalon" RELATED LATIN [http://en.wikipedia.org/wiki/Midbrain] +xref: AAO:0010149 +xref: BAMS:MES +xref: birnlex:1667 +xref: BM:MB +xref: BTO:0000138 +xref: CALOHA:TS-0630 +xref: DHBA:10648 +xref: DMBA:16649 +xref: EFO:0000919 +xref: EHDAA2:0001162 +xref: EHDAA:3694 +xref: EMAPA:16974 +xref: EV:0100242 +xref: FMA:61993 +xref: HBA:9001 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 {source="NIFSTD:birnlex_1667"} +xref: http://en.wikipedia.org/wiki/Midbrain +xref: http://linkedlifedata.com/resource/umls/id/C0025462 +xref: http://www.snomedbrowser.com/Codes/Details/279099009 +xref: MA:0000207 +xref: MAT:0000106 +xref: MBA:313 +xref: MESH:D008636 +xref: MIAA:0000106 +xref: NCIT:C12510 +xref: OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA +xref: RETIRED_EHDAA2:0001104 +xref: TAO:0000128 +xref: UMLS:C0025462 {source="ncithesaurus:Mesencephalon"} +xref: UMLS:C0025462 {source="NIFSTD:birnlex_1667"} +xref: VHOG:0000069 +xref: XAO:0000014 +xref: ZFA:0000128 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: contributes_to_morphology_of UBERON:0000955 ! brain +relationship: develops_from UBERON:0009616 ! presumptive midbrain +relationship: has_developmental_contribution_from UBERON:0003849 {evidence="definitional"} ! mesencephalic neural crest +relationship: immediate_transformation_of UBERON:0009616 {source="Bgee:AN"} ! presumptive midbrain +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG +property_value: IAO:0000116 "developmental relationships need revised" xsd:string +property_value: UBPROP:0000001 "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010149", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000128", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000069", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)"} +property_value: UBPROP:0000007 "mesencephalic" xsd:string +property_value: UBPROP:0000012 "part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships" xsd:string {external_ontology="ABA"} + +[Term] +id: UBERON:0001892 +name: rhombomere +namespace: uberon +def: "A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]." [http://en.wikipedia.org/wiki/Rhombomere, ZFIN:curator] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "future rhombencephalon" RELATED [MIAA:0000272] +synonym: "hindbrain neuromere" EXACT [] +synonym: "hindbrain neuromeres" EXACT PLURAL [DHBA:HNM] +synonym: "hindbrain segment" BROAD [ZFA:0001064] +synonym: "rhombomere" EXACT [] +synonym: "rhombomeres" RELATED PLURAL [VHOG:0000672] +synonym: "segment of hindbrain" BROAD [ZFA:0001064] +xref: DHBA:12664 +xref: EFO:0003617 +xref: EMAPA:16148 +xref: FMA:295666 +xref: http://en.wikipedia.org/wiki/Rhombomere +xref: MAT:0000272 +xref: MIAA:0000272 +xref: RETIRED_EHDAA2:0000669 +xref: TAO:0001064 +xref: VHOG:0000672 +xref: XAO:0004079 +xref: ZFA:0001064 +is_a: UBERON:0004731 ! neuromere +intersection_of: UBERON:0004731 ! neuromere +intersection_of: part_of UBERON:0007277 ! presumptive hindbrain +relationship: part_of UBERON:0007277 ! presumptive hindbrain +property_value: UBPROP:0000001 "A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001064", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000672", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)"} +property_value: UBPROP:0000008 "In human embryonic development, the rhombomeres are present by day 29" xsd:string +property_value: UBPROP:0000012 "DHBA divides this into A(1-3),B(4),C(5-7) and D(8)" xsd:string + +[Term] +id: UBERON:0001896 +name: medulla oblongata +namespace: uberon +def: "Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]." [FMA:62004, GO:0021550, http://en.wikipedia.org/wiki/Bone_marrow_of_ovary_oblongata] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "bulb" BROAD [] +synonym: "bulbus" EXACT LATIN [FMA:62004, FMA:TA] +synonym: "medulla" BROAD [ABA:MY] +synonym: "medulla oblonzata" RELATED LATIN [http://en.wikipedia.org/wiki/Medulla_oblongata] +synonym: "metepencephalon" RELATED [FMA:62004] +xref: AAO:0010486 +xref: BAMS:Md +xref: BAMS:MY +xref: birnlex:957 +xref: BM:Me +xref: BTO:0000041 +xref: CALOHA:TS-0607 +xref: DMBA:17352 +xref: EFO:0000924 +xref: EHDAA2:0001088 +xref: EHDAA:7588 +xref: EMAPA:17550 +xref: EV:0100275 +xref: FMA:62004 +xref: GAID:590 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 {source="NIFSTD:birnlex_957"} +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 +xref: http://en.wikipedia.org/wiki/Bone_marrow_of_ovary_oblongata +xref: http://linkedlifedata.com/resource/umls/id/C0025148 +xref: http://linkedlifedata.com/resource/umls/id/C1269575 +xref: http://www.snomedbrowser.com/Codes/Details/279104005 +xref: MA:0000206 +xref: MAT:0000111 +xref: MAT:0000367 +xref: MBA:354 +xref: MESH:D008526 +xref: MIAA:0000111 +xref: NCIT:C12442 +xref: OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA +xref: OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA +xref: TAO:0000545 +xref: UMLS:C0025148 {source="ncithesaurus:Medulla_Oblongata"} +xref: UMLS:C0025148 {source="NIFSTD:birnlex_957"} +xref: UMLS:C1269575 {source="NIFSTD:birnlex_957"} +xref: VHOG:0000181 +xref: XAO:0003100 +xref: ZFA:0000545 +is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: part_of UBERON:0002298 ! brainstem +relationship: part_of UBERON:0005290 ! myelencephalon +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg +property_value: UBPROP:0000001 "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010486", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="http://bgee.unil.ch/"} +property_value: UBPROP:0000003 "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)"} + +[Term] +id: UBERON:0001915 +name: endothelium of capillary +namespace: uberon +def: "An endothelium that is part of a capillary [Automatically generated definition]." [OBOL:automatic] +synonym: "blood capillary endothelium" EXACT [OBOL:automatic] +synonym: "capillary endothelium" EXACT [] +synonym: "capillary vessel endothelium" EXACT [OBOL:automatic] +synonym: "endothelium of blood capillary" EXACT [OBOL:automatic] +synonym: "endothelium of capillary vessel" EXACT [OBOL:automatic] +xref: BTO:0004954 +xref: CALOHA:TS-0112 +xref: EMAPA:36292 +xref: FMA:62114 +xref: http://linkedlifedata.com/resource/umls/id/C0006904 +xref: MA:0000711 +xref: NCIT:C49215 +xref: UMLS:C0006904 {source="ncithesaurus:Capillary_Endothelium"} +is_a: UBERON:0004638 ! blood vessel endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001982 ! capillary +relationship: part_of UBERON:0001982 ! capillary + +[Term] +id: UBERON:0001916 +name: endothelium of arteriole +namespace: uberon +def: "An endothelium that is part of an arteriole [Automatically generated definition]." [OBOL:automatic] +synonym: "arteriole endothelium" EXACT [] +xref: EMAPA:36286 +xref: FMA:62115 +xref: http://linkedlifedata.com/resource/umls/id/C1179024 +xref: MA:0000705 +xref: NCIT:C49192 +xref: UMLS:C1179024 {source="ncithesaurus:Arteriole_Endothelium"} +is_a: UBERON:0004638 ! blood vessel endothelium +is_a: UBERON:0004700 ! arterial system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001980 ! arteriole +relationship: part_of UBERON:0001980 ! arteriole + +[Term] +id: UBERON:0001917 +name: endothelium of artery +namespace: uberon +def: "An endothelium that is part of an artery [Automatically generated definition]." [OBOL:automatic] +synonym: "arterial endothelium" EXACT [] +synonym: "artery endothelium" EXACT [] +xref: AAO:0011013 +xref: BTO:0004757 +xref: EMAPA:35148 +xref: FMA:62116 +xref: http://linkedlifedata.com/resource/umls/id/C1179025 +xref: MA:0000707 +xref: NCIT:C49194 +xref: UMLS:C1179025 {source="ncithesaurus:Artery_Endothelium"} +xref: VHOG:0001215 +xref: XAO:0000357 +is_a: UBERON:0003915 ! endothelial tube +is_a: UBERON:0004638 ! blood vessel endothelium +is_a: UBERON:0004700 ! arterial system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0001637 ! artery +property_value: UBPROP:0000001 "The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011013", ontology="AAO", source="XAO:curator"} +property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001215", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207"} + +[Term] +id: UBERON:0001918 +name: endothelium of venule +namespace: uberon +def: "An endothelium that is part of a venule [Automatically generated definition]." [OBOL:automatic] +synonym: "venule endothelium" EXACT [] +xref: EMAPA:36290 +xref: FMA:62117 +xref: http://linkedlifedata.com/resource/umls/id/C1179026 +xref: MA:0000716 +xref: NCIT:C49319 +xref: UMLS:C1179026 {source="ncithesaurus:Venule_Endothelium"} +is_a: UBERON:0004638 ! blood vessel endothelium +is_a: UBERON:0004701 ! venous system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001979 ! venule +relationship: part_of UBERON:0001979 ! venule + +[Term] +id: UBERON:0001919 +name: endothelium of vein +namespace: uberon +def: "An endothelium that is part of a vein [Automatically generated definition]." [OBOL:automatic] +synonym: "vein endothelium" EXACT [] +synonym: "veinous endothelium" RELATED [VHOG:0001216] +synonym: "venous endothelium" EXACT [] +xref: AAO:0011110 +xref: BTO:0004756 +xref: EMAPA:36288 +xref: FMA:62118 +xref: http://linkedlifedata.com/resource/umls/id/C1179027 +xref: MA:0000712 +xref: NCIT:C49317 +xref: UMLS:C1179027 {source="ncithesaurus:Vein_Endothelium"} +xref: VHOG:0001216 +xref: XAO:0000358 +is_a: UBERON:0004638 ! blood vessel endothelium +is_a: UBERON:0004701 ! venous system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001638 ! vein +relationship: part_of UBERON:0001638 ! vein +property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001216", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207"} + +[Term] +id: UBERON:0001943 +name: midbrain tegmentum +namespace: uberon +def: "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]." [FMA:FMA, http://en.wikipedia.org/wiki/Midbrain_tegmentum, ISBN10:0471888893] +comment: 'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mesencephalic tegmentum" RELATED [VHOG:0001367] +synonym: "MTg" BROAD ABBREVIATION [http://uri.neuinfo.org/nif/nifstd/birnlex_1200, NIFSTD:NeuroNames_abbrevSource] +synonym: "tegmentum" BROAD [ISBN10:0471888893] +synonym: "tegmentum mesencephali" EXACT LATIN [http://en.wikipedia.org/wiki/Midbrain_tegmentum] +synonym: "tegmentum mesencephalicum" RELATED LATIN [NeuroNames:491] +synonym: "tegmentum of midbrain" EXACT [] +xref: BAMS:MTg +xref: birnlex:1200 +xref: BTO:0003388 +xref: DHBA:12195 +xref: EFO:0000921 +xref: EHDAA2:0004475 +xref: EMAPA:18215 +xref: FMA:62393 +xref: HBA:9002 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 {source="NIFSTD:birnlex_1200"} +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 +xref: http://linkedlifedata.com/resource/umls/id/C0039441 +xref: http://www.snomedbrowser.com/Codes/Details/362392007 +xref: MA:0000212 +xref: MAT:0000452 +xref: Midbrain:tegmentum +xref: TAO:0000160 +xref: UMLS:C0039441 {source="NIFSTD:birnlex_1200"} +xref: VHOG:0001367 +xref: XAO:0004271 +xref: ZFA:0000160 +is_a: UBERON:0002616 ! regional part of brain +relationship: develops_from UBERON:0010285 {source="ZFA"} ! midbrain basal plate +relationship: part_of UBERON:0001891 ! midbrain +relationship: part_of UBERON:0002298 ! brainstem +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png +property_value: UBPROP:0000003 "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001367", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)"} + +[Term] +id: UBERON:0001948 +name: regional part of spinal cord +namespace: uberon +def: "A multi-tissue structure that is part of a spinal cord." [OBOL:automatic] +subset: non_informative +synonym: "spinal cord part" RELATED [] +xref: birnlex:1496 +xref: http://linkedlifedata.com/resource/umls/id/C1268166 +xref: http://www.snomedbrowser.com/Codes/Details/244437008 +xref: NCIT:C33969 +xref: UMLS:C1268166 {source="ncithesaurus:Spinal_Cord_Part"} +is_a: UBERON:0000073 ! regional part of nervous system +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0002240 ! spinal cord +relationship: part_of UBERON:0002240 ! spinal cord + +[Term] +id: UBERON:0001969 +name: blood plasma +namespace: uberon +def: "The liquid component of blood, in which erythrocytes are suspended." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "blood plasm" EXACT [] +synonym: "plasma" BROAD [MA:0002501] +synonym: "portion of blood plasma" EXACT [] +synonym: "portion of plasma" BROAD [FMA:62970] +xref: Blood:plasma +xref: BTO:0000131 +xref: CALOHA:TS-0800 +xref: EFO:0001905 +xref: EMAPA:35690 +xref: FMA:62970 +xref: GAID:1178 +xref: http://linkedlifedata.com/resource/umls/id/C0032105 +xref: MA:0002501 +xref: MAT:0000052 +xref: MESH:D010949 +xref: MIAA:0000052 +xref: NCIT:C13356 +xref: OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw +xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} +is_a: UBERON:0000179 ! haemolymphatic fluid +relationship: part_of UBERON:0000178 ! blood + +[Term] +id: UBERON:0001979 +name: venule +namespace: uberon +def: "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins" [MESH:A07.231.432.952, MP:0004125] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "venula" RELATED LATIN [http://en.wikipedia.org/wiki/Venule] +xref: BTO:0002626 +xref: EMAPA:35917 +xref: FMA:63130 +xref: http://en.wikipedia.org/wiki/Venule +xref: http://linkedlifedata.com/resource/umls/id/C0042520 +xref: http://www.snomedbrowser.com/Codes/Details/341687009 +xref: MA:0000071 +xref: MESH:A07.231.432.952 +xref: NCIT:C12818 +xref: TAO:0005315 +xref: UMLS:C0042520 {source="ncithesaurus:Venule"} +xref: VHOG:0001765 +xref: ZFA:0005315 +is_a: UBERON:0003920 ! venous blood vessel +relationship: connects UBERON:0001638 ! vein +relationship: connects UBERON:0001982 ! capillary +property_value: depicted:by Illu:capillary.jpg +property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005315", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0001980 +name: arteriole +namespace: uberon +def: "The smallest division of the artery located between the muscular arteries and the capillaries[GO]." [GO:0014830] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arteriola" RELATED LATIN [http://en.wikipedia.org/wiki/Arteriole] +xref: AAO:0010253 +xref: BTO:0001997 +xref: EMAPA:35146 +xref: FMA:63182 +xref: http://en.wikipedia.org/wiki/Arteriole +xref: http://linkedlifedata.com/resource/umls/id/C0003847 +xref: http://www.snomedbrowser.com/Codes/Details/337724002 +xref: MA:0000063 +xref: MESH:D001160 +xref: NCIT:C12672 +xref: TAO:0002138 +xref: UMLS:C0003847 {source="ncithesaurus:Arteriole"} +xref: VHOG:0001763 +xref: ZFA:0005255 +is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: connects UBERON:0001637 ! artery +intersection_of: connects UBERON:0001982 ! capillary +relationship: connects UBERON:0001637 ! artery +relationship: connects UBERON:0001982 ! capillary +relationship: contributes_to_morphology_of UBERON:0001637 ! artery +property_value: depicted:by Illu:capillary.jpg +property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002138", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010253", ontology="AAO", source="AAO:BJB"} + +[Term] +id: UBERON:0001981 +name: blood vessel +namespace: uberon +def: "A vessel through which blood circulates in the body." [BTO:0001102, http://en.wikipedia.org/wiki/Blood_vessel] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "region of vascular tree organ" EXACT [FMA:50722] +synonym: "vas sanguineum" RELATED LATIN [http://en.wikipedia.org/wiki/Blood_vessel] +synonym: "vascular element" BROAD [EMAPA:35993] +synonym: "vascular tree organ region" EXACT [FMA:50722] +xref: AAO:0011004 +xref: AEO:0000207 +xref: Blood:vessel +xref: BTO:0001102 +xref: CALOHA:TS-0080 +xref: EFO:0000817 +xref: EHDAA2:0003252 +xref: EHDAA:240 +xref: EMAPA:32743 +xref: EMAPA:35993 +xref: FMA:50722 +xref: FMA:63183 +xref: GAID:169 +xref: http://linkedlifedata.com/resource/umls/id/C0005847 +xref: http://www.snomedbrowser.com/Codes/Details/361097006 +xref: MA:0000060 +xref: MAT:0000393 +xref: MESH:D001808 +xref: NCIT:C12679 +xref: nlx_anat:090901 +xref: OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA +xref: TAO:0002137 +xref: UMLS:C0005847 {source="ncithesaurus:Blood_Vessel"} +xref: VHOG:0001250 +xref: XAO:0001011 +xref: ZFA:0005314 +is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: channel_for UBERON:0000178 ! blood +relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm +relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord +relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends +relationship: part_of UBERON:0004537 ! blood vasculature +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} +property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)"} +property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string +property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0001982 +name: capillary +namespace: uberon +def: "Any of the smallest blood vessels connecting arterioles with venules." [http://en.wikipedia.org/wiki/Capillary, https://github.com/obophenotype/uberon/issues/137, ISBN10:0073040584] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood capillary" EXACT [] +synonym: "capillary vessel" EXACT [] +xref: AAO:0010252 +xref: BTO:0002045 +xref: CALOHA:TS-2006 +xref: EFO:0001906 +xref: EMAPA:35198 +xref: EV:0100035 +xref: FMA:63194 +xref: http://en.wikipedia.org/wiki/Capillary +xref: http://linkedlifedata.com/resource/umls/id/C0935624 +xref: MA:0000065 +xref: MESH:A07.231.432.410 +xref: NCIT:C12685 +xref: nlx_anat:090902 +xref: OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA +xref: TAO:0005250 +xref: UMLS:C0935624 {source="ncithesaurus:Capillary"} +xref: VHOG:0001253 +xref: XAO:0000116 +xref: ZFA:0005250 +is_a: UBERON:0001981 {source="FMA", source="MA", source="XAO"} ! blood vessel +is_a: UBERON:0010523 {source="ZFA"} ! microcirculatory vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: connects UBERON:0001979 ! venule +intersection_of: connects UBERON:0001980 ! arteriole +relationship: connects UBERON:0001979 ! venule +relationship: connects UBERON:0001980 ! arteriole +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: UBPROP:0000001 "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010252", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001253", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)"} +property_value: UBPROP:0000010 "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" xsd:string + +[Term] +id: UBERON:0001986 +name: endothelium +namespace: uberon +def: "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]" [FMA:63916, https://github.com/obophenotype/uberon/issues/225, MESH:A10.272.491] +comment: The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) +subset: efo_slim +subset: uberon_slim +xref: BTO:0000393 +xref: CALOHA:TS-0278 +xref: EFO:0002548 +xref: FMA:63916 +xref: GAID:520 +xref: galen:Endothelium +xref: http://linkedlifedata.com/resource/umls/id/C0014257 +xref: http://www.snomedbrowser.com/Codes/Details/27168002 +xref: MESH:D004727 +xref: NCIT:C12481 +xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} +is_a: UBERON:0000487 {source="https://github.com/obophenotype/uberon/issues/225", source="FMA-text-def"} ! simple squamous epithelium +is_a: UBERON:0012275 ! meso-epithelium +property_value: UBPROP:0000007 "endothelial" xsd:string + +[Term] +id: UBERON:0002012 +name: pulmonary artery +namespace: uberon +def: "An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.." [http://en.wikipedia.org/wiki/Pulmonary_artery, http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "arteria pulmonalis" RELATED LATIN [http://en.wikipedia.org/wiki/Pulmonary_artery] +synonym: "pulmonary arterial subtree" RELATED [FMA:66326] +synonym: "pulmonary arterial tree" EXACT [FMA:66326] +synonym: "pulmonary arterial tree organ part" EXACT [FMA:66326] +synonym: "truncus pulmonalis" RELATED LATIN [http://en.wikipedia.org/wiki/Pulmonary_artery] +xref: AAO:0010221 +xref: BTO:0000778 +xref: CALOHA:TS-0839 +xref: EFO:0001399 +xref: EHDAA2:0001575 +xref: EHDAA:4351 +xref: EMAPA:17008 +xref: FMA:66326 +xref: GAID:505 +xref: galen:PulmonaryArtery +xref: http://linkedlifedata.com/resource/umls/id/C0034052 +xref: http://www.snomedbrowser.com/Codes/Details/181380003 +xref: MA:0002031 +xref: MESH:D011651 +xref: NCIT:C12774 +xref: OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA +xref: Pulmonary:artery +xref: UMLS:C0034052 {source="ncithesaurus:Pulmonary_Artery"} +xref: VHOG:0000982 +xref: XAO:0004162 +is_a: UBERON:0001637 ! artery +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0013768 ! great vessel of heart +intersection_of: UBERON:0001637 ! artery +intersection_of: part_of UBERON:0008886 ! pulmonary vascular system +intersection_of: supplies UBERON:0002048 ! lung +disjoint_from: UBERON:0004573 ! systemic artery +relationship: continuous_with UBERON:0002333 ! pulmonary trunk +relationship: develops_from UBERON:0002061 {source="Wikipedia"} ! truncus arteriosus +relationship: develops_from UBERON:0003123 {source="EHDAA2", source="XAO"} ! pharyngeal arch artery 6 +relationship: develops_from UBERON:0005339 {source="EHDAA2"} ! outflow tract pulmonary component +relationship: part_of UBERON:0008886 ! pulmonary vascular system +relationship: supplies UBERON:0002048 ! lung +property_value: depicted:by Alveoli:diagram.png +property_value: UBPROP:0000001 "Major artery which supplies blood to the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010221", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000982", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+artery"} +property_value: UBPROP:0000003 "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000982", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620"} +property_value: UBPROP:0000008 "In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]" xsd:string + +[Term] +id: UBERON:0002016 +name: pulmonary vein +namespace: uberon +def: "Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]." [GO:0060577] +subset: pheno_slim +subset: uberon_slim +synonym: "pulmonary venous tree organ part" EXACT [] +synonym: "venae pulmonales" RELATED LATIN [http://en.wikipedia.org/wiki/Pulmonary_vein] +xref: AAO:0010521 +xref: BTO:0001799 +xref: CALOHA:TS-0840 +xref: EHDAA2:0001579 +xref: EHDAA:2629 +xref: EMAPA:18645 +xref: FMA:66643 +xref: GAID:543 +xref: galen:PulmonaryVein +xref: http://linkedlifedata.com/resource/umls/id/C0034090 +xref: http://www.snomedbrowser.com/Codes/Details/430160002 +xref: MA:0002206 +xref: MESH:D011667 +xref: NCIT:C12776 +xref: Pulmonary:vein +xref: UMLS:C0034090 {source="ncithesaurus:Pulmonary_Vein"} +xref: VHOG:0001133 +xref: XAO:0000394 +is_a: UBERON:0001638 ! vein +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0013768 ! great vessel of heart +intersection_of: UBERON:0001638 ! vein +intersection_of: drains UBERON:0002048 ! lung +relationship: develops_from UBERON:0002061 ! truncus arteriosus +relationship: drains UBERON:0002048 ! lung +relationship: part_of UBERON:0008886 ! pulmonary vascular system +property_value: depicted:by Alveoli:diagram.png +property_value: UBPROP:0000001 "Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010521", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001133", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+vein"} +property_value: UBPROP:0000001 "the veins that return oxygenated blood from the lungs to the left atrium of the heart" xsd:string {source="MP:0002726,MGI:cwg"} +property_value: UBPROP:0000003 "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001133", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620"} +property_value: UBPROP:0000202 FMA:70827 + +[Term] +id: UBERON:0002020 +name: gray matter +namespace: uberon +def: "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons." [http://en.wikipedia.org/wiki/Gray_matter, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "gray mater" RELATED [ZFA:0001681] +synonym: "gray matter" EXACT [] +synonym: "gray matter of neuraxis" EXACT [FMA:67242] +synonym: "grey matter" EXACT [] +synonym: "grey matter of neuraxis" EXACT [] +synonym: "grey substance" EXACT [] +synonym: "grisea" RELATED LATIN [] +synonym: "neuronal grey matter" EXACT [AEO:0001012] +synonym: "substantia grisea" EXACT LATIN [FMA:67242, FMA:TA] +xref: AEO:0001012 +xref: EHDAA2:0003136 +xref: EHDAA2_RETIRED:0004658 +xref: EMAPA:37596 {source="MA:th"} +xref: FMA:67242 +xref: Gray:matter +xref: HBA:4006 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2869 +xref: http://linkedlifedata.com/resource/umls/id/C0018220 +xref: MA:0001112 +xref: NCIT:C32695 +xref: OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA +xref: TAO:0002197 +xref: UMLS:C0018220 {source="ncithesaurus:Gray_Matter"} +xref: VHOG:0001768 +xref: ZFA:0001681 +is_a: UBERON:0011215 ! central nervous system cell part cluster +property_value: depicted:by Spinal:nerve.svg +property_value: UBPROP:0000001 "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002197", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0002028 +name: hindbrain +namespace: uberon +def: "The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]." [http://en.wikipedia.org/wiki/Rhombencephalon, ZFA:0000029, ZFIN:curator] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "rhombencephalon" RELATED [] +xref: AAO:0010150 +xref: BAMS:HB +xref: birnlex:942 +xref: BTO:0000672 +xref: CALOHA:TS-0457 +xref: DHBA:10653 +xref: DMBA:16808 +xref: EFO:0000923 +xref: EHDAA2:0000746 +xref: EHDAA:3514 +xref: EHDAA:6487 +xref: EMAPA:16916 +xref: FMA:67687 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 {source="NIFSTD:birnlex_942"} +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 +xref: http://en.wikipedia.org/wiki/Rhombencephalon +xref: http://linkedlifedata.com/resource/umls/id/C0035507 +xref: http://linkedlifedata.com/resource/umls/id/C1522180 +xref: http://www.snomedbrowser.com/Codes/Details/303456008 +xref: MA:0000195 +xref: MAT:0000107 +xref: MBA:1065 +xref: MESH:D012249 +xref: MIAA:0000107 +xref: NCIT:C40336 +xref: TAO:0000029 +xref: UMLS:C0035507 {source="ncithesaurus:Hind-Brain"} +xref: UMLS:C0035507 {source="NIFSTD:birnlex_942"} +xref: UMLS:C1522180 {source="NIFSTD:birnlex_942"} +xref: VHOG:0000070 +xref: XAO:0000015 +xref: ZFA:0000029 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: contributes_to_morphology_of UBERON:0000955 ! brain +relationship: develops_from UBERON:0007277 ! presumptive hindbrain +relationship: immediate_transformation_of UBERON:0007277 {source="Bgee:AN"} ! presumptive hindbrain +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg +property_value: RO:0002175 NCBITaxon:7762 {source="http://www.ncbi.nlm.nih.gov/pubmed/8932866"} +property_value: UBPROP:0000001 "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010150", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000002 "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO"} +property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000070", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)"} +property_value: UBPROP:0000007 "rhombencephalic" xsd:string +property_value: UBPROP:0000012 "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0002040 +name: bronchial artery +namespace: uberon +def: "A systemic artery that supplies the lung with with oxygenated blood." [http://en.wikipedia.org/wiki/Bronchial_artery, UBERON:cjm] +comment: Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. +subset: uberon_slim +synonym: "arteriae bronchiales" RELATED LATIN [http://en.wikipedia.org/wiki/Bronchial_artery] +synonym: "bronchial arterial tree" EXACT [] +synonym: "rami bronchiales partis thoracicae aortae" RELATED LATIN [http://en.wikipedia.org/wiki/Bronchial_artery] +xref: Bronchial:artery +xref: EMAPA:18608 +xref: FMA:68109 +xref: GAID:477 +xref: http://linkedlifedata.com/resource/umls/id/C0006257 +xref: http://www.snomedbrowser.com/Codes/Details/244247009 +xref: MA:0001923 +xref: MESH:D001981 +xref: NCIT:C32230 +xref: OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg +xref: UMLS:C0006257 {source="ncithesaurus:Bronchial_Artery"} +is_a: UBERON:0004573 ! systemic artery +intersection_of: UBERON:0004573 ! systemic artery +intersection_of: part_of UBERON:0004571 ! systemic arterial system +intersection_of: supplies UBERON:0002048 ! lung +relationship: supplies UBERON:0002048 ! lung +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png + +[Term] +id: UBERON:0002048 +name: lung +namespace: uberon +def: "Respiration organ that develops as an oupocketing of the esophagus." [http://orcid.org/0000-0002-6601-2165] +comment: Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "pulmo" EXACT LATIN [] +xref: AAO:0000275 +xref: AAO:0010567 +xref: BTO:0000763 +xref: CALOHA:TS-0568 +xref: EFO:0000934 +xref: EHDAA2:0001042 +xref: EHDAA:1554 +xref: EHDAA:2205 +xref: EMAPA:16728 +xref: EV:0100042 +xref: FMA:7195 +xref: GAID:345 +xref: galen:Lung +xref: http://en.wikipedia.org/wiki/Lung +xref: http://linkedlifedata.com/resource/umls/id/C0024109 +xref: http://www.snomedbrowser.com/Codes/Details/181216001 +xref: MA:0000415 +xref: MAT:0000135 +xref: MESH:D008168 +xref: MIAA:0000135 +xref: NCIT:C12468 +xref: OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA +xref: UMLS:C0024109 {source="ncithesaurus:Lung"} +xref: VHOG:0000310 +xref: XAO:0000119 +is_a: UBERON:0000171 ! respiration organ +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0005178 ! thoracic cavity element +is_a: UBERON:0015212 ! lateral structure +relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system +relationship: develops_from UBERON:0000118 ! lung bud +relationship: in_lateral_side_of UBERON:0000170 ! pair of lungs +relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs +property_value: seeAlso https://github.com/obophenotype/uberon/issues/701 +property_value: UBPROP:0000001 "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010567", ontology="AAO", source="AAO:SBH"} +property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000310", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)"} +property_value: UBPROP:0000007 "pulmonary" xsd:string +property_value: UBPROP:0000008 "respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi" xsd:string + +[Term] +id: UBERON:0002049 +name: vasculature +namespace: uberon +def: "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face." [ZFA:0005249] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "vascular network" EXACT [FMA:69050] +xref: BTO:0003718 +xref: FMA:69050 +xref: TAO:0005249 +xref: ZFA:0005249 +is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster +relationship: composed_primarily_of UBERON:0000055 ! vessel +relationship: has_part UBERON:0000179 ! haemolymphatic fluid +relationship: part_of UBERON:0007798 ! vascular system +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: UBPROP:0000007 "vascular" xsd:string + +[Term] +id: UBERON:0002050 +name: embryonic structure +namespace: uberon +def: "Anatomical structure that is part of an embryo." [BTO:0000174, ZFIN:curator] +subset: efo_slim +subset: inconsistent_with_fma +subset: vertebrate_core +synonym: "developing embryonic structure" EXACT [FBbt:00004208] +synonym: "developing structure" RELATED [] +synonym: "embryonale Struktur" RELATED [BTO:0000174] +synonym: "embryonic anatomical structure" EXACT [RETIRED_EHDAA2:0003169] +synonym: "embryonic structures" RELATED PLURAL [ZFA:0001105] +xref: AAO:0000138 +xref: BILA:0000034 +xref: BTO:0000174 +xref: CALOHA:TS-2110 +xref: EFO:0000461 +xref: FBbt:00004208 +xref: FMA:69067 +xref: GAID:407 +xref: http://linkedlifedata.com/resource/umls/id/C0013948 +xref: http://www.snomedbrowser.com/Codes/Details/667009 +xref: MESH:D004628 +xref: NCIT:C13229 +xref: RETIRED_EHDAA2:0003169 +xref: TAO:0001105 +xref: UMLS:C0013948 {source="ncithesaurus:Embryonic_Structure"} +xref: VSAO:0000178 +xref: XAO:0003042 +xref: ZFA:0001105 +is_a: UBERON:0005423 ! developing anatomical structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: part_of UBERON:0000922 ! embryo +relationship: part_of UBERON:0000922 ! embryo +property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} +property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0002061 +name: truncus arteriosus +namespace: uberon +def: "The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles." [http://en.wikipedia.org/wiki/Truncus_arteriosus_(embryology)] +subset: uberon_slim +xref: EHDAA2:0004143 +xref: EMAPA:35887 +xref: FMA:70301 +xref: GAID:554 +xref: http://en.wikipedia.org/wiki/Truncus_arteriosus_(embryology) +xref: http://linkedlifedata.com/resource/umls/id/C1519589 +xref: http://www.snomedbrowser.com/Codes/Details/308828009 +xref: MA:0000103 +xref: MESH:D014338 +xref: NCIT:C34317 +xref: OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw +xref: UMLS:C1519589 {source="ncithesaurus:Trancus_Arteriosus"} +is_a: UBERON:0001637 {source="EHDAA2"} ! artery +is_a: UBERON:0002050 {source="FMA"} ! embryonic structure +is_a: UBERON:0003498 ! heart blood vessel +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: develops_from UBERON:0005432 {source="EHDAA2"} ! aortic sac +relationship: part_of UBERON:0004145 {source="MA"} ! outflow tract +relationship: part_of UBERON:0005498 {source="EHDAA2"} ! primitive heart tube +property_value: UBPROP:0000012 "assume spelling error for ncit" xsd:string {external_ontology="ncit"} + +[Term] +id: UBERON:0002067 +name: dermis +namespace: uberon +def: "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]." [http://en.wikipedia.org/wiki/Dermis, ZFIN:curator] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "corium" RELATED [BTO:0000294] +synonym: "corium" RELATED LATIN [http://en.wikipedia.org/wiki/Dermis] +synonym: "cutis" RELATED [BTO:0000294] +synonym: "vertebrate dermis" EXACT [] +xref: AAO:0000128 +xref: BTO:0000294 +xref: CALOHA:TS-2076 +xref: EFO:0000953 +xref: EMAPA:17527 +xref: EV:0100154 +xref: FMA:70323 +xref: GAID:1321 +xref: http://en.wikipedia.org/wiki/Dermis +xref: http://linkedlifedata.com/resource/umls/id/C0011646 +xref: http://www.snomedbrowser.com/Codes/Details/361696001 +xref: MA:0000152 +xref: MAT:0000153 +xref: MESH:D020405 +xref: MIAA:0000153 +xref: NCIT:C12701 +xref: TAO:0001119 +xref: UMLS:C0011646 {source="ncithesaurus:Dermis"} +xref: VHOG:0000108 +xref: XAO:0000217 +xref: ZFA:0001119 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0013754 ! integumentary system layer +relationship: composed_primarily_of UBERON:0002384 ! connective tissue +relationship: deep_to UBERON:0001003 ! skin epidermis +relationship: develops_from UBERON:0010083 ! future dermis +relationship: has_part UBERON:0011860 ! collection of collagen fibrils +relationship: immediate_transformation_of UBERON:0010083 {evidence="definitional"} ! future dermis +relationship: part_of UBERON:0002097 {source="FMA"} ! skin of body +relationship: superficial_to UBERON:0002072 ! hypodermis +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg +property_value: IAO:0000116 "Consider adding a layer-of-skin grouping class for all skin layers" xsd:string +property_value: UBPROP:0000001 "A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001119", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000108", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1"} +property_value: UBPROP:0000007 "dermal" xsd:string + +[Term] +id: UBERON:0002072 +name: hypodermis +namespace: uberon +def: "Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]." [http://en.wikipedia.org/wiki/Hypodermis] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "hypoderm" EXACT [] +synonym: "sub-tegumental tissue" RELATED [BTO:0004525] +synonym: "subcutaneous tissue" RELATED [http://en.wikipedia.org/wiki/Hypodermis] +synonym: "subcutis" RELATED [] +synonym: "subtegumental tissue" RELATED [BTO:0004525] +synonym: "superficial fascia" RELATED INCONSISTENT [] +synonym: "tela subcutanea" RELATED LATIN [http://en.wikipedia.org/wiki/Hypodermis] +synonym: "vertebrate hypodermis" EXACT [] +xref: BTO:0001314 +xref: CALOHA:TS-2366 +xref: EMAPA:37505 {source="MA:th"} +xref: FMA:70544 +xref: http://en.wikipedia.org/wiki/Hypodermis +xref: http://linkedlifedata.com/resource/umls/id/C0278403 +xref: NCIT:C33645 +xref: TAO:0001136 +xref: UMLS:C0278403 {source="ncithesaurus:Subcutis"} +xref: ZFA:0001136 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0013754 ! integumentary system layer +relationship: composed_primarily_of UBERON:0001013 ! adipose tissue +relationship: composed_primarily_of UBERON:0011825 {source="FMA-modified"} ! loose connective tissue +relationship: deep_to UBERON:0002067 ! dermis +relationship: part_of UBERON:0002199 {source="ZFA"} ! integument +relationship: superficial_to UBERON:0001015 ! musculature +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg +property_value: UBPROP:0000001 "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001136", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]." xsd:string {source="FMA:70544"} +property_value: UBPROP:0000007 "hypodermal" xsd:string +property_value: UBPROP:0000007 "subcutaneous" xsd:string +property_value: UBPROP:0000007 "subcutaneus" xsd:string +property_value: UBPROP:0000012 "BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument." xsd:string {external_ontology="BTO"} + +[Term] +id: UBERON:0002075 +name: viscus +namespace: uberon +def: "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen." [BTO:0001491, http://en.wikipedia.org/wiki/Viscus, https://github.com/obophenotype/mouse-anatomy-ontology/issues/14] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: upper_level +synonym: "Organsystem@de" RELATED [BTO:0001491] +synonym: "splanchnic tissue" RELATED [BTO:0001491] +synonym: "viscera" RELATED [] +synonym: "visceral organ" EXACT [RETIRED_EHDAA2:0002201] +synonym: "visceral organ system" EXACT [MA:0000019] +synonym: "visceral tissue" RELATED [BTO:0001491] +xref: AAO:0010386 +xref: BTO:0001491 +xref: EHDAA:512 +xref: EMAPA:16245 +xref: FMA:7085 +xref: http://en.wikipedia.org/wiki/Viscus +xref: http://linkedlifedata.com/resource/umls/id/C0042779 +xref: http://www.snomedbrowser.com/Codes/Details/118760003 +xref: MA:0000019 +xref: MESH:D014781 +xref: NCIT:C28287 +xref: RETIRED_EHDAA2:0002201 +xref: UMLS:C0042779 {source="ncithesaurus:Viscera"} +xref: XAO:0003034 +is_a: UBERON:0005177 ! trunk region element +intersection_of: UBERON:0000062 ! organ +intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen +relationship: located_in UBERON:0002323 ! coelemic cavity lumen +property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} +property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0002090 +name: postcranial axial skeleton +namespace: uberon +def: "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]." [https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957, https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834, ZFA:0000317] +comment: previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "axial skeleton" BROAD [FMA:71221, https://github.com/obophenotype/uberon/wiki/The-axial-skeleton] +synonym: "post-cranial axial skeleton" EXACT [] +xref: AAO:0000034 +xref: EFO:0000942 +xref: EHDAA2:0000161 +xref: EHDAA:5049 +xref: EMAPA:17214 +xref: EMAPA:37721 {source="MA:th"} +xref: FMA:71221 +xref: MA:0002986 +xref: MAT:0000148 +xref: MIAA:0000148 +xref: TAO:0000317 +xref: VHOG:0000317 +xref: VSAO:0000093 +xref: XAO:0003073 +xref: ZFA:0000317 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: develops_from UBERON:0003089 ! sclerotome +relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton +relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI +property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} +property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)"} + +[Term] +id: UBERON:0002097 +name: skin of body +namespace: uberon +def: "The organ covering the body that consists of the dermis and epidermis." [UBERON:cjm] +subset: efo_slim +subset: major_organ +subset: pheno_slim +subset: uberon_slim +synonym: "entire integument" RELATED [] +synonym: "entire skin" EXACT [] +synonym: "integument" RELATED [] +synonym: "integumental organ" RELATED [] +synonym: "pelt" RELATED [] +synonym: "skin" RELATED [] +synonym: "skin organ" EXACT [] +xref: BTO:0001253 +xref: CALOHA:TS-0934 +xref: EFO:0000962 +xref: EHDAA2:0001844 +xref: EMAPA:17525 +xref: FMA:7163 +xref: galen:Skin +xref: http://en.wikipedia.org/wiki/Skin +xref: http://linkedlifedata.com/resource/umls/id/C1123023 +xref: http://www.snomedbrowser.com/Codes/Details/181469002 +xref: MESH:D012867 +xref: MFMO:0000099 +xref: NCIT:C12470 +xref: OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA +xref: UMLS:C1123023 {source="ncithesaurus:Skin"} +xref: XAO:0000023 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: composed_primarily_of UBERON:0000014 ! zone of skin +relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer +relationship: part_of UBERON:0002199 ! integument +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg +property_value: IAO:0000232 "consider 'integumentary system' for invertebrates" xsd:string +property_value: UBPROP:0000012 "MA uses the term skin to refer to what is called here: zone of skin" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0002099 +name: cardiac septum +namespace: uberon +def: "The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles." [MESH:A07.541.459] +subset: pheno_slim +subset: uberon_slim +synonym: "cardiac septa" EXACT PLURAL [] +synonym: "heart septa" EXACT PLURAL [] +synonym: "heart septum" EXACT [] +synonym: "septum of heart" EXACT [] +synonym: "spiral septa" RELATED PLURAL [XAO:0004141] +xref: EMAPA:35400 +xref: FMA:7180 +xref: GAID:562 +xref: http://linkedlifedata.com/resource/umls/id/C0018819 +xref: http://www.snomedbrowser.com/Codes/Details/362014000 +xref: MA:0000083 +xref: MESH:D006346 +xref: NCIT:C49485 +xref: UMLS:C0018819 {source="ncithesaurus:Heart_Septum"} +xref: XAO:0004141 +is_a: UBERON:0003037 ! septum +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0003037 ! septum +intersection_of: part_of UBERON:0000948 ! heart +relationship: adjacent_to UBERON:0004151 ! cardiac chamber +relationship: contributes_to_morphology_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart +property_value: UBPROP:0000008 "'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'" xsd:string +property_value: UBPROP:0000012 "in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this" xsd:string {external_ontology="GO"} + +[Term] +id: UBERON:0002100 +name: trunk +namespace: uberon +def: "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." [http://en.wikipedia.org/wiki/Torso, TAO:0001115, UBERONREF:0000006] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Rumpf" RELATED [BTO:0001493] +synonym: "thoracolumbar region" EXACT [] +synonym: "torso" EXACT [] +synonym: "trunk region" EXACT [XAO:0000054] +xref: AAO:0010339 +xref: BILA:0000116 +xref: BTO:0001493 +xref: CALOHA:TS-1071 +xref: EFO:0000966 +xref: EMAPA:31857 +xref: FMA:7181 +xref: galen:Trunk +xref: http://en.wikipedia.org/wiki/Torso +xref: http://linkedlifedata.com/resource/umls/id/C0460005 +xref: http://www.snomedbrowser.com/Codes/Details/262225004 +xref: MA:0000004 +xref: MAT:0000296 +xref: MIAA:0000296 +xref: NCIT:C33816 +xref: OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA +xref: TAO:0001115 +xref: UMLS:C0460005 {source="ncithesaurus:Trunk"} +xref: XAO:0000054 +xref: XAO:0003025 +xref: ZFA:0001115 +is_a: UBERON:0011676 ! subdivision of organism along main body axis +relationship: part_of UBERON:0013702 ! body proper +property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0002111 +name: artery smooth muscle tissue +namespace: uberon +def: "A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]." [OBOL:automatic] +synonym: "arterial smooth muscle" EXACT [BTO:0000087] +synonym: "arterial smooth muscle cell" RELATED [BTO:0000087] +synonym: "artery smooth muscle" EXACT [] +synonym: "artery smooth muscle tissue" EXACT [] +synonym: "smooth muscle of artery" EXACT [FMA:72024] +xref: BTO:0000087 +xref: CALOHA:TS-1198 +xref: EMAPA:36285 +xref: FMA:72024 +xref: http://linkedlifedata.com/resource/umls/id/C1706851 +xref: MA:0000708 +xref: NCIT:C49195 +xref: UMLS:C1706851 {source="ncithesaurus:Artery_Smooth_Muscle_Tissue"} +is_a: UBERON:0004237 ! blood vessel smooth muscle +is_a: UBERON:0004695 ! arterial system smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0001637 ! artery + +[Term] +id: UBERON:0002165 +name: endocardium +namespace: uberon +alt_id: UBERON:0006225 +def: "The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]." [GO:0003157] +comment: fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "endocardial lining" EXACT [EMAPA:32686] +synonym: "endocardial tissue" EXACT [EMAPA:17868] +synonym: "heart endocardial tissue" RELATED [VHOG:0000084] +synonym: "heart endocardium" EXACT [] +xref: AAO:0010408 +xref: BTO:0000387 +xref: CALOHA:TS-2075 +xref: EFO:0000821 +xref: EHDAA2:0004153 +xref: EMAPA:17868 +xref: EMAPA:32686 +xref: EV:0100021 +xref: FMA:7280 +xref: GAID:550 +xref: galen:Endocardium +xref: http://en.wikipedia.org/wiki/Endocardium +xref: http://linkedlifedata.com/resource/umls/id/C0014124 +xref: http://www.snomedbrowser.com/Codes/Details/362013006 +xref: MA:0000076 +xref: MAT:0000455 +xref: MESH:D004699 +xref: NCIT:C13004 +xref: OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw +xref: TAO:0001320 +xref: UMLS:C0014124 {source="ncithesaurus:Endocardium"} +xref: VHOG:0000084 +xref: XAO:0000066 +xref: ZFA:0001320 +is_a: UBERON:0002523 ! tunica intima +is_a: UBERON:0005983 ! heart layer +relationship: develops_from UBERON:0007280 ! presumptive endocardium +relationship: has_part UBERON:0005316 ! endocardial endothelium +relationship: immediate_transformation_of UBERON:0007280 {source="Bgee:AN"} ! presumptive endocardium +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png +property_value: UBPROP:0000001 "Layer that lines the lumen of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001320", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010408", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000001 "Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber." xsd:string {source="FMA:7280"} + +[Term] +id: UBERON:0002167 +name: right lung +namespace: uberon +def: "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Right_lung] +subset: pheno_slim +subset: uberon_slim +xref: EHDAA2:0001730 +xref: EHDAA:4969 +xref: EMAPA:17661 +xref: FMA:7309 +xref: http://linkedlifedata.com/resource/umls/id/C0225706 +xref: http://www.snomedbrowser.com/Codes/Details/361967000 +xref: MA:0000426 +xref: NCIT:C33483 +xref: OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA +xref: Right:lung +xref: UMLS:C0225706 {source="ncithesaurus:Right_Lung"} +xref: VHOG:0000301 +is_a: UBERON:0002048 ! lung +intersection_of: UBERON:0002048 ! lung +intersection_of: in_right_side_of UBERON:0000170 ! pair of lungs +relationship: in_right_side_of UBERON:0000170 ! pair of lungs +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png +property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000301", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210"} +property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI + +[Term] +id: UBERON:0002168 +name: left lung +namespace: uberon +def: "Lung which consists of the left upper lobe and left lower lobe.[FMA]" [FMA:FMA, http://en.wikipedia.org/wiki/Left_lung] +subset: pheno_slim +subset: uberon_slim +xref: EHDAA2:0000943 +xref: EHDAA:4947 +xref: EMAPA:17653 +xref: FMA:7310 +xref: http://linkedlifedata.com/resource/umls/id/C0225730 +xref: http://www.snomedbrowser.com/Codes/Details/361982005 +xref: Left:lung +xref: MA:0000425 +xref: NCIT:C32967 +xref: OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA +xref: UMLS:C0225730 {source="ncithesaurus:Left_Lung"} +xref: VHOG:0000618 +is_a: UBERON:0002048 ! lung +intersection_of: UBERON:0002048 ! lung +intersection_of: in_left_side_of UBERON:0000170 ! pair of lungs +relationship: in_left_side_of UBERON:0000170 ! pair of lungs +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png +property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000618", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210"} +property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI + +[Term] +id: UBERON:0002190 +name: subcutaneous adipose tissue +namespace: uberon +alt_id: UBERON:0008875 +def: "A portion of adipose tissue that is part of the hypodermis, beneath the dermis." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "fatty layer of subcutaneous tissue" EXACT [FMA:74315] +synonym: "fatty layer of superficial fascia" RELATED [FMA:74315] +synonym: "hypodermis fat layer" EXACT [MP:0011156] +synonym: "panniculus adiposus" BROAD [MP:0011156] +synonym: "panniculus adiposus (tela subcutanea)" EXACT LATIN [FMA:74315, FMA:TA] +synonym: "panniculus adiposus telae subcutaneae" EXACT LATIN [FMA:74315, FMA:TA] +synonym: "subcutaneous fat" RELATED [BTO:0004042] +synonym: "subcutaneous fat layer" EXACT [MP:0011156] +xref: BTO:0004042 +xref: EMAPA:35829 +xref: FMA:74315 +xref: MA:0000473 +is_a: UBERON:0001013 ! adipose tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0001013 ! adipose tissue +intersection_of: part_of UBERON:0002072 ! hypodermis +relationship: contributes_to_morphology_of UBERON:0002072 ! hypodermis +relationship: part_of UBERON:0002072 ! hypodermis +property_value: UBPROP:0000001 "the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]" xsd:string {source="MP:0011156"} + +[Term] +id: UBERON:0002193 +name: hemolymphoid system +namespace: uberon +def: "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs." [http://orcid.org/0000-0002-6601-2165] +synonym: "haemolymphoid system" RELATED [] +synonym: "hematolymphoid system" EXACT [] +synonym: "lymphomyeloid complex" EXACT [] +xref: CALOHA:TS-2018 +xref: EHDAA2:0004615 +xref: EMAPA:18765 +xref: FMA:74562 +xref: MA:0000013 +is_a: UBERON:0000467 {source="MA"} ! anatomical system + +[Term] +id: UBERON:0002199 +name: integument +namespace: uberon +def: "The dermis, epidermis and hypodermis." [http://en.wikipedia.org/wiki/Integument] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "dermal system" RELATED [BTO:0000634] +synonym: "dermis plus epidermis plus hypodermis" EXACT [] +synonym: "dermoid system" RELATED [BTO:0000634] +synonym: "Hautsystem@de" RELATED [BTO:0000634] +synonym: "integumentum commune" EXACT LATIN [FMA:74657, FMA:TA] +synonym: "skin" RELATED [] +synonym: "skin and subcutaneous tissue" EXACT [] +synonym: "skin plus hypodermis" EXACT [] +synonym: "tegument" RELATED [BTO:0000634] +synonym: "the integument" EXACT [FMA:74657] +synonym: "vertebrate integument" RELATED [] +xref: AAO:0000239 +xref: BTO:0000634 +xref: EMAPA:37504 {source="MA:th"} +xref: FMA:74657 +xref: galen:Integument +xref: http://en.wikipedia.org/wiki/Integument +xref: TAO:0000368 +xref: VSAO:0000029 +xref: ZFA:0000368 +is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision +relationship: bounding_layer_of UBERON:0000468 ! multicellular organism +relationship: has_part UBERON:0002072 ! hypodermis +relationship: has_part UBERON:0002097 ! skin of body +relationship: part_of UBERON:0002416 {source="FMA"} ! integumental system +property_value: IAO:0000232 "in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition." xsd:string +property_value: UBPROP:0000001 "Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000239", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000001 "Surface structure that is the outer protective covering of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000029", ontology="VSAO", source="PSPUB:0000170"} +property_value: UBPROP:0000001 "The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000368", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000007 "integumental" xsd:string +property_value: UBPROP:0000007 "integumentary" xsd:string + +[Term] +id: UBERON:0002200 +name: vasculature of head +namespace: uberon +def: "Vasculature that is part of a head [Automatically generated definition]." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "adult head vascular network" EXACT [OBOL:automatic] +synonym: "adult head vasculature" EXACT [OBOL:automatic] +synonym: "cranial vasculature" EXACT [] +synonym: "head vascular network" EXACT [OBOL:automatic] +synonym: "head vasculature" RELATED [] +synonym: "vascular network of adult head" EXACT [OBOL:automatic] +synonym: "vascular network of head" EXACT [OBOL:automatic] +synonym: "vasculature of adult head" EXACT [OBOL:automatic] +xref: EFO:0003656 +xref: FMA:74710 +xref: TAO:0001267 +xref: XAO:0004152 +xref: ZFA:0001267 +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0000033 ! head + +[Term] +id: UBERON:0002201 +name: vasculature of trunk +namespace: uberon +def: "A vasculature that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +subset: vertebrate_core +synonym: "torso vascular network" EXACT [OBOL:automatic] +synonym: "torso vasculature" EXACT [OBOL:automatic] +synonym: "trunk vascular network" EXACT [OBOL:automatic] +synonym: "trunk vasculature" EXACT [] +synonym: "vascular network of torso" EXACT [OBOL:automatic] +synonym: "vascular network of trunk" EXACT [OBOL:automatic] +synonym: "vasculature of torso" EXACT [OBOL:automatic] +xref: FMA:74712 +xref: TAO:0005024 +xref: ZFA:0005024 +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk + +[Term] +id: UBERON:0002204 +name: musculoskeletal system +namespace: uberon +def: "Anatomical system that consists of the muscular and skeletal systems." [https://github.com/obophenotype/uberon/issues/77, VSAO:0000031, VSAO:curator] +subset: uberon_slim +synonym: "musculo-skeletal system" EXACT [] +xref: AAO:0010546 +xref: CALOHA:TS-1311 +xref: EMAPA:32714 +xref: EV:0100139 +xref: FMA:7482 +xref: GAID:98 +xref: http://linkedlifedata.com/resource/umls/id/C0026860 +xref: http://www.snomedbrowser.com/Codes/Details/278858007 +xref: MA:0002418 +xref: MESH:D009141 +xref: Musculoskeletal:system +xref: NCIT:C12754 +xref: OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g +xref: UMLS:C0026860 {source="ncithesaurus:Musculoskeletal_System"} +xref: VHOG:0001275 +xref: VSAO:0000031 +xref: XAO:0000168 +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0002330 ! exocrine system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm +relationship: has_part UBERON:0000383 ! musculature of body +relationship: has_part UBERON:0001434 ! skeletal system +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)"} +property_value: UBPROP:0000007 "musculoskeletal" xsd:string + +[Term] +id: UBERON:0002217 +name: synovial joint +namespace: uberon +def: "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]" [FMA:7501, http://en.wikipedia.org/wiki/Synovial_joint] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "articulatio synoviale" EXACT [] +synonym: "diarthrodial joints" RELATED PLURAL [ZFA:0005153] +synonym: "diarthroses" EXACT PLURAL [ZFA:0005153] +synonym: "diarthrosis" EXACT [] +synonym: "diarthrosis joint" EXACT [] +xref: AEO:0000183 +xref: CALOHA:TS-2138 +xref: EHDAA2:0003183 +xref: FMA:7501 +xref: galen:SynovialJoint +xref: http://www.snomedbrowser.com/Codes/Details/113234001 +xref: MA:0000322 +xref: NCIT:C32461 +xref: OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA +xref: Synovial:joint +xref: TAO:0005153 +xref: ZFA:0005153 +is_a: UBERON:0000982 ! skeletal joint +intersection_of: UBERON:0000982 ! skeletal joint +intersection_of: surrounded_by UBERON:0001484 ! articular capsule +disjoint_from: UBERON:0011134 ! nonsynovial joint +relationship: surrounded_by UBERON:0001484 ! articular capsule +property_value: UBPROP:0000001 "Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005153", ontology="TAO", source="ZFIN:Curator"} + +[Term] +id: UBERON:0002224 +name: thoracic cavity +namespace: uberon +def: "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax." [http://en.wikipedia.org/wiki/Thoracic_cavity, UBERON:cjm] +subset: pheno_slim +subset: uberon_slim +synonym: "cavitas thoracis" EXACT LATIN [http://en.wikipedia.org/wiki/Thoracic_cavity] +synonym: "cavity of chest" EXACT [] +synonym: "cavity of thorax" EXACT [] +synonym: "chest cavity" EXACT [] +synonym: "pectoral cavity" EXACT [] +synonym: "space of thoracic compartment" EXACT [FMA:7565] +synonym: "thoracic lumen" EXACT [] +xref: EMAPA:36497 +xref: FMA:7565 +xref: GAID:93 +xref: http://linkedlifedata.com/resource/umls/id/C0230139 +xref: http://www.snomedbrowser.com/Codes/Details/243949006 +xref: MA:0000032 +xref: MESH:A01.911.800 +xref: NCIT:C12905 +xref: OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg +xref: OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA +xref: Thoracic:cavity +xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen +relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0002323 ! coelemic cavity lumen +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg +property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string + +[Term] +id: UBERON:0002240 +name: spinal cord +namespace: uberon +def: "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)" [NIFSTD:birnlex_1709] +subset: cumbo +subset: efo_slim +subset: major_organ +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cerebro-cerebellar fissure" RELATED [NeuroNames:22] +synonym: "cerebrocerebellar fissure" RELATED [NeuroNames:22] +synonym: "fissura cerebro-cerebellaris" RELATED LATIN [NeuroNames:22] +synonym: "fissura cerebrocerebellaris" RELATED LATIN [NeuroNames:22] +synonym: "medulla spinalis" RELATED [BTO:0001279] +synonym: "medulla spinalis" RELATED LATIN [http://en.wikipedia.org/wiki/Spinal_cord] +synonym: "SpC" RELATED ABBREVIATION [] +synonym: "spinal cord structure" RELATED [ZFA:0000075] +synonym: "spinal medulla" RELATED [BTO:0001279] +xref: AAO:0010151 +xref: BAMS:SP +xref: BAMS:Spinal +xref: birnlex:1709 +xref: BM:SpC +xref: BTO:0001279 +xref: CALOHA:TS-0953 +xref: DHBA:12890 +xref: DMBA:17651 +xref: EFO:0000110 +xref: EHDAA2:0001255 +xref: EHDAA:2863 +xref: EMAPA:17577 +xref: EV:0100316 +xref: FMA:7647 +xref: GAID:695 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 {source="NIFSTD:birnlex_1709"} +xref: http://linkedlifedata.com/resource/umls/id/C0037925 +xref: http://www.snomedbrowser.com/Codes/Details/180959008 +xref: MA:0000216 +xref: MAT:0000183 +xref: MESH:D013116 +xref: MIAA:0000183 +xref: NCIT:C12464 +xref: OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA +xref: Spinal:cord +xref: TAO:0000075 +xref: UMLS:C0037925 {source="NIFSTD:birnlex_1709"} +xref: UMLS:C0037925 {source="ncithesaurus:Spinal_Cord"} +xref: VHOG:0000601 +xref: XAO:0000020 +xref: ZFA:0000075 +is_a: UBERON:0000489 ! cavitated compound organ +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005174 ! dorsal region element +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: develops_from UBERON:0003076 ! posterior neural tube +relationship: develops_from UBERON:0006241 ! future spinal cord +relationship: has_developmental_contribution_from UBERON:0003853 {evidence="definitional"} ! spinal cord neural crest +relationship: immediate_transformation_of UBERON:0006241 {evidence="definitional"} ! future spinal cord +relationship: part_of UBERON:0001017 ! central nervous system +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg +property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string +property_value: UBPROP:0000001 "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010151", ontology="AAO", source="AAO:BJB"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000601", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165"} + +[Term] +id: UBERON:0002298 +name: brainstem +namespace: uberon +def: "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]." [http://en.wikipedia.org/wiki/Brainstem, ISBN10:0471888893, MP:0005277, ZFA:0001707] +comment: 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "accessory medullary lamina of pallidum" RELATED [NeuroNames:236] +synonym: "brain stem" EXACT [ABA:BS] +synonym: "lamella pallidi incompleta" RELATED LATIN [NeuroNames:236] +synonym: "lamina medullaris accessoria" RELATED LATIN [NeuroNames:236] +synonym: "lamina medullaris incompleta pallidi" RELATED LATIN [NeuroNames:236] +synonym: "lamina pallidi incompleta" RELATED LATIN [NeuroNames:236] +synonym: "truncus encephali" EXACT LATIN [http://en.wikipedia.org/wiki/Brainstem] +synonym: "truncus encephalicus" RELATED LATIN [BTO:0000146] +xref: BAMS:BS +xref: birnlex:1565 +xref: BTO:0000146 +xref: CALOHA:TS-0093 +xref: EFO:0001962 +xref: EMAPA:32678 +xref: EV:0100241 +xref: FMA:79876 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 {source="NIFSTD:birnlex_1565"} +xref: http://en.wikipedia.org/wiki/Brainstem +xref: http://linkedlifedata.com/resource/umls/id/C0006121 +xref: http://www.snomedbrowser.com/Codes/Details/180925009 +xref: MA:0000169 +xref: MBA:343 +xref: MESH:D001933 +xref: NCIT:C12441 +xref: TAO:0002156 +xref: UMLS:C0006121 {source="NIFSTD:birnlex_1565"} +xref: UMLS:C0006121 {source="ncithesaurus:Brain_Stem"} +xref: VHOG:0001457 +xref: ZFA:0001707 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: continuous_with UBERON:0002240 ! spinal cord +relationship: contributes_to_morphology_of UBERON:0000955 ! brain +relationship: has_part UBERON:0001896 ! medulla oblongata +relationship: has_part UBERON:0001943 ! midbrain tegmentum +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png +property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002156", ontology="TAO", source="ISBN:3764351209"} +property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." xsd:string {source="ZFA:0001707"} +property_value: UBPROP:0000001 "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" xsd:string {source="MP:0005277"} + +[Term] +id: UBERON:0002315 +name: gray matter of spinal cord +namespace: uberon +def: "The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue." [MP:0008503] +subset: pheno_slim +synonym: "gray matter of spinal cord" EXACT [OBOL:automatic] +synonym: "gray substance of spinal cord" EXACT [FMA:256580] +synonym: "grey matter of spinal cord" EXACT [] +synonym: "grey substance of spinal cord" EXACT [] +synonym: "spinal cord gray matter" EXACT [OBOL:automatic] +synonym: "spinal cord grey matter" EXACT [] +synonym: "spinal cord grey substance" EXACT [OBOL:automatic] +synonym: "substantia grisea medullae spinalis" EXACT LATIN [FMA:256580, FMA:TA] +xref: BAMS:Scgrey +xref: DHBA:146035048 +xref: EMAPA:35792 +xref: FMA:256580 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2619 +xref: http://linkedlifedata.com/resource/umls/id/C0475853 +xref: http://www.snomedbrowser.com/Codes/Details/279441003 +xref: MA:0000002 +xref: NCIT:C32696 +xref: nlx_anat:100204 +xref: UMLS:C0475853 {source="ncithesaurus:Gray_Matter_of_the_Spinal_Cord"} +is_a: UBERON:0002020 ! gray matter +intersection_of: UBERON:0002020 ! gray matter +intersection_of: part_of UBERON:0002240 ! spinal cord +relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord +relationship: part_of UBERON:0002240 ! spinal cord + +[Term] +id: UBERON:0002323 +name: coelemic cavity lumen +namespace: uberon +alt_id: UBERON:0000169 +def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] +subset: uberon_slim +subset: vertebrate_core +synonym: "body cavity" BROAD [BTO:0001707] +synonym: "celom" RELATED [BTO:0001707] +synonym: "coelom" RELATED [] +synonym: "coelome" RELATED [BTO:0001707] +synonym: "coelomic cavity" EXACT [EHDAA2:0000267] +synonym: "coelomic cavity lumen" EXACT [EHDAA2:0000267] +synonym: "hemocoel" RELATED [FBbt:00005060] +synonym: "main body cavity" EXACT [] +synonym: "space of body compartment" EXACT [FMA:85006] +synonym: "ventral body cavity" NARROW [NCBITaxon:7742] +xref: AEO:0000186 +xref: BTO:0001707 +xref: EHDAA2:0000267 +xref: FBbt:00005060 +xref: FMA:85006 +xref: galen:BodyCavity +xref: http://linkedlifedata.com/resource/umls/id/C0333343 +xref: http://www.snomedbrowser.com/Codes/Details/361348008 +xref: NCIT:C25444 +xref: RETIRED_EHDAA2:0003186 +xref: TAO:0001438 +xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} +xref: ZFA:0001438 +is_a: UBERON:0002553 ! anatomical cavity +relationship: develops_from UBERON:0003886 ! future coelemic cavity lumen +relationship: luminal_space_of UBERON:0011997 ! coelom +relationship: part_of UBERON:0011997 ! coelom +relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen +property_value: IAO:0000116 "check the FMA placement here; ncit placement of body cavity here probably not correct" xsd:string +property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} +property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} +property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string + +[Term] +id: UBERON:0002328 +name: notochord +namespace: uberon +def: "A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube." [http://en.wikipedia.org/wiki/Notochord, http://tolweb.org/Chordata/2499, https://github.com/obophenotype/uberon/issues/25, https://github.com/obophenotype/uberon/issues/271, ISBN:0815318960] +comment: The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "embryonic notocord" EXACT [] +synonym: "notochorda" RELATED LATIN [http://en.wikipedia.org/wiki/Notochord] +synonym: "notocord" EXACT [ZFA:0000135] +xref: AAO:0000327 +xref: BTO:0001768 +xref: CALOHA:TS-0690 +xref: EHDAA2:0001277 +xref: EHDAA:1241 +xref: EHDAA:6021 +xref: EMAPA:16191 +xref: EV:0100002 +xref: FMA:85521 +xref: GAID:1311 +xref: http://en.wikipedia.org/wiki/Notochord +xref: http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg +xref: http://linkedlifedata.com/resource/umls/id/C0028439 +xref: http://www.snomedbrowser.com/Codes/Details/308820002 +xref: MAT:0000281 +xref: MESH:A16.254.610 +xref: NCIT:C12463 +xref: TAO:0000135 +xref: UMLS:C0028439 {source="ncithesaurus:Notochord"} +xref: VHOG:0000199 +xref: VSAO:0000032 +xref: XAO:0000055 +xref: ZFA:0000135 +is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm +relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate +relationship: dorsal_to UBERON:0001555 ! digestive tract +relationship: existence_starts_during UBERON:0000068 ! embryo stage +relationship: part_of UBERON:0011137 ! axial skeletal system +relationship: ventral_to UBERON:0001049 ! neural tube +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul +property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} +property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} +property_value: UBPROP:0000007 "notochordal" xsd:string +property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string + +[Term] +id: UBERON:0002329 +name: somite +namespace: uberon +def: "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm." [http://dx.doi.org/10.1111/j.1439-0426.2012.01987.x, http://en.wikipedia.org/wiki/Somite] +comment: When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "epimere" RELATED [ISBN10:0073040584] +synonym: "epimere mesoderm" RELATED [] +synonym: "epithelial somite" RELATED [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "mesodermal cluster" BROAD [GO:0001756] +synonym: "somites" RELATED PLURAL [] +synonym: "somitic mesoderm" RELATED [] +synonym: "somitus" RELATED LATIN [http://en.wikipedia.org/wiki/Somite] +xref: AAO:0010569 +xref: AEO:0001015 +xref: BTO:0001558 +xref: EHDAA2:0003436 +xref: EHDAA:366 +xref: EHDAA:699 +xref: EMAPA:31169 +xref: FMA:85522 +xref: GAID:1306 +xref: http://en.wikipedia.org/wiki/Somite +xref: http://linkedlifedata.com/resource/umls/id/C0376449 +xref: MAT:0000068 +xref: MESH:A16.254.425.660.750 +xref: MIAA:0000068 +xref: NCIT:C34302 +xref: TAO:0000155 +xref: UMLS:C0376449 {source="ncithesaurus:Somite"} +xref: VHOG:0000191 +xref: XAO:0000058 +xref: ZFA:0000155 +is_a: UBERON:0005423 ! developing anatomical structure +is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle +relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png +property_value: IAO:0000116 "currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string +property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} +property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} +property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} +property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)"} +property_value: UBPROP:0000007 "somitic" xsd:string + +[Term] +id: UBERON:0002330 +name: exocrine system +namespace: uberon +def: "Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]." [http://en.wikipedia.org/wiki/Exocrine_gland] +subset: pheno_slim +subset: uberon_slim +synonym: "exocrine glandular system" EXACT [EHDAA2:0002225] +xref: CALOHA:TS-2057 +xref: EHDAA2:0002225 +xref: EMAPA:35329 +xref: Exocrine:gland +xref: FMA:85539 +xref: http://linkedlifedata.com/resource/umls/id/C1516995 +xref: MA:0002411 +xref: NCIT:C12957 +xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} +xref: WikipediaCategory:Exocrine_system +is_a: UBERON:0000467 ! anatomical system +disjoint_from: UBERON:0002390 ! hematopoietic system +disjoint_from: UBERON:0002416 ! integumental system +relationship: composed_primarily_of UBERON:0002365 ! exocrine gland +relationship: existence_ends_during UBERON:0000066 ! fully formed stage + +[Term] +id: UBERON:0002333 +name: pulmonary trunk +namespace: uberon +def: "An arterial trunk which is continuous with the heart and branches into the pulmonary arteries." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "main pulmonary artery" RELATED [http://en.wikipedia.org/wiki/Pulmonary_artery] +synonym: "pulmonary artery (trunk)" EXACT [] +synonym: "trunk of pulmonary arterial tree" EXACT [] +xref: EHDAA2:0001576 +xref: EHDAA:9831 +xref: EMAPA:17015 +xref: FMA:8612 +xref: galen:PulmonaryTrunk +xref: MA:0002033 +xref: NCIT:C116918 +xref: OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA +xref: VHOG:0001134 +is_a: UBERON:0001637 {source="MA"} ! artery +relationship: continuous_with UBERON:0000948 ! heart +relationship: part_of UBERON:0008886 ! pulmonary vascular system +property_value: depicted:by Alveoli:diagram.png +property_value: UBPROP:0000001 "An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001134", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+trunk"} +property_value: UBPROP:0000003 "As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001134", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481"} + +[Term] +id: UBERON:0002342 +name: neural crest +namespace: uberon +def: "A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]." [MP:0009846] +comment: Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "crista neuralis" RELATED LATIN [http://en.wikipedia.org/wiki/Neural_crest] +synonym: "NC" EXACT ABBREVIATION [XAO:0000048] +synonym: "neural crest material" RELATED [VHOG:0000057] +xref: AAO:0010578 +xref: BTO:0001764 +xref: CALOHA:TS-0676 +xref: EHDAA2:0004419 +xref: EMAPA:32737 +xref: FMA:86666 +xref: GAID:1310 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1366 +xref: http://linkedlifedata.com/resource/umls/id/C0027789 +xref: http://www.snomedbrowser.com/Codes/Details/361462002 +xref: MAT:0000066 +xref: MESH:A16.254.600 +xref: MIAA:0000066 +xref: NCIT:C34222 +xref: Neural:crest +xref: TAO:0000045 +xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} +xref: VHOG:0000057 +xref: XAO:0000048 +xref: ZFA:0000045 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0010316 ! germ layer / neural crest +relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate +relationship: develops_from UBERON:0005062 {source="http://www.ncbi.nlm.nih.gov/pubmed/11523831"} ! neural fold +relationship: existence_starts_during UBERON:0000110 {source="http://www.ncbi.nlm.nih.gov/pubmed/11523831"} ! neurula stage +relationship: part_of UBERON:0002346 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="XAO"} ! neurectoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png +property_value: depicted:by Neural:Crest.png +property_value: IAO:0000116 "consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string +property_value: RO:0002174 NCBITaxon:117565 {source="http://www.ncbi.nlm.nih.gov/pubmed/17377535", source="ISBN10:0073040584"} +property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="http://www.ncbi.nlm.nih.gov/pubmed/11523831"} +property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)"} + +[Term] +id: UBERON:0002346 +name: neurectoderm +namespace: uberon +def: "Embryonic ectoderm that gives rise to nervous tissue." [http://en.wikipedia.org/wiki/Neuroectoderm] +subset: uberon_slim +subset: vertebrate_core +synonym: "epithelium tubi neuralis; neuroectoderma" RELATED LATIN [http://en.wikipedia.org/wiki/Neuroectoderm] +synonym: "neuaral ectoderm" RELATED [] +synonym: "neural ectoderm" EXACT [] +synonym: "neuroectoderm" EXACT [] +synonym: "presumptive central nervous system" RELATED [] +synonym: "ventral neurogenic region" RELATED [VHOG:0000150] +xref: AAO:0011074 +xref: BILA:0000039 +xref: CALOHA:TS-1212 +xref: EHDAA2:0001248 +xref: EHDAA:1498 +xref: EHDAA:255 +xref: EMAPA:16073 +xref: EV:0100004 +xref: FBbt:00001061 +xref: FMA:87657 +xref: http://en.wikipedia.org/wiki/Neuroectoderm +xref: http://linkedlifedata.com/resource/umls/id/C1518271 +xref: MAT:0000176 +xref: MIAA:0000176 +xref: NCIT:C34228 +xref: TAO:0001120 +xref: UMLS:C1518271 {source="ncithesaurus:Neuroectoderm"} +xref: VHOG:0000150 +xref: XAO:0000042 +xref: ZFA:0001120 +is_a: UBERON:0000923 ! germ layer +is_a: UBERON:0004121 ! ectoderm-derived structure +property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)"} +property_value: UBPROP:0000007 "neurectodermal" xsd:string +property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string + +[Term] +id: UBERON:0002365 +name: exocrine gland +namespace: uberon +def: "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas" [http://en.wikipedia.org/wiki/Exocrine_gland] +subset: organ_slim +subset: pheno_slim +subset: uberon_slim +synonym: "ducted gland" EXACT [AEO:0000097] +synonym: "glandula exocrina" EXACT LATIN [http://en.wikipedia.org/wiki/Exocrine_gland] +xref: AEO:0000097 +xref: BTO:0000765 +xref: CALOHA:TS-2012 +xref: EHDAA2:0003097 +xref: EMAPA:35327 +xref: Exocrine:gland +xref: FMA:9596 +xref: GAID:34 +xref: http://linkedlifedata.com/resource/umls/id/C0015282 +xref: http://www.snomedbrowser.com/Codes/Details/115976003 +xref: MA:0002564 +xref: MESH:D005088 +xref: NCIT:C12712 +xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} +is_a: UBERON:0002530 ! gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0002330 ! exocrine system +relationship: has_part UBERON:0000058 ! duct +relationship: part_of UBERON:0002330 ! exocrine system +property_value: IAO:0000116 "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string + +[Term] +id: UBERON:0002384 +name: connective tissue +namespace: uberon +def: "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, https://github.com/obophenotype/uberon/issues/23, PSPUB:0000170, VSAO:0000017] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Bindegewebe" RELATED [BTO:0000421] +synonym: "portion of connective tissue" EXACT [FMA:9640] +synonym: "textus connectivus" EXACT [] +xref: AAO:0000098 +xref: BTO:0000421 +xref: CALOHA:TS-2009 +xref: EFO:0000952 +xref: EMAPA:35251 +xref: FMA:9640 +xref: GAID:100 +xref: galen:ConnectiveTissue +xref: http://linkedlifedata.com/resource/umls/id/C0009780 +xref: http://www.snomedbrowser.com/Codes/Details/361919005 +xref: MA:0000011 +xref: MAT:0000301 +xref: MESH:D003238 +xref: MIAA:0000301 +xref: NCIT:C12374 +xref: OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA +xref: TAO:0001641 +xref: UMLS:C0009780 {source="ncithesaurus:Connective_Tissue"} +xref: VSAO:0000017 +xref: XAO:0001017 +xref: ZFA:0001632 +is_a: UBERON:0000479 ! tissue +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul +property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} +property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0002385 +name: muscle tissue +namespace: uberon +def: "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." [GO:0060537, http://en.wikipedia.org/wiki/Muscle_tissue, https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764] +comment: Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. +subset: uberon_slim +synonym: "muscular tissue" EXACT SENSU [] +synonym: "portion of muscle tissue" EXACT [FMA:9641] +synonym: "textus muscularis" EXACT [] +xref: AAO:0000306 +xref: AEO:0000122 +xref: CALOHA:TS-0642 +xref: EHDAA2:0003122 +xref: EMAPA:32715 +xref: FMA:9641 +xref: galen:MuscleTissue +xref: http://linkedlifedata.com/resource/umls/id/C2328219 +xref: http://www.snomedbrowser.com/Codes/Details/91727004 +xref: MA:0002437 +xref: MESH:D009132 +xref: Muscle:tissue +xref: NCIT:C12435 +xref: UMLS:C2328219 {source="ncithesaurus:Muscle_Tissue"} +is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +disjoint_from: UBERON:0003714 ! neural tissue +relationship: part_of UBERON:0001015 ! musculature +property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} + +[Term] +id: UBERON:0002390 +name: hematopoietic system +namespace: uberon +def: "Anatomical system that is involved in the production of hematopoietic cells." [http://en.wikipedia.org/wiki/Haematopoiesis] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "Blutbildungssystem" RELATED [BTO:0000570] +synonym: "haematological system" EXACT [] +synonym: "haematopoietic system" RELATED [] +synonym: "haemopoietic system" EXACT [] +synonym: "hematological system" RELATED [] +synonym: "hematolymphoid system" RELATED [] +synonym: "hemopoietic system" RELATED [] +synonym: "organa haemopoietica" EXACT [] +xref: AAO:0011002 +xref: BTO:0000570 +xref: CALOHA:TS-0449 +xref: EFO:0000798 +xref: EMAPA:35402 +xref: EV:0100045 +xref: FMA:9667 +xref: GAID:1008 +xref: http://en.wikipedia.org/wiki/Haematopoiesis +xref: http://linkedlifedata.com/resource/umls/id/C0018957 +xref: http://www.snomedbrowser.com/Codes/Details/362587009 +xref: MA:0002434 +xref: MAT:0000022 +xref: MESH:D006413 +xref: MIAA:0000022 +xref: NCIT:C12909 +xref: TAO:0005023 +xref: UMLS:C0018957 {source="ncithesaurus:Hematopoietic_System"} +xref: VHOG:0001624 +xref: XAO:0000122 +xref: ZFA:0005023 +is_a: UBERON:0000467 ! anatomical system +is_a: UBERON:0004120 ! mesoderm-derived structure +disjoint_from: UBERON:0002416 ! integumental system +relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island +relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system +property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)"} +property_value: UBPROP:0000007 "hematopoietic" xsd:string +property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} + +[Term] +id: UBERON:0002416 +name: integumental system +namespace: uberon +alt_id: UBERON:0007029 +def: "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle." [CARO:0002001, http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/29] +subset: efo_slim +subset: grouping_class +subset: pheno_slim +synonym: "body surface" RELATED [] +synonym: "dermal system" RELATED [MIAA:0000033] +synonym: "external covering of organism" RELATED [] +synonym: "integumentary system" EXACT [FMA:72979] +synonym: "integumentum commune" RELATED LATIN [http://en.wikipedia.org/wiki/Integumentary_system] +synonym: "organism surface" RELATED [EHDAA2:0003154] +synonym: "surface" RELATED [BILA:0000118] +xref: AEO:0000154 +xref: BILA:0000118 +xref: CALOHA:TS-1299 +xref: CARO:0002001 +xref: EFO:0000807 +xref: EHDAA2:0000836 +xref: EHDAA2_RETIRED:0003154 +xref: EHDAA:6520 +xref: EMAPA:17524 +xref: EV:0100151 +xref: FBbt:00004969 +xref: FMA:72979 +xref: galen:Surface +xref: HAO:0000421 +xref: http://linkedlifedata.com/resource/umls/id/C0037267 +xref: http://www.snomedbrowser.com/Codes/Details/361692004 +xref: Integumentary:system +xref: MA:0000014 +xref: MAT:0000033 +xref: MESH:D034582 +xref: MIAA:0000033 +xref: NCIT:C12907 +xref: TADS:0000108 +xref: UMLS:C0037267 {source="ncithesaurus:Integumentary_System"} +xref: VHOG:0000403 +xref: XAO:0000176 +is_a: UBERON:0000467 ! anatomical system +relationship: bounding_layer_of UBERON:0000468 ! multicellular organism +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: has_part UBERON:0007376 ! outer epithelium +relationship: surrounded_by UBERON:0013514 ! space surrounding organism +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/tfhayamizu +property_value: UBPROP:0000003 "(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000403", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)"} + +[Term] +id: UBERON:0002419 +name: skin gland +namespace: uberon +def: "A gland that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] +subset: organ_slim +synonym: "glandulae cutis" EXACT LATIN [FMA:71878, FMA:TA] +synonym: "set of skin glands" RELATED [FMA:71878] +synonym: "skin glands" RELATED PLURAL [] +synonym: "skin glands set" RELATED PLURAL [] +xref: EMAPA:35774 +xref: FMA:71878 +xref: http://www.snomedbrowser.com/Codes/Details/110485007 +xref: MA:0000146 +is_a: UBERON:0003297 ! gland of integumental system +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0006003 ! integumentary adnexa +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0002097 ! skin of body +relationship: part_of UBERON:0002097 ! skin of body +property_value: IAO:0000116 "check FMA, use plural for now as general class not there" xsd:string + +[Term] +id: UBERON:0002424 +name: oral epithelium +namespace: uberon +def: "An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues" [https://orcid.org/0000-0002-6601-2165] +subset: vertebrate_core +synonym: "epithelium of mucosa of mouth" EXACT [FMA:265152] +synonym: "epithelium of oral mucosa" EXACT [FMA:265152] +xref: AAO:0010357 +xref: BTO:0001775 +xref: CALOHA:TS-0715 +xref: EHDAA2:0001325 +xref: EHDAA:2187 +xref: EMAPA:16839 +xref: EMAPA:26942 +xref: FMA:265152 +xref: http://linkedlifedata.com/resource/umls/id/C1709332 +xref: MA:0000344 +xref: NCIT:C49595 +xref: TAO:0000816 +xref: UMLS:C1709332 {source="ncithesaurus:Oral_Cavity_Epithelium"} +xref: VHOG:0000187 +xref: XAO:0003201 +xref: ZFA:0000816 +is_a: UBERON:0003350 ! epithelium of mucosa +is_a: UBERON:0003929 ! digestive tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0003729 ! mouth mucosa +relationship: adjacent_to UBERON:0000167 {source="AAO-modified"} ! oral cavity +relationship: part_of UBERON:0003729 ! mouth mucosa +property_value: IAO:0000116 "consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)" xsd:string +property_value: UBPROP:0000001 "The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]." xsd:string {source="ZFA:0000816"} +property_value: UBPROP:0000011 "the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme" xsd:string {source="http://www.ncbi.nlm.nih.gov/pubmed/16488870"} + +[Term] +id: UBERON:0002458 +name: spinal artery +namespace: uberon +def: "Arteries that supply the spinal cord." [http://en.wikipedia.org/wiki/Spinal_artery, https://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +subset: vertebrate_core +synonym: "spinal arteries" EXACT PLURAL [ZFA:0000682] +xref: EHDAA2:0001890 +xref: EHDAA:4355 +xref: EMAPA:18241 +xref: http://linkedlifedata.com/resource/umls/id/C0447043 +xref: http://www.snomedbrowser.com/Codes/Details/244228006 +xref: MA:0002043 +xref: NCIT:C33587 +xref: Spinal:artery +xref: TAO:0000682 +xref: UMLS:C0447043 {source="ncithesaurus:Spinal_Artery"} +xref: ZFA:0000682 +is_a: UBERON:0004573 ! systemic artery +intersection_of: UBERON:0001637 ! artery +intersection_of: supplies UBERON:0002240 ! spinal cord +relationship: supplies UBERON:0002240 ! spinal cord + +[Term] +id: UBERON:0002521 +name: elastic tissue +namespace: uberon +def: "Connective tissue composed of elastic fibers." [http://orcid.org/0000-0002-6601-2165] +subset: uberon_slim +synonym: "elastic connective tissue" EXACT [] +synonym: "elastic fiber" NARROW [] +synonym: "textus connectivus elasticus" EXACT LATIN [] +xref: Elastic:fiber +xref: FMA:20113 +xref: GAID:926 +xref: http://www.snomedbrowser.com/Codes/Details/27197004 +xref: MA:0002853 +xref: MESH:D004547 +xref: NCIT:C32495 +is_a: UBERON:0002384 ! connective tissue +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png + +[Term] +id: UBERON:0002522 +name: tunica media +namespace: uberon +def: "The middle layer of an artery or vein. [WP,unvetted]." [http://en.wikipedia.org/wiki/Tunica_media] +comment: May be composed of smooth muscle and elastic tissue +subset: uberon_slim +synonym: "tunica media vasorum" RELATED [BTO:0002011] +synonym: "tunica media vasorum" RELATED LATIN [http://en.wikipedia.org/wiki/Tunica_media] +xref: BTO:0002011 +xref: EMAPA:36298 +xref: FMA:55590 +xref: GAID:170 +xref: http://linkedlifedata.com/resource/umls/id/C0162867 +xref: http://www.snomedbrowser.com/Codes/Details/61695000 +xref: MA:0002855 +xref: MESH:D017540 +xref: NCIT:C33821 +xref: Tunica:media +xref: UMLS:C0162867 {source="ncithesaurus:Tunica_Media"} +is_a: UBERON:0004797 {source="MA"} ! blood vessel layer +relationship: has_part UBERON:0002521 {source="cjm"} ! elastic tissue +relationship: has_part UBERON:0004237 {source="cjm"} ! blood vessel smooth muscle +relationship: surrounded_by UBERON:0005734 ! tunica adventitia of blood vessel +property_value: depicted:by Illu:artery.jpg + +[Term] +id: UBERON:0002523 +name: tunica intima +namespace: uberon +def: "The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]." [http://en.wikipedia.org/wiki/Tunica_intima, ISBN10:0073040584, NCIT:C33820] +subset: uberon_slim +synonym: "Bichat's tunic" RELATED [BTO:0002012] +synonym: "intima" RELATED [BTO:0002012] +synonym: "tunica intima vasorum" RELATED [BTO:0002012] +xref: BTO:0002012 +xref: EMAPA:36297 +xref: FMA:55589 +xref: GAID:523 +xref: http://linkedlifedata.com/resource/umls/id/C0162864 +xref: http://www.snomedbrowser.com/Codes/Details/8361002 +xref: http://www.snomedbrowser.com/Codes/Details/87483006 +xref: MA:0002861 +xref: MESH:D017539 +xref: NCIT:C33820 +xref: Tunica:intima +xref: UMLS:C0162864 {source="ncithesaurus:Tunica_Intima"} +is_a: UBERON:0004923 {source="FMA"} ! organ component layer +relationship: adjacent_to UBERON:0010161 {source="ISBN10:0073040584"} ! lumen of blood vessel +relationship: has_part UBERON:0001986 ! endothelium +relationship: surrounded_by UBERON:0002522 {notes="check for exceptions, e.g. capillaries"} ! tunica media +property_value: depicted:by Illu:artery.jpg +property_value: IAO:0000116 "the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure" xsd:string +property_value: IAO:0000116 "the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts" xsd:string +property_value: UBPROP:0000001 "The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]" xsd:string {ontology="Wikipedia", source="Tunica:intima"} + +[Term] +id: UBERON:0002530 +name: gland +namespace: uberon +alt_id: UBERON:MIAA_0000021 +def: "an organ that functions as a secretory or excretory organ" [MGI:csmith, MP:0002163] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "Druese" RELATED [BTO:0000522] +synonym: "glandula" RELATED [BTO:0000522] +synonym: "glandula" RELATED LATIN [http://en.wikipedia.org/wiki/Gland] +synonym: "glandular organ" EXACT [http://orcid.org/0000-0002-6601-2165] +xref: AAO:0000212 +xref: AEO:0000096 +xref: BTO:0000522 +xref: EFO:0000797 +xref: EHDAA2:0003096 +xref: EHDAA:2161 +xref: EHDAA:4475 +xref: EHDAA:6522 +xref: EMAPA:18425 +xref: FBbt:00100317 +xref: FMA:7146 +xref: FMA:86294 +xref: galen:Gland +xref: HAO:0000375 +xref: http://en.wikipedia.org/wiki/Gland +xref: http://linkedlifedata.com/resource/umls/id/C1285092 +xref: http://www.snomedbrowser.com/Codes/Details/134358001 +xref: MA:0003038 +xref: MAT:0000021 +xref: MIAA:0000021 +xref: NCIT:C13319 +xref: OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA +xref: UMLS:C1285092 {source="ncithesaurus:Gland"} +xref: WikipediaCategory:Glands +is_a: UBERON:0000062 ! organ +relationship: produces UBERON:0000463 ! organism substance +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png +property_value: UBPROP:0000007 "glandular" xsd:string + +[Term] +id: UBERON:0002532 +name: epiblast (generic) +namespace: uberon +def: "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]" [http://en.wikipedia.org/wiki/Epiblast, ZFIN:curator] +subset: early_development +subset: grouping_class +subset: uberon_slim +subset: vertebrate_core +synonym: "blastocyst" RELATED [] +synonym: "ectoblast" RELATED [MP:0003886] +synonym: "epiblast" EXACT [VHOG:0000243] +synonym: "epiblastus" RELATED LATIN [http://en.wikipedia.org/wiki/Epiblast] +synonym: "primitive ectoderm" RELATED [VHOG:0000243] +xref: BTO:0004593 +xref: FMA:296704 +xref: http://en.wikipedia.org/wiki/Epiblast +xref: MAT:0000067 +xref: MIAA:0000067 +xref: VHOG:0000243 +is_a: UBERON:0002050 ! embryonic structure +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string +property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)"} + +[Term] +id: UBERON:0002539 +name: pharyngeal arch +namespace: uberon +def: "One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches." [http://orcid.org/0000-0002-6601-2165, http://www.ncbi.nlm.nih.gov/pubmed/16313389, ZFA:yb] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "arcus pharyngei" RELATED LATIN [http://en.wikipedia.org/wiki/Pharyngeal_arch] +synonym: "branchial arch" NARROW [BTO:0001785, MP:0002884] +synonym: "pharyngeal arches" EXACT PLURAL [] +synonym: "visceral arch" RELATED [] +xref: AAO:0010359 +xref: BTO:0001785 +xref: EFO:0000959 +xref: EHDAA:571 +xref: EMAPA:16117 +xref: FMA:293015 +xref: GAID:1292 +xref: http://linkedlifedata.com/resource/umls/id/C0080322 +xref: http://www.snomedbrowser.com/Codes/Details/308766004 +xref: MAT:0000242 +xref: MESH:A16.254.160 +xref: MIAA:0000242 +xref: NCIT:C34249 +xref: Pharyngeal:arch +xref: TAO:0001306 +xref: UMLS:C0080322 {source="ncithesaurus:Pharyngeal_Arch"} +xref: VHOG:0000155 +xref: XAO:0000096 +xref: ZFA:0001306 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: developmentally_induced_by UBERON:0007690 {source="http://www.ncbi.nlm.nih.gov/pubmed/16313389"} ! early pharyngeal endoderm +relationship: part_of UBERON:0008814 ! pharyngeal arch system +relationship: part_of UBERON:0008816 {source="http://www.ncbi.nlm.nih.gov/pubmed/16313389"} ! embryonic head +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png +property_value: UBPROP:0000001 "One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010359", ontology="AAO", source="NLM:branchial+arch"} +property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000155", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)"} +property_value: UBPROP:0000013 "Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering" xsd:string + +[Term] +id: UBERON:0002553 +name: anatomical cavity +namespace: uberon +def: "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina." [FMA:67552] +subset: upper_level +synonym: "cavity" BROAD [] +xref: birnlex:1011 +xref: EMAPA:37442 {source="MA:th"} +xref: FMA:67552 +xref: galen:Cavity +xref: MA:0002447 +xref: NCIT:C34007 +is_a: UBERON:0000464 ! anatomical space +relationship: location_of UBERON:0000463 ! organism substance + +[Term] +id: UBERON:0002616 +name: regional part of brain +namespace: uberon +def: "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia." [NIFSTD:birnlex_1167] +subset: non_informative +synonym: "anatomical structure of brain" EXACT [OBOL:automatic] +synonym: "biological structure of brain" EXACT [OBOL:automatic] +synonym: "brain anatomical structure" EXACT [OBOL:automatic] +synonym: "brain biological structure" EXACT [OBOL:automatic] +synonym: "brain part" EXACT [] +synonym: "neuraxis segment" EXACT [FMA:55676] +synonym: "neuroanatomical region" EXACT [] +synonym: "segment of brain" EXACT [NIFSTD:birnlex_1167] +xref: birnlex:1167 +xref: FMA:55676 +xref: http://linkedlifedata.com/resource/umls/id/C0445620 +xref: http://www.snomedbrowser.com/Codes/Details/384763002 +xref: NCIT:C13031 +xref: UMLS:C0445620 {source="ncithesaurus:Brain_Part"} +is_a: UBERON:0000073 ! regional part of nervous system +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0000955 ! brain +relationship: composed_primarily_of UBERON:0003714 ! neural tissue +relationship: part_of UBERON:0000955 ! brain + +[Term] +id: UBERON:0003037 +name: septum +namespace: uberon +def: "A wall, dividing a cavity or structure into smaller ones[WP]." [http://en.wikipedia.org/wiki/Septum] +comment: general anatomical term in FMA +subset: pheno_slim +synonym: "septa" EXACT PLURAL [] +xref: AAO:0011127 +xref: FMA:86461 +xref: http://en.wikipedia.org/wiki/Septum +xref: OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ +is_a: UBERON:0000061 ! anatomical structure +relationship: located_in UBERON:0002553 ! anatomical cavity +property_value: UBPROP:0000007 "septal" xsd:string + +[Term] +id: UBERON:0003052 +name: midbrain-hindbrain boundary +namespace: uberon +def: "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate." [GO:0021555] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "isthmic organizer territory" RELATED [XAO:0000016] +synonym: "isthmo-cerebellar region" RELATED [VHOG:0000649] +synonym: "isthmus" RELATED [] +synonym: "isthmus/MHB" RELATED [Geisha:syn, NCBITaxon:8782] +synonym: "MHB" EXACT [] +synonym: "mid-hindbrain boundary" EXACT [] +synonym: "mid-hindbrain junction" EXACT [] +synonym: "midbrain hindbrain boundary" EXACT [] +xref: AAO:0011064 +xref: DMBA:16810 +xref: EHDAA2:0004395 +xref: EHDAA:5789 +xref: EMAPA:32857 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2076 +xref: NCIT:C93172 +xref: TAO:0000042 +xref: VHOG:0000649 +xref: XAO:0000016 +xref: ZFA:0000042 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: develops_from UBERON:0009615 ! midbrain hindbrain boundary neural plate +relationship: immediate_transformation_of UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate +relationship: part_of UBERON:0000955 {source="ZFA"} ! brain +property_value: IAO:0000116 "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string +property_value: UBPROP:0000003 "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000649", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)"} + +[Term] +id: UBERON:0003055 +name: periderm +namespace: uberon +def: "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis." [ISBN:9780878932504] +subset: pheno_slim +subset: uberon_slim +synonym: "epidermis epithelial layer" RELATED [] +synonym: "epidermis outer layer" RELATED [] +synonym: "epitrichium" RELATED [MP:0013530] +synonym: "EVL" RELATED [ZFA:0001185] +synonym: "periderm" RELATED [] +synonym: "skin periderm" EXACT [EHDAA2:0001846] +xref: EHDAA2:0001846 +xref: EHDAA:6538 +xref: FMA:295662 +xref: http://linkedlifedata.com/resource/umls/id/C1518973 +xref: NCIT:C34247 +xref: TAO:0001185 +xref: UMLS:C1518973 {source="ncithesaurus:Periderm"} +xref: VHOG:0001680 +xref: XAO:0000029 +xref: ZFA:0001185 +is_a: UBERON:0000487 {source="EHDAA2"} ! simple squamous epithelium +is_a: UBERON:0010371 ! ecto-epithelium +relationship: develops_from UBERON:0007383 {source="ZFA"} ! enveloping layer of ectoderm +relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument +property_value: UBPROP:0000001 "The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001185", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001185", ontology="TAO"} +property_value: UBPROP:0000008 "In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]" xsd:string +property_value: UBPROP:0000011 "In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis" xsd:string +property_value: UBPROP:0000011 "Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)" xsd:string + +[Term] +id: UBERON:0003056 +name: pre-chordal neural plate +namespace: uberon +def: "The portion of neural plate anterior to the mid-hindbrain junction." [XB:curator] +synonym: "anterior neural plate" RELATED [] +xref: AAO:0011084 +xref: TAO:0007016 +xref: VHOG:0001200 +xref: XAO:0000045 +xref: ZFA:0007016 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: anterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate +relationship: part_of UBERON:0003075 ! neural plate +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001200", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003057 +name: chordal neural plate +namespace: uberon +def: "The portion of neural plate posterior to the mid-hindbrain junction." [XB:curator] +synonym: "posterior neural plate" RELATED [] +xref: TAO:0007017 +xref: VHOG:0001201 +xref: XAO:0000046 +xref: ZFA:0007017 +is_a: UBERON:0002050 ! embryonic structure +relationship: part_of UBERON:0003075 ! neural plate +relationship: posterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001201", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003059 +name: presomitic mesoderm +namespace: uberon +def: "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." [ZFIN:curator] +subset: efo_slim +subset: pheno_slim +synonym: "presumptive somite mesoderm" RELATED [] +synonym: "PSM" RELATED [] +synonym: "segmental plate" EXACT [] +synonym: "somitogenic mesoderm" RELATED [] +synonym: "somitomeric mesoderm" RELATED [GO:0002075] +synonym: "unsegmented mesenchyme" RELATED [VHOG:0000559] +synonym: "unsegmented paraxial mesoderm" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: AAO:0011086 +xref: EFO:0001982 +xref: EMAPA:16189 +xref: EMAPA:16752 +xref: TAO:0000279 +xref: VHOG:0000559 +xref: XAO:0000057 +xref: ZFA:0000279 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite +intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate +relationship: develops_from UBERON:0007282 ! presumptive segmental plate +relationship: has_potential_to_develop_into UBERON:0002329 ! somite +relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +relationship: part_of UBERON:0003077 ! paraxial mesoderm +property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)"} + +[Term] +id: UBERON:0003061 +name: blood island +namespace: uberon +def: "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." [http://en.wikipedia.org/wiki/Blood_island_of_umbilical_vesicle] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "blood islands" EXACT PLURAL [] +synonym: "caudal hematopoietic tissue" RELATED [] +synonym: "posterior blood island" RELATED [] +synonym: "posterior ICM" RELATED [] +synonym: "VBI" RELATED [] +synonym: "ventral blood island" RELATED [] +synonym: "ventral lateral plate mesoderm" BROAD [] +xref: AAO:0011006 +xref: EFO:0003489 +xref: EHDAA:207 +xref: http://en.wikipedia.org/wiki/Blood_island_of_umbilical_vesicle +xref: http://linkedlifedata.com/resource/umls/id/C1511224 +xref: NCIT:C34113 +xref: TAO:0000094 +xref: TE:E5.11.2.0.0.0.4 +xref: UMLS:C1511224 {source="ncithesaurus:Blood_Island"} +xref: VHOG:0000085 +xref: XAO:0000067 +xref: ZFA:0000094 +is_a: UBERON:0006598 ! presumptive structure +relationship: develops_from UBERON:0003081 ! lateral plate mesoderm +relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system +property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} +property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)"} +property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} + +[Term] +id: UBERON:0003063 +name: prechordal plate +namespace: uberon +alt_id: UBERON:0004881 +def: "A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue" [ISBN:0838580343, MP:0004387] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "head mesenchyme" BROAD [XAO:0000079] +synonym: "head mesoderm" BROAD [XAO:0000079] +xref: AAO:0011085 +xref: EHDAA2:0001493 +xref: EHDAA:181 +xref: FMA:295532 +xref: Prechordal:plate +xref: TAO:0000060 +xref: VHOG:0000086 +xref: XAO:0000079 +xref: ZFA:0000060 +is_a: UBERON:0002050 ! embryonic structure +relationship: develops_from UBERON:0034878 ! prechordal mesoderm +relationship: part_of UBERON:0003068 {source="ZFA"} ! axial mesoderm +relationship: transformation_of UBERON:0034878 {todo="PMID:16313393"} ! prechordal mesoderm +property_value: IAO:0000116 "TODO - check; developmental relationship to anterior hypoblast in ZFA?" xsd:string +property_value: UBPROP:0000001 "Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000060", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="http://bgee.unil.ch/"} +property_value: UBPROP:0000003 "There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)"} + +[Term] +id: UBERON:0003068 +name: axial mesoderm +namespace: uberon +def: "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." [GO:0048318, http://en.wikipedia.org/wiki/Chordamesoderm] +subset: efo_slim +subset: uberon_slim +synonym: "chordamesoderm" RELATED [http://en.wikipedia.org/wiki/Chordamesoderm] +xref: AAO:0011017 +xref: EFO:0003647 +xref: http://en.wikipedia.org/wiki/Chordamesoderm +xref: TAO:0001204 +xref: VHOG:0000107 +xref: XAO:0000205 +xref: ZFA:0001204 +is_a: UBERON:0002050 ! embryonic structure +relationship: develops_from UBERON:0000926 ! mesoderm +relationship: part_of UBERON:0000926 ! mesoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png +property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} + +[Term] +id: UBERON:0003075 +name: neural plate +namespace: uberon +def: "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]" [http://en.wikipedia.org/wiki/Neural_plate, ISBN:0815318960, OMD:neural+plate, ZFIN:curator] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "lamina neuralis" RELATED LATIN [http://en.wikipedia.org/wiki/Neural_plate] +synonym: "presumptive central nervous system" RELATED [] +xref: AAO:0011072 +xref: BTO:0001765 +xref: DHBA:10153 +xref: DMBA:15565 +xref: EHDAA:346 +xref: EHDAA:902 +xref: EMAPA:35593 +xref: FMA:293879 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1362 +xref: http://linkedlifedata.com/resource/umls/id/C0920623 +xref: NCIT:C34225 +xref: Neural:plate +xref: RETIRED_EHDAA2:0001252 +xref: TAO:0000132 +xref: UMLS:C0920623 {source="ncithesaurus:Neural_Plate"} +xref: VHOG:0000068 +xref: XAO:0000249 +xref: ZFA:0000132 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0016879 ! future central nervous system +relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord +relationship: develops_from UBERON:0007284 ! presumptive neural plate +relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate +property_value: depicted:by Neural:Crest.png +property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003076 +name: posterior neural tube +namespace: uberon +xref: AAO:0011082 +xref: TAO:0007037 +xref: VHOG:0001383 +xref: XAO:0000250 +xref: ZFA:0007037 +is_a: UBERON:0002050 ! embryonic structure +disjoint_from: UBERON:0003080 {source="lexical"} ! anterior neural tube +relationship: develops_from UBERON:0003057 ! chordal neural plate +relationship: part_of UBERON:0001049 ! neural tube +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001383", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003077 +name: paraxial mesoderm +namespace: uberon +def: "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]" [GO:0048339, https://github.com/obophenotype/uberon/issues/30] +subset: efo_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mesoderma paraxiale" RELATED LATIN [http://en.wikipedia.org/wiki/Paraxial_mesoderm] +synonym: "paraxial mesenchyme" EXACT [https://github.com/obophenotype/uberon/issues/30, https://github.com/obophenotype/uberon/wiki/The-neural-crest, ZFA:0000255] +synonym: "somitic mesoderm" EXACT [ISBN:9780878932504] +xref: AAO:0010568 +xref: EFO:0003515 +xref: EMAPA:16183 +xref: EMAPA:16751 +xref: FMA:293145 +xref: http://linkedlifedata.com/resource/umls/id/C1284009 +xref: http://www.snomedbrowser.com/Codes/Details/361475002 +xref: NCIT:C34244 +xref: Paraxial:mesoderm +xref: TAO:0000255 +xref: UMLS:C1284009 {source="ncithesaurus:Paraxial_Mesoderm"} +xref: VHOG:0000114 +xref: XAO:0000259 +xref: ZFA:0000255 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue +is_a: UBERON:0015212 ! lateral structure +relationship: develops_from UBERON:0007285 ! presumptive paraxial mesoderm +relationship: existence_starts_during UBERON:0000109 ! gastrula stage +relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm +relationship: in_lateral_side_of UBERON:0000922 ! embryo +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png +property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)"} +property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} + +[Term] +id: UBERON:0003080 +name: anterior neural tube +namespace: uberon +xref: AAO:0011012 +xref: TAO:0007038 +xref: VHOG:0001384 +xref: XAO:0000307 +xref: ZFA:0007038 +is_a: UBERON:0002050 ! embryonic structure +relationship: develops_from UBERON:0003056 ! pre-chordal neural plate +relationship: part_of UBERON:0001049 ! neural tube +property_value: IAO:0000116 "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001384", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003081 +name: lateral plate mesoderm +namespace: uberon +alt_id: UBERON:0006258 +def: "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." [http://en.wikipedia.org/wiki/Lateral_plate_mesoderm, MP:0010117] +subset: pheno_slim +subset: uberon_slim +synonym: "lateral mesoderm" EXACT [GO:0048368] +synonym: "lateral plate" RELATED [] +synonym: "lateral plate mesenchyme" RELATED [EHDAA2:0000919] +synonym: "LPM" EXACT ABBREVIATION [ZFA:0000121] +synonym: "mesoderma laminae lateralis" RELATED LATIN [http://en.wikipedia.org/wiki/Lateral_plate_mesoderm] +xref: AAO:0010574 +xref: EHDAA2:0000919 +xref: EHDAA:379 +xref: EMAPA:16179 +xref: FMA:293149 +xref: http://en.wikipedia.org/wiki/Lateral_plate_mesoderm +xref: http://linkedlifedata.com/resource/umls/id/C1517749 +xref: http://www.snomedbrowser.com/Codes/Details/361477005 +xref: NCIT:C34199 +xref: TAO:0000121 +xref: UMLS:C1517749 {source="ncithesaurus:Lateral_Mesoderm"} +xref: VHOG:0000118 +xref: XAO:0000311 +xref: ZFA:0000121 +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue +relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm +relationship: surrounds UBERON:0003887 ! intraembryonic coelom +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png +property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} +property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)"} +property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} + +[Term] +id: UBERON:0003084 +name: heart primordium +namespace: uberon +def: "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone." [ZFIN:curator] +subset: uberon_slim +synonym: "cardiac field" RELATED [ZFA:0000028] +synonym: "fused heart primordium" RELATED [] +xref: AAO:0011044 +xref: BTO:0001887 +xref: http://linkedlifedata.com/resource/umls/id/C1514450 +xref: NCIT:C34276 +xref: TAO:0000028 +xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} +xref: XAO:0000336 +xref: ZFA:0000028 +is_a: UBERON:0001048 {source="Obol"} ! primordium +relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm +relationship: develops_from UBERON:0004140 ! primary heart field +relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm +relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string +property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} +property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} + +[Term] +id: UBERON:0003089 +name: sclerotome +namespace: uberon +def: "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." [http://en.wikipedia.org/wiki/Sclerotome, https://github.com/obophenotype/uberon/issues/316, XB:curator] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "sclerotomes" EXACT PLURAL [TAO:0001080] +synonym: "sclerotomus" RELATED LATIN [http://en.wikipedia.org/wiki/Sclerotome] +xref: AAO:0010571 +xref: AEO:0000212 +xref: EHDAA2:0003439 +xref: EMAPA:31159 +xref: FMA:295652 +xref: http://en.wikipedia.org/wiki/Sclerotome +xref: http://linkedlifedata.com/resource/umls/id/C0183176 +xref: NCIT:C34287 +xref: TAO:0001080 +xref: UMLS:C0183176 {source="ncithesaurus:Sclerotome"} +xref: VHOG:0000680 +xref: XAO:0000397 +xref: ZFA:0001080 +is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation +is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population +relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png +property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)"} +property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} + +[Term] +id: UBERON:0003099 +name: cranial neural crest +namespace: uberon +def: "neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage." [MGI:anna] +subset: efo_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "cephalic neural crest" EXACT [EMAPA:16091] +synonym: "CNC" EXACT ABBREVIATION [XAO:0001001] +synonym: "cranial NCC population" EXACT [] +synonym: "crista neuralis cranialis" RELATED LATIN [http://en.wikipedia.org/wiki/Cranial_neural_crest] +synonym: "head crest" RELATED [] +synonym: "head NCC population" EXACT [] +synonym: "head neural crest" RELATED [] +xref: AAO:0010580 +xref: EFO:0003645 +xref: EHDAA2:0004420 +xref: EMAPA:16091 +xref: http://en.wikipedia.org/wiki/Cranial_neural_crest +xref: TAO:0001194 +xref: VHOG:0000063 +xref: XAO:0001001 +xref: ZFA:0001194 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: part_of UBERON:0002342 ! neural crest +property_value: UBPROP:0000001 "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010580", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000001 "Neural crest that is part of the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001194", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000063", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43"} + +[Term] +id: UBERON:0003102 +name: surface structure +namespace: uberon +def: "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/24] +subset: upper_level +synonym: "anatomical surface feature" EXACT [EHDAA2:0003010] +synonym: "surface feature" RELATED [] +synonym: "surface region" RELATED [] +synonym: "surface structures" RELATED PLURAL [ZFA:0000292] +xref: AAO:0010337 +xref: AEO_RETIRED:0000010 +xref: EHDAA2_RETIRED:0003010 +xref: galen:SurfaceRegion +xref: Surface:structure +xref: TAO:0000292 +xref: VSAO:0000001 +xref: XAO:0003028 +xref: ZFA:0000292 +is_a: UBERON:0000061 ! anatomical structure +relationship: adjacent_to UBERON:0013514 ! space surrounding organism +relationship: part_of UBERON:0002416 ! integumental system +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/wdahdul +property_value: IAO:0000116 "consider obsoleting. See issue/1305" xsd:string +property_value: UBPROP:0000001 "Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000292", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0003103 +name: compound organ +namespace: uberon +def: "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." [CARO:0000024] +subset: organ_slim +subset: upper_level +synonym: "organ" RELATED [] +xref: AAO:0010015 +xref: AEO:0000024 +xref: BILA:0000024 +xref: CARO:0000024 +xref: EHDAA2:0003024 +xref: HAO:0000024 +xref: TADS:0000598 +xref: TAO:0000496 +xref: TGMA:0001837 +xref: VHOG:0001723 +xref: XAO:0003041 +xref: ZFA:0000496 +is_a: UBERON:0000062 ! organ +property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string + +[Term] +id: UBERON:0003104 +name: mesenchyme +namespace: uberon +def: "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]." [BTO:0001393, http://en.wikipedia.org/wiki/Mesenchyme, ZFIN:curator] +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "mesenchyma" RELATED LATIN [http://en.wikipedia.org/wiki/Mesenchyme] +synonym: "mesenchymal tissue" EXACT [] +synonym: "mesenchyme tissue" EXACT [] +synonym: "portion of mesenchymal tissue" EXACT [] +synonym: "portion of mesenchyme tissue" EXACT [] +xref: AAO:0010427 +xref: AEO:0000145 +xref: BTO:0001393 +xref: CALOHA:TS-0620 +xref: EHDAA2:0003145 +xref: EV:0100007 +xref: http://en.wikipedia.org/wiki/Mesenchyme +xref: http://linkedlifedata.com/resource/umls/id/C0162415 +xref: NCIT:C13301 +xref: TAO:0000393 +xref: UMLS:C0162415 {source="ncithesaurus:Mesenchyme"} +xref: VHOG:0000170 +xref: XAO:0003046 +xref: ZFA:0000393 +is_a: UBERON:0000479 ! tissue +relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string +property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000007 "mesenchymal" xsd:string + +[Term] +id: UBERON:0003117 +name: pharyngeal arch 6 +namespace: uberon +alt_id: UBERON:0004349 +def: "The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles" [MP:0006347] +subset: pheno_slim +synonym: "6th arch" EXACT [EHDAA2:0004075] +synonym: "6th pharyngeal arch" RELATED [VHOG:0001205] +synonym: "6th visceral arch" RELATED [VHOG:0001205] +synonym: "branchial arch 4" RELATED SENSU [AAO:0010368, ZFA:0001609] +synonym: "fourth branchial arch" RELATED SENSU [] +synonym: "gill arch 4" EXACT [ZFA:0001609] +synonym: "sixth branchial arch" EXACT [] +synonym: "sixth pharyngeal arch" RELATED [VHOG:0001205] +synonym: "sixth visceral arch" RELATED [XAO:0000453] +synonym: "visceral arch 6" EXACT [ZFA:0001609] +xref: AAO:0010368 +xref: EHDAA2:0004075 +xref: EMAPA:32766 +xref: FMA:293047 +xref: http://www.snomedbrowser.com/Codes/Details/308772004 +xref: TAO:0001601 +xref: VHOG:0001205 +xref: XAO:0000453 +xref: ZFA:0001609 +is_a: UBERON:0002539 ! pharyngeal arch +property_value: UBPROP:0000001 "The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010368", ontology="AAO", source="ISBN:0-02-377110-0"} +property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001205", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)"} +property_value: UBPROP:0000103 "6" xsd:nonNegativeInteger + +[Term] +id: UBERON:0003123 +name: pharyngeal arch artery 6 +namespace: uberon +alt_id: UBERON:0004351 +def: "The vessels formed within the sixth pair of branchial arches in embryogenesis" [MP:0006355] +subset: pheno_slim +subset: vertebrate_core +synonym: "6th aortic arch artery" RELATED [EMAPA:17005] +synonym: "6th arch artery" EXACT [EMAPA:17005] +synonym: "6th branchial arch artery" RELATED [EMAPA:17005] +synonym: "6th pharyngeal arch artery" RELATED [EMAPA:17005] +synonym: "AA6" EXACT [ZFA:0005016] +synonym: "aortic arch 6" EXACT [ZFA:0005016] +synonym: "pulmonary arch" RELATED [ISBN10:0073040584] +synonym: "sixth aortic arch" EXACT [XAO:0000353] +synonym: "sixth branchial arch artery" EXACT [] +xref: AAO:0010422 +xref: Arch_6 +xref: EHDAA2:0000102 +xref: EMAPA:17005 +xref: http://www.snomedbrowser.com/Codes/Details/308779008 +xref: TAO:0005016 +xref: VHOG:0000144 +xref: XAO:0000353 +xref: ZFA:0005016 +is_a: UBERON:0004363 ! pharyngeal arch artery +intersection_of: UBERON:0004363 ! pharyngeal arch artery +intersection_of: part_of UBERON:0003117 ! pharyngeal arch 6 +relationship: part_of UBERON:0003117 ! pharyngeal arch 6 +property_value: UBPROP:0000001 "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005016", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010422", ontology="AAO", source="ISBN:0-02-377110-0"} +property_value: UBPROP:0000001 "The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]." xsd:string {source="Arch_6"} +property_value: UBPROP:0000011 "the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} + +[Term] +id: UBERON:0003258 +name: endoderm of foregut +namespace: uberon +def: "An endoderm that is part of a foregut [Automatically generated definition]." [OBOL:automatic] +synonym: "foregut endoderm" EXACT [OBOL:automatic] +xref: EHDAA2:0004568 +xref: EHDAA:524 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0015833 ! foregut epithelium +intersection_of: UBERON:0000490 ! unilaminar epithelium +intersection_of: develops_from UBERON:0000925 ! endoderm +intersection_of: part_of UBERON:0001041 ! foregut +property_value: IAO:0000116 "TODO - check" xsd:string + +[Term] +id: UBERON:0003294 +name: gland of foregut +namespace: uberon +def: "A gland that is part of a foregut [Automatically generated definition]." [OBOL:automatic] +synonym: "foregut gland" EXACT [OBOL:automatic] +xref: EHDAA2:0000567 +xref: EHDAA:950 +xref: EMAPA:16557 +xref: VHOG:0000650 +is_a: UBERON:0003408 ! gland of digestive tract +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0001041 ! foregut +relationship: part_of UBERON:0001041 ! foregut + +[Term] +id: UBERON:0003295 +name: pharyngeal gland +namespace: uberon +def: "Racemose mucous glands beneath the mucous membrane of the pharynx." [Biology-Online_Dictionary:http\://www.biology-online.org/dictionary/] +subset: organ_slim +synonym: "glandulae pharyngeae" RELATED [BTO:0004849] +synonym: "pharynx gland" EXACT [EHDAA2:0001461] +xref: BTO:0004849 +xref: EHDAA2:0001461 +xref: EHDAA:2967 +xref: FMA:55075 +is_a: UBERON:0003408 ! gland of digestive tract +is_a: UBERON:0036225 ! respiratory system gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0001042 ! chordate pharynx +relationship: part_of UBERON:0001042 {source="BTO"} ! chordate pharynx + +[Term] +id: UBERON:0003297 +name: gland of integumental system +namespace: uberon +def: "A gland that is part of a integumental system [Automatically generated definition]." [OBOL:automatic] +synonym: "integumental gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "integumental system gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "integumentary gland" EXACT [http://orcid.org/0000-0002-6601-2165] +xref: EHDAA2:0000837 +xref: EHDAA:6522 +xref: EMAPA:17758 +xref: MA:0000144 +xref: VHOG:0000654 +is_a: UBERON:0002530 ! gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0002416 ! integumental system +relationship: part_of UBERON:0002416 ! integumental system + +[Term] +id: UBERON:0003304 +name: mesoderm blood island +namespace: uberon +alt_id: UBERON:0003305 +def: "A blood island that is part of a mesoderm." [OBOL:automatic] +synonym: "mesenchyme blood island" RELATED [OBOL:automatic] +synonym: "mesoderm blood islands" EXACT PLURAL [EHDAA2:0003241] +xref: EHDAA2:0003241 +xref: EHDAA:170 +xref: EMAPA:16115 +is_a: UBERON:0003061 ! blood island +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle +is_a: UBERON:0012275 ! meso-epithelium +intersection_of: UBERON:0003061 ! blood island +intersection_of: part_of UBERON:0000926 ! mesoderm +relationship: part_of UBERON:0000926 ! mesoderm +relationship: part_of UBERON:0007798 {source="EHDAA2"} ! vascular system +property_value: UBPROP:0000012 "in EHDAA2, gives rise to blood and dorsal aorta" xsd:string {external_ontology="EHDAA2"} + +[Term] +id: UBERON:0003343 +name: mucosa of oral region +namespace: uberon +def: "A mucosa that is part of a oral opening [Automatically generated definition]." [OBOL:automatic] +synonym: "mucosa of oral opening" EXACT [OBOL:automatic] +synonym: "mucosa of oral part of face" EXACT [OBOL:automatic] +synonym: "mucosa of organ of oral opening" EXACT [OBOL:automatic] +synonym: "mucosa of organ of oral part of face" EXACT [OBOL:automatic] +synonym: "mucosa of organ of oral region" EXACT [OBOL:automatic] +synonym: "mucosa of organ of subdivision of mouth" EXACT [OBOL:automatic] +synonym: "mucosa of subdivision of mouth" EXACT [OBOL:automatic] +synonym: "mucous membrane of oral opening" EXACT [OBOL:automatic] +synonym: "mucous membrane of oral part of face" EXACT [OBOL:automatic] +synonym: "mucous membrane of oral region" EXACT [OBOL:automatic] +synonym: "mucous membrane of subdivision of mouth" EXACT [OBOL:automatic] +synonym: "oral opening mucosa" EXACT [OBOL:automatic] +synonym: "oral opening mucosa of organ" EXACT [OBOL:automatic] +synonym: "oral opening mucous membrane" EXACT [OBOL:automatic] +synonym: "oral opening organ mucosa" EXACT [OBOL:automatic] +synonym: "oral part of face mucosa" EXACT [OBOL:automatic] +synonym: "oral part of face mucosa of organ" EXACT [OBOL:automatic] +synonym: "oral part of face mucous membrane" EXACT [OBOL:automatic] +synonym: "oral part of face organ mucosa" EXACT [OBOL:automatic] +synonym: "oral region mucosa" EXACT [OBOL:automatic] +synonym: "oral region mucosa of organ" EXACT [OBOL:automatic] +synonym: "oral region mucous membrane" EXACT [OBOL:automatic] +synonym: "oral region organ mucosa" EXACT [OBOL:automatic] +synonym: "organ mucosa of oral opening" EXACT [OBOL:automatic] +synonym: "organ mucosa of oral part of face" EXACT [OBOL:automatic] +synonym: "organ mucosa of oral region" EXACT [OBOL:automatic] +synonym: "organ mucosa of subdivision of mouth" EXACT [OBOL:automatic] +synonym: "subdivision of mouth mucosa" EXACT [OBOL:automatic] +synonym: "subdivision of mouth mucosa of organ" EXACT [OBOL:automatic] +synonym: "subdivision of mouth mucous membrane" EXACT [OBOL:automatic] +synonym: "subdivision of mouth organ mucosa" EXACT [OBOL:automatic] +xref: EMAPA:26937 +xref: http://www.snomedbrowser.com/Codes/Details/362083000 +is_a: UBERON:0003729 ! mouth mucosa +intersection_of: UBERON:0000344 ! mucosa +intersection_of: part_of UBERON:0000166 ! oral opening +relationship: part_of UBERON:0000166 ! oral opening + +[Term] +id: UBERON:0003350 +name: epithelium of mucosa +namespace: uberon +def: "A layer of epithelial cells on the surface of the mucosa." [BTO:0003752] +comment: lies on top of lamina propria +synonym: "lamina epithelialis mucosa" RELATED [BTO:0003752] +synonym: "lamina epithelialis mucosae" RELATED [BTO:0003752] +xref: BTO:0003752 +is_a: UBERON:0000483 ! epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0000344 ! mucosa +relationship: part_of UBERON:0000344 ! mucosa + +[Term] +id: UBERON:0003351 +name: pharyngeal epithelium +namespace: uberon +def: "An epithelium that is part of a pharynx [Automatically generated definition]." [OBOL:automatic] +subset: vertebrate_core +synonym: "epithelial tissue of pharynx" EXACT [OBOL:automatic] +synonym: "epithelium of pharynx" EXACT [OBOL:automatic] +synonym: "pharynx epithelial tissue" EXACT [OBOL:automatic] +synonym: "pharynx epithelium" EXACT [OBOL:automatic] +xref: BSA:0000112 +xref: BTO:0005240 +xref: EMAPA:16708 +xref: MA:0002725 +xref: RETIRED_EHDAA2:0001460 +xref: TAO:0001174 +xref: XAO:0003202 +xref: ZFA:0001174 +is_a: UBERON:0003929 ! digestive tract epithelium +is_a: UBERON:0004807 ! respiratory system epithelium +is_a: UBERON:0005911 ! endo-epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001042 ! chordate pharynx +relationship: develops_from UBERON:0007690 {source="ZFA"} ! early pharyngeal endoderm +relationship: part_of UBERON:0001042 {source="ZFA"} ! chordate pharynx +property_value: UBPROP:0000001 "Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001174", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0003364 +name: epithelium of right lung +namespace: uberon +def: "An epithelium that is part of a right lung [Automatically generated definition]." [OBOL:automatic] +synonym: "epithelial tissue of right lung" EXACT [OBOL:automatic] +synonym: "right lung epithelial tissue" EXACT [OBOL:automatic] +synonym: "right lung epithelium" EXACT [OBOL:automatic] +xref: EMAPA:17663 +xref: MA:0003132 +is_a: UBERON:0000115 ! lung epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0002167 ! right lung +relationship: part_of UBERON:0002167 ! right lung + +[Term] +id: UBERON:0003365 +name: epithelium of left lung +namespace: uberon +def: "An epithelium that is part of a left lung [Automatically generated definition]." [OBOL:automatic] +synonym: "epithelial tissue of left lung" EXACT [OBOL:automatic] +synonym: "left lung epithelial tissue" EXACT [OBOL:automatic] +synonym: "left lung epithelium" EXACT [OBOL:automatic] +xref: EMAPA:17655 +xref: MA:0003131 +is_a: UBERON:0000115 ! lung epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0002168 ! left lung +relationship: part_of UBERON:0002168 ! left lung + +[Term] +id: UBERON:0003408 +name: gland of digestive tract +namespace: uberon +def: "A gland that is part of a digestive tract [Automatically generated definition]." [OBOL:automatic] +synonym: "digestive tract gland" EXACT [OBOL:automatic] +synonym: "gland of digestive tract" EXACT [OBOL:automatic] +synonym: "gland of lower gastrointestinal tract" EXACT [OBOL:automatic] +synonym: "gut gland" EXACT [MA:0003202] +synonym: "lower gastrointestinal tract gland" EXACT [OBOL:automatic] +xref: EMAPA:18815 +xref: MA:0003202 +is_a: UBERON:0002530 ! gland +is_a: UBERON:0013765 ! digestive system element +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0001555 ! digestive tract +relationship: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0003426 +name: dermis adipose tissue +namespace: uberon +def: "An adipose tissue that is part of a dermis [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "adipose tissue of dermis" EXACT [OBOL:automatic] +synonym: "dermis fat tissue" EXACT [OBOL:automatic] +synonym: "dermis fatty tissue" EXACT [OBOL:automatic] +synonym: "fat tissue of dermis" EXACT [OBOL:automatic] +synonym: "fatty tissue of dermis" EXACT [OBOL:automatic] +xref: MA:0000798 +is_a: UBERON:0001013 ! adipose tissue +is_a: UBERON:0003585 ! dermis connective tissue +intersection_of: UBERON:0001013 ! adipose tissue +intersection_of: part_of UBERON:0002067 ! dermis + +[Term] +id: UBERON:0003469 +name: respiratory system artery +namespace: uberon +def: "An artery that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:37569 {source="MA:th"} +xref: MA:0001804 +is_a: UBERON:0001637 ! artery +is_a: UBERON:0003643 ! respiratory system arterial blood vessel +intersection_of: UBERON:0001637 ! artery +intersection_of: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003473 +name: thoracic cavity artery +namespace: uberon +def: "An artery that is part of a thoracic cavity[cjm]." [https://sourceforge.net/tracker/index.php?func=detail&aid=3317815&group_id=76834&atid=1205376] +synonym: "thoracic artery" RELATED [MESH:A07.231.114.891] +xref: EMAPA:37241 {source="MA:th"} +xref: MA:0001902 +xref: MESH:D013895 +is_a: UBERON:0001637 ! artery +is_a: UBERON:0003519 ! thoracic cavity blood vessel +intersection_of: UBERON:0001637 ! artery +intersection_of: located_in UBERON:0002224 ! thoracic cavity +property_value: UBPROP:0000012 "in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0003476 +name: respiratory system venous blood vessel +namespace: uberon +def: "A vein that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius vein" EXACT [OBOL:automatic] +synonym: "respiratory system vein" EXACT [OBOL:automatic] +synonym: "vein of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "vein of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:37584 {source="MA:th"} +xref: MA:0001809 +xref: MA:0001810 +is_a: UBERON:0001638 ! vein +intersection_of: UBERON:0001638 ! vein +intersection_of: drains UBERON:0001004 ! respiratory system +relationship: drains UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003479 +name: thoracic cavity vein +namespace: uberon +def: "A vein that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] +synonym: "cavity of chest vein" EXACT [OBOL:automatic] +synonym: "cavity of thorax vein" EXACT [OBOL:automatic] +synonym: "chest cavity vein" EXACT [OBOL:automatic] +synonym: "pectoral cavity vein" EXACT [OBOL:automatic] +synonym: "vein of cavity of chest" EXACT [OBOL:automatic] +synonym: "vein of cavity of thorax" EXACT [OBOL:automatic] +synonym: "vein of chest cavity" EXACT [OBOL:automatic] +synonym: "vein of pectoral cavity" EXACT [OBOL:automatic] +synonym: "vein of thoracic cavity" EXACT [OBOL:automatic] +xref: EMAPA:37242 {source="MA:th"} +xref: MA:0001903 +is_a: UBERON:0001638 ! vein +is_a: UBERON:0003519 ! thoracic cavity blood vessel +intersection_of: UBERON:0001638 ! vein +intersection_of: located_in UBERON:0002224 ! thoracic cavity + +[Term] +id: UBERON:0003489 +name: respiratory system capillary endothelium +namespace: uberon +def: "An endothelium of capillary that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius blood capillary endothelium" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius capillary endothelium" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius capillary vessel endothelium" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius endothelium of blood capillary" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius endothelium of capillary" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius endothelium of capillary vessel" EXACT [OBOL:automatic] +synonym: "blood capillary endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "blood capillary endothelium of respiratory system" EXACT [OBOL:automatic] +synonym: "capillary endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "capillary endothelium of respiratory system" EXACT [OBOL:automatic] +synonym: "capillary vessel endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "capillary vessel endothelium of respiratory system" EXACT [OBOL:automatic] +synonym: "endothelium of blood capillary of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "endothelium of blood capillary of respiratory system" EXACT [OBOL:automatic] +synonym: "endothelium of capillary of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "endothelium of capillary of respiratory system" EXACT [OBOL:automatic] +synonym: "endothelium of capillary vessel of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "endothelium of capillary vessel of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system blood capillary endothelium" EXACT [OBOL:automatic] +synonym: "respiratory system capillary vessel endothelium" EXACT [OBOL:automatic] +synonym: "respiratory system endothelium of blood capillary" EXACT [OBOL:automatic] +synonym: "respiratory system endothelium of capillary" EXACT [OBOL:automatic] +synonym: "respiratory system endothelium of capillary vessel" EXACT [OBOL:automatic] +xref: EMAPA:37575 {source="MA:th"} +xref: MA:0001808 +is_a: UBERON:0001915 ! endothelium of capillary +is_a: UBERON:0004702 ! respiratory system blood vessel endothelium +intersection_of: UBERON:0001915 ! endothelium of capillary +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003526 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system capillary + +[Term] +id: UBERON:0003494 +name: respiratory system venule +namespace: uberon +def: "A venule that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius venule" EXACT [OBOL:automatic] +synonym: "venule of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "venule of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:37587 {source="MA:th"} +xref: MA:0001813 +is_a: UBERON:0001979 ! venule +is_a: UBERON:0003504 ! respiratory system blood vessel +intersection_of: UBERON:0001979 ! venule +intersection_of: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003495 +name: respiratory system arteriole +namespace: uberon +def: "An arteriole that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:37568 {source="MA:th"} +xref: MA:0001803 +is_a: UBERON:0001980 ! arteriole +is_a: UBERON:0003643 ! respiratory system arterial blood vessel +intersection_of: UBERON:0001980 ! arteriole +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003469 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system artery + +[Term] +id: UBERON:0003496 +name: head blood vessel +namespace: uberon +def: "A blood vessel that is part of a head [Automatically generated definition]." [OBOL:automatic] +synonym: "adult head blood vessel" EXACT [OBOL:automatic] +synonym: "blood vessel of adult head" EXACT [OBOL:automatic] +synonym: "blood vessel of head" EXACT [OBOL:automatic] +xref: EMAPA:36610 +xref: http://www.snomedbrowser.com/Codes/Details/127865000 +xref: MA:0000575 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0011362 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! cranial blood vasculature + +[Term] +id: UBERON:0003498 +name: heart blood vessel +namespace: uberon +def: "A blood vessel that is part of a heart [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "blood vessel of heart" EXACT [OBOL:automatic] +synonym: "cardiac blood vessel" RELATED [EMAPA:35397] +xref: EMAPA:35397 +xref: MA:0002483 +is_a: UBERON:0003834 ! thoracic segment blood vessel +is_a: UBERON:0005985 ! coronary vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0000948 ! heart +relationship: part_of UBERON:0018674 ! heart vasculature + +[Term] +id: UBERON:0003499 +name: brain blood vessel +namespace: uberon +def: "A blood vessel that is part of a brain [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "blood vessel of brain" EXACT [OBOL:automatic] +xref: EMAPA:35182 +xref: MA:0002769 +is_a: UBERON:0001981 ! blood vessel +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0000955 ! brain +relationship: part_of UBERON:0008998 ! vasculature of brain + +[Term] +id: UBERON:0003502 +name: neck blood vessel +namespace: uberon +def: "A blood vessel that is part of a neck [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of neck" EXACT [OBOL:automatic] +synonym: "blood vessel of neck (volume)" EXACT [OBOL:automatic] +synonym: "neck (volume) blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37236 {source="MA:th"} +xref: MA:0000583 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0000974 ! neck +relationship: part_of UBERON:0000974 ! neck + +[Term] +id: UBERON:0003504 +name: respiratory system blood vessel +namespace: uberon +def: "A blood vessel that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius blood vessel" EXACT [OBOL:automatic] +synonym: "blood vessel of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "blood vessel of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:35731 +xref: EMAPA:35995 +xref: MA:0001799 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003509 +name: arterial blood vessel +namespace: uberon +def: "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." [https://orcid.org/0000-0002-6601-2165] +comment: only in MA - supertype of artery, arteriole, aorta. +subset: pheno_slim +xref: EMAPA:35144 +xref: MA:0000061 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0004572 ! arterial system +relationship: part_of UBERON:0004572 ! arterial system + +[Term] +id: UBERON:0003512 +name: lung blood vessel +namespace: uberon +def: "A blood vessel that is part of a lung [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "blood vessel of lung" EXACT [OBOL:automatic] +synonym: "pulmonary vascular element" RELATED [EMAPA:32867] +xref: EMAPA:32867 +xref: MA:0002457 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003504 ! respiratory system blood vessel +is_a: UBERON:0003834 ! thoracic segment blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0002048 ! lung +relationship: contributes_to_morphology_of UBERON:0002048 ! lung +relationship: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0003513 +name: trunk blood vessel +namespace: uberon +def: "A blood vessel that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of torso" EXACT [OBOL:automatic] +synonym: "blood vessel of trunk" EXACT [OBOL:automatic] +synonym: "torso blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37237 {source="MA:th"} +xref: MA:0000511 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk + +[Term] +id: UBERON:0003519 +name: thoracic cavity blood vessel +namespace: uberon +def: "A blood vessel that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of cavity of chest" EXACT [OBOL:automatic] +synonym: "blood vessel of cavity of thorax" EXACT [OBOL:automatic] +synonym: "blood vessel of chest cavity" EXACT [OBOL:automatic] +synonym: "blood vessel of pectoral cavity" EXACT [OBOL:automatic] +synonym: "blood vessel of thoracic cavity" EXACT [OBOL:automatic] +synonym: "cavity of chest blood vessel" EXACT [OBOL:automatic] +synonym: "cavity of thorax blood vessel" EXACT [OBOL:automatic] +synonym: "chest cavity blood vessel" EXACT [OBOL:automatic] +synonym: "pectoral cavity blood vessel" EXACT [OBOL:automatic] +xref: EMAPA:37240 {source="MA:th"} +xref: MA:0000554 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: located_in UBERON:0002224 ! thoracic cavity +relationship: located_in UBERON:0002224 ! thoracic cavity + +[Term] +id: UBERON:0003526 +name: respiratory system capillary +namespace: uberon +def: "A capillary that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius blood capillary" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius capillary" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius capillary vessel" EXACT [OBOL:automatic] +synonym: "blood capillary of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "blood capillary of respiratory system" EXACT [OBOL:automatic] +synonym: "capillary of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "capillary of respiratory system" EXACT [OBOL:automatic] +synonym: "capillary vessel of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "capillary vessel of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system blood capillary" EXACT [OBOL:automatic] +synonym: "respiratory system capillary vessel" EXACT [OBOL:automatic] +xref: EMAPA:37574 {source="MA:th"} +xref: MA:0001807 +is_a: UBERON:0001982 ! capillary +is_a: UBERON:0003504 ! respiratory system blood vessel +intersection_of: UBERON:0001982 ! capillary +intersection_of: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003528 +name: brain gray matter +namespace: uberon +def: "A gray matter that is part of a brain [Automatically generated definition]." [OBOL:automatic] +synonym: "brain grey matter" EXACT [MA:0000810] +synonym: "brain grey substance" EXACT [OBOL:automatic] +synonym: "gray matter of brain" EXACT [OBOL:automatic] +synonym: "grey matter of brain" EXACT [OBOL:automatic] +synonym: "grey substance of brain" EXACT [OBOL:automatic] +xref: EMAPA:35184 +xref: http://linkedlifedata.com/resource/umls/id/C1707348 +xref: MA:0000810 +xref: NCIT:C49333 +xref: UMLS:C1707348 {source="ncithesaurus:Cerebral_Gray_Matter"} +is_a: UBERON:0002020 ! gray matter +intersection_of: UBERON:0002020 ! gray matter +intersection_of: part_of UBERON:0000955 ! brain +relationship: part_of UBERON:0000955 ! brain + +[Term] +id: UBERON:0003566 +name: head connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a head [Automatically generated definition]." [OBOL:automatic] +synonym: "adult head connective tissue" EXACT [OBOL:automatic] +synonym: "adult head portion of connective tissue" EXACT [OBOL:automatic] +synonym: "adult head textus connectivus" EXACT [OBOL:automatic] +synonym: "connective tissue of adult head" EXACT [OBOL:automatic] +synonym: "connective tissue of head" EXACT [OBOL:automatic] +synonym: "head portion of connective tissue" EXACT [OBOL:automatic] +synonym: "head textus connectivus" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of adult head" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of head" EXACT [OBOL:automatic] +synonym: "textus connectivus of adult head" EXACT [OBOL:automatic] +synonym: "textus connectivus of head" EXACT [OBOL:automatic] +xref: EMAPA:16098 +xref: MA:0000577 +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0000033 ! head +relationship: develops_from UBERON:0005253 ! head mesenchyme +relationship: part_of UBERON:0000033 ! head +relationship: transformation_of UBERON:0005253 ! head mesenchyme + +[Term] +id: UBERON:0003568 +name: neck connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a neck [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of neck" EXACT [OBOL:automatic] +synonym: "connective tissue of neck (volume)" EXACT [OBOL:automatic] +synonym: "neck (volume) connective tissue" EXACT [OBOL:automatic] +synonym: "neck (volume) portion of connective tissue" EXACT [OBOL:automatic] +synonym: "neck (volume) textus connectivus" EXACT [OBOL:automatic] +synonym: "neck portion of connective tissue" EXACT [OBOL:automatic] +synonym: "neck textus connectivus" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of neck" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of neck (volume)" EXACT [OBOL:automatic] +synonym: "textus connectivus of neck" EXACT [OBOL:automatic] +synonym: "textus connectivus of neck (volume)" EXACT [OBOL:automatic] +xref: EMAPA:37250 {source="MA:th"} +xref: MA:0000585 +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0000974 ! neck +relationship: part_of UBERON:0000974 ! neck + +[Term] +id: UBERON:0003570 +name: respiratory system connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius connective tissue" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius portion of connective tissue" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius textus connectivus" EXACT [OBOL:automatic] +synonym: "connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "connective tissue of respiratory system" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system portion of connective tissue" EXACT [OBOL:automatic] +synonym: "respiratory system textus connectivus" EXACT [OBOL:automatic] +synonym: "textus connectivus of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "textus connectivus of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:35968 +xref: EMAPA:35977 +xref: MA:0001814 +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003580 +name: lower respiratory tract connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "lower respiratory tract portion of connective tissue" EXACT [OBOL:automatic] +synonym: "lower respiratory tract textus connectivus" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "textus connectivus of lower respiratory tract" EXACT [OBOL:automatic] +xref: EMAPA:37548 {source="MA:th"} +xref: MA:0002409 +is_a: UBERON:0003570 ! respiratory system connective tissue +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0001558 ! lower respiratory tract +relationship: part_of UBERON:0001558 ! lower respiratory tract + +[Term] +id: UBERON:0003585 +name: dermis connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a dermis [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "connective tissue of dermis" EXACT [OBOL:automatic] +synonym: "dermis portion of connective tissue" EXACT [OBOL:automatic] +synonym: "dermis textus connectivus" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of dermis" EXACT [OBOL:automatic] +synonym: "textus connectivus of dermis" EXACT [OBOL:automatic] +xref: EMAPA:36509 +xref: MA:0000799 +is_a: UBERON:0002384 ! connective tissue +is_a: UBERON:0010313 ! neural crest-derived structure +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0002067 ! dermis +relationship: develops_from UBERON:0004016 ! dermatome +relationship: part_of UBERON:0002067 ! dermis + +[Term] +id: UBERON:0003586 +name: trunk connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of torso" EXACT [OBOL:automatic] +synonym: "connective tissue of trunk" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of torso" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of trunk" EXACT [OBOL:automatic] +synonym: "textus connectivus of torso" EXACT [OBOL:automatic] +synonym: "textus connectivus of trunk" EXACT [OBOL:automatic] +synonym: "torso connective tissue" EXACT [OBOL:automatic] +synonym: "torso portion of connective tissue" EXACT [OBOL:automatic] +synonym: "torso textus connectivus" EXACT [OBOL:automatic] +synonym: "trunk portion of connective tissue" EXACT [OBOL:automatic] +synonym: "trunk textus connectivus" EXACT [OBOL:automatic] +xref: EMAPA:37252 {source="MA:th"} +xref: MA:0000513 +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk + +[Term] +id: UBERON:0003593 +name: thoracic cavity connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]." [OBOL:automatic] +synonym: "cavity of chest connective tissue" EXACT [OBOL:automatic] +synonym: "cavity of chest portion of connective tissue" EXACT [OBOL:automatic] +synonym: "cavity of chest textus connectivus" EXACT [OBOL:automatic] +synonym: "cavity of thorax connective tissue" EXACT [OBOL:automatic] +synonym: "cavity of thorax portion of connective tissue" EXACT [OBOL:automatic] +synonym: "cavity of thorax textus connectivus" EXACT [OBOL:automatic] +synonym: "chest cavity connective tissue" EXACT [OBOL:automatic] +synonym: "chest cavity portion of connective tissue" EXACT [OBOL:automatic] +synonym: "chest cavity textus connectivus" EXACT [OBOL:automatic] +synonym: "connective tissue of cavity of chest" EXACT [OBOL:automatic] +synonym: "connective tissue of cavity of thorax" EXACT [OBOL:automatic] +synonym: "connective tissue of chest cavity" EXACT [OBOL:automatic] +synonym: "connective tissue of pectoral cavity" EXACT [OBOL:automatic] +synonym: "connective tissue of thoracic cavity" EXACT [OBOL:automatic] +synonym: "pectoral cavity connective tissue" EXACT [OBOL:automatic] +synonym: "pectoral cavity portion of connective tissue" EXACT [OBOL:automatic] +synonym: "pectoral cavity textus connectivus" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of cavity of chest" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of cavity of thorax" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of chest cavity" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of pectoral cavity" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of thoracic cavity" EXACT [OBOL:automatic] +synonym: "textus connectivus of cavity of chest" EXACT [OBOL:automatic] +synonym: "textus connectivus of cavity of thorax" EXACT [OBOL:automatic] +synonym: "textus connectivus of chest cavity" EXACT [OBOL:automatic] +synonym: "textus connectivus of pectoral cavity" EXACT [OBOL:automatic] +synonym: "textus connectivus of thoracic cavity" EXACT [OBOL:automatic] +synonym: "thoracic cavity portion of connective tissue" EXACT [OBOL:automatic] +synonym: "thoracic cavity textus connectivus" EXACT [OBOL:automatic] +xref: EMAPA:37255 {source="MA:th"} +xref: MA:0000555 +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: located_in UBERON:0002224 ! thoracic cavity +relationship: located_in UBERON:0002224 ! thoracic cavity + +[Term] +id: UBERON:0003610 +name: heart elastic tissue +namespace: uberon +def: "The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers." [MP:0009863] +subset: pheno_slim +synonym: "cardiac elastic tissue" EXACT [MP:0009863] +synonym: "elastic connective tissue of heart" EXACT [OBOL:automatic] +synonym: "elastic tissue of heart" EXACT [OBOL:automatic] +synonym: "heart elastic connective tissue" EXACT [OBOL:automatic] +synonym: "heart textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "textus connectivus elasticus of heart" EXACT [OBOL:automatic] +xref: MA:0002858 +is_a: UBERON:0003613 ! cardiovascular system elastic tissue +is_a: UBERON:0003837 ! thoracic segment connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0002521 ! elastic tissue +intersection_of: part_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0003611 +name: respiratory system elastic tissue +namespace: uberon +def: "An elastic tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius elastic connective tissue" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius elastic tissue" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "elastic connective tissue of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "elastic connective tissue of respiratory system" EXACT [OBOL:automatic] +synonym: "elastic tissue of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "elastic tissue of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system elastic connective tissue" EXACT [OBOL:automatic] +synonym: "respiratory system textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "textus connectivus elasticus of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "textus connectivus elasticus of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:37579 {source="MA:th"} +xref: MA:0001820 +is_a: UBERON:0002521 ! elastic tissue +is_a: UBERON:0003570 ! respiratory system connective tissue +intersection_of: UBERON:0002521 ! elastic tissue +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0004777 ! respiratory system submucosa + +[Term] +id: UBERON:0003613 +name: cardiovascular system elastic tissue +namespace: uberon +def: "An elastic tissue that is part of a circulatory system [Automatically generated definition]." [OBOL:automatic] +synonym: "cardiovascular system elastic connective tissue" EXACT [OBOL:automatic] +synonym: "cardiovascular system textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "circulatory system elastic connective tissue" EXACT [OBOL:automatic] +synonym: "circulatory system elastic tissue" EXACT [OBOL:automatic] +synonym: "circulatory system textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "elastic connective tissue of cardiovascular system" EXACT [OBOL:automatic] +synonym: "elastic connective tissue of circulatory system" EXACT [OBOL:automatic] +synonym: "elastic tissue of cardiovascular system" EXACT [OBOL:automatic] +synonym: "elastic tissue of circulatory system" EXACT [OBOL:automatic] +synonym: "textus connectivus elasticus of cardiovascular system" EXACT [OBOL:automatic] +synonym: "textus connectivus elasticus of circulatory system" EXACT [OBOL:automatic] +xref: MA:0002857 +is_a: UBERON:0002521 ! elastic tissue +intersection_of: UBERON:0002521 ! elastic tissue +intersection_of: part_of UBERON:0001009 ! circulatory system +relationship: part_of UBERON:0004535 ! cardiovascular system + +[Term] +id: UBERON:0003614 +name: blood vessel elastic tissue +namespace: uberon +def: "Elastic tissue layer that lines a blood vessel layer." [http://orcid.org/0000-0002-6601-2165, https://sourceforge.net/p/obo/mammalian-phenotype-requests/2026/] +subset: pheno_slim +synonym: "blood vessel elastic connective tissue" EXACT [OBOL:automatic] +synonym: "blood vessel textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "elastic connective tissue of blood vessel" EXACT [OBOL:automatic] +synonym: "elastic lamina" BROAD [MP:0006083] +synonym: "elastic laminae" BROAD PLURAL [MP:0006083] +synonym: "elastic tissue of blood vessel" EXACT [OBOL:automatic] +synonym: "textus connectivus elasticus of blood vessel" EXACT [OBOL:automatic] +synonym: "vascular elastic lamina" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "vascular elastic laminae" EXACT PLURAL [http://orcid.org/0000-0002-6601-2165] +synonym: "vascular elastic tissue" EXACT [MP:0006083] +xref: EMAPA:36300 +xref: MA:0002856 +is_a: UBERON:0003613 ! cardiovascular system elastic tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0002521 ! elastic tissue +intersection_of: part_of UBERON:0001981 ! blood vessel +relationship: part_of UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0003615 +name: lung elastic tissue +namespace: uberon +def: "Elastic tissue that is part of a lung [Automatically generated definition]." [OBOL:automatic] +synonym: "elastic connective tissue of lung" EXACT [OBOL:automatic] +synonym: "elastic tissue of lung" EXACT [OBOL:automatic] +synonym: "lung elastic connective tissue" EXACT [OBOL:automatic] +synonym: "lung textus connectivus elasticus" EXACT [OBOL:automatic] +synonym: "pulmonary elastic fiber" NARROW [http://orcid.org/0000-0002-6601-2165] +synonym: "textus connectivus elasticus of lung" EXACT [OBOL:automatic] +xref: MA:0002860 +is_a: UBERON:0000114 ! lung connective tissue +is_a: UBERON:0003611 ! respiratory system elastic tissue +intersection_of: UBERON:0002521 ! elastic tissue +intersection_of: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0003643 +name: respiratory system arterial blood vessel +namespace: uberon +def: "An arterial blood vessel that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:37565 {source="MA:th"} +xref: MA:0001800 +is_a: UBERON:0003504 ! respiratory system blood vessel +is_a: UBERON:0003509 ! arterial blood vessel +intersection_of: UBERON:0003509 ! arterial blood vessel +intersection_of: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003714 +name: neural tissue +namespace: uberon +def: "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature." [FMA:9642] +synonym: "nerve tissue" EXACT [FMA:9642] +synonym: "nervous tissue" EXACT [FMA:9642] +synonym: "portion of neural tissue" EXACT [FMA:9642] +xref: AAO:0000325 +xref: AEO:0000123 +xref: EHDAA2:0003123 +xref: FMA:9642 +xref: GAID:609 +xref: http://linkedlifedata.com/resource/umls/id/C0027757 +xref: http://www.snomedbrowser.com/Codes/Details/91728009 +xref: MESH:D009417 +xref: NCIT:C13052 +xref: OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ +xref: UMLS:C0027757 {source="ncithesaurus:Nervous_Tissue"} +is_a: UBERON:0000479 ! tissue +relationship: part_of UBERON:0001016 ! nervous system +property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000325", ontology="AAO", source="AAO:LAP"} +property_value: UBPROP:0000012 "FMA definition includes vasculature" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0003729 +name: mouth mucosa +namespace: uberon +def: "A mucous membrane that lines the mouth." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "buccal mucosa" RELATED [GAID:951] +synonym: "mouth mucosa" EXACT [FMA:59660] +synonym: "mouth mucous membrane" EXACT [OBOL:accepted] +synonym: "mouth organ mucosa" EXACT [OBOL:accepted] +synonym: "mucosa of mouth" EXACT [OBOL:accepted] +synonym: "mucosal lining of mouth" RELATED [MA:0002794] +synonym: "mucous membrane of mouth" EXACT [FMA:59660] +synonym: "oral mucosa" RELATED [GAID:951] +synonym: "oral mucous membrane" EXACT [] +synonym: "oral part of viscerocranial mucosa" EXACT [FMA:59660] +synonym: "tunica mucosa oris" EXACT LATIN [FMA:59660, FMA:TA] +synonym: "tunica mucosa oris" RELATED LATIN [http://en.wikipedia.org/wiki/Oral_mucosa] +xref: BTO:0002860 +xref: CALOHA:TS-0716 +xref: EMAPA:26937 +xref: FMA:59660 +xref: GAID:951 +xref: http://linkedlifedata.com/resource/umls/id/C0026639 +xref: MA:0002794 +xref: MESH:D009061 +xref: NCIT:C77637 +xref: Oral:mucosa +xref: UMLS:C0026639 {source="ncithesaurus:Oral_Mucosa"} +is_a: UBERON:0000344 ! mucosa +intersection_of: UBERON:0000344 ! mucosa +intersection_of: part_of UBERON:0000165 ! mouth +relationship: bounding_layer_of UBERON:0000165 ! mouth +relationship: continuous_with UBERON:0000355 ! pharyngeal mucosa +relationship: continuous_with UBERON:0001458 ! skin of lip +relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system +relationship: part_of UBERON:0000165 ! mouth +property_value: IAO:0000232 "this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)" xsd:string +property_value: UBPROP:0000001 "the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]." xsd:string {source="Oral:mucosa"} + +[Term] +id: UBERON:0003831 +name: respiratory system muscle +namespace: uberon +def: "Any muscle organ that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius muscle organ" EXACT [OBOL:automatic] +synonym: "muscle organ of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "muscle organ of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system muscle organ" EXACT [OBOL:automatic] +xref: EMAPA:35733 +xref: MA:0001828 +is_a: UBERON:0001630 ! muscle organ +intersection_of: UBERON:0001630 ! muscle organ +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0003834 +name: thoracic segment blood vessel +namespace: uberon +def: "A blood vessel that is part of a thorax [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of thorax" EXACT [OBOL:automatic] +synonym: "thorax blood vessel" EXACT [OBOL:automatic] +synonym: "upper body blood vessel" RELATED [MA:0000558] +xref: EMAPA:37238 {source="MA:th"} +xref: MA:0000558 +is_a: UBERON:0003513 ! trunk blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0000915 ! thoracic segment of trunk + +[Term] +id: UBERON:0003837 +name: thoracic segment connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a thorax [Automatically generated definition]." [OBOL:automatic] +synonym: "connective tissue of thorax" EXACT [OBOL:automatic] +synonym: "portion of connective tissue of thorax" EXACT [OBOL:automatic] +synonym: "textus connectivus of thorax" EXACT [OBOL:automatic] +synonym: "thorax connective tissue" EXACT [OBOL:automatic] +synonym: "thorax portion of connective tissue" EXACT [OBOL:automatic] +synonym: "thorax textus connectivus" EXACT [OBOL:automatic] +synonym: "upper body connective tissue" RELATED [MA:0000560] +xref: EMAPA:37253 {source="MA:th"} +xref: MA:0000560 +is_a: UBERON:0003586 ! trunk connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0000915 ! thoracic segment of trunk + +[Term] +id: UBERON:0003842 +name: neural tube lumen +namespace: uberon +alt_id: UBERON:0005713 +def: "An anatomical space that surrounded_by a neural tube." [OBOL:automatic] +synonym: "cavity of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "central lumen" RELATED [] +synonym: "lumen of neural tube" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "neural lumen" RELATED [EHDAA:2889] +synonym: "neural tube neural lumen" EXACT [EHDAA2:0001269] +synonym: "neurocoel" RELATED [VHOG:0001119] +synonym: "prosencoel" NARROW [] +xref: AAO:0011073 +xref: EHDAA2:0001269 +xref: EHDAA:2889 +xref: EHDAA:914 +xref: EMAPA:16167 +xref: VHOG:0001119 +xref: XAO:0000252 +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0001049 ! neural tube +relationship: luminal_space_of UBERON:0001049 ! neural tube +relationship: part_of UBERON:0001049 ! neural tube +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001119", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003849 +name: mesencephalic neural crest +namespace: uberon +def: "A neural crest that has_potential_to_developmentally_contribute_to a midbrain." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "mesencephalic neural crest" EXACT [ZFA:0000935] +synonym: "neural crest midbrain" EXACT [ZFA:0000935] +xref: EFO:0003591 +xref: EHDAA2:0001101 +xref: EHDAA:360 +xref: TAO:0000935 +xref: VHOG:0000796 +xref: ZFA:0000935 +is_a: UBERON:0002342 ! neural crest +is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest +intersection_of: UBERON:0002342 ! neural crest +intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain +relationship: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain +property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000796", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43"} + +[Term] +id: UBERON:0003852 +name: rhombencephalon neural crest +namespace: uberon +def: "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain." [OBOL:automatic] +subset: vertebrate_core +synonym: "neural crest hindbrain" EXACT [ZFA:0007063] +synonym: "rhombencephalic neural crest" EXACT [ZFA:0007063] +synonym: "rhombomere neural crest" RELATED [EMAPA:35747] +xref: EHDAA2:0001628 +xref: EHDAA:362 +xref: EMAPA:35747 +xref: TAO:0007063 +xref: VHOG:0001210 +xref: ZFA:0007063 +is_a: UBERON:0002342 ! neural crest +is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest +intersection_of: UBERON:0002342 ! neural crest +intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain +relationship: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain +property_value: UBPROP:0000001 "Cranial neural crest that is part of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007063", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001210", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43"} + +[Term] +id: UBERON:0003853 +name: spinal cord neural crest +namespace: uberon +def: "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord." [OBOL:automatic] +synonym: "neural crest spinal cord" EXACT [VHOG:0001006] +synonym: "spinal neural crest" RELATED [VHOG:0001006] +xref: EHDAA:696 +xref: EMAPA:16163 +xref: EMAPA:16881 +xref: VHOG:0001006 +is_a: UBERON:0002342 ! neural crest +intersection_of: UBERON:0002342 ! neural crest +intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord +relationship: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord +property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001006", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43"} + +[Term] +id: UBERON:0003854 +name: spinal cord neural plate +namespace: uberon +def: "A neural plate that develops_from a future spinal cord." [OBOL:automatic] +synonym: "neural plate of spinal cord" EXACT [OBOL:automatic] +xref: FMA:312957 +xref: TAO:0007021 +xref: VHOG:0000439 +xref: ZFA:0007021 +is_a: UBERON:0003075 ! neural plate +intersection_of: UBERON:0003075 ! neural plate +intersection_of: develops_from UBERON:0006241 ! future spinal cord +relationship: develops_from UBERON:0006241 {source="ZFA"} ! future spinal cord +property_value: UBPROP:0000001 "Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000439", ontology="VHOG", source="http://bgee.unil.ch/"} +property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000439", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28"} + +[Term] +id: UBERON:0003886 +name: future coelemic cavity lumen +namespace: uberon +def: "An anatomical cavity that has the potential to develop into a coelemic cavity lumen." [OBOL:automatic] +subset: grouping_class +subset: non_informative +synonym: "body cavity precursor" RELATED [] +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +relationship: existence_ends_during UBERON:0000111 ! organogenesis stage +relationship: existence_starts_during UBERON:0000109 ! gastrula stage +relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +relationship: part_of UBERON:0000926 ! mesoderm + +[Term] +id: UBERON:0003887 +name: intraembryonic coelom +namespace: uberon +def: "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom" [MGI:anna, MP:0012187] +subset: pheno_slim +synonym: "somatic coelom" EXACT [http://en.wikipedia.org/wiki/Intraembryonic_coelom] +xref: EHDAA:251 +xref: EMAPA:16088 +xref: http://linkedlifedata.com/resource/umls/id/C1512940 +xref: Intraembryonic:coelom +xref: NCIT:C34195 +xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} +xref: VHOG:0000316 +is_a: UBERON:0002050 ! embryonic structure +relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm +relationship: part_of UBERON:0011997 ! coelom +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string +property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166"} + +[Term] +id: UBERON:0003914 +name: epithelial tube +namespace: uberon +def: "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." [GO:0060562, http://www.ncbi.nlm.nih.gov/pubmed/12526790] +synonym: "epithelial or endothelial tube" EXACT [] +xref: AEO:0000114 +xref: EHDAA2:0003114 +xref: FBbt:00007474 +is_a: UBERON:0000025 ! tube +is_a: UBERON:0000483 ! epithelium +property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string + +[Term] +id: UBERON:0003915 +name: endothelial tube +namespace: uberon +def: "Any endothelium that has the quality of being cylindrical [Automatically generated definition]." [OBOL:automatic] +is_a: UBERON:0001986 ! endothelium +is_a: UBERON:0003914 ! epithelial tube + +[Term] +id: UBERON:0003920 +name: venous blood vessel +namespace: uberon +def: "A blood vessel that carries blood from the capillaries toward the heart" [http://www.thefreedictionary.com/venous+blood+vessel] +comment: Compare to: vein +synonym: "segment of venous tree organ" EXACT [FMA:86188] +synonym: "venous tree organ segment" EXACT [FMA:86188] +xref: EMAPA:35932 +xref: FMA:86188 +xref: MA:0000066 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0004582 ! venous system +relationship: part_of UBERON:0004582 ! venous system + +[Term] +id: UBERON:0003928 +name: digestive system duct +namespace: uberon +def: "A duct that is part of a digestive system [Automatically generated definition]." [OBOL:automatic] +synonym: "duct of digestive system" EXACT [OBOL:automatic] +synonym: "duct of gastrointestinal system" EXACT [OBOL:automatic] +synonym: "gastrointestinal system duct" EXACT [OBOL:automatic] +xref: TAO:0005162 +xref: ZFA:0005162 +is_a: UBERON:0000058 ! duct +intersection_of: UBERON:0000058 ! duct +intersection_of: part_of UBERON:0001007 ! digestive system +relationship: part_of UBERON:0001007 ! digestive system + +[Term] +id: UBERON:0003929 +name: digestive tract epithelium +namespace: uberon +def: "An epithelium that lines the lumen of the digestive tract." [http://orcid.org/0000-0002-6601-2165] +synonym: "alimentary tract epithelium" RELATED [OBOL:automatic] +synonym: "digestive tract epithelial tissue" EXACT [OBOL:automatic] +synonym: "epithelial tissue of digestive tract" EXACT [OBOL:automatic] +synonym: "epithelial tissue of gut" EXACT [OBOL:automatic] +synonym: "epithelium of digestive tract" EXACT [OBOL:automatic] +synonym: "epithelium of gut" EXACT [OBOL:automatic] +synonym: "gastrodermis" EXACT SENSU [BGEE:ANN, NCBITaxon:6073] +synonym: "gut epithelial tissue" EXACT [OBOL:automatic] +synonym: "gut epithelium" EXACT [EHDAA2:0004567, MA:0003201, ZFA:0005123] +xref: BTO:0000956 +xref: EHDAA2:0004567 +xref: EMAPA:32928 +xref: http://linkedlifedata.com/resource/umls/id/C0836205 +xref: MA:0003201 +xref: NCIT:C12963 +xref: TAO:0005123 +xref: UMLS:C0836205 {source="ncithesaurus:Gut_Epithelium"} +xref: XAO:0003200 +xref: ZFA:0005123 +is_a: UBERON:0000483 ! epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001555 ! digestive tract +relationship: part_of UBERON:0001555 ! digestive tract +property_value: UBPROP:0000001 "Epithelium lining the lumen of the gut.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005123", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000008 "" xsd:string + +[Term] +id: UBERON:0003967 +name: cutaneous elastic tissue +namespace: uberon +def: "The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity" [MP:0008418] +subset: pheno_slim +synonym: "cutaneous elastic fiber" NARROW [MP:0008418] +synonym: "dermal elastic fiber" NARROW [MP:0008418] +xref: EMAPA:37841 {source="MA:th"} +is_a: UBERON:0002521 ! elastic tissue +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0002521 ! elastic tissue +intersection_of: part_of UBERON:0000014 ! zone of skin +relationship: contributes_to_morphology_of UBERON:0000014 ! zone of skin +relationship: part_of UBERON:0000014 ! zone of skin + +[Term] +id: UBERON:0004015 +name: embryonic-extraembryonic boundary +namespace: uberon +def: "The connection between the embryo proper and extraembryonic tissues" [MP:0003890] +subset: pheno_slim +is_a: UBERON:0000015 ! non-material anatomical boundary +intersection_of: UBERON:0000015 ! non-material anatomical boundary +intersection_of: adjacent_to UBERON:0000478 ! extraembryonic structure +intersection_of: adjacent_to UBERON:0002050 ! embryonic structure +relationship: adjacent_to UBERON:0000478 ! extraembryonic structure +relationship: adjacent_to UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0004016 +name: dermatome +namespace: uberon +def: "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." [AEO:0001017, AEO:JB] +subset: pheno_slim +synonym: "cutis plate" EXACT [http://en.wikipedia.org/wiki/Cutis_plate] +synonym: "dermatomal mesenchyme" EXACT [http://en.wikipedia.org/wiki/Cutis_plate] +synonym: "epimere mesoderm" RELATED [] +synonym: "mesenchyma dermatomiale" RELATED LATIN [http://en.wikipedia.org/wiki/Dermatomal_mesenchyme] +xref: AAO:0011028 +xref: AEO:0001017 +xref: Dermatome:(embryology) +xref: EHDAA2_RETIRED:0003428 +xref: EHDAA:1719 +xref: EHDAA:1725 +xref: EHDAA:1731 +xref: EHDAA:1737 +xref: EMAPA:32838 +xref: FMA:295656 +xref: http://linkedlifedata.com/resource/umls/id/C0180383 +xref: NCIT:C61572 +xref: UMLS:C0180383 {source="ncithesaurus:Dermatome"} +xref: XAO:0000220 +is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure +relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png +property_value: UBPROP:0000013 "Not to be confused with 'dermatome segment of skin'." xsd:string + +[Term] +id: UBERON:0004022 +name: germinal neuroepithelium +namespace: uberon +def: "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells" [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0004261] +subset: pheno_slim +synonym: "germinal neuroepithelial layer" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "germinal neuroepithelium" EXACT [NCBIBook:NBK10047] +synonym: "original neural tube" EXACT [NCBIBook:NBK10047] +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium +relationship: adjacent_to UBERON:0003842 ! neural tube lumen +relationship: bounding_layer_of UBERON:0001049 ! neural tube +relationship: part_of UBERON:0001049 ! neural tube +property_value: UBPROP:0000011 "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" xsd:string + +[Term] +id: UBERON:0004060 +name: neural tube ventricular layer +namespace: uberon +def: "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium" [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009689] +subset: pheno_slim +synonym: "ependymal layer" BROAD [NCBIBook:NBK10047] +synonym: "neural tube ependymal layer" EXACT [NCBIBook:NBK10047] +synonym: "neural tube ependymal zone" NARROW [MP:0009689] +synonym: "neural tube ventricular germinal zone" EXACT [NCBIBook:NBK10047] +synonym: "neural tube ventricular zone" EXACT [MP:0009689] +xref: EMAPA:17152 +xref: EMAPA:35362 +xref: EMAPA_RETIRED:16783 +xref: MA:0003193 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium +relationship: adjacent_to UBERON:0003842 ! neural tube lumen +relationship: develops_from UBERON:0004022 ! germinal neuroepithelium +relationship: immediate_transformation_of UBERON:0004022 {source="NCBIBook:NBK10047"} ! germinal neuroepithelium +relationship: part_of UBERON:0001049 ! neural tube +property_value: IAO:0000116 "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string +property_value: UBPROP:0000001 "The layer of undifferentiated, proliferating cells that line the neural tube lumen" xsd:string {source="MP:0009689"} + +[Term] +id: UBERON:0004061 +name: neural tube mantle layer +namespace: uberon +def: "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer." [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] +subset: pheno_slim +synonym: "future brain marginal layer" RELATED [EMAPA:35360] +synonym: "neural tube intermediate zone" EXACT [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009690] +xref: EMAPA:17148 +xref: EMAPA:35360 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1367 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0034707 {source="NCBIBook:NBK10047"} ! differentiating neuroepithelium +relationship: adjacent_to UBERON:0004060 ! neural tube ventricular layer +relationship: adjacent_to UBERON:0004062 ! neural tube marginal layer +relationship: develops_from UBERON:0004022 {notes="by division", source="NCBIBook:NBK10047"} ! germinal neuroepithelium +relationship: part_of UBERON:0001049 ! neural tube + +[Term] +id: UBERON:0004062 +name: neural tube marginal layer +namespace: uberon +def: "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter" [http://www.ncbi.nlm.nih.gov/books/NBK10047, MP:0009691] +subset: pheno_slim +synonym: "brain marginal zone" RELATED [] +synonym: "neural tube marginal zone" EXACT [MP:0009691] +xref: EMAPA:17151 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1368 +is_a: UBERON:0005162 ! multi cell part structure +relationship: adjacent_to UBERON:0004061 ! neural tube mantle layer +relationship: develops_from UBERON:0004061 {notes="forms from axons"} ! neural tube mantle layer +relationship: part_of UBERON:0001049 ! neural tube + +[Term] +id: UBERON:0004111 +name: anatomical conduit +namespace: uberon +def: "Any tube, opening or passage that connects two distinct anatomical spaces." [http://orcid.org/0000-0002-6601-2165] +synonym: "foramen" NARROW [EHDAA2:0003080] +synonym: "foramina" NARROW PLURAL [https://orcid.org/0000-0002-6601-2165] +synonym: "opening" RELATED [] +synonym: "ostia" RELATED PLURAL [] +synonym: "ostium" RELATED [] +xref: AEO:0000080 +xref: EHDAA2:0003080 +xref: FMA:242873 +xref: http://en.wikipedia.org/wiki/Foramen +xref: http://www.snomedbrowser.com/Codes/Details/346902003 +is_a: UBERON:0010000 ! multicellular anatomical structure +intersection_of: UBERON:0010000 ! multicellular anatomical structure +intersection_of: conduit_for UBERON:0000061 ! anatomical structure +intersection_of: has_part UBERON:0013686 ! anatomical conduit space +relationship: conduit_for UBERON:0000061 ! anatomical structure +relationship: connects UBERON:0000464 {minCardinality="2", maxCardinality="2"} ! anatomical space +relationship: has_part UBERON:0013686 ! anatomical conduit space +property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0004119 +name: endoderm-derived structure +namespace: uberon +def: "An anatomical structure that develops (entirely or partially) from the endoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: develops_from UBERON:0000925 ! endoderm +relationship: develops_from UBERON:0000925 ! endoderm +property_value: IAO:0000232 "Grouping term for query purposes" xsd:string + +[Term] +id: UBERON:0004120 +name: mesoderm-derived structure +namespace: uberon +def: "An anatomical structure that develops (entirely or partially) from the mesoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "mesodermal derivative" EXACT [FBbt:00025998] +xref: FBbt:00025998 +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: develops_from UBERON:0000926 ! mesoderm +relationship: develops_from UBERON:0000926 ! mesoderm +property_value: IAO:0000232 "Grouping term for query purposes" xsd:string + +[Term] +id: UBERON:0004121 +name: ectoderm-derived structure +namespace: uberon +def: "An anatomical structure that develops (entirely or partially) from the ectoderm." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "ectodermal deriviative" EXACT [FBbt:00025990] +xref: FBbt:00025990 +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: develops_from UBERON:0000924 ! ectoderm +relationship: develops_from UBERON:0000924 ! ectoderm +property_value: IAO:0000232 "Grouping term for query purposes" xsd:string + +[Term] +id: UBERON:0004139 +name: cardiogenic plate +namespace: uberon +def: "The first recognizable structure derived from the heart field" [GO:0003142] +subset: pheno_slim +synonym: "cardiac crescent" RELATED [EMAPA:16106] +synonym: "cardiogenic crescent" RELATED [GO:0003142] +synonym: "heart rudiment" RELATED [] +synonym: "myocardial plate" EXACT [EHDAA2:0000215] +xref: EHDAA2:0000215 +xref: EMAPA:16106 +xref: VHOG:0000975 +is_a: UBERON:0002050 ! embryonic structure +relationship: develops_from UBERON:0003084 ! heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string +property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="http://bgee.unil.ch/", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)"} + +[Term] +id: UBERON:0004140 +name: primary heart field +namespace: uberon +def: "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle." [GO:0003138, GOC:mtg_heart, GOC:rl] +synonym: "FHF" RELATED ABBREVIATION [XAO:0004185] +synonym: "first heart field" EXACT [XAO:0004185] +synonym: "heart field" RELATED [XAO:0004185] +synonym: "PHF" RELATED ABBREVIATION [XAO:0004185] +synonym: "primary heart field" EXACT [http://www.ncbi.nlm.nih.gov/pubmed/17276708, XAO:0004185] +xref: XAO:0004185 +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007688 ! anlage +relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm +relationship: part_of UBERON:0036146 {source="BGEE:ann"} ! cardiopharyngeal field +property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} + +[Term] +id: UBERON:0004141 +name: heart tube +namespace: uberon +def: "An epithelial tube that will give rise to the mature heart." [GO:0003143, GOC:mtg_heart] +subset: efo_slim +subset: pheno_slim +subset: vertebrate_core +synonym: "embryonic heart tube" EXACT [GO:0003143] +synonym: "endocardial heart tube" EXACT [MP:0012700] +synonym: "endocardial tube" EXACT [XAO:0000337] +xref: AAO:0010411 +xref: EFO:0003526 +xref: EMAPA:32685 +xref: NCIT:C34161 +xref: TAO:0000360 +xref: XAO:0000337 +xref: ZFA:0000360 +is_a: UBERON:0003914 ! epithelial tube +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0012275 ! meso-epithelium +relationship: develops_from UBERON:0005498 ! primitive heart tube +relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube +property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} + +[Term] +id: UBERON:0004142 +name: outflow tract septum +namespace: uberon +def: "The outflow tract septum is a partition in the outflow tract" [GO:0003148] +is_a: UBERON:0002099 ! cardiac septum +intersection_of: UBERON:0002099 ! cardiac septum +intersection_of: part_of UBERON:0004145 ! outflow tract +relationship: part_of UBERON:0004145 ! outflow tract + +[Term] +id: UBERON:0004145 +name: outflow tract +namespace: uberon +def: "The outflow tract is the portion of the heart through which blood flows into the arteries" [GO:0003151] +subset: pheno_slim +synonym: "arterial (outflow) pole" RELATED [http://www.ncbi.nlm.nih.gov/pubmed/20735616] +synonym: "cardiac outflow tract" EXACT [http://www.ncbi.nlm.nih.gov/pubmed/20735616] +synonym: "heart outflow tract" EXACT [] +xref: EHDAA2:0001351 +xref: EHDAA:464 +xref: EHDAA:798 +xref: EMAPA:16346 +xref: MA:0000100 +xref: VHOG:0000670 +xref: XAO:0004139 +is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: channel_for UBERON:0000178 ! blood +relationship: channels_from UBERON:0000948 ! heart +relationship: channels_into UBERON:0001637 ! artery +relationship: part_of UBERON:0000948 ! heart +property_value: UBPROP:0000008 "Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]" xsd:string + +[Term] +id: UBERON:0004151 +name: cardiac chamber +namespace: uberon +def: "A cardiac chamber surrounds an enclosed cavity within the heart" [GO:0003205] +comment: generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus +synonym: "chamber of heart" EXACT [] +synonym: "heart chamber" EXACT [] +xref: FMA:7095 +xref: http://www.snomedbrowser.com/Codes/Details/276456008 +xref: OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw +is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: part_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0004177 +name: hemopoietic organ +namespace: uberon +def: "Organ that is part of the hematopoietic system." [GOC:Obol] +subset: organ_slim +subset: pheno_slim +synonym: "haematological system organ" EXACT [OBOL:automatic] +synonym: "haemopoietic system organ" EXACT [OBOL:automatic] +synonym: "hematopoeitic or lymphoid organ" NARROW [] +synonym: "hematopoeitic organ" EXACT [] +synonym: "hematopoietic system organ" EXACT [OBOL:automatic] +synonym: "lymph organ" NARROW [MA:0000747] +synonym: "lymphoid organ" NARROW [BTO:0004605, FMA:7143] +synonym: "organ of haematological system" EXACT [OBOL:automatic] +synonym: "organ of haemopoietic system" EXACT [OBOL:automatic] +synonym: "organ of hematopoietic system" EXACT [OBOL:automatic] +synonym: "organ of organa haemopoietica" EXACT [OBOL:automatic] +synonym: "organa haemopoietica organ" EXACT [OBOL:automatic] +xref: BTO:0004605 +xref: EMAPA:37665 {source="MA:th"} +xref: FMA:7143 +xref: http://www.snomedbrowser.com/Codes/Details/361338006 +xref: MA:0000747 +is_a: UBERON:0000062 ! organ +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000062 ! organ +intersection_of: part_of UBERON:0002390 ! hematopoietic system +relationship: part_of UBERON:0002390 ! hematopoietic system +property_value: IAO:0000116 "consider splitting out lymph organ, compare with lymph node" xsd:string +property_value: UBPROP:0000001 "the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]." xsd:string {source="http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs"} +property_value: UBPROP:0000012 "the FMA class 'lymphoid organ' is a general anatomical term" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0004185 +name: endodermal part of digestive tract +namespace: uberon +def: "A portions of the gut that is derived from endoderm." [GO:0061031] +synonym: "endodermal gut" EXACT [] +synonym: "gut endoderm" EXACT [EMAPA:32930] +xref: EMAPA:32930 +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004921 ! subdivision of digestive tract +intersection_of: UBERON:0004921 ! subdivision of digestive tract +intersection_of: develops_from UBERON:0000925 ! endoderm +intersection_of: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0004225 +name: respiratory system smooth muscle +namespace: uberon +def: "A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "airway smooth muscle" RELATED [BTO:0001660] +synonym: "airway smooth muscle cell" RELATED [BTO:0001660] +synonym: "respiratory smooth muscle" EXACT [BTO:0001660] +synonym: "smooth muscle of respiratory system" EXACT [OBOL:automatic] +xref: BTO:0001660 +xref: EMAPA:35734 +xref: MA:0001830 +is_a: UBERON:0001135 ! smooth muscle tissue +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0004233 +name: lower respiratory tract smooth muscle +namespace: uberon +def: "A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] +synonym: "involuntary muscle of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "lower respiratory tract involuntary muscle" EXACT [OBOL:automatic] +synonym: "lower respiratory tract non-striated muscle" EXACT [OBOL:automatic] +synonym: "lower respiratory tract smooth muscle tissue" EXACT [OBOL:automatic] +synonym: "non-striated muscle of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "smooth muscle of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "smooth muscle tissue of lower respiratory tract" EXACT [OBOL:automatic] +xref: EMAPA:35520 +xref: MA:0002410 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0004225 ! respiratory system smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0001558 ! lower respiratory tract +relationship: part_of UBERON:0001558 ! lower respiratory tract + +[Term] +id: UBERON:0004236 +name: arteriole smooth muscle +namespace: uberon +def: "A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:36287 +xref: FMA:312251 +xref: MA:0000706 +is_a: UBERON:0004237 ! blood vessel smooth muscle +is_a: UBERON:0004695 ! arterial system smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0001980 ! arteriole +relationship: part_of UBERON:0001980 ! arteriole + +[Term] +id: UBERON:0004237 +name: blood vessel smooth muscle +namespace: uberon +alt_id: UBERON:0010508 +def: "smooth muscle found within, and composing the majority of the wall of blood vessels." [http://en.wikipedia.org/wiki/Vascular_smooth_muscle] +subset: pheno_slim +synonym: "blood vessel involuntary muscle" EXACT [OBOL:automatic] +synonym: "blood vessel non-striated muscle" EXACT [OBOL:automatic] +synonym: "blood vessel smooth muscle tissue" EXACT [OBOL:automatic] +synonym: "involuntary muscle of blood vessel" EXACT [OBOL:automatic] +synonym: "non-striated muscle of blood vessel" EXACT [OBOL:automatic] +synonym: "smooth muscle of blood vessel" EXACT [OBOL:automatic] +synonym: "smooth muscle tissue of blood vessel" EXACT [OBOL:automatic] +synonym: "vascular smooth muscle" EXACT [ZFA:0005321] +synonym: "vascular smooth muscle tissue" EXACT [] +xref: BTO:0001431 +xref: CALOHA:TS-1107 +xref: EMAPA:35177 +xref: http://en.wikipedia.org/wiki/Vascular_smooth_muscle +xref: http://linkedlifedata.com/resource/umls/id/C1519956 +xref: MA:0000710 +xref: MESH:D009131 +xref: NCIT:C33853 +xref: TAO:0005321 +xref: UMLS:C1519956 {source="ncithesaurus:Vascular_Smooth_Muscle_Tissue"} +xref: ZFA:0005321 +is_a: UBERON:0001135 ! smooth muscle tissue +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0001981 ! blood vessel +relationship: part_of UBERON:0001981 ! blood vessel +property_value: UBPROP:0000009 "Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension." xsd:string + +[Term] +id: UBERON:0004246 +name: outflow tract smooth muscle +namespace: uberon +def: "A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]." [OBOL:automatic] +synonym: "involuntary muscle of outflow tract" EXACT [OBOL:automatic] +synonym: "non-striated muscle of outflow tract" EXACT [OBOL:automatic] +synonym: "outflow tract involuntary muscle" EXACT [OBOL:automatic] +synonym: "outflow tract non-striated muscle" EXACT [OBOL:automatic] +synonym: "outflow tract smooth muscle tissue" EXACT [OBOL:automatic] +synonym: "smooth muscle of outflow tract" EXACT [OBOL:automatic] +synonym: "smooth muscle tissue of outflow tract" EXACT [OBOL:automatic] +xref: EMAPA:37708 {source="MA:th"} +xref: MA:0000492 +is_a: UBERON:0001135 ! smooth muscle tissue +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0004145 ! outflow tract +relationship: part_of UBERON:0004145 ! outflow tract + +[Term] +id: UBERON:0004253 +name: skin muscle +namespace: uberon +alt_id: UBERON:0015797 +def: "Any muscle organ that is part of a skin of body [Automatically generated definition]." [OBOL:automatic] +synonym: "integumental system muscle" EXACT [MA:0003139] +synonym: "muscle of integumental system" EXACT [EMAPA:18187] +synonym: "muscle organ of skin" EXACT [OBOL:automatic] +synonym: "skin muscle organ" EXACT [OBOL:automatic] +xref: EMAPA:18187 +xref: EMAPA:35776 +xref: MA:0002710 +xref: MA:0003139 +is_a: UBERON:0001630 ! muscle organ +intersection_of: UBERON:0001630 ! muscle organ +intersection_of: part_of UBERON:0002416 ! integumental system +relationship: located_in UBERON:0002097 ! skin of body +relationship: part_of UBERON:0002416 ! integumental system +property_value: IAO:0000116 "review as part of general integumentary system review - part of skin, or more generally, integumental system" xsd:string +property_value: UBPROP:0000012 "in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0004258 +name: back blood vessel +namespace: uberon +def: "A blood vessel that is part of a back [Automatically generated definition]." [OBOL:automatic] +synonym: "blood vessel of back" EXACT [OBOL:automatic] +xref: EMAPA:37243 {source="MA:th"} +xref: MA:0000493 +is_a: UBERON:0001981 ! blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0001137 ! dorsum +relationship: part_of UBERON:0001137 ! dorsum + +[Term] +id: UBERON:0004267 +name: back connective tissue +namespace: uberon +def: "A portion of connective tissue that is part of a back [Automatically generated definition]." [OBOL:automatic] +synonym: "mesenchyne of back" RELATED [OBOL:automatic] +xref: EMAPA:37256 {source="MA:th"} +xref: MA:0000495 +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: part_of UBERON:0001137 ! dorsum +relationship: part_of UBERON:0001137 ! dorsum + +[Term] +id: UBERON:0004288 +name: skeleton +namespace: uberon +def: "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." [VSAO:0000026] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +synonym: "set of all bones" EXACT [] +synonym: "set of bones of body" EXACT [] +xref: AEO:0000168 +xref: EHDAA2:0001843 +xref: EHDAA:5047 +xref: EMAPA:17213 +xref: FMA:23875 +xref: GAID:177 +xref: galen:Skeleton +xref: http://en.wikipedia.org/wiki/Skeleton +xref: http://www.snomedbrowser.com/Codes/Details/361378004 +xref: MA:0003006 +xref: MAT:0000032 +xref: MESH:D012863 +xref: MIAA:0000032 +xref: OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA +xref: VSAO:0000026 +xref: XAO:0004053 +is_a: UBERON:0034925 ! anatomical collection +disjoint_from: UBERON:0004770 ! articular system +relationship: has_member UBERON:0004765 ! skeletal element +relationship: part_of UBERON:0001434 ! skeletal system +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/The-skeletal-system xsd:anyURI +property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} +property_value: UBPROP:0000007 "skeletal" xsd:string + +[Term] +id: UBERON:0004290 +name: dermomyotome +namespace: uberon +def: "The bilaminar epithelium formed from the myotome and dermatome." [AEO:0000214] +synonym: "dermamyotome" RELATED [VHOG:0000676] +synonym: "dermomyotomes" RELATED PLURAL [VHOG:0000676] +xref: AAO:0010572 +xref: AEO:0000214 +xref: EHDAA2:0003259 +xref: EMAPA:31109 +xref: FMA:295654 +xref: http://linkedlifedata.com/resource/umls/id/C1511786 +xref: NCIT:C34140 +xref: TAO:0001513 +xref: UMLS:C1511786 {source="ncithesaurus:Dermomyotome"} +xref: VHOG:0000676 +xref: ZFA:0001513 +is_a: UBERON:0000486 {source="AEO"} ! multilaminar epithelium +is_a: UBERON:0016888 {source="AEO"} ! transitional anatomical structure +relationship: develops_from UBERON:0002329 {source="EHDAA2", source="ZFA"} ! somite +property_value: UBPROP:0000001 "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." xsd:string {source="http://medical-dictionary.thefreedictionary.com/dermomyotome"} +property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." xsd:string {source="http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768"} +property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001513", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000001 "Portion of somites that gives rise to dermis and muscles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010572", ontology="AAO", source="AAO:EJS"} +property_value: UBPROP:0000003 "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000676", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)"} + +[Term] +id: UBERON:0004291 +name: heart rudiment +namespace: uberon +def: "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube." [GO:0003313] +synonym: "heart cone" EXACT [GO:0003313] +synonym: "rudimentary heart" EXACT [ZFA:0000115] +xref: TAO:0000115 +xref: ZFA:0000115 +is_a: UBERON:0012275 ! meso-epithelium +relationship: develops_from UBERON:0004139 ! cardiogenic plate +property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0004297 +name: respiratory system blood vessel smooth muscle +namespace: uberon +def: "A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "smooth muscle tissue of blood vessel of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:37573 {source="MA:th"} +xref: MA:0001806 +is_a: UBERON:0004225 ! respiratory system smooth muscle +is_a: UBERON:0004237 ! blood vessel smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0003504 ! respiratory system blood vessel +relationship: part_of UBERON:0003504 ! respiratory system blood vessel + +[Term] +id: UBERON:0004363 +name: pharyngeal arch artery +namespace: uberon +alt_id: UBERON:0004342 +def: "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]" [MP:0002672] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "a. arcuum pharyngeorum" RELATED LATIN [http://en.wikipedia.org/wiki/Aortic_arches] +synonym: "aortic arch" EXACT [ZFA:0005004] +synonym: "aortic arch artery" RELATED [EMAPA:16684] +synonym: "aortic arches" EXACT PLURAL [ZFA:0005004] +synonym: "arteriae arcuum pharyngeorum" RELATED LATIN [http://en.wikipedia.org/wiki/Aortic_arches] +synonym: "branchial aortic arches" EXACT PLURAL [ZFIN:ZDB-PUB-080512-6] +synonym: "branchial aortic arches" RELATED PLURAL [ZFA:0005004\,ZFIN\:ZDB-PUB-080512-6] +synonym: "branchial arch artery" EXACT [EMAPA:16684] +synonym: "embryonic aortic arch artery" EXACT [EMAPA:16684, MP:0002672] +synonym: "PAA" EXACT ABBREVIATION [MP:0002672] +synonym: "pharyngeal arch arteries" RELATED PLURAL [] +synonym: "pharyngeal arch artery" EXACT [MP:0002672] +synonym: "pharyngeal arch artery" RELATED [VHOG:0000122] +xref: AAO:0010414 +xref: Aortic:arches +xref: EFO:0003695 +xref: EHDAA2:0000186 +xref: EHDAA:398 +xref: EHDAA:7327 +xref: EMAPA:16684 +xref: http://linkedlifedata.com/resource/umls/id/C0003489 +xref: NCIT:C32123 +xref: TAO:0005004 +xref: UMLS:C0003489 {source="ncithesaurus:Aortic_Arch"} +xref: VHOG:0000122 +xref: XAO:0000341 +xref: ZFA:0005004 +is_a: UBERON:0003469 ! respiratory system artery +is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: contributes_to_morphology_of UBERON:0002539 ! pharyngeal arch +relationship: has_potential_to_develop_into UBERON:0001637 ! artery +relationship: part_of UBERON:0002539 ! pharyngeal arch +relationship: part_of UBERON:0007303 {source="ZFA"} ! pharyngeal vasculature +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png +property_value: IAO:0000116 "add specific artery derivatives" xsd:string +property_value: IAO:0000232 "Do not confuse with arch of aorta." xsd:string +property_value: UBPROP:0000001 "Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aortic+arches"} +property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620"} +property_value: UBPROP:0000008 "Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods" xsd:string +property_value: UBPROP:0000011 "The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches" xsd:string + +[Term] +id: UBERON:0004455 +name: neurula embryo +namespace: uberon +alt_id: UBERON:0007013 +def: "An embryo at the neurula stage." [http://orcid.org/0000-0002-6601-2165] +synonym: "neurula" EXACT [BTO:0001766] +xref: BILA:0000061 +xref: BTO:0001766 +xref: http://linkedlifedata.com/resource/umls/id/C1518306 +xref: NCIT:C34229 +xref: UMLS:C1518306 {source="ncithesaurus:Neurula"} +is_a: UBERON:0000922 ! embryo +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: existence_starts_and_ends_during UBERON:0000110 ! neurula stage +relationship: develops_from UBERON:0004734 ! gastrula +relationship: existence_starts_and_ends_during UBERON:0000110 ! neurula stage + +[Term] +id: UBERON:0004464 +name: musculature of thorax +namespace: uberon +def: "Any collection of muscles that is part of a thorax [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "muscle group of thorax" EXACT [FMA:71293] +synonym: "muscles of thorax" EXACT [FMA:71293] +synonym: "musculi thoracis" EXACT LATIN [FMA:71293, FMA:TA] +synonym: "set of muscles of thorax" EXACT [FMA:71293] +synonym: "thoracic musculature" EXACT [FMA:71293] +xref: BTO:0000508 +xref: EMAPA:37260 {source="MA:th"} +xref: FMA:71293 +is_a: UBERON:0004479 ! musculature of trunk +intersection_of: UBERON:0001015 ! musculature +intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0000915 ! thoracic segment of trunk +property_value: UBPROP:0000012 "BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm" xsd:string {external_ontology="BTO"} + +[Term] +id: UBERON:0004465 +name: musculature of neck +namespace: uberon +def: "Any collection of muscles that is part of a neck [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "cervical muscles" EXACT [AAO:0000091] +synonym: "muscle group of neck" EXACT [FMA:71290] +synonym: "muscles of neck" EXACT [FMA:71290] +synonym: "musculi cervicis" EXACT LATIN [FMA:71290, FMA:TA] +synonym: "musculi colli" EXACT LATIN [FMA:71290, FMA:TA] +synonym: "neck musculature" EXACT [FMA:71290] +synonym: "set of muscles of neck" EXACT [FMA:71290] +xref: AAO:0000091 +xref: EMAPA:36050 +xref: FMA:71290 +xref: MESH:D009334 +is_a: UBERON:0008229 ! craniocervical region musculature +intersection_of: UBERON:0001015 ! musculature +intersection_of: part_of UBERON:0000974 ! neck +relationship: part_of UBERON:0000974 ! neck + +[Term] +id: UBERON:0004469 +name: musculature of back +namespace: uberon +def: "Any collection of muscles that is part of a back [Automatically generated definition]." [OBOL:automatic] +synonym: "muscle group of back" EXACT [FMA:71291] +synonym: "muscles of back" EXACT [FMA:71291] +synonym: "musculi dorsi" EXACT LATIN [FMA:71291, FMA:TA] +synonym: "set of muscles of back" EXACT [FMA:71291] +xref: FMA:71291 +is_a: UBERON:0001015 ! musculature +intersection_of: UBERON:0001015 ! musculature +intersection_of: part_of UBERON:0001137 ! dorsum +relationship: part_of UBERON:0001137 ! dorsum + +[Term] +id: UBERON:0004473 +name: musculature of face +namespace: uberon +def: "Any collection of muscles that is part of a face." [OBOL:automatic] +subset: pheno_slim +synonym: "entire facial musculature" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "facial muscles" EXACT [FMA:71288] +synonym: "muscle group of face" EXACT [FMA:71288] +synonym: "musculi faciei" EXACT LATIN [FMA:71288, FMA:TA] +synonym: "set of facial muscles" RELATED [FMA:71288] +synonym: "set of muscles of face" RELATED [FMA:71288] +xref: FMA:71288 +is_a: UBERON:0008229 ! craniocervical region musculature +intersection_of: UBERON:0001015 ! musculature +intersection_of: part_of UBERON:0001456 ! face +relationship: part_of UBERON:0001456 ! face +property_value: IAO:0000116 "originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose" xsd:string + +[Term] +id: UBERON:0004479 +name: musculature of trunk +namespace: uberon +def: "Any collection of muscles that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +subset: efo_slim +subset: pheno_slim +synonym: "muscle group of trunk" EXACT [FMA:50187] +synonym: "muscular system of trunk" RELATED [FMA:50187] +synonym: "set of muscles of trunk" EXACT [FMA:50187] +xref: AAO:0011572 +xref: EFO:0003531 +xref: FMA:50187 +is_a: UBERON:0001015 ! musculature +intersection_of: UBERON:0001015 ! musculature +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string + +[Term] +id: UBERON:0004521 +name: vasculature of muscle organ +namespace: uberon +def: "A vasculature that is part of a muscle organ [Automatically generated definition]." [OBOL:automatic] +synonym: "muscular organ vasculature" EXACT [FMA:87123] +xref: FMA:87123 +is_a: UBERON:0004522 ! vasculature of musculoskeletal system +is_a: UBERON:0006876 ! vasculature of organ +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0001630 ! muscle organ +relationship: part_of UBERON:0001630 ! muscle organ + +[Term] +id: UBERON:0004522 +name: vasculature of musculoskeletal system +namespace: uberon +def: "A vasculature that is part of a musculoskeletal system [Automatically generated definition]." [OBOL:automatic] +xref: FMA:239607 +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0002204 ! musculoskeletal system +relationship: part_of UBERON:0002204 ! musculoskeletal system + +[Term] +id: UBERON:0004535 +name: cardiovascular system +namespace: uberon +def: "Anatomical system that has as its parts the heart and blood vessels." [BTO:0000088] +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "CV system" RELATED [BTO:0000088] +synonym: "Herz und Gefaesssystem" RELATED [BTO:0000088] +xref: AAO:0011001 +xref: BILA:0000016 +xref: BTO:0000088 +xref: CALOHA:TS-1297 +xref: EFO:0000791 +xref: EHDAA2:0000216 +xref: EHDAA:394 +xref: EMAPA:16104 +xref: EMAPA:16370 +xref: EV:0100017 +xref: FMA:7161 +xref: GAID:467 +xref: http://linkedlifedata.com/resource/umls/id/C0007226 +xref: http://www.snomedbrowser.com/Codes/Details/278198007 +xref: MA:0000010 +xref: MAT:0000016 +xref: MESH:D002319 +xref: MIAA:0000016 +xref: NCIT:C12686 +xref: OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA +xref: TAO:0000010 +xref: UMLS:C0007226 {source="ncithesaurus:Cardiovascular_System"} +xref: VHOG:0000302 +xref: WikipediaCategory:Cardiovascular_system +xref: XAO:0000100 +xref: XAO:0001010 +xref: ZFA:0000010 +is_a: UBERON:0000467 ! anatomical system +intersection_of: UBERON:0000467 ! anatomical system +intersection_of: has_part UBERON:0000948 ! heart +intersection_of: has_part UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0001009 ! circulatory system +relationship: has_part UBERON:0000948 ! heart +relationship: has_part UBERON:0001981 ! blood vessel +relationship: part_of UBERON:0001009 ! circulatory system +property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string +property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451"} + +[Term] +id: UBERON:0004537 +name: blood vasculature +namespace: uberon +def: "A vascular network consisting of blood vessels." [https://orcid.org/0000-0002-6601-2165] +synonym: "blood system" RELATED [] +synonym: "blood vascular network" EXACT [] +synonym: "blood vessel system" RELATED [] +synonym: "blood vessels" RELATED [TAO:0001079] +synonym: "set of blood vessels" EXACT [] +xref: TAO:0001079 +xref: ZFA:0001079 +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel +relationship: composed_primarily_of UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0004571 +name: systemic arterial system +namespace: uberon +def: "The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart." [http://en.wikipedia.org/wiki/Systemic_circulation#Arteries, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "systemic arterial circulatory system" EXACT [FMA:45623] +xref: Arteries +xref: FMA:45623 +is_a: UBERON:0007798 {source="MA-inferred"} ! vascular system +relationship: part_of UBERON:0004572 ! arterial system + +[Term] +id: UBERON:0004572 +name: arterial system +namespace: uberon +def: "The part of the cardiovascular system consisting of all arteries." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +xref: BTO:0004690 +xref: EHDAA2:0000143 +xref: EHDAA:396 +xref: EMAPA:16201 +xref: EMAPA:16371 +xref: http://www.snomedbrowser.com/Codes/Details/362030008 +xref: MA:0002719 +xref: VHOG:0000273 +is_a: UBERON:0007798 {source="MA"} ! vascular system +relationship: has_member UBERON:0001637 ! artery +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000273", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)"} + +[Term] +id: UBERON:0004573 +name: systemic artery +namespace: uberon +def: "An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart." [http://en.wikipedia.org/wiki/Artery#Systemic_arteries, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "systemic arterial subtree" EXACT [FMA:66464] +xref: EMAPA:37126 {source="MA:th"} +xref: FMA:66464 +xref: Systemic_arteries +is_a: UBERON:0001637 ! artery +intersection_of: UBERON:0001637 ! artery +intersection_of: part_of UBERON:0004571 ! systemic arterial system +relationship: part_of UBERON:0004571 ! systemic arterial system + +[Term] +id: UBERON:0004581 +name: systemic venous system +namespace: uberon +def: "The part of the venous system that drains the general body tissues[Kardong]" [http://en.wikipedia.org/wiki/Systemic_venous_system, ISBN10:0073040584] +synonym: "systemic venous circulatory system" EXACT [FMA:45626] +xref: FMA:45626 +xref: http://en.wikipedia.org/wiki/Systemic_venous_system +is_a: UBERON:0002049 ! vasculature +relationship: part_of UBERON:0004582 ! venous system +property_value: UBPROP:0000001 "In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]" xsd:string {source="http://en.wikipedia.org/wiki/Systemic_venous_system"} +property_value: UBPROP:0000001 "Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]" xsd:string {ontology="FMA", source="FMA:45626"} +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)"} + +[Term] +id: UBERON:0004582 +name: venous system +namespace: uberon +def: "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." [https://orcid.org/0000-0002-6601-2165] +synonym: "vein system" EXACT [] +xref: BTO:0004692 +xref: EHDAA2:0002171 +xref: EHDAA:486 +xref: EMAPA:16240 +xref: http://linkedlifedata.com/resource/umls/id/C1267406 +xref: http://www.snomedbrowser.com/Codes/Details/362060003 +xref: MA:0002720 +xref: NCIT:C33858 +xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} +xref: VHOG:0000277 +is_a: UBERON:0007798 {source="MA"} ! vascular system +relationship: composed_primarily_of UBERON:0001638 ! vein +property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)"} + +[Term] +id: UBERON:0004638 +name: blood vessel endothelium +namespace: uberon +def: "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart" [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +subset: vertebrate_core +xref: BTO:0000766 +xref: CALOHA:TS-2155 +xref: EMAPA:35176 +xref: http://linkedlifedata.com/resource/umls/id/C1706972 +xref: MA:0000709 +xref: NCIT:C53395 +xref: TAO:0005257 +xref: UMLS:C1706972 {source="ncithesaurus:Blood_Vessel_Endothelium"} +xref: ZFA:0005257 +is_a: UBERON:0004852 ! cardiovascular system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0001981 ! blood vessel +relationship: part_of UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0004688 +name: costo-cervical trunk +namespace: uberon +def: "The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]." [http://en.wikipedia.org/wiki/Costocervical_trunk] +synonym: "costocervical trunk" EXACT [FMA:10636] +synonym: "truncus costocervicalis" RELATED LATIN [http://en.wikipedia.org/wiki/Costocervical_trunk] +synonym: "trunk of costocervical artery" EXACT [FMA:10636] +xref: Costocervical:trunk +xref: EMAPA:37496 {source="MA:th"} +xref: FMA:10636 +xref: http://www.snomedbrowser.com/Codes/Details/244225009 +xref: MA:0001939 +is_a: UBERON:0001637 ! artery +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png + +[Term] +id: UBERON:0004695 +name: arterial system smooth muscle +namespace: uberon +def: "A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:36503 +xref: MA:0000704 +is_a: UBERON:0001135 ! smooth muscle tissue +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0004572 ! arterial system +relationship: part_of UBERON:0004572 ! arterial system + +[Term] +id: UBERON:0004696 +name: venous system smooth muscle +namespace: uberon +def: "A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:36613 +xref: MA:0000715 +is_a: UBERON:0004237 ! blood vessel smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0004582 ! venous system +relationship: part_of UBERON:0004582 ! venous system + +[Term] +id: UBERON:0004699 +name: outflow tract endothelium +namespace: uberon +def: "An endothelium that is part of a outflow tract [Automatically generated definition]." [OBOL:automatic] +xref: MA:0000490 +xref: VHOG:0001524 +is_a: UBERON:0008307 ! heart endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0004145 ! outflow tract +relationship: part_of UBERON:0004145 ! outflow tract +property_value: UBPROP:0000003 "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001524", ontology="VHOG", source="http://bgee.unil.ch/", source="DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)"} + +[Term] +id: UBERON:0004700 +name: arterial system endothelium +namespace: uberon +def: "An endothelium that is part of an arterial system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:35145 +xref: http://linkedlifedata.com/resource/umls/id/C1706849 +xref: MA:0000703 +xref: NCIT:C49329 +xref: UMLS:C1706849 {source="ncithesaurus:Arterial_System_Endothelium"} +is_a: UBERON:0004852 ! cardiovascular system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0004572 ! arterial system +relationship: part_of UBERON:0004572 ! arterial system + +[Term] +id: UBERON:0004701 +name: venous system endothelium +namespace: uberon +def: "An endothelium that is part of a venous system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:35907 +xref: http://linkedlifedata.com/resource/umls/id/C1710626 +xref: MA:0000714 +xref: NCIT:C49320 +xref: UMLS:C1710626 {source="ncithesaurus:Venous_System_Endothelium"} +is_a: UBERON:0004852 ! cardiovascular system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0004582 ! venous system +relationship: part_of UBERON:0004582 ! venous system + +[Term] +id: UBERON:0004702 +name: respiratory system blood vessel endothelium +namespace: uberon +def: "A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:35732 +xref: MA:0001805 +is_a: UBERON:0004638 ! blood vessel endothelium +is_a: UBERON:0004807 ! respiratory system epithelium +intersection_of: UBERON:0004638 ! blood vessel endothelium +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003504 ! respiratory system blood vessel + +[Term] +id: UBERON:0004711 +name: jugular vein +namespace: uberon +def: "The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava." [http://en.wikipedia.org/wiki/Jugular_vein] +synonym: "jugular" RELATED [] +synonym: "vena jugularis" RELATED [BTO:0001744] +xref: BTO:0001744 +xref: CALOHA:TS-0497 +xref: EMAPA:18638 +xref: GAID:536 +xref: http://linkedlifedata.com/resource/umls/id/C0022427 +xref: http://www.snomedbrowser.com/Codes/Details/244403000 +xref: Jugular:vein +xref: MA:0002154 +xref: MESH:D007601 +xref: NCIT:C12738 +xref: UMLS:C0022427 {source="ncithesaurus:Jugular_Vein"} +is_a: UBERON:0003502 ! neck blood vessel +is_a: UBERON:0009141 ! craniocervical region vein +relationship: drains UBERON:0000033 ! head +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png + +[Term] +id: UBERON:0004716 +name: conceptus +namespace: uberon +def: "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." [BTO:0003834, http://en.wikipedia.org/wiki/Conceptus] +synonym: "embryo plus adnexa" EXACT [] +xref: AEO:0000194 +xref: BTO:0003834 +xref: EHDAA2:0000001 +xref: EHDAA2:0003235 +xref: EMAPA:36040 +xref: http://en.wikipedia.org/wiki/Conceptus +xref: http://linkedlifedata.com/resource/umls/id/C1516779 +xref: NCIT:C34131 +xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} +is_a: UBERON:0000061 ! anatomical structure +relationship: existence_ends_with UBERON:0000068 ! embryo stage +relationship: existence_starts_with UBERON:0000068 ! embryo stage +relationship: has_part UBERON:0002050 ! embryonic structure +relationship: has_part UBERON:0016887 ! entire extraembryonic component +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string + +[Term] +id: UBERON:0004731 +name: neuromere +namespace: uberon +def: "A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres)." [http://dx.doi.org/10.1016/j.tins.2013.06.004, https://github.com/obophenotype/uberon/issues/318] +subset: pheno_slim +synonym: "neural metamere" RELATED [] +synonym: "neural segment" RELATED [] +synonym: "neural tube metameric segment" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "neural tube segment" EXACT [] +synonym: "neuromere" EXACT [] +synonym: "neuromeres" EXACT PLURAL [TAO:0001328] +xref: http://en.wikipedia.org/wiki/Neuromere +xref: nlx:147842 +xref: TAO:0001328 +xref: ZFA:0001328 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0004732 ! segmental subdivision of nervous system +intersection_of: UBERON:0004732 ! segmental subdivision of nervous system +intersection_of: part_of UBERON:0001049 ! neural tube +relationship: part_of UBERON:0001049 ! neural tube +property_value: IAO:0000116 "We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted" xsd:string +property_value: UBPROP:0000001 "A metameric segment of the central nervous system.[ZFA]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001328", ontology="TAO", source="ZFIN:curator"} +created_by: Melissa Haendel +creation_date: 2009-06-18T09:00:04Z + +[Term] +id: UBERON:0004732 +name: segmental subdivision of nervous system +namespace: uberon +def: "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres." [FBbt:00005140, http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "neuromere" RELATED [FBbt:00005140] +xref: FBbt:00005140 +is_a: UBERON:0000063 ! organ subunit +intersection_of: UBERON:0000063 ! organ subunit +intersection_of: part_of UBERON:0001016 ! nervous system +relationship: part_of UBERON:0001016 ! nervous system +property_value: IAO:0000116 "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string + +[Term] +id: UBERON:0004733 +name: segmental subdivision of hindbrain +namespace: uberon +def: "An organ subunit that is part of a hindbrain [Automatically generated definition]." [OBOL:automatic] +subset: non_informative +synonym: "hindbrain segment" EXACT [FMA:61998] +synonym: "segment of hindbrain" EXACT [FMA:61998] +xref: FMA:61998 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0004732 ! segmental subdivision of nervous system +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0000063 ! organ subunit +intersection_of: part_of UBERON:0002028 ! hindbrain +relationship: part_of UBERON:0002028 ! hindbrain + +[Term] +id: UBERON:0004734 +name: gastrula +namespace: uberon +alt_id: UBERON:0007012 +def: "Organism at the gastrula stage." [http://en.wikipedia.org/wiki/Gastrula, http://en.wikipedia.org/wiki/Trilaminar_blastocyst] +subset: pheno_slim +synonym: "blastocystis trilaminaris" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "gastrula embryo" EXACT [BILA:0000060] +synonym: "tri-laminar disc" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "tri-laminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastocyst" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar blastoderm" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar disc" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] +xref: BILA:0000060 +xref: BTO:0001403 +xref: FBbt:00005317 +xref: FMA:293108 +xref: GAID:1302 +xref: http://en.wikipedia.org/wiki/Gastrula +xref: http://linkedlifedata.com/resource/umls/id/C0017199 +xref: http://linkedlifedata.com/resource/umls/id/C1284022 +xref: MESH:A16.254.412 +xref: MIAA:0000179 +xref: NCIT:C34057 +xref: NCIT:C34058 +xref: Trilaminar:blastocyst +xref: UMLS:C0017199 {source="ncithesaurus:Gastrula"} +xref: UMLS:C1284022 {source="ncithesaurus:Trilaminar_Embryonic_Disc"} +is_a: UBERON:0000922 ! embryo +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage +relationship: develops_from UBERON:0000307 ! blastula +relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage +property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} + +[Term] +id: UBERON:0004765 +name: skeletal element +namespace: uberon +def: "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." [https://orcid.org/0000-0002-6601-2165] +subset: organ_slim +subset: uberon_slim +xref: AAO:0011129 +xref: galen:SkeletalStructure +xref: TAO:0001890 +xref: VSAO:0000128 +xref: XAO:0004012 +xref: ZFA:0005494 +is_a: UBERON:0000062 ! organ +relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system +property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} +property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} + +[Term] +id: UBERON:0004770 +name: articular system +namespace: uberon +def: "Anatomical system that consists of all the joints of the body." [VSAO:0000181] +synonym: "joint system" EXACT [FMA:23878] +synonym: "set of all joints" RELATED [] +synonym: "set of all joints of body" EXACT [FMA:23878] +synonym: "set of joints of body" RELATED [FMA:23878] +xref: EMAPA:35150 +xref: FMA:23878 +xref: http://www.snomedbrowser.com/Codes/Details/361827000 +xref: MA:0003007 +xref: VSAO:0000181 +is_a: UBERON:0034925 ! anatomical collection +intersection_of: UBERON:0034925 ! anatomical collection +intersection_of: has_member UBERON:0000982 ! skeletal joint +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: has_member UBERON:0000982 ! skeletal joint +relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system + +[Term] +id: UBERON:0004777 +name: respiratory system submucosa +namespace: uberon +def: "A submucosa that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius submucosa" EXACT [OBOL:automatic] +synonym: "submucosa of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "submucosa of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:37578 {source="MA:th"} +xref: MA:0001822 +is_a: UBERON:0000009 ! submucosa +intersection_of: UBERON:0000009 ! submucosa +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003570 ! respiratory system connective tissue + +[Term] +id: UBERON:0004785 +name: respiratory system mucosa +namespace: uberon +def: "the mucous membrane lining the respiratory tract" [MESH:A04.760, MGI:cwg, MP:0002277] +subset: pheno_slim +synonym: "apparatus respiratorius mucosa" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius mucosa of organ" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius mucous membrane" EXACT [OBOL:automatic] +synonym: "laryngeal mucous membrane" RELATED [EMAPA:18334] +synonym: "mucosa of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "mucosa of organ of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "mucosa of organ of respiratory system" EXACT [OBOL:automatic] +synonym: "mucosa of respiratory system" EXACT [OBOL:automatic] +synonym: "mucous membrane of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "mucous membrane of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory mucosa" RELATED [BTO:0000973] +synonym: "respiratory system mucosa of organ" EXACT [OBOL:automatic] +synonym: "respiratory system mucous membrane" EXACT [OBOL:automatic] +synonym: "respiratory tract mucosa" RELATED [] +xref: BTO:0000973 +xref: EMAPA:18334 +xref: EMAPA:37577 {source="MA:th"} +xref: FMA:302092 +xref: GAID:304 +xref: MA:0001827 +xref: MESH:D020545 +is_a: UBERON:0000344 ! mucosa +intersection_of: UBERON:0000344 ! mucosa +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system +property_value: IAO:0000116 "TODO - split respiratory tract mucosa from respiratory system mucosa" xsd:string + +[Term] +id: UBERON:0004797 +name: blood vessel layer +namespace: uberon +def: "Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia." [http://orcid.org/0000-0002-6601-2165] +xref: EMAPA:36296 +xref: MA:0002854 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: part_of UBERON:0001981 ! blood vessel +relationship: part_of UBERON:0035965 ! wall of blood vessel +property_value: depicted:by Blood:vessels.svg + +[Term] +id: UBERON:0004802 +name: respiratory tract epithelium +namespace: uberon +def: "the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi" [ISBN:0-683-40008-8, MGI:anna, MP:0010942] +subset: pheno_slim +synonym: "airway epithelium" RELATED [BTO:0000419] +synonym: "epithelial tissue of respiratory tract" EXACT [OBOL:automatic] +synonym: "epithelium of respiratory tract" EXACT [OBOL:automatic] +synonym: "respiratory epithelium" RELATED [BTO:0000419] +synonym: "respiratory tract epithelial tissue" EXACT [OBOL:automatic] +xref: BTO:0000419 +xref: CALOHA:TS-0023 +xref: EMAPA:32827 +xref: http://www.snomedbrowser.com/Codes/Details/321764001 +xref: MA:0001480 +xref: VHOG:0000981 +is_a: UBERON:0004807 ! respiratory system epithelium +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0010499 ! pseudostratified ciliated columnar epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0000065 ! respiratory tract +relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0000072 ! proximo-distal subdivision of respiratory tract + +[Term] +id: UBERON:0004807 +name: respiratory system epithelium +namespace: uberon +def: "An epithelium that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +subset: pheno_slim +synonym: "apparatus respiratorius epithelial tissue" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius epithelium" EXACT [OBOL:automatic] +synonym: "epithelial tissue of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "epithelial tissue of respiratory system" EXACT [OBOL:automatic] +synonym: "epithelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "epithelium of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system epithelial tissue" EXACT [OBOL:automatic] +xref: CALOHA:TS-0023 +xref: EMAPA:32826 +xref: MA:0001823 +xref: VHOG:0000981 +is_a: UBERON:0000483 ! epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0004815 +name: lower respiratory tract epithelium +namespace: uberon +def: "An epithelium that is part of a lower respiratory tract [Automatically generated definition]." [OBOL:automatic] +synonym: "epithelial tissue of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "epithelium of lower respiratory tract" EXACT [OBOL:automatic] +synonym: "lower respiratory tract epithelial tissue" EXACT [OBOL:automatic] +xref: EMAPA:37549 {source="MA:th"} +xref: MA:0001481 +is_a: UBERON:0004802 ! respiratory tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001558 ! lower respiratory tract +relationship: part_of UBERON:0001558 ! lower respiratory tract + +[Term] +id: UBERON:0004848 +name: respiratory system arterial endothelium +namespace: uberon +def: "An endothelium of artery that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius arterial endothelium" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius artery endothelium" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius endothelium of artery" EXACT [OBOL:automatic] +synonym: "arterial endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "arterial endothelium of respiratory system" EXACT [OBOL:automatic] +synonym: "artery endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "artery endothelium of respiratory system" EXACT [OBOL:automatic] +synonym: "endothelium of artery of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "endothelium of artery of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system artery endothelium" EXACT [OBOL:automatic] +synonym: "respiratory system endothelium of artery" EXACT [OBOL:automatic] +xref: EMAPA:37566 {source="MA:th"} +xref: MA:0001801 +is_a: UBERON:0001917 ! endothelium of artery +is_a: UBERON:0004702 ! respiratory system blood vessel endothelium +intersection_of: UBERON:0001917 ! endothelium of artery +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003469 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system artery + +[Term] +id: UBERON:0004849 +name: respiratory system venous endothelium +namespace: uberon +def: "An endothelium of vein that is part of a respiratory system [Automatically generated definition]." [OBOL:automatic] +synonym: "apparatus respiratorius endothelium of vein" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius vein endothelium" EXACT [OBOL:automatic] +synonym: "apparatus respiratorius venous endothelium" EXACT [OBOL:automatic] +synonym: "endothelium of vein of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "endothelium of vein of respiratory system" EXACT [OBOL:automatic] +synonym: "respiratory system endothelium of vein" EXACT [OBOL:automatic] +synonym: "respiratory system vein endothelium" EXACT [OBOL:automatic] +synonym: "vein endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "vein endothelium of respiratory system" EXACT [OBOL:automatic] +synonym: "venous endothelium of apparatus respiratorius" EXACT [OBOL:automatic] +synonym: "venous endothelium of respiratory system" EXACT [OBOL:automatic] +xref: EMAPA:37585 {source="MA:th"} +xref: MA:0001811 +is_a: UBERON:0001919 ! endothelium of vein +is_a: UBERON:0004702 ! respiratory system blood vessel endothelium +intersection_of: UBERON:0001919 ! endothelium of vein +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003476 ! respiratory system venous blood vessel + +[Term] +id: UBERON:0004852 +name: cardiovascular system endothelium +namespace: uberon +def: "An endothelium that is part of the cardiovascular system." [https://orcid.org/0000-0002-6601-2165] +subset: vertebrate_core +synonym: "endothelia" RELATED PLURAL [ZFA:0001639] +synonym: "vascular endothelia" RELATED PLURAL [XAO:0000356] +xref: BTO:0001853 +xref: EMAPA:35201 +xref: GAID:519 +xref: http://linkedlifedata.com/resource/umls/id/C0014261 +xref: MA:0000717 +xref: MESH:D004730 +xref: NCIT:C13053 +xref: TAO:0002171 +xref: UMLS:C0014261 {source="ncithesaurus:Vascular_Endothelium"} +xref: VHOG:0001217 +xref: XAO:0000356 +xref: ZFA:0001639 +is_a: UBERON:0001986 ! endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0004535 ! cardiovascular system +relationship: part_of UBERON:0004535 ! cardiovascular system +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string +property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207"} + +[Term] +id: UBERON:0004872 +name: splanchnic layer of lateral plate mesoderm +namespace: uberon +def: "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]." [http://en.wikipedia.org/wiki/Lateral_plate_mesoderm#Division_into_layers] +subset: pheno_slim +synonym: "inner layer of lateral plate mesoderm" EXACT [] +synonym: "splanchnic mesoderm" RELATED [ISBN:9780878932504] +synonym: "visceral mesoderm" BROAD [BILA:0000044, http://www.drugs.com/dict/visceral-mesoderm.html, http://www.stedmans.com/] +xref: AAO:0011102 +xref: BILA:0000044 +xref: Division_into_layers +xref: FMA:295568 +xref: XAO:0000276 +is_a: UBERON:0002050 ! embryonic structure +relationship: part_of UBERON:0003081 ! lateral plate mesoderm +property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} + +[Term] +id: UBERON:0004873 +name: splanchnopleure +namespace: uberon +def: "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]." [http://en.wikipedia.org/wiki/Splanchnopleure] +synonym: "ventral splanchnic mesoderm" RELATED [http://en.wikipedia.org/wiki/Intraembryonic_coelom] +xref: EHDAA2:0001903 +xref: EHDAA:383 +xref: EMAPA:16181 +xref: FMA:295564 +xref: http://en.wikipedia.org/wiki/Splanchnopleure +xref: http://linkedlifedata.com/resource/umls/id/C1519472 +xref: NCIT:C34303 +xref: UMLS:C1519472 {source="ncithesaurus:Splanchnopleure"} +xref: VHOG:0000558 +is_a: UBERON:0002050 ! embryonic structure +relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png +property_value: IAO:0000116 "TODO - check relationship to LPM" xsd:string + +[Term] +id: UBERON:0004880 +name: chordamesoderm +namespace: uberon +def: "The central region of trunk mesoderm. This tissue forms the notochord" [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +subset: pheno_slim +synonym: "axial chorda mesoderm" EXACT [ZFA:0000091] +synonym: "chorda mesoderm" EXACT [] +synonym: "dorsal mesoderm" EXACT [https://github.com/obophenotype/uberon/wiki/The-neural-crest] +synonym: "presumptive notochord" EXACT [ZFA:0000091] +xref: AAO:0000478 +xref: EFO:0003426 +xref: TAO:0000091 +xref: ZFA:0000091 +is_a: UBERON:0002050 ! embryonic structure +relationship: part_of UBERON:0003068 ! axial mesoderm +property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} +property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string + +[Term] +id: UBERON:0004883 +name: lung mesenchyme +namespace: uberon +def: "The mass of tissue made up of mesenchymal cells in the lung." [GO:0060484] +subset: pheno_slim +synonym: "lung-associated mesenchyme" EXACT [GO:0060484] +synonym: "mesenchyme of lung" EXACT [OBOL:automatic] +synonym: "pulmonary mesenchyme" EXACT [GO:0060484] +xref: EMAPA:32866 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003104 ! mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0002048 ! lung +relationship: develops_from UBERON:0003081 ! lateral plate mesoderm +relationship: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0004905 +name: articulation +namespace: uberon +def: "Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "joint" NARROW [] +xref: FBbt:00005811 +is_a: UBERON:0034921 ! multi organ part structure +relationship: part_of UBERON:0004770 ! articular system + +[Term] +id: UBERON:0004906 +name: ectodermal part of digestive tract +namespace: uberon +def: "A portion of the gut that is derived from ectoderm." [GO:0007439] +synonym: "ectodermal gut" EXACT [] +synonym: "gut ectoderm" EXACT [EMAPA:32930] +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0004921 ! subdivision of digestive tract +intersection_of: UBERON:0004921 ! subdivision of digestive tract +intersection_of: develops_from UBERON:0000924 ! ectoderm +intersection_of: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0004921 +name: subdivision of digestive tract +namespace: uberon +def: "A proximal-distal subdivision of the digestive tract." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "alimentary system subdivision" RELATED [FMA:71131] +synonym: "intestinal tract" RELATED [] +synonym: "segment of intestinal tract" RELATED [] +synonym: "subdivision of alimentary system" RELATED [FMA:71131] +xref: FBbt:00100315 +xref: FMA:71131 +is_a: UBERON:0013522 ! subdivision of tube +intersection_of: UBERON:0013522 ! subdivision of tube +intersection_of: subdivision_of UBERON:0001555 ! digestive tract +relationship: part_of UBERON:0001555 ! digestive tract +relationship: subdivision_of UBERON:0001555 ! digestive tract +property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string + +[Term] +id: UBERON:0004923 +name: organ component layer +namespace: uberon +def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +xref: FMA:82485 +is_a: UBERON:0000064 ! organ part +relationship: part_of UBERON:0000060 ! anatomical wall + +[Term] +id: UBERON:0004924 +name: submucosa of pharynx +namespace: uberon +def: "The tissue underlying the tunica mucosa of the pharynx." [BTO:0002113] +synonym: "pharyngeal submucosa" EXACT [FMA:75144] +synonym: "pharyngobasilar fascia" RELATED [] +synonym: "pharynx submucosa" EXACT [OBOL:automatic] +synonym: "submucous coat of pharynx" RELATED [BTO:0002113] +synonym: "submucous layer of pharynx" RELATED [BTO:0002113] +synonym: "tela submucosa pharyngea" EXACT LATIN [FMA:75144, FMA:TA] +synonym: "tela submucosa pharyngis" EXACT LATIN [BTO:0002113] +xref: BTO:0002113 +xref: FMA:75144 +xref: http://www.snomedbrowser.com/Codes/Details/19594009 +is_a: UBERON:0004777 ! respiratory system submucosa +is_a: UBERON:0018257 ! submucosa of digestive tract +intersection_of: UBERON:0000009 ! submucosa +intersection_of: part_of UBERON:0001042 ! chordate pharynx +relationship: part_of UBERON:0001042 ! chordate pharynx + +[Term] +id: UBERON:0005058 +name: hemolymphoid system gland +namespace: uberon +def: "A gland that is part of a hemolymphoid system [Automatically generated definition]." [OBOL:automatic] +subset: organ_slim +synonym: "haemolymphoid system gland" RELATED [EMAPA:18766] +synonym: "hemopoietic or lymphoid gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "hemopoietic or lymphoid organ" BROAD [GO:0048534] +xref: EMAPA:18766 +xref: MA:0002962 +is_a: UBERON:0002530 ! gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0002193 ! hemolymphoid system +relationship: part_of UBERON:0002193 ! hemolymphoid system + +[Term] +id: UBERON:0005061 +name: neural groove +namespace: uberon +def: "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds." [GO:0001842, http://en.wikipedia.org/wiki/Neural_groove, http://orcid.org/0000-0002-6601-2165] +xref: AAO:0011071 +xref: EMAPA:35594 +xref: FMA:295624 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1363 +xref: http://linkedlifedata.com/resource/umls/id/C0814992 +xref: http://www.snomedbrowser.com/Codes/Details/361463007 +xref: NCIT:C34224 +xref: Neural:groove +xref: UMLS:C0814992 {source="ncithesaurus:Neural_Groove"} +xref: XAO:0000248 +is_a: UBERON:0002050 ! embryonic structure +relationship: part_of UBERON:0003075 ! neural plate +property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Neural:groove"} + +[Term] +id: UBERON:0005062 +name: neural fold +namespace: uberon +def: "One of the two elevated edges of the neural groove[GO,MP]." [GO:0001842, http://en.wikipedia.org/wiki/Neural_fold, MP:0011256] +subset: pheno_slim +synonym: "medullary fold" EXACT [MP:0011256] +xref: EHDAA2:0001249 +xref: FMA:295618 +xref: http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1364 +xref: http://linkedlifedata.com/resource/umls/id/C0814993 +xref: http://www.snomedbrowser.com/Codes/Details/361461009 +xref: NCIT:C34223 +xref: Neural:fold +xref: UMLS:C0814993 {source="ncithesaurus:Neural_Fold"} +xref: XAO:0004087 +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005157 ! epithelial fold +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0015212 ! lateral structure +relationship: in_lateral_side_of UBERON:0005061 ! neural groove +relationship: part_of UBERON:0005061 ! neural groove +property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Neural:fold"} + +[Term] +id: UBERON:0005068 +name: neural rod +namespace: uberon +def: "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]." [GO:0014024, ZFA:0000133] +subset: efo_slim +synonym: "neural tube rod" RELATED [GO:0014027] +xref: EFO:0003498 +xref: TAO:0000133 +xref: ZFA:0000133 +is_a: UBERON:0016879 ! future central nervous system +relationship: develops_from UBERON:0007135 ! neural keel +property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0005076 +name: hindbrain-spinal cord boundary +namespace: uberon +def: "An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord." [OBOL:automatic] +synonym: "hindbrain-spinal cord boundary region" EXACT [] +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0007651 ! anatomical junction +intersection_of: UBERON:0007651 ! anatomical junction +intersection_of: adjacent_to UBERON:0002028 ! hindbrain +intersection_of: adjacent_to UBERON:0002240 ! spinal cord +relationship: adjacent_to UBERON:0002028 ! hindbrain +relationship: adjacent_to UBERON:0002240 ! spinal cord +relationship: part_of UBERON:0001017 ! central nervous system + +[Term] +id: UBERON:0005082 +name: tube lumen +namespace: uberon +def: "A hole in a tube[GO]." [GO:0060609] +xref: AEO:0000078 +xref: EHDAA2:0004618 +xref: RETIRED_EHDAA2:0003078 +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: surrounded_by UBERON:0000025 ! tube +relationship: surrounded_by UBERON:0000025 ! tube + +[Term] +id: UBERON:0005090 +name: muscle structure +namespace: uberon +def: "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." [GO:0061061] +synonym: "muscle" RELATED [] +synonym: "muscle element" RELATED [] +synonym: "musculus" EXACT [FMA:30316] +xref: EMAPA:32715 +xref: FBbt:00005073 +xref: FMA:30316 +is_a: UBERON:0000061 ! anatomical structure +property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string + +[Term] +id: UBERON:0005153 +name: epithelial bud +namespace: uberon +def: "A bud is a protrusion that forms from an epithelial sheet by localized folding." [GO:0060572] +xref: BTO:0001639 +is_a: UBERON:0005157 ! epithelial fold + +[Term] +id: UBERON:0005157 +name: epithelial fold +namespace: uberon +def: "An epithelial sheet bent on a linear axis." [GO:0060571] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0005162 +name: multi cell part structure +namespace: uberon +def: "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." [CARO:0001000] +subset: upper_level +synonym: "cell part cluster" RELATED [FMA:83115] +synonym: "multi-cell-component structure" EXACT [CARO:0001000] +synonym: "multi-cell-part structure" EXACT [CARO:0001000] +xref: AAO:0011000 +xref: CARO:0001000 +xref: FBbt:00007060 +xref: FMA:83115 +is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster +property_value: UBPROP:0000012 "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" xsd:string {external_ontology="CARO", external_ontology="FMA"} + +[Term] +id: UBERON:0005174 +name: dorsal region element +namespace: uberon +def: "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "back organ" EXACT [MA:0001901] +synonym: "dorsal region organ" EXACT [] +xref: EMAPA:37274 {source="MA:th"} +xref: MA:0001901 +is_a: UBERON:0000062 ! organ +intersection_of: UBERON:0000062 ! organ +intersection_of: part_of UBERON:0001137 ! dorsum +relationship: part_of UBERON:0001137 ! dorsum + +[Term] +id: UBERON:0005177 +name: trunk region element +namespace: uberon +def: "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +subset: organ_slim +synonym: "trunk organ" EXACT [MA:0000516] +xref: EMAPA:37270 {source="MA:th"} +xref: MA:0000516 +is_a: UBERON:0000062 ! organ +intersection_of: UBERON:0000062 ! organ +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk + +[Term] +id: UBERON:0005178 +name: thoracic cavity element +namespace: uberon +def: "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +subset: pheno_slim +synonym: "thoracic cavity organ" EXACT [MA:0000557] +xref: EMAPA:37273 {source="MA:th"} +xref: MA:0000557 +is_a: UBERON:0005181 ! thoracic segment organ +intersection_of: UBERON:0000062 ! organ +intersection_of: located_in UBERON:0002224 ! thoracic cavity +relationship: located_in UBERON:0002224 ! thoracic cavity + +[Term] +id: UBERON:0005181 +name: thoracic segment organ +namespace: uberon +def: "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." [http://orcid.org/0000-0002-6601-2165] +subset: non_informative +synonym: "upper body organ" RELATED [MA:0000563] +xref: EMAPA:37271 {source="MA:th"} +xref: MA:0000563 +is_a: UBERON:0005177 ! trunk region element +intersection_of: UBERON:0000062 ! organ +intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0000915 ! thoracic segment of trunk + +[Term] +id: UBERON:0005194 +name: thoracic vein +namespace: uberon +def: "A vein that is part of a thorax [Automatically generated definition]." [OBOL:automatic] +xref: EMAPA:37197 {source="MA:th"} +xref: http://linkedlifedata.com/resource/umls/id/C0226629 +xref: http://www.snomedbrowser.com/Codes/Details/281472008 +xref: MA:0002235 +xref: NCIT:C53142 +xref: UMLS:C0226629 {source="ncithesaurus:Thoracic_Vein"} +is_a: UBERON:0001638 ! vein +is_a: UBERON:0003834 ! thoracic segment blood vessel +intersection_of: UBERON:0001638 ! vein +intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk + +[Term] +id: UBERON:0005250 +name: stomatodeum gland +namespace: uberon +def: "A gland that is part of a stomodeum." [OBOL:automatic] +subset: organ_slim +synonym: "stomatodaeum gland" EXACT [VHOG:0000658] +xref: VHOG:0000658 +is_a: UBERON:0002530 ! gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0000930 ! stomodeum +relationship: part_of UBERON:0000930 ! stomodeum +property_value: IAO:0000116 "check this" xsd:string + +[Term] +id: UBERON:0005253 +name: head mesenchyme +namespace: uberon +def: "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." [ISBN:0683400088, MP:0011260] +subset: efo_slim +subset: pheno_slim +subset: vertebrate_core +synonym: "cephalic mesenchyme" EXACT [MP:0011260] +synonym: "cranial mesenchyme" RELATED [MGI:anna] +synonym: "desmocranium" RELATED PENDING_REVIEW [FMA:76622] +xref: EFO:0003492 +xref: EHDAA2:0000732 +xref: EHDAA:179 +xref: EMAPA:16098 +xref: EMAPA_RETIRED:16269 +xref: FMA:76622 +xref: TAO:0000113 +xref: VHOG:0000332 +xref: ZFA:0000113 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0005291 ! embryonic tissue +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme +property_value: UBPROP:0000001 "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000113", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0005256 +name: trunk mesenchyme +namespace: uberon +def: "Mesenchyme that is part of a developing trunk." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "trunk and cervical mesenchyme" RELATED [EHDAA2:0002092] +xref: EFO:0003485 +xref: EHDAA2:0002092 +xref: EHDAA:377 +xref: EMAPA:16177 +xref: TAO:0000081 +xref: VHOG:0000281 +xref: ZFA:0000081 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0005291 ! embryonic tissue +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0000922 ! embryo +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme + +[Term] +id: UBERON:0005290 +name: myelencephalon +namespace: uberon +def: "The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]." [BTO:0000758, http://en.wikipedia.org/wiki/Myelencephalon] +subset: uberon_slim +synonym: "myelencephalon (medulla oblongata)" RELATED [DHBA:10662] +xref: BTO:0000758 +xref: CALOHA:TS-0607 +xref: CALOHA:TS-2365 +xref: DHBA:10662 +xref: EHDAA2:0001207 +xref: EHDAA:5526 +xref: EMAPA:17082 +xref: HBA:9512 +xref: http://en.wikipedia.org/wiki/Myelencephalon +xref: MA:0000205 +xref: VHOG:0000456 +is_a: UBERON:0004733 ! segmental subdivision of hindbrain +relationship: develops_from UBERON:0010096 ! future myelencephalon +relationship: immediate_transformation_of UBERON:0010096 {evidence="definitional"} ! future myelencephalon +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg +property_value: RO:0002174 NCBITaxon:7955 +property_value: UBPROP:0000001 "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myelencephalon"} +property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="http://bgee.unil.ch/", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500"} +property_value: UBPROP:0000013 "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" xsd:string + +[Term] +id: UBERON:0005291 +name: embryonic tissue +namespace: uberon +def: "A portion of tissue that is part of an embryo." [OBOL:automatic] +subset: pheno_slim +subset: upper_level +synonym: "developing tissue" RELATED [] +synonym: "portion of embryonic tissue" EXACT [OBOL:automatic] +xref: CALOHA:TS-2100 +is_a: UBERON:0000479 ! tissue +intersection_of: UBERON:0000479 ! tissue +intersection_of: part_of UBERON:0000922 ! embryo +relationship: part_of UBERON:0002050 ! embryonic structure + +[Term] +id: UBERON:0005292 +name: extraembryonic tissue +namespace: uberon +def: "Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." [https://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "extra-embryonic tissue" EXACT [] +xref: BTO:0003360 +xref: CALOHA:TS-2119 +xref: EFO:0001406 +xref: MAT:0000061 +xref: MIAA:0000061 +is_a: UBERON:0000479 ! tissue +intersection_of: UBERON:0000479 ! tissue +intersection_of: part_of UBERON:0016887 ! entire extraembryonic component +relationship: part_of UBERON:0016887 ! entire extraembryonic component + +[Term] +id: UBERON:0005316 +name: endocardial endothelium +namespace: uberon +def: "The endothelial lining of the endocardium." [UBERON:cjm] +synonym: "endocardium endothelium" EXACT [FMA:83596] +synonym: "endothelium of endocardium" EXACT [FMA:83596] +xref: FMA:83596 +is_a: UBERON:0008307 ! heart endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0002165 ! endocardium +relationship: part_of UBERON:0002165 ! endocardium + +[Term] +id: UBERON:0005317 +name: pulmonary artery endothelium +namespace: uberon +def: "An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]." [GO:0061155] +synonym: "pulmonary artery endothelial tube" EXACT [GO:0061155] +xref: BTO:0000137 +is_a: UBERON:0001917 ! endothelium of artery +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0002012 ! pulmonary artery +relationship: part_of UBERON:0002012 ! pulmonary artery + +[Term] +id: UBERON:0005339 +name: outflow tract pulmonary component +namespace: uberon +xref: EHDAA2:0001359 +xref: EHDAA:4401 +xref: EMAPA:17330 +xref: MA:0000102 +xref: VHOG:0001395 +is_a: UBERON:0004145 ! outflow tract +property_value: IAO:0000116 "merge with RVOT?" xsd:string + +[Term] +id: UBERON:0005423 +name: developing anatomical structure +namespace: uberon +synonym: "developing structure" RELATED [] +synonym: "developmental structure" RELATED [] +synonym: "developmental tissue" RELATED [MIAA:0000019] +xref: AEO:0000125 +xref: CALOHA:TS-2122 +xref: EHDAA2:0003125 +xref: FBbt:00007006 +xref: FMA:292313 +xref: MIAA:0000019 +is_a: UBERON:0000465 ! material anatomical entity + +[Term] +id: UBERON:0005432 +name: aortic sac +namespace: uberon +def: "The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates" [MP:0012510] +subset: pheno_slim +synonym: "saccus aorticus" EXACT LATIN [] +xref: EHDAA2:0004145 +xref: EHDAA:9826 +xref: EMAPA:36461 +xref: FMA:71008 +xref: http://www.snomedbrowser.com/Codes/Details/361527005 +xref: RETIRED_EHDAA2:0000133 +is_a: UBERON:0001637 {source="EHDAA2"} ! artery +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0003498 ! heart blood vessel +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: develops_from UBERON:0004363 {source="EHDAA2"} ! pharyngeal arch artery +relationship: part_of UBERON:0004145 ! outflow tract +property_value: UBPROP:0000001 "the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]." xsd:string {source="http://medical-dictionary.thefreedictionary.com/aortic+sac"} + +[Term] +id: UBERON:0005496 +name: neural tube lateral wall +namespace: uberon +def: "Portion of tissue on the side of the lumen of the neural tube." [ZFA:0001435] +subset: vertebrate_core +synonym: "lateral wall neural tube" EXACT [ZFA:0001435] +xref: EHDAA2:0001257 +xref: EHDAA:2873 +xref: EHDAA:912 +xref: EMAPA:16166 +xref: TAO:0001435 +xref: VHOG:0000513 +xref: ZFA:0001435 +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: part_of UBERON:0001049 ! neural tube + +[Term] +id: UBERON:0005498 +name: primitive heart tube +namespace: uberon +def: "Multi-tissue structure that arises from the heart rudiment and will become the heart tube." [ZFA:0000149] +subset: vertebrate_core +synonym: "early primitive heart tube" NARROW [EMAPA:16208] +synonym: "primitive heart tube" EXACT [EMAPA:16215] +xref: EHDAA2:0001512 +xref: EHDAA:424 +xref: EHDAA:436 +xref: EMAPA:16215 +xref: FMA:321916 +xref: http://en.wikipedia.org/wiki/Primitive_heart_tube +xref: http://www.snomedbrowser.com/Codes/Details/361522004 +xref: TAO:0000149 +xref: ZFA:0000149 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment +relationship: part_of UBERON:0000922 ! embryo + +[Term] +id: UBERON:0005501 +name: rhombomere lateral wall +namespace: uberon +def: "A neural tube lateral wall that is part of a rhombomere." [OBOL:automatic] +synonym: "future hindbrain lateral wall" RELATED [EMAPA:35364] +xref: EMAPA:32819 +xref: EMAPA:35364 +is_a: UBERON:0005496 ! neural tube lateral wall +intersection_of: UBERON:0005496 ! neural tube lateral wall +intersection_of: part_of UBERON:0001892 ! rhombomere +relationship: part_of UBERON:0001892 ! rhombomere + +[Term] +id: UBERON:0005597 +name: lung primordium +namespace: uberon +alt_id: UBERON:3010717 +def: "A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum." [XAO:0001002] +subset: efo_slim +synonym: "lateral diverticula" RELATED [XAO:0001002] +synonym: "lung diverticulum" RELATED [AAO:3010717] +synonym: "lung endoderm" RELATED [EFO:0002578] +xref: AAO:0011059 +xref: EFO:0002578 +xref: EMAPA:36007 +xref: XAO:0001002 +is_a: UBERON:0001048 {source="XAO"} ! primordium +relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut +relationship: has_potential_to_develop_into UBERON:0000170 ! pair of lungs +relationship: part_of UBERON:0008947 ! respiratory primordium + +[Term] +id: UBERON:0005598 +name: trunk somite +namespace: uberon +def: "A somite that is part of a trunk." [OBOL:automatic] +xref: AAO:0010385 +xref: EHDAA2:0003438 +xref: EMAPA:16184 +xref: XAO:0000314 +is_a: UBERON:0002329 ! somite +intersection_of: UBERON:0002329 ! somite +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk + +[Term] +id: UBERON:0005672 +name: right lung endothelium +namespace: uberon +def: "An endothelium that is part of a right lung." [OBOL:automatic] +xref: EHDAA2:0001755 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0001986 ! endothelium +is_a: UBERON:0003364 ! epithelium of right lung +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0002167 ! right lung + +[Term] +id: UBERON:0005673 +name: left lung endothelium +namespace: uberon +def: "An endothelium that is part of a left lung." [OBOL:automatic] +xref: EHDAA2:0000961 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0001986 ! endothelium +is_a: UBERON:0003365 ! epithelium of left lung +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0002168 ! left lung + +[Term] +id: UBERON:0005720 +name: hindbrain venous system +namespace: uberon +def: "A venous system that is part of a hindbrain." [OBOL:automatic] +synonym: "rhombencephalon venous system" RELATED [VHOG:0001322] +xref: EHDAA2:0000776 +xref: EMAPA:18632 +xref: VHOG:0001322 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0004582 ! venous system +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0004582 ! venous system +intersection_of: part_of UBERON:0002028 ! hindbrain +relationship: part_of UBERON:0002028 ! hindbrain + +[Term] +id: UBERON:0005734 +name: tunica adventitia of blood vessel +namespace: uberon +def: "The outermost layer of a blood vessel, composed mainly of fibrous tissue." [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29, ISBN10:0073040584] +synonym: "adventitia externa" EXACT [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29] +synonym: "external coat" RELATED [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29] +synonym: "tunica adventitia" EXACT [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29] +synonym: "tunica adventitia of vessel" EXACT [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29] +synonym: "tunica adventitia vasorum" RELATED LATIN [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29] +synonym: "tunica externa vasorum" RELATED LATIN [http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29] +xref: BTO:0002010 +xref: EMAPA:36299 +xref: http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29 +xref: http://linkedlifedata.com/resource/umls/id/C0225342 +xref: http://www.snomedbrowser.com/Codes/Details/61066005 +xref: NCIT:C33818 +xref: UMLS:C0225342 {source="ncithesaurus:Tunica_Adventitia"} +is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer +is_a: UBERON:0005742 ! adventitia +relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue +property_value: depicted:by Illu:artery.jpg +property_value: IAO:0000116 "TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings" xsd:string +property_value: UBPROP:0000001 "The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29]." xsd:string {source="http://en.wikipedia.org/wiki/Tunica_externa_%28vessels%29"} + +[Term] +id: UBERON:0005740 +name: tunica intima of artery +namespace: uberon +def: "A tunica intima that is part of a artery." [OBOL:automatic] +synonym: "arterial intima" EXACT [EV:0100028] +synonym: "tunica interna (intima)(arteriae)" EXACT [FMA:14272] +xref: EMAPA:36293 +xref: EV:0100028 +xref: FMA:14272 +xref: galen:IntimaOfArtery +xref: http://www.snomedbrowser.com/Codes/Details/40022005 +is_a: UBERON:0002523 ! tunica intima +is_a: UBERON:0004797 ! blood vessel layer +intersection_of: UBERON:0002523 ! tunica intima +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0000415 ! artery wall + +[Term] +id: UBERON:0005742 +name: adventitia +namespace: uberon +def: "An outermost connective tissue covering of an organ, vessel, or other structure[WP]." [http://en.wikipedia.org/wiki/Adventitia] +subset: grouping_class +synonym: "tunica advetitia" NARROW [http://en.wikipedia.org/wiki/Adventitia] +synonym: "tunica externa" NARROW [FMA:45635] +xref: BTO:0002010 +xref: FMA:45635 +xref: http://en.wikipedia.org/wiki/Adventitia +xref: http://www.snomedbrowser.com/Codes/Details/30180000 +is_a: UBERON:0004923 ! organ component layer +relationship: composed_primarily_of UBERON:0002384 ! connective tissue +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg + +[Term] +id: UBERON:0005764 +name: acellular membrane +namespace: uberon +def: "A acellular anatomical structure that is the bounding layer of a anatomical structure." [OBOL:automatic] +xref: FMA:63871 +is_a: UBERON:0000476 ! acellular anatomical structure +intersection_of: UBERON:0000476 ! acellular anatomical structure +intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure +relationship: bounding_layer_of UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0005769 +name: basement membrane of epithelium +namespace: uberon +def: "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina." [http://en.wikipedia.org/wiki/Basement_membrane, http://orcid.org/0000-0002-6601-2165] +synonym: "basement membrane" RELATED [FMA:63872] +synonym: "basement membrane of connective tissue" EXACT [FMA:63872] +synonym: "membrana basalis" EXACT LATIN [http://en.wikipedia.org/wiki/Basement_membrane] +xref: AAO:0010596 +xref: Basement:membrane +xref: FMA:63872 +xref: GAID:915 +xref: http://linkedlifedata.com/resource/umls/id/C0004799 +xref: http://www.snomedbrowser.com/Codes/Details/68989006 +xref: NCIT:C13191 +xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} +is_a: UBERON:0005764 {source="FMA"} ! acellular membrane +relationship: part_of UBERON:0000483 ! epithelium +property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} + +[Term] +id: UBERON:0005856 +name: developing mesenchymal condensation +namespace: uberon +def: "A delimited region of dense mesenchyme within looser mesenchyme." [AEO:0000148] +synonym: "mesenchyme condensation" EXACT [EMAPA:25351] +xref: AEO:0000148 +xref: EHDAA2_RETIRED:0003148 +xref: EHDAA:8979 +is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue +is_a: UBERON:0011585 {source="cjm"} ! cell condensation + +[Term] +id: UBERON:0005906 +name: serous sac +namespace: uberon +def: "Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]" [FMA:9689, https://github.com/obophenotype/uberon/issues/86] +comment: See notes for serous membrane +xref: EMAPA:16060 +xref: FMA:9689 +xref: http://www.snomedbrowser.com/Codes/Details/362890006 +xref: MA:0000005 +is_a: UBERON:0000062 ! organ +relationship: has_part UBERON:0000042 ! serous membrane +relationship: has_part UBERON:0002553 ! anatomical cavity +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall + +[Term] +id: UBERON:0005911 +name: endo-epithelium +namespace: uberon +def: "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]" [FMA:69065] +synonym: "endoderm-derived epithelium" EXACT [] +synonym: "endoepithelium" EXACT [] +xref: FMA:69065 +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004119 ! endoderm-derived structure +intersection_of: UBERON:0000483 ! epithelium +intersection_of: develops_from UBERON:0000925 ! endoderm + +[Term] +id: UBERON:0005944 +name: axial skeleton plus cranial skeleton +namespace: uberon +def: "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]." [FMA:71221, http://en.wikipedia.org/wiki/Axial_skeleton, https://github.com/obophenotype/uberon/issues/44, https://github.com/obophenotype/uberon/wiki/The-axial-skeleton, VSAO:0000056] +subset: pheno_slim +subset: uberon_slim +synonym: "skeleton axiale" RELATED LATIN [http://en.wikipedia.org/wiki/Axial_skeleton] +xref: AAO:0000963 +xref: Axial:skeleton +xref: EMAPA:17214 +xref: EMAPA:18043 +xref: http://linkedlifedata.com/resource/umls/id/C0222645 +xref: http://www.snomedbrowser.com/Codes/Details/361725000 +xref: MA:0000308 +xref: NCIT:C32172 +xref: UMLS:C0222645 {source="ncithesaurus:Axial_Skeleton"} +xref: VSAO:0000056 +xref: XAO:0004011 +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system +relationship: develops_from UBERON:0003089 ! sclerotome +relationship: part_of UBERON:0011137 ! axial skeletal system +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI +property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} + +[Term] +id: UBERON:0005983 +name: heart layer +namespace: uberon +def: "The laminar structure of the heart" [MP:0010545] +subset: non_informative +subset: pheno_slim +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: part_of UBERON:0000948 ! heart +relationship: contributes_to_morphology_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0005985 +name: coronary vessel +namespace: uberon +def: "Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation" [MP:0010551] +subset: pheno_slim +xref: Coronary:circulation +xref: MESH:D003331 +is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000055 ! vessel +intersection_of: part_of UBERON:0000948 ! heart +relationship: contributes_to_morphology_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart +property_value: IAO:0000116 "TODO - change relation from part_of" xsd:string + +[Term] +id: UBERON:0006003 +name: integumentary adnexa +namespace: uberon +def: "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers." [http://code.google.com/p/caro2/issues/detail?id=5, http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "adnexae cutis" RELATED LATIN [http://en.wikipedia.org/wiki/Skin_appendage] +synonym: "body hair or bristle" NARROW [GO:GO] +synonym: "skin adnexa" RELATED [http://en.wikipedia.org/wiki/Skin_appendage] +synonym: "skin adnexal structure" RELATED [] +synonym: "skin appendage" RELATED [http://en.wikipedia.org/wiki/Skin_appendage] +xref: EMAPA:37883 {source="MA:th"} +xref: Skin:appendage +is_a: UBERON:0000064 ! organ part +relationship: part_of UBERON:0002416 ! integumental system +property_value: IAO:0000116 "add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis." xsd:string +property_value: UBPROP:0000001 "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]" xsd:string {source="MP:0010678"} + +[Term] +id: UBERON:0006211 +name: buccopharyngeal membrane +namespace: uberon +def: "The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx." [MP:0012521] +subset: emapa_ehdaa2 +subset: pheno_slim +synonym: "oral membrane" RELATED [MP:0012521] +synonym: "oral plate" RELATED [MP:0012521] +synonym: "oropharyngeal membrane" RELATED [http://en.wikipedia.org/wiki/Buccopharyngeal_membrane] +synonym: "pharyngeal membrane" RELATED INCONSISTENT [MP:0012521] +xref: Buccopharyngeal:membrane +xref: EHDAA2:0000189 +xref: EHDAA:536 +xref: EMAPA:16259 +xref: FMA:313607 +xref: http://www.snomedbrowser.com/Codes/Details/361412007 +xref: VHOG:0000380 +is_a: UBERON:0003037 ! septum +relationship: has_developmental_contribution_from UBERON:0000924 ! ectoderm +relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm +relationship: part_of UBERON:0000922 ! embryo +relationship: part_of UBERON:0006264 {source="EHDAA2"} ! mouth-foregut junction +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png + +[Term] +id: UBERON:0006238 +name: future brain +namespace: uberon +def: "The embryonic precursor of the brain." [NIFSTD:nlx_94995] +subset: cumbo +subset: efo_slim +subset: emapa_ehdaa2 +subset: vertebrate_core +synonym: "brain rudiment" EXACT [TAO:0000146] +synonym: "embryonic brain" RELATED [BTO:0004726] +synonym: "encephalon" NARROW [NIFSTD:nlx_94995] +synonym: "presumptive brain" EXACT [ZFA:0000146] +xref: BAMS:Enc +xref: BTO:0004726 +xref: EFO:0003431 +xref: EHDAA:300 +xref: EHDAA:830 +xref: EMAPA:16089 +xref: FMA:312967 +xref: RETIRED_EHDAA2:0000591 +xref: TAO:0000146 +xref: ZFA:0000146 +is_a: UBERON:0006598 ! presumptive structure +relationship: has_potential_to_develop_into UBERON:0000955 ! brain +relationship: part_of UBERON:0002346 ! neurectoderm +property_value: UBPROP:0000001 "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="Cumbo:terms"} + +[Term] +id: UBERON:0006241 +name: future spinal cord +namespace: uberon +subset: efo_slim +subset: vertebrate_core +synonym: "presumptive spinal cord" EXACT [ZFA:0000417] +synonym: "presumptive spinal cord neural keel" EXACT [TAO:0000417] +synonym: "presumptive spinal cord neural plate" EXACT [TAO:0000417] +synonym: "presumptive spinal cord neural rod" EXACT [TAO:0000417] +xref: EFO:0003438 +xref: EHDAA2:0000674 +xref: EHDAA:898 +xref: EMAPA:16092 +xref: EMAPA:16755 +xref: TAO:0000417 +xref: ZFA:0000417 +is_a: UBERON:0006598 ! presumptive structure +relationship: has_potential_to_develop_into UBERON:0001049 {source="EHDAA2"} ! neural tube +relationship: has_potential_to_develop_into UBERON:0002240 ! spinal cord +relationship: part_of UBERON:0001017 ! central nervous system + +[Term] +id: UBERON:0006264 +name: mouth-foregut junction +namespace: uberon +def: "An anatomical junctions that overlaps the mouth and foregut." [OBOL:automatic] +subset: emapa_ehdaa2 +xref: EHDAA:534 +xref: EMAPA:16258 +xref: RETIRED_EHDAA2:0001205 +xref: VHOG:0000592 +is_a: UBERON:0007651 ! anatomical junction +relationship: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0006267 +name: notochordal plate +namespace: uberon +def: "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord." [VHOG:0001212] +subset: emapa_ehdaa2 +xref: EHDAA2:0001278 +xref: EHDAA:264 +xref: EMAPA:16101 +xref: http://linkedlifedata.com/resource/umls/id/C1518429 +xref: NCIT:C34231 +xref: UMLS:C1518429 {source="ncithesaurus:Notochordal_Plate"} +xref: VHOG:0001212 +is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string +property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} + +[Term] +id: UBERON:0006268 +name: notochordal process +namespace: uberon +def: "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot" [http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm] +comment: The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. +subset: emapa_ehdaa2 +synonym: "chordamesoderm" RELATED [] +synonym: "presumptive notochord" RELATED [] +xref: EHDAA2:0001279 +xref: EHDAA:224 +xref: EMAPA:16102 +xref: FMA:293135 +xref: http://linkedlifedata.com/resource/umls/id/C1518430 +xref: NCIT:C34232 +xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} +xref: VHOG:0001213 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm + +[Term] +id: UBERON:0006314 +name: bodily fluid +namespace: uberon +def: "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." [http://en.wikipedia.org/wiki/Body_fluid, MESH:A12.207] +subset: pheno_slim +synonym: "body fluid" EXACT [GAID:266] +synonym: "fluid" BROAD [] +xref: birnlex:20 +xref: Body:fluid +xref: EMAPA:37441 {source="MA:th"} +xref: FMA:280556 +xref: GAID:266 +xref: galen:BodyFluid +xref: MESH:D001826 +is_a: UBERON:0000463 ! organism substance + +[Term] +id: UBERON:0006347 +name: communicating artery +namespace: uberon +def: "An artery that connects two larger arteries." [ncithesaurus:Communicating_Artery] +comment: Grouping for anterior and posterior +xref: EMAPA:18598 +xref: http://linkedlifedata.com/resource/umls/id/C1707451 +xref: MA:0001938 +xref: NCIT:C52851 +xref: UMLS:C1707451 {source="ncithesaurus:Communicating_Artery"} +is_a: UBERON:0001637 ! artery +intersection_of: UBERON:0001637 ! artery +intersection_of: connects UBERON:0001637 {minCardinality="2", maxCardinality="2"} ! artery +relationship: connects UBERON:0001637 ! artery + +[Term] +id: UBERON:0006535 +name: skin secretion +namespace: uberon +def: "A portion of organism substance that secreted_by a zone of skin." [OBOL:automatic] +synonym: "skin fluid" RELATED [] +synonym: "skin fluid/secretion" EXACT [MA:0002537] +synonym: "skin substance" RELATED [] +xref: MA:0002537 +is_a: UBERON:0000463 ! organism substance +intersection_of: UBERON:0000463 ! organism substance +intersection_of: produced_by UBERON:0000014 ! zone of skin +relationship: produced_by UBERON:0000014 ! zone of skin + +[Term] +id: UBERON:0006538 +name: respiratory system fluid/secretion +namespace: uberon +def: "A portion of organism substance that secreted_by a respiratory system." [OBOL:automatic] +synonym: "respiratory system fluid" RELATED [] +synonym: "respiratory system secretion" RELATED [] +xref: EMAPA:36550 +xref: http://linkedlifedata.com/resource/umls/id/C1514899 +xref: MA:0002533 +xref: NCIT:C13722 +xref: UMLS:C1514899 {source="ncithesaurus:Respiratory_System_Fluid_or_Secretion"} +is_a: UBERON:0000463 ! organism substance +intersection_of: UBERON:0000463 ! organism substance +intersection_of: produced_by UBERON:0001004 ! respiratory system +relationship: produced_by UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0006562 +name: pharynx +namespace: uberon +def: "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." [GO:0060465] +subset: grouping_class +subset: uberon_slim +synonym: "anterior part of foregut" RELATED [] +synonym: "pharyngeal tube" RELATED [] +xref: FBbt:00005380 +xref: MAT:0000049 +xref: MIAA:0000049 +is_a: UBERON:0004921 ! subdivision of digestive tract +property_value: IAO:0000232 "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string +property_value: UBPROP:0000007 "branchial" xsd:string +property_value: UBPROP:0000007 "pharyngeal" xsd:string + +[Term] +id: UBERON:0006563 +name: tunica media of pulmonary trunk +namespace: uberon +def: "Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]" [FMA:85030, FMA:FMA] +xref: FMA:85030 +is_a: UBERON:0007239 ! tunica media of artery +intersection_of: UBERON:0002522 ! tunica media +intersection_of: part_of UBERON:0002333 ! pulmonary trunk +relationship: part_of UBERON:0002333 ! pulmonary trunk + +[Term] +id: UBERON:0006595 +name: presumptive endoderm +namespace: uberon +def: "Presumptive structure of the blastula that will develop into endoderm." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +xref: AAO:0000471 +xref: EFO:0003437 +xref: TAO:0000416 +xref: ZFA:0000416 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm +intersection_of: part_of UBERON:0000307 ! blastula +relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm +relationship: part_of UBERON:0000307 ! blastula + +[Term] +id: UBERON:0006596 +name: presumptive blood +namespace: uberon +subset: efo_slim +synonym: "future blood" EXACT [] +xref: AAO:0000468 +xref: EFO:0003439 +xref: TAO:0000568 +xref: ZFA:0000568 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood +relationship: has_potential_to_develop_into UBERON:0000178 ! blood + +[Term] +id: UBERON:0006598 +name: presumptive structure +namespace: uberon +def: "Portion of embryonic tissue determined by fate mapping to become a structure." [GOC:CVS, GOC:YMB, ZFA:0001116] +synonym: "future structure" EXACT [] +synonym: "presumptive structures" EXACT [ZFA:0001116] +xref: AAO:0000479 +xref: TAO:0001116 +xref: ZFA:0001116 +is_a: UBERON:0002050 ! embryonic structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure +intersection_of: part_of UBERON:0000922 ! embryo +relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string + +[Term] +id: UBERON:0006601 +name: presumptive ectoderm +namespace: uberon +def: "Presumptive structure of the blastula that will develop into ectoderm." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "presumptive epidermis" RELATED [ZFA:0001376] +xref: AAO:0000470 +xref: EFO:0003466 +xref: TAO:0001376 +xref: XAO:0004132 +xref: ZFA:0001376 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm +intersection_of: part_of UBERON:0000307 ! blastula +relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm +relationship: part_of UBERON:0000307 ! blastula + +[Term] +id: UBERON:0006603 +name: presumptive mesoderm +namespace: uberon +def: "Presumptive structure of the blastula that will develop into mesoderm." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +xref: AAO:0000476 +xref: EFO:0003467 +xref: TAO:0001377 +xref: ZFA:0001377 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm +intersection_of: part_of UBERON:0000307 ! blastula +relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm +relationship: part_of UBERON:0000307 ! blastula + +[Term] +id: UBERON:0006876 +name: vasculature of organ +namespace: uberon +def: "A vasculature that is part of a organ." [OBOL:automatic] +subset: non_informative +synonym: "organ vasculature" EXACT [FMA:74612] +synonym: "set of blood vessels of organ" EXACT [FMA:74612] +xref: FMA:74612 +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0000062 ! organ +relationship: part_of UBERON:0000062 ! organ + +[Term] +id: UBERON:0006904 +name: head mesenchyme from mesoderm +namespace: uberon +def: "A head mesenchyme that develops_from a mesoderm." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "cranial mesoderm" RELATED [UBERON:0005280] +synonym: "head mesenchyme derived from mesoderm" EXACT [] +synonym: "head mesenchyme from head mesoderm" EXACT [EHDAA2:0001118] +synonym: "head mesenchyme from mesoderm" EXACT [] +synonym: "head mesoderm" RELATED [AAO:0011051, UBERON:0005280] +synonym: "mesenchyme derived from head mesoderm" EXACT [EHDAA:1057] +synonym: "mesenchyme from head mesoderm" EXACT [] +xref: AAO:0011051 +xref: EFO:0003337 +xref: EFO:0003603 +xref: EHDAA2:0001118 +xref: EHDAA:655 +xref: EMAPA:16099 +xref: EMAPA_RETIRED:16270 +xref: FMA:293859 +xref: TAO:0000998 +xref: VHOG:0000185 +xref: XAO:0000053 +xref: ZFA:0000998 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme +intersection_of: UBERON:0005253 ! head mesenchyme +intersection_of: develops_from UBERON:0000926 ! mesoderm +relationship: develops_from UBERON:0003063 {source="EHDAA2", source="XAO"} ! prechordal plate +property_value: IAO:0000116 "merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme" xsd:string + +[Term] +id: UBERON:0006909 +name: lumen of digestive tract +namespace: uberon +def: "An anatomical space that surrounded_by a digestive tract." [OBOL:automatic] +synonym: "digestive tract lumen" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "gut cavity" EXACT [BTO:0000349] +synonym: "gut lumen" EXACT [FMA:45677] +synonym: "lumen of alimentary tract" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "lumen of digestive tract" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "lumen of gut" EXACT [FMA:45677] +xref: BTO:0000349 +xref: EMAPA:32908 +xref: FMA:45677 +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0001555 ! digestive tract +relationship: luminal_space_of UBERON:0001555 ! digestive tract +relationship: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0006913 +name: lip epithelium +namespace: uberon +def: "An epithelium that is part of a lip." [OBOL:automatic] +xref: BTO:0004468 +xref: TAO:0005334 +xref: ZFA:0005334 +is_a: UBERON:0003929 ! digestive tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001833 ! lip +relationship: part_of UBERON:0001833 ! lip +property_value: UBPROP:0000001 "The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005334", ontology="TAO", source="ZFIN:ZDB-PUB-060921-12"} + +[Term] +id: UBERON:0006914 +name: squamous epithelium +namespace: uberon +def: "An epithelium characterised by its most superficial layer consisting of squamous epithelial cells." [http://en.wikipedia.org/wiki/Squamous_epithelium] +xref: BTO:0002072 +xref: http://linkedlifedata.com/resource/umls/id/C0221909 +xref: http://www.snomedbrowser.com/Codes/Details/40118003 +xref: NCIT:C12848 +xref: Squamous:epithelium +xref: UMLS:C0221909 {source="ncithesaurus:Squamous_Epithelium"} +is_a: UBERON:0000483 ! epithelium +property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} + +[Term] +id: UBERON:0006965 +name: vascular cord +namespace: uberon +def: "The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]." [GO:0072360, ZFA:0005077] +subset: efo_slim +xref: EFO:0003709 +xref: TAO:0005077 +xref: ZFA:0005077 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: part_of UBERON:0014903 ! primordial vasculature + +[Term] +id: UBERON:0006966 +name: coronary capillary +namespace: uberon +def: "A capillary that is part of the coronary system." [http://orcid.org/0000-0002-6601-2165] +synonym: "heart capillary" EXACT [GO:0003248] +xref: ZFA:0005813 +is_a: UBERON:0001982 ! capillary +is_a: UBERON:0003498 ! heart blood vessel +intersection_of: UBERON:0001982 ! capillary +intersection_of: part_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0006984 +name: anatomical surface +namespace: uberon +def: "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n" [CARO:0001002] +comment: Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. +subset: upper_level +xref: BILA:0000010 +xref: CARO:0001002 +xref: EHDAA2_RETIRED:0003192 +xref: FMA:24137 +xref: http://linkedlifedata.com/resource/umls/id/C1515977 +xref: NCIT:C34022 +xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} +is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary + +[Term] +id: UBERON:0007005 +name: cardiogenic splanchnic mesoderm +namespace: uberon +def: "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]." [http://www.drugs.com/dict/cardiogenic-mesoderm.html, https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7, XAO:0000235] +subset: efo_slim +subset: pheno_slim +synonym: "cardiac mesoderm" RELATED [XAO:0000235] +synonym: "cardiogenic mesoderm" RELATED [http://www.drugs.com/dict/cardiogenic-mesoderm.html] +synonym: "cardiogenic region" RELATED [http://orcid.org/0000-0002-6601-2165] +synonym: "cardiogenic splanchnopleure" EXACT [EHDAA2:0000214] +synonym: "heart primordia" RELATED [XAO:0000235] +xref: AAO:0011021 +xref: BILA:0000051 +xref: EFO:0000315 +xref: EHDAA2:0000214 +xref: EHDAA:385 +xref: FMA:293143 +xref: http://www.snomedbrowser.com/Codes/Details/360387000 +xref: VHOG:0001641 +xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm +relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm +relationship: part_of UBERON:0004140 ! primary heart field +relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string + +[Term] +id: UBERON:0007010 +name: cleaving embryo +namespace: uberon +def: "Organism at the cleavage stage." [OBOL:automatic] +xref: BILA:0000058 +is_a: UBERON:0000922 ! embryo +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage +intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage +relationship: existence_ends_with UBERON:0000107 ! cleavage stage +relationship: existence_starts_with UBERON:0000107 ! cleavage stage + +[Term] +id: UBERON:0007026 +name: presumptive gut +namespace: uberon +synonym: "embryonic digestive tube" RELATED [] +synonym: "future digestive tract" EXACT [] +synonym: "future digestive tube" EXACT [] +synonym: "future gut" EXACT [] +synonym: "primitive gut" EXACT [] +synonym: "primordial digestive tube" RELATED [] +synonym: "primordial gut" RELATED [] +xref: BILA:0000084 +xref: http://linkedlifedata.com/resource/umls/id/C1514442 +xref: http://www.snomedbrowser.com/Codes/Details/360394002 +xref: NCIT:C34268 +xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract +relationship: existence_starts_during UBERON:0000109 ! gastrula stage +relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm +relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm +relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract +property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} + +[Term] +id: UBERON:0007100 +name: primary circulatory organ +namespace: uberon +def: "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]." [GO:0007507] +comment: Gene notes: Bmp, Nkx, Gata +subset: grouping_class +synonym: "adult heart" RELATED [FBbt:00003154] +synonym: "dorsal tube" NARROW [http://en.wikipedia.org/wiki/Heart] +synonym: "heart" NARROW [GO:0007507] +xref: FBbt:00003154 +xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg +xref: SPD:0000130 +xref: TADS:0000147 +is_a: UBERON:0015228 ! circulatory organ +property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string + +[Term] +id: UBERON:0007135 +name: neural keel +namespace: uberon +def: "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section." [ZFIN:ZDB-PUB-961014-576] +subset: efo_slim +synonym: "presumptive central nervous system" RELATED [ZFA:0000131] +xref: EFO:0003497 +xref: TAO:0000131 +xref: ZFA:0000131 +is_a: UBERON:0016879 ! future central nervous system +relationship: develops_from UBERON:0003075 ! neural plate +property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0007213 +name: mesenchyme derived from head neural crest +namespace: uberon +def: "Mesenchyme that develops_from a cranial neural crest." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "head mesenchyme from cranial neural crest" EXACT [] +synonym: "head mesenchyme from neural crest" EXACT [EHDAA2:0000735] +synonym: "head neural crest derived mesenchyme" EXACT [] +xref: EFO:0003572 +xref: EHDAA2:0000735 +xref: EMAPA:16169 +xref: EMAPA:16271 +xref: EMAPA_RETIRED:16271 +xref: TAO:0000787 +xref: ZFA:0000787 +is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0003099 ! cranial neural crest +relationship: develops_from UBERON:0003099 ! cranial neural crest + +[Term] +id: UBERON:0007239 +name: tunica media of artery +namespace: uberon +def: "A tunica media that is part of a artery." [OBOL:automatic] +synonym: "arterial media" EXACT [EV:0100029] +synonym: "tunica media (arteriae)" EXACT [FMA:14273] +xref: EMAPA:36294 +xref: EV:0100029 +xref: FMA:14273 +xref: http://linkedlifedata.com/resource/umls/id/C1710627 +xref: http://www.snomedbrowser.com/Codes/Details/84300001 +xref: NCIT:C49321 +xref: UMLS:C1710627 {source="ncithesaurus:Venous_System_Smooth_Muscle_Tissue"} +is_a: UBERON:0002522 ! tunica media +intersection_of: UBERON:0002522 ! tunica media +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0000415 ! artery wall + +[Term] +id: UBERON:0007240 +name: tunica adventitia of artery +namespace: uberon +def: "A tunica adventitia that is part of a artery." [OBOL:automatic] +synonym: "arterial adventitia" EXACT [EV:0100030] +synonym: "tunica externa (adventitia)(arteriae)" EXACT [FMA:14274] +xref: EMAPA:36295 +xref: EV:0100030 +xref: FMA:14274 +xref: http://www.snomedbrowser.com/Codes/Details/113261001 +is_a: UBERON:0005734 ! tunica adventitia of blood vessel +intersection_of: UBERON:0005734 ! tunica adventitia of blood vessel +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0000415 ! artery wall + +[Term] +id: UBERON:0007241 +name: tunica adventitia of vein +namespace: uberon +def: "A tunica adventitia that is part of a vein." [OBOL:automatic] +synonym: "tunica externa (adventitia)(venae)" EXACT [FMA:14355] +synonym: "venous adventitia" EXACT [EV:0100034] +xref: EMAPA:36310 +xref: EV:0100034 +xref: FMA:14355 +xref: http://www.snomedbrowser.com/Codes/Details/13202006 +is_a: UBERON:0005734 ! tunica adventitia of blood vessel +intersection_of: UBERON:0005734 ! tunica adventitia of blood vessel +intersection_of: part_of UBERON:0001638 ! vein +relationship: part_of UBERON:0001638 ! vein + +[Term] +id: UBERON:0007242 +name: tunica intima of vein +namespace: uberon +def: "A tunica intima that is part of a vein." [OBOL:automatic] +synonym: "tunica interna (intima)(venae)" EXACT [FMA:14353] +synonym: "venous intima" EXACT [EV:0100032] +xref: EMAPA:36308 +xref: EV:0100032 +xref: FMA:14353 +xref: http://www.snomedbrowser.com/Codes/Details/2436009 +is_a: UBERON:0002523 ! tunica intima +is_a: UBERON:0004797 ! blood vessel layer +intersection_of: UBERON:0002523 ! tunica intima +intersection_of: part_of UBERON:0001638 ! vein +relationship: part_of UBERON:0001638 ! vein + +[Term] +id: UBERON:0007243 +name: tunica media of vein +namespace: uberon +def: "A tunica media that is part of a vein." [OBOL:automatic] +synonym: "tunica media (venae)" EXACT [FMA:14354] +synonym: "venous media" EXACT [EV:0100033] +xref: EMAPA:36309 +xref: EV:0100033 +xref: FMA:14354 +xref: http://www.snomedbrowser.com/Codes/Details/42049001 +is_a: UBERON:0002522 ! tunica media +intersection_of: UBERON:0002522 ! tunica media +intersection_of: part_of UBERON:0001638 ! vein +relationship: part_of UBERON:0001638 ! vein + +[Term] +id: UBERON:0007277 +name: presumptive hindbrain +namespace: uberon +def: "The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure." [http://en.wikipedia.org/wiki/Rhombencephalon] +subset: efo_slim +synonym: "embryonic rhombencephalon" RELATED [CALOHA:TS-2118] +synonym: "future hindbrain" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "presumptive rhombencephalon" EXACT [ZFA:0000569] +synonym: "rhombencephalon" RELATED [EHDAA2:0001630] +xref: BAMS:HB +xref: CALOHA:TS-2118 +xref: EFO:0003440 +xref: EHDAA2:0001630 +xref: FMA:295640 +xref: http://en.wikipedia.org/wiki/Rhombencephalon +xref: TAO:0000569 +xref: ZFA:0000569 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0002028 ! hindbrain +relationship: develops_from UBERON:0003076 {source="XAO-abduced"} ! posterior neural tube +relationship: has_developmental_contribution_from UBERON:0003852 {source="cjm"} ! rhombencephalon neural crest +relationship: has_potential_to_develop_into UBERON:0002028 ! hindbrain +relationship: part_of UBERON:0006238 ! future brain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string +property_value: UBPROP:0000001 "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." xsd:string {source="NPX:PDR"} + +[Term] +id: UBERON:0007280 +name: presumptive endocardium +namespace: uberon +def: "A presumptive structure that has the potential to develop into a endocardium." [OBOL:automatic] +xref: TAO:0002233 +xref: ZFA:0001724 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0002165 ! endocardium +relationship: develops_from UBERON:0003084 ! heart primordium +relationship: has_potential_to_develop_into UBERON:0002165 ! endocardium +relationship: part_of UBERON:0005498 ! primitive heart tube +property_value: UBPROP:0000001 "Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002233", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0007281 +name: presumptive midbrain hindbrain boundary +namespace: uberon +def: "Embryonic structure that gives rise to the midbrain hindbrain boundary." [ZFA:0001187] +subset: efo_slim +synonym: "presumptive MHB" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "presumptive midbrain-hindbrain boundary" EXACT [ZFA:0001187] +xref: EFO:0003446 +xref: TAO:0001187 +xref: XAO:0004086 +xref: ZFA:0001187 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary +relationship: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary +relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain + +[Term] +id: UBERON:0007282 +name: presumptive segmental plate +namespace: uberon +def: "A presumptive structure that has the potential to develop into a presomitic mesoderm." [OBOL:automatic] +subset: efo_slim +synonym: "presumptive segmental plates" RELATED PLURAL [ZFA:0000053] +xref: EFO:0003421 +xref: TAO:0000053 +xref: ZFA:0000053 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm +relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm + +[Term] +id: UBERON:0007284 +name: presumptive neural plate +namespace: uberon +def: "A presumptive structure that has the potential to develop into a neural plate." [OBOL:automatic] +subset: efo_slim +synonym: "prospective neuroectoderm" EXACT [ZFA:0000063] +synonym: "prospective vegetal ectoderm" EXACT [ZFA:0000063] +xref: EFO:0003424 +xref: TAO:0000063 +xref: ZFA:0000063 +is_a: UBERON:0016879 ! future central nervous system +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate +relationship: develops_from UBERON:0002346 ! neurectoderm +relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +relationship: part_of UBERON:0004734 ! gastrula +property_value: IAO:0000116 "consider merging" xsd:string +property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0007285 +name: presumptive paraxial mesoderm +namespace: uberon +def: "The part of the blastula that has the potential to develop into a paraxial mesoderm." [https://github.com/obophenotype/uberon/issues/1277, UBERON:cjm] +subset: efo_slim +synonym: "future paraxial mesenchyme" EXACT [UBERON:cjm] +synonym: "future paraxial mesoderm" EXACT [] +xref: EFO:0003443 +xref: TAO:0000591 +xref: XAO:0004134 +xref: ZFA:0000591 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm +intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula +relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +relationship: part_of UBERON:0000307 ! blastula + +[Term] +id: UBERON:0007303 +name: pharyngeal vasculature +namespace: uberon +def: "A vasculature that is part of a chordate pharynx." [OBOL:automatic] +synonym: "branchial vasculature" EXACT [ZFA:0005003] +xref: TAO:0005003 +xref: ZFA:0005003 +is_a: UBERON:0006876 ! vasculature of organ +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0001042 ! chordate pharynx +relationship: part_of UBERON:0001042 ! chordate pharynx + +[Term] +id: UBERON:0007376 +name: outer epithelium +namespace: uberon +def: "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]." [GO:0008544] +subset: grouping_class +synonym: "epidermis" EXACT [GO:0008544] +synonym: "epidermis (sensu Metazoa)" EXACT [] +synonym: "hypoderm" RELATED INCONSISTENT [BTO:0000313] +synonym: "hypodermis" RELATED INCONSISTENT [GO:0008544, WBbt:0005733] +synonym: "outer epidermal layer" EXACT [] +synonym: "outer epithelial layer" EXACT [] +xref: BSA:0000073 +xref: BTO:0000313 +xref: Epidermis:(zoology) +xref: FBbt:00004993 +xref: HAO:0000298 +xref: TADS:0000109 +xref: WBbt:0005733 +is_a: UBERON:0003102 ! surface structure +is_a: UBERON:0010371 ! ecto-epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: bounding_layer_of UBERON:0000468 ! multicellular organism +intersection_of: develops_from UBERON:0007383 ! enveloping layer of ectoderm +relationship: bounding_layer_of UBERON:0000468 ! multicellular organism +relationship: develops_from UBERON:0007383 ! enveloping layer of ectoderm +property_value: IAO:0000116 "this grouping class exists primarily to align with GO - see GO:0008544." xsd:string + +[Term] +id: UBERON:0007383 +name: enveloping layer of ectoderm +namespace: uberon +def: "Outermost layer of cells surrounding the embryo." [http://orcid.org/0000-0002-6601-2165] +subset: efo_slim +synonym: "enveloping layer" EXACT [ZFIN:ZDB-PUB-961014-576] +synonym: "EVL" EXACT [ZFA:0000086] +xref: EFO:0003425 +xref: TAO:0000086 +xref: ZFA:0000086 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium +relationship: bounding_layer_of UBERON:0000922 ! embryo +relationship: develops_from UBERON:0000076 ! external ectoderm +property_value: UBPROP:0000001 "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO", source="ZFIN:curator"} +property_value: UBPROP:0000002 "relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO"} +property_value: UBPROP:0000008 "Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm." xsd:string + +[Term] +id: UBERON:0007473 +name: lumen of epithelial sac +namespace: uberon +alt_id: EHDAA2:0003079 +def: "The space within an epithelial sphere." [AEO:JB] +synonym: "cavity of vesicle" EXACT [AEO:0000079] +xref: AEO:0000079 +is_a: UBERON:0012467 ! enclosed anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0007499 ! epithelial sac +relationship: luminal_space_of UBERON:0007499 ! epithelial sac +relationship: part_of UBERON:0007499 ! epithelial sac + +[Term] +id: UBERON:0007499 +name: epithelial sac +namespace: uberon +def: "An epithelial tube that is open at one end only." [AEO:JB, UBERONREF:0000001] +xref: AEO:0000115 +xref: EHDAA2:0003115 +is_a: UBERON:0003914 {source="AEO"} ! epithelial tube +is_a: UBERON:0009856 ! sac + +[Term] +id: UBERON:0007500 +name: epithelial tube open at both ends +namespace: uberon +def: "An epithelial tube open at both ends that allows fluid flow." [AEO:JB, UBERONREF:0000001] +xref: AEO_RETIRED:0000116 +xref: RETIRED_EHDAA2:0003116 +is_a: UBERON:0003914 {source="AEO"} ! epithelial tube + +[Term] +id: UBERON:0007503 +name: epithelial vesicle +namespace: uberon +alt_id: EHDAA2:0003119 +def: "A closed epithelium with a lumen." [AEO:JB] +xref: AEO:0000119 +xref: EHDAA2:0003119 +is_a: UBERON:0000483 {source="AEO"} ! epithelium + +[Term] +id: UBERON:0007524 +name: dense mesenchyme tissue +namespace: uberon +alt_id: EHDAA2:0003146 +def: "Mesenchyme with little extracellular matrix." [AEO:JB] +xref: AEO:0000146 +xref: EHDAA2:0003146 +is_a: UBERON:0003104 {source="AEO"} ! mesenchyme + +[Term] +id: UBERON:0007530 +name: migrating mesenchyme population +namespace: uberon +alt_id: EHDAA2:0003152 +def: "Mesenchymal cells that are migrating." [AEO:JB] +xref: AEO:0000152 +xref: EHDAA2:0003152 +is_a: UBERON:0003104 ! mesenchyme +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string + +[Term] +id: UBERON:0007592 +name: ciliated columnar epithelium +namespace: uberon +def: "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]" [FMA:64798] +xref: FMA:64798 +is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium +is_a: UBERON:0007601 ! ciliated epithelium +property_value: UBPROP:0000008 "In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system" xsd:string +property_value: UBPROP:0000009 "Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]" xsd:string + +[Term] +id: UBERON:0007601 +name: ciliated epithelium +namespace: uberon +def: "Epithelium bearing vibratile cilia on the free surface." [http://medical-dictionary.thefreedictionary.com/ciliated+epithelium] +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0007616 +name: layer of synovial tissue +namespace: uberon +def: "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." [BTO:0001338, http://www.britannica.com/EBchecked/topic/578563/synovial-tissue] +synonym: "stratum synoviale" NARROW [FMA:TA] +synonym: "synovial layer" NARROW [FMA:66762] +synonym: "synovial membrane" NARROW [FMA:66762] +synonym: "synovial tissue" RELATED [BTO:0001338] +synonym: "synovium" EXACT [CALOHA:TS-0998] +xref: BTO:0001338 +xref: CALOHA:TS-0998 +xref: FMA:66762 +is_a: UBERON:0000042 ! serous membrane +intersection_of: UBERON:0000042 ! serous membrane +intersection_of: produces UBERON:0001090 ! synovial fluid +relationship: composed_primarily_of UBERON:0002384 {source="BTO"} ! connective tissue +relationship: produces UBERON:0001090 ! synovial fluid + +[Term] +id: UBERON:0007617 +name: synovial cavity of joint +namespace: uberon +def: "An anatomical cavity that surrounded_by a synovial joint." [OBOL:automatic] +synonym: "articular cavity (synovial joint)" EXACT [FMA:11356] +synonym: "cavitas articularis (junctura synovialis)" EXACT [FMA:11356] +synonym: "cavity of synovial joint" EXACT [FMA:11356] +synonym: "joint cavity" RELATED [FMA:11356] +synonym: "synovial cavity" RELATED [FMA:11356] +xref: FMA:11356 +is_a: UBERON:0002553 ! anatomical cavity +intersection_of: UBERON:0002553 ! anatomical cavity +intersection_of: luminal_space_of UBERON:0002217 ! synovial joint +relationship: luminal_space_of UBERON:0002217 ! synovial joint +relationship: part_of UBERON:0002217 ! synovial joint + +[Term] +id: UBERON:0007651 +name: anatomical junction +namespace: uberon +def: "An anatomical structure that connects two structures" [http://code.google.com/p/caro2/issues/detail?id=15] +subset: upper_level +synonym: "anatomical junction" EXACT [] +synonym: "junction" BROAD [] +xref: FMA:5898 +xref: http://www.snomedbrowser.com/Codes/Details/91833003 +is_a: UBERON:0000061 {source="FMA"} ! anatomical structure +relationship: connects UBERON:0000061 {minCardinality="2"} ! anatomical structure + +[Term] +id: UBERON:0007688 +name: anlage +namespace: uberon +def: "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue." [FBbt:00005426, http://flybase.org/reports/FBrf0178740.html, JB:DEF] +subset: efo_slim +synonym: "developmental field" EXACT [] +synonym: "field" BROAD [] +synonym: "future organ" RELATED [] +synonym: "organ field" RELATED [] +xref: AEO:0000170 +xref: Anlage:(biology) +xref: EFO:0001649 +xref: EHDAA2:0003170 +xref: FBbt:00005426 +is_a: UBERON:0000479 {source="FBbt"} ! tissue +is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure + +[Term] +id: UBERON:0007690 +name: early pharyngeal endoderm +namespace: uberon +def: "." [http://dev.biologists.org/content/128/22/4573.full] +comment: relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' +subset: efo_slim +synonym: "early pharyngeal arch endoderm" EXACT [EHDAA2:0001457] +synonym: "pharyngeal arch endoderm" RELATED [] +synonym: "pharyngeal endoderm" RELATED [ZFA:0001104] +synonym: "pharyngeal region endoderm" RELATED [EHDAA2:0001456] +xref: EFO:0003626 +xref: EHDAA2:0001457 +xref: EHDAA:962 +xref: EMAPA:32754 +xref: FMA:293087 +xref: TAO:0001104 +xref: ZFA:0001104 +is_a: UBERON:0003258 ! endoderm of foregut +is_a: UBERON:0005291 ! embryonic tissue +relationship: part_of UBERON:0009722 {source="cjm"} ! entire pharyngeal arch endoderm + +[Term] +id: UBERON:0007771 +name: epidermis gland +namespace: uberon +def: "A gland that is part of a epidermis." [OBOL:automatic] +subset: grouping_class +synonym: "epidermal gland" EXACT [] +synonym: "gland of epidermis" EXACT [FMA:59153] +xref: FMA:59153 +is_a: UBERON:0002419 ! skin gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0001003 ! skin epidermis +relationship: part_of UBERON:0001003 ! skin epidermis + +[Term] +id: UBERON:0007779 +name: transudate +namespace: uberon +def: "Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces" [http://medical-dictionary.thefreedictionary.com/transudate] +synonym: "plasma ultrafiltrate" RELATED [] +xref: FMA:12276 +xref: GAID:1195 +xref: MESH:D005122 +xref: ncithesaurus:Transudate +is_a: UBERON:0006314 ! bodily fluid +relationship: develops_from UBERON:0001969 ! blood plasma +relationship: filtered_through UBERON:0001982 ! capillary +relationship: transformation_of UBERON:0001969 ! blood plasma +property_value: UBPROP:0000007 "transudative" xsd:string +property_value: UBPROP:0000010 "characteristically low in protein and cellular content (unless there has been secondary concentration)" xsd:string + +[Term] +id: UBERON:0007794 +name: secretion of serous gland +namespace: uberon +def: "Any fluid produced by a serous gland." [UBERON:cjm] +synonym: "serosal fluid" EXACT [http://en.wikipedia.org/wiki/Serous_fluid] +synonym: "serous fluid" BROAD [] +synonym: "serous gland fluid" EXACT [] +xref: Serous:fluid +is_a: UBERON:0000456 ! secretion of exocrine gland +is_a: UBERON:0006314 ! bodily fluid +intersection_of: UBERON:0006314 ! bodily fluid +intersection_of: produced_by UBERON:0000409 ! serous gland +relationship: produced_by UBERON:0000409 ! serous gland + +[Term] +id: UBERON:0007798 +name: vascular system +namespace: uberon +def: "Anatomical system that consists of all blood and lymph vessels." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "Gefaesssystem@de" RELATED [BTO:0001085] +xref: BTO:0001085 +xref: CALOHA:TS-2053 +xref: EHDAA2:0004520 +xref: EMAPA:35905 +xref: http://linkedlifedata.com/resource/umls/id/C0489903 +xref: MA:0002718 +xref: NCIT:C33854 +xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} +is_a: UBERON:0000467 ! anatomical system +relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} +property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0007811 +name: craniocervical region +namespace: uberon +def: "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "cephalic area" RELATED [https://github.com/obophenotype/uberon/issues/379] +synonym: "cephalic part of animal" RELATED [http://en.wikipedia.org/wiki/Head] +synonym: "cephalic region" RELATED [https://github.com/obophenotype/uberon/issues/379] +synonym: "head and neck" RELATED [FMA:280881] +synonym: "head or neck" RELATED [] +xref: CALOHA:TS-2356 +xref: EV:0100009 +xref: FMA:280881 +xref: galen:HeadAndNeck +xref: http://linkedlifedata.com/resource/umls/id/C0460004 +xref: http://www.snomedbrowser.com/Codes/Details/361355005 +xref: MA:0000006 +xref: NCIT:C12418 +xref: UMLS:C0460004 {source="ncithesaurus:Head_and_Neck"} +xref: WikipediaCategory:Head_and_neck +is_a: UBERON:0000475 {source="MA"} ! organism subdivision +relationship: has_part UBERON:0000033 ! head +relationship: has_part UBERON:0006562 ! pharynx +relationship: part_of UBERON:0000153 ! anterior region of body +relationship: part_of UBERON:0013702 ! body proper + +[Term] +id: UBERON:0008229 +name: craniocervical region musculature +namespace: uberon +def: "Musculature system of the pharyngeal and head regions." [ZFA:0000328, ZFA:curator] +synonym: "head muscles" RELATED [ZFA:0000328] +synonym: "head or neck muscle" EXACT [MA:0000571] +synonym: "head or neck muscle" RELATED [MA:0000571] +xref: EMAPA:37259 {source="MA:th"} +xref: MA:0000571 +xref: TAO:0000328 +xref: ZFA:0000328 +is_a: UBERON:0001015 {source="MA"} ! musculature +intersection_of: UBERON:0001015 ! musculature +intersection_of: part_of UBERON:0007811 ! craniocervical region +relationship: part_of UBERON:0007811 {source="MA"} ! craniocervical region +property_value: UBPROP:0000012 "in MA this is restricted to skeletal muscles" xsd:string {external_ontology="MA"} + +[Term] +id: UBERON:0008307 +name: heart endothelium +namespace: uberon +def: "An endothelium that is part of a heart [Automatically generated definition]." [OBOL:automatic] +synonym: "cardiac endothelium" RELATED [BTO:0004293] +xref: BTO:0004293 +is_a: UBERON:0004852 ! cardiovascular system endothelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart +property_value: IAO:0000232 "this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class." xsd:string + +[Term] +id: UBERON:0008814 +name: pharyngeal arch system +namespace: uberon +def: "A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]." [GO:0060037, GOC:dph] +synonym: "embryonic pharyngeal complex" EXACT [] +synonym: "pharyngeal apparatus" EXACT [] +synonym: "pharyngeal arch complex" RELATED [] +synonym: "pharyngeal arch region" RELATED [EHDAA2:0000187] +synonym: "pharyngeal arches and clefts" RELATED [] +synonym: "pharyngeal complex" RELATED [] +synonym: "pharyngeal system" EXACT [GO:0060037] +xref: EHDAA2:0000187 +xref: FMA:293041 +xref: http://linkedlifedata.com/resource/umls/id/C1519038 +xref: NCIT:C34248 +xref: UMLS:C1519038 {source="ncithesaurus:Pharyngeal_Apparatus"} +is_a: UBERON:0000477 ! anatomical cluster +relationship: part_of UBERON:0000922 ! embryo +relationship: part_of UBERON:0009145 ! pharyngeal region of foregut +property_value: IAO:0000116 "Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing" xsd:string + +[Term] +id: UBERON:0008816 +name: embryonic head +namespace: uberon +def: "A head that is part of a embryo." [OBOL:automatic] +subset: non_informative +xref: CALOHA:TS-0246 +xref: FBbt:00000155 +xref: FMA:293011 +is_a: UBERON:0000033 ! head +intersection_of: UBERON:0000033 ! head +intersection_of: part_of UBERON:0000922 ! embryo +relationship: part_of UBERON:0000922 ! embryo + +[Term] +id: UBERON:0008823 +name: neural tube derived brain +namespace: uberon +def: "A brain that develops_from a neural tube." [https://github.com/obophenotype/uberon/issues/338, OBOL:automatic] +synonym: "vertebrate brain" NARROW [] +is_a: UBERON:0000489 {source="ZFA"} ! cavitated compound organ +is_a: UBERON:0000955 ! brain +intersection_of: UBERON:0000955 ! brain +intersection_of: develops_from UBERON:0001049 ! neural tube +relationship: develops_from UBERON:0001049 ! neural tube +relationship: part_of UBERON:0000033 {source="FMA"} ! head +property_value: IAO:0000116 "a reasoner should automatically classify all the vertebrate ontology brain classes here" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/338 + +[Term] +id: UBERON:0008886 +name: pulmonary vascular system +namespace: uberon +def: "The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins." [http://en.wikipedia.org/wiki/Pulmonary_circulation, ISBN10:0073040584] +synonym: "pulmonary circulatory system" EXACT [FMA:45621] +synonym: "pulmonary system" EXACT [ISBN10:0073040584] +xref: FMA:45621 +xref: Pulmonary:circulation +is_a: UBERON:0007798 {source="Obol"} ! vascular system +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: has_part UBERON:0002012 ! pulmonary artery +relationship: has_part UBERON:0002016 ! pulmonary vein +property_value: UBPROP:0000001 "Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]" xsd:string {ontology="FMA", source="FMA:45621"} + +[Term] +id: UBERON:0008947 +name: respiratory primordium +namespace: uberon +xref: EHDAA2:0004069 +xref: http://linkedlifedata.com/resource/umls/id/C1514898 +xref: NCIT:C34283 +xref: UMLS:C1514898 {source="ncithesaurus:Respiratory_Primordium"} +is_a: UBERON:0001048 {source="Obol"} ! primordium +relationship: has_potential_to_develop_into UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003258 ! endoderm of foregut + +[Term] +id: UBERON:0008998 +name: vasculature of brain +namespace: uberon +alt_id: UBERON:0005284 +def: "System pertaining to blood vessels in the brain." [BTO:0003840] +subset: efo_slim +synonym: "brain vasculature" EXACT [] +synonym: "cerebrovascular system" EXACT [BTO:0003840] +synonym: "intracerebral vasculature" EXACT [FMA:61935] +xref: BTO:0003840 +xref: EFO:0003491 +xref: EMAPA:35186 +xref: FMA:242007 +xref: FMA:61935 +xref: http://www.snomedbrowser.com/Codes/Details/362029003 +xref: TAO:0000099 +xref: ZFA:0000099 +is_a: UBERON:0006876 ! vasculature of organ +relationship: part_of UBERON:0000955 ! brain + +[Term] +id: UBERON:0009030 +name: left pulmonary vein +namespace: uberon +def: "Vein that drains left lung and returns blood to the heart." [http://orcid.org/0000-0002-6601-2165] +xref: EMAPA:37165 {source="MA:th"} +xref: http://linkedlifedata.com/resource/umls/id/C0226670 +xref: http://www.snomedbrowser.com/Codes/Details/304057004 +xref: MA:0002207 +xref: NCIT:C48946 +xref: UMLS:C0226670 {source="ncithesaurus:Left_Pulmonary_Vein"} +is_a: UBERON:0002016 ! pulmonary vein +intersection_of: UBERON:0002016 ! pulmonary vein +intersection_of: drains UBERON:0002168 ! left lung +relationship: drains UBERON:0002168 ! left lung +property_value: UBPROP:0000001 "A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]." xsd:string {source="ncithesaurus:Left_Pulmonary_Vein"} + +[Term] +id: UBERON:0009032 +name: right pulmonary vein +namespace: uberon +def: "Vein that drains right lung and returns blood to the heart." [http://orcid.org/0000-0002-6601-2165] +xref: EMAPA:37379 {source="MA:th"} +xref: http://linkedlifedata.com/resource/umls/id/C0226669 +xref: http://www.snomedbrowser.com/Codes/Details/304056008 +xref: MA:0002208 +xref: NCIT:C48947 +xref: UMLS:C0226669 {source="ncithesaurus:Right_Pulmonary_Vein"} +is_a: UBERON:0002016 ! pulmonary vein +intersection_of: UBERON:0002016 ! pulmonary vein +intersection_of: drains UBERON:0002167 ! right lung +relationship: drains UBERON:0002167 ! right lung +property_value: UBPROP:0000001 "A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]." xsd:string {source="ncithesaurus:Right_Pulmonary_Vein"} + +[Term] +id: UBERON:0009141 +name: craniocervical region vein +namespace: uberon +def: "A vein that is part of a craniocervical region." [OBOL:automatic] +synonym: "craniocervical vein" EXACT [] +synonym: "head and neck veins" EXACT [EHDAA2:0004542] +synonym: "vein of head and neck" EXACT [] +xref: EHDAA2:0004542 +xref: http://www.snomedbrowser.com/Codes/Details/32945007 +is_a: UBERON:0013140 ! systemic vein +intersection_of: UBERON:0001638 ! vein +intersection_of: part_of UBERON:0007811 ! craniocervical region +relationship: part_of UBERON:0007811 ! craniocervical region + +[Term] +id: UBERON:0009142 +name: entire embryonic mesenchyme +namespace: uberon +alt_id: UBERON:0003313 +def: "Sum total of mesenchyme in the embryo." [https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7] +xref: EHDAA2:0001113 +xref: EHDAA:177 +xref: EMAPA:16097 +is_a: UBERON:0000477 ! anatomical cluster +relationship: composed_primarily_of UBERON:0003104 ! mesenchyme +relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm +relationship: part_of UBERON:0000922 ! embryo +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string + +[Term] +id: UBERON:0009145 +name: pharyngeal region of foregut +namespace: uberon +synonym: "pharyngeal region" EXACT [EMAPA:16549] +xref: EMAPA:16549 +xref: RETIRED_EHDAA2:0001454 +is_a: UBERON:0005423 ! developing anatomical structure +relationship: part_of UBERON:0001041 {source="EHDAA2"} ! foregut + +[Term] +id: UBERON:0009479 +name: ectoderm of buccopharyngeal membrane +namespace: uberon +def: "An ectoderm that is part of a buccopharyngeal membrane." [OBOL:automatic] +subset: emapa_ehdaa2 +xref: EHDAA2:0000190 +xref: EMAPA:16260 +is_a: UBERON:0000924 ! ectoderm +intersection_of: UBERON:0000924 ! ectoderm +intersection_of: part_of UBERON:0006211 ! buccopharyngeal membrane +relationship: part_of UBERON:0006211 ! buccopharyngeal membrane + +[Term] +id: UBERON:0009480 +name: endoderm of buccopharyngeal membrane +namespace: uberon +def: "An endoderm that is part of a buccopharyngeal membrane." [OBOL:automatic] +subset: emapa_ehdaa2 +xref: EHDAA2:0000191 +xref: EMAPA:16261 +is_a: UBERON:0000925 ! endoderm +intersection_of: UBERON:0000925 ! endoderm +intersection_of: part_of UBERON:0006211 ! buccopharyngeal membrane +relationship: part_of UBERON:0006211 ! buccopharyngeal membrane + +[Term] +id: UBERON:0009494 +name: pharyngeal arch mesenchymal region +namespace: uberon +def: "A portion of mesenchymal tissue associated with an individual pharyngeal arch." [https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "branchial arch mesenchyme" EXACT [MP:0011262] +synonym: "pharyngeal arch mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] +xref: EMAPA:32755 +xref: FMA:295694 +is_a: UBERON:0005253 ! head mesenchyme +is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0002539 ! pharyngeal arch +relationship: has_developmental_contribution_from UBERON:0003099 {source="cjm"} ! cranial neural crest +relationship: part_of UBERON:0002539 ! pharyngeal arch +relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme +property_value: IAO:0000116 "this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures." xsd:string {source="MP:0011262"} + +[Term] +id: UBERON:0009569 +name: subdivision of trunk +namespace: uberon +subset: non_informative +synonym: "region of trunk" EXACT [FMA:25054] +synonym: "trunk subdivision" EXACT [FMA:25054] +xref: FMA:25054 +xref: http://www.snomedbrowser.com/Codes/Details/22943007 +is_a: UBERON:0000475 ! organism subdivision +relationship: part_of UBERON:0002100 ! trunk + +[Term] +id: UBERON:0009581 +name: midbrain mantle layer +namespace: uberon +synonym: "mantle layer lateral wall mesencephalon" RELATED [VHOG:0000910] +synonym: "mantle layer lateral wall midbrain" EXACT [VHOG:0000910] +synonym: "midbrain lateral wall mantle layer" EXACT [] +xref: EHDAA2:0001172 +xref: EMAPA:16977 +xref: VHOG:0000910 +is_a: UBERON:0004061 ! neural tube mantle layer +intersection_of: UBERON:0004061 ! neural tube mantle layer +intersection_of: part_of UBERON:0009616 ! presumptive midbrain +relationship: part_of UBERON:0009616 ! presumptive midbrain + +[Term] +id: UBERON:0009583 +name: spinal cord mantle layer +namespace: uberon +synonym: "mantle layer lateral wall spinal cord" EXACT [VHOG:0000911] +synonym: "spinal cord lateral wall mantle layer" EXACT [] +xref: EMAPA:17580 +xref: VHOG:0000911 +is_a: UBERON:0004061 ! neural tube mantle layer +intersection_of: UBERON:0004061 ! neural tube mantle layer +intersection_of: part_of UBERON:0006241 ! future spinal cord +relationship: part_of UBERON:0006241 ! future spinal cord + +[Term] +id: UBERON:0009602 +name: left lung associated mesenchyme +namespace: uberon +def: "Mesenchyme that is part of a developing left lung." [OBOL:automatic] +synonym: "left lung mesenchyme" EXACT [EMAPA:17654] +xref: EHDAA2:0000944 +xref: EMAPA:16730 +xref: EMAPA:17654 +is_a: UBERON:0004883 ! lung mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0002168 ! left lung +relationship: part_of UBERON:0002168 ! left lung + +[Term] +id: UBERON:0009603 +name: right lung associated mesenchyme +namespace: uberon +def: "Mesenchyme that is part of a developing right lung." [OBOL:automatic] +synonym: "right lung mesenchyme" EXACT [EMAPA:17662] +xref: EHDAA2:0001739 +xref: EMAPA:17662 +is_a: UBERON:0004883 ! lung mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0002167 ! right lung +relationship: part_of UBERON:0002167 ! right lung + +[Term] +id: UBERON:0009611 +name: midbrain neural plate +namespace: uberon +def: "A neural plate that develops_from a presumptive midbrain." [OBOL:automatic] +xref: TAO:0007019 +xref: ZFA:0007019 +is_a: UBERON:0003075 ! neural plate +intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate +intersection_of: develops_from UBERON:0009616 {source="ZFA"} ! presumptive midbrain +relationship: develops_from UBERON:0009616 ! presumptive midbrain +relationship: part_of UBERON:0003056 {source="ZFA"} ! pre-chordal neural plate + +[Term] +id: UBERON:0009614 +name: hindbrain neural plate +namespace: uberon +def: "A neural plate that develops_from a presumptive hindbrain." [OBOL:automatic] +xref: TAO:0007022 +xref: ZFA:0007022 +is_a: UBERON:0003075 ! neural plate +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate +intersection_of: develops_from UBERON:0007277 {source="ZFA"} ! presumptive hindbrain +relationship: develops_from UBERON:0007277 ! presumptive hindbrain +relationship: part_of UBERON:0003057 {source="ZFA"} ! chordal neural plate + +[Term] +id: UBERON:0009615 +name: midbrain hindbrain boundary neural plate +namespace: uberon +synonym: "MHB neural plate" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] +xref: TAO:0007044 +xref: ZFA:0007044 +is_a: UBERON:0006598 ! presumptive structure +relationship: develops_from UBERON:0007281 ! presumptive midbrain hindbrain boundary +relationship: immediate_transformation_of UBERON:0007281 {notes="https://github.com/obophenotype/uberon/issues/438", source="Bgee:AN"} ! presumptive midbrain hindbrain boundary +relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate +property_value: IAO:0000116 "TODO - developmental relationships for lines" xsd:string + +[Term] +id: UBERON:0009616 +name: presumptive midbrain +namespace: uberon +def: "A presumptive structure that has the potential to develop into a midbrain." [OBOL:automatic] +subset: efo_slim +synonym: "early midbrain" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "future midbrain" RELATED [https://orcid.org/0000-0002-6601-2165] +synonym: "mesencephalon" RELATED [EHDAA2:0000615] +synonym: "presumptive mesencephalon" EXACT [ZFA:0000148] +xref: BAMS:MES +xref: EFO:0003432 +xref: EHDAA2:0000615 +xref: EMAPA:16140 +xref: http://en.wikipedia.org/wiki/Mesencephalon +xref: TAO:0000148 +xref: ZFA:0000148 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0001891 ! midbrain +relationship: develops_from UBERON:0003080 ! anterior neural tube +relationship: develops_from UBERON:0010286 {source="ZFA"} ! midbrain neural tube +relationship: has_potential_to_develop_into UBERON:0001891 ! midbrain +relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string + +[Term] +id: UBERON:0009618 +name: trunk paraxial mesoderm +namespace: uberon +synonym: "trunk and cervical paraxial mesenchyme" EXACT [EHDAA2:0002094] +synonym: "trunk paraxial mesenchyme" RELATED [https://github.com/obophenotype/uberon/issues/30] +xref: EHDAA2:0002094 +is_a: UBERON:0005256 ! trunk mesenchyme +relationship: part_of UBERON:0003077 ! paraxial mesoderm + +[Term] +id: UBERON:0009657 +name: artery of lip +namespace: uberon +synonym: "labial artery" EXACT [MA:0001987] +xref: EMAPA:37092 {source="MA:th"} +xref: http://linkedlifedata.com/resource/umls/id/C1708633 +xref: MA:0001987 +xref: NCIT:C52947 +xref: UMLS:C1708633 {source="ncithesaurus:Labial_Artery"} +is_a: UBERON:0001637 ! artery +intersection_of: UBERON:0001637 ! artery +intersection_of: supplies UBERON:0001833 ! lip +relationship: supplies UBERON:0001833 ! lip + +[Term] +id: UBERON:0009715 +name: stomodeal lumen +namespace: uberon +def: "An anatomical cavity that surrounded_by a stomodeum." [OBOL:automatic] +synonym: "lumen of stomatodaeum" EXACT [] +synonym: "lumen of stomodeum" EXACT [] +synonym: "stomatodeal cavity" EXACT [] +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0000930 ! stomodeum +relationship: luminal_space_of UBERON:0000930 ! stomodeum +relationship: part_of UBERON:0000930 ! stomodeum + +[Term] +id: UBERON:0009722 +name: entire pharyngeal arch endoderm +namespace: uberon +synonym: "pharyngeal arch endoderm" RELATED [EHDAA2:0004621] +xref: EHDAA2:0004621 +xref: EMAPA:32754 +xref: FMA:293087 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0015833 ! foregut epithelium +relationship: part_of UBERON:0008814 ! pharyngeal arch system + +[Term] +id: UBERON:0009751 +name: cardiac mesenchyme +namespace: uberon +def: "The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures" [MP:0011264] +subset: pheno_slim +synonym: "heart mesenchyme" EXACT [EMAPA:36438] +xref: EHDAA2:0004162 +xref: EMAPA:36438 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart +property_value: IAO:0000116 "decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts" xsd:string + +[Term] +id: UBERON:0009842 +name: glandular acinus +namespace: uberon +def: "The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form." [http://en.wikipedia.org/wiki/Acinus] +synonym: "acini" RELATED PLURAL [http://en.wikipedia.org/wiki/Acinus] +synonym: "acinus" BROAD [FMA:55588] +xref: FMA:55588 +xref: http://en.wikipedia.org/wiki/Acinus +is_a: UBERON:0034922 ! cell cluster +relationship: part_of UBERON:0002530 ! gland +property_value: depicted:by http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png +property_value: UBPROP:0000007 "acinar" xsd:string + +[Term] +id: UBERON:0009854 +name: digestive tract diverticulum +namespace: uberon +def: "Branch or outpocketing of the digestive tract." [https://orcid.org/0000-0002-6601-2165] +synonym: "diverticulum of gut" RELATED [FBbt:00100316] +synonym: "intestinal pouch" RELATED [] +xref: FBbt:00100316 +is_a: UBERON:0004921 ! subdivision of digestive tract +is_a: UBERON:0009856 ! sac +intersection_of: UBERON:0009856 ! sac +intersection_of: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0009856 +name: sac +namespace: uberon +synonym: "diverticulum" RELATED [] +synonym: "pouch" EXACT [] +xref: galen:Diverticulum +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0009881 +name: anterior lateral plate mesoderm +namespace: uberon +subset: efo_slim +synonym: "ALPM" EXACT [ZFA:0005041] +xref: EFO:0003704 +xref: TAO:0005041 +xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm + +[Term] +id: UBERON:0009891 +name: facial mesenchyme +namespace: uberon +def: "Mesenchyme that is part of a developing face." [OBOL:automatic] +synonym: "face mesenchyme" EXACT [] +synonym: "mesenchyme of face" EXACT [] +xref: EMAPA:35337 +xref: FMA:302884 +is_a: UBERON:0005253 ! head mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0001456 ! face +relationship: part_of UBERON:0001456 ! face + +[Term] +id: UBERON:0009953 +name: post-embryonic organism +namespace: uberon +def: "A multicellular organism that existence_starts_with a post-embryonic stage." [OBOL:automatic] +synonym: "post-hatching organism" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "post-natal organism" NARROW [https://orcid.org/0000-0002-6601-2165] +synonym: "postnatal mouse" NARROW [MA:0002405] +synonym: "postnatal organism" EXACT [] +synonym: "TS28 mouse" NARROW [MA:0002405] +xref: MA:0002405 +is_a: UBERON:0000468 ! multicellular organism +intersection_of: UBERON:0000468 ! multicellular organism +intersection_of: existence_starts_with UBERON:0000092 ! post-embryonic stage +relationship: existence_starts_with UBERON:0000092 ! post-embryonic stage +property_value: seeAlso https://github.com/obophenotype/uberon/issues/667 + +[Term] +id: UBERON:0010000 +name: multicellular anatomical structure +namespace: uberon +def: "An anatomical structure that has more than one cell as a part." [CARO:0010000] +subset: upper_level +synonym: "multicellular structure" EXACT [FBbt:00100313] +xref: CARO:0010000 +xref: FBbt:00100313 +is_a: UBERON:0000061 ! anatomical structure + +[Term] +id: UBERON:0010031 +name: 6th arch mesenchyme +namespace: uberon +def: "Mesenchyme that is part of a pharyngeal arch 6." [OBOL:automatic] +synonym: "6th branchial arch mesenchyme" RELATED [] +synonym: "6th pharyngeal arch mesenchyme" EXACT [] +synonym: "pharyngeal arch 6 mesenchyme" RELATED [] +xref: EHDAA2:0004076 +xref: EMAPA:32765 +xref: FMA:318209 +is_a: UBERON:0009494 ! pharyngeal arch mesenchymal region +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0003117 ! pharyngeal arch 6 +relationship: part_of UBERON:0003117 ! pharyngeal arch 6 + +[Term] +id: UBERON:0010046 +name: entire pharyngeal arch associated mesenchyme +namespace: uberon +def: "The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells." [https://orcid.org/0000-0002-6601-2165, XAO:0004524] +synonym: "associated mesenchyme of pharyngeal region" EXACT [EMAPA:16550] +synonym: "entire branchial arch associated mesenchyme" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "pharyngeal arch associated mesenchyme" EXACT [EHDAA2:0001459] +xref: EHDAA2:0001459 +xref: EMAPA:16550 +xref: XAO:0004524 +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: has_developmental_contribution_from UBERON:0003099 {source="cjm"} ! cranial neural crest +relationship: part_of UBERON:0008814 {source="EHDAA2"} ! pharyngeal arch system + +[Term] +id: UBERON:0010047 +name: oral gland +namespace: uberon +alt_id: UBERON:0003293 +def: "Gland of the epithelium lining the oral cavity. The most common are the salivary glands." [ISBN10:0073040584] +synonym: "buccal gland" NARROW [] +synonym: "gland of oral opening" RELATED [] +synonym: "gland of oral region" RELATED [] +synonym: "mouth gland" RELATED [] +synonym: "oral cavity gland" RELATED [] +synonym: "oral region gland" RELATED [] +xref: EHDAA2:0001327 +xref: EHDAA:2181 +xref: EMAPA:16572 +xref: EMAPA:16723 +xref: VHOG:0000652 +is_a: UBERON:0002365 ! exocrine gland +is_a: UBERON:0003408 ! gland of digestive tract +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0000165 ! mouth +relationship: part_of UBERON:0000165 ! mouth +property_value: UBPROP:0000012 "Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa" xsd:string {external_ontology="EHDAA2"} + +[Term] +id: UBERON:0010083 +name: future dermis +namespace: uberon +def: "Mesenchyme that has the potential to develop into a dermis." [OBOL:automatic] +xref: EHDAA2:0000598 +is_a: UBERON:0003104 ! mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: has_potential_to_develop_into UBERON:0002067 ! dermis +relationship: develops_from UBERON:0003089 {source="EHDAA2"} ! sclerotome +relationship: develops_from UBERON:0004016 {source="XAO"} ! dermatome +relationship: has_potential_to_develop_into UBERON:0002067 ! dermis +relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument +property_value: IAO:0000116 "check development" xsd:string + +[Term] +id: UBERON:0010096 +name: future myelencephalon +namespace: uberon +def: "A developing anatomical structure that has the potential to develop into a myelencephalon." [OBOL:automatic] +xref: EHDAA2:0000640 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0005290 ! myelencephalon +relationship: has_potential_to_develop_into UBERON:0005290 ! myelencephalon +relationship: part_of UBERON:0002028 ! hindbrain + +[Term] +id: UBERON:0010161 +name: lumen of blood vessel +namespace: uberon +def: "An anatomical cavity that surrounded_by a blood vessel." [OBOL:automatic] +synonym: "blood vessel lumen" EXACT [] +xref: FMA:312610 +xref: http://www.snomedbrowser.com/Codes/Details/91747007 +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0001981 ! blood vessel +relationship: luminal_space_of UBERON:0001981 ! blood vessel +relationship: part_of UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0010188 +name: protuberance +namespace: uberon +def: "A roughly circular bulge in a surface." [EHDAA2:0003250] +xref: AEO:0000205 +xref: EHDAA2:0003250 +xref: FMA:82506 +is_a: UBERON:0003102 {source="EHDAA2"} ! surface structure +property_value: IAO:0000116 "requires review" xsd:string + +[Term] +id: UBERON:0010199 +name: bona-fide anatomical boundary +namespace: uberon +def: "An anatomical boundary that corresponds to some physical discontinuity." [CARO:0001004] +comment: One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) +subset: upper_level +xref: CARO:0001004 +is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity + +[Term] +id: UBERON:0010257 +name: 6th arch mesenchyme from neural crest +namespace: uberon +def: "Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme." [OBOL:automatic] +synonym: "branchial arch 6 mesenchyme from neural crest" RELATED [] +synonym: "neural crest derived arch 6 mesenchyme" EXACT [] +synonym: "pharyngeal arch 6 mesenchyme from neural crest" EXACT [] +xref: EHDAA2:0004077 +is_a: UBERON:0010031 ! 6th arch mesenchyme +is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest +is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0002342 ! neural crest +intersection_of: part_of UBERON:0010031 ! 6th arch mesenchyme + +[Term] +id: UBERON:0010258 +name: mesenchyme from rhombencephalic neural crest +namespace: uberon +def: "Mesenchyme that develops_from a rhombencephalon neural crest." [OBOL:automatic] +xref: EHDAA2:0004423 +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0003852 ! rhombencephalon neural crest +relationship: develops_from UBERON:0003852 ! rhombencephalon neural crest + +[Term] +id: UBERON:0010285 +name: midbrain basal plate +namespace: uberon +def: "Portion of tissue that is dorsolateral to the floor plate and part of the midbrain." [ZFA:0000761] +subset: efo_slim +synonym: "basal plate midbrain" EXACT [TAO:0000761] +synonym: "basal plate midbrain region" EXACT [ZFA:0000761] +xref: DHBA:12322 +xref: EFO:0003567 +xref: EHDAA2:0004375 +xref: TAO:0000761 +xref: ZFA:0000761 +is_a: UBERON:0002020 {source="EHDAA2"} ! gray matter +relationship: part_of UBERON:0009581 {source="EHDAA2"} ! midbrain mantle layer +relationship: part_of UBERON:0010286 {source="ZFA"} ! midbrain neural tube + +[Term] +id: UBERON:0010286 +name: midbrain neural tube +namespace: uberon +def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] +xref: TAO:0007039 +xref: ZFA:0007039 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: part_of UBERON:0003080 {source="ZFA"} ! anterior neural tube +property_value: IAO:0000116 "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string + +[Term] +id: UBERON:0010303 +name: extraembryonic epithelium +namespace: uberon +def: "An epithelium that is part of a extraembryonic structure." [OBOL:automatic] +synonym: "extra-embryonic epithelium" EXACT [] +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0005292 ! extraembryonic tissue +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0000478 ! extraembryonic structure +relationship: part_of UBERON:0000478 ! extraembryonic structure + +[Term] +id: UBERON:0010313 +name: neural crest-derived structure +namespace: uberon +def: "An anatomical structure that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: develops_from UBERON:0002342 ! neural crest +relationship: develops_from UBERON:0002342 ! neural crest +property_value: IAO:0000232 "Grouping term for query purposes" xsd:string + +[Term] +id: UBERON:0010314 +name: structure with developmental contribution from neural crest +namespace: uberon +def: "An anatomical structure that has some part that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest +relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest +property_value: IAO:0000232 "Grouping term for query purposes" xsd:string + +[Term] +id: UBERON:0010316 +name: germ layer / neural crest +namespace: uberon +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: develops_from UBERON:0002532 ! epiblast (generic) + +[Term] +id: UBERON:0010347 +name: 6th arch mesenchyme from head mesenchyme +namespace: uberon +def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme." [OBOL:automatic] +synonym: "branchial arch 6 mesenchyme from head mesenchyme" RELATED [] +synonym: "head mesenchyme derived arch 6 mesenchyme" EXACT [] +synonym: "pharyngeal arch 6 mesenchyme from head mesenchyme" EXACT [] +xref: EHDAA2:0004078 +is_a: UBERON:0006904 ! head mesenchyme from mesoderm +is_a: UBERON:0010031 ! 6th arch mesenchyme +is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm +intersection_of: part_of UBERON:0010031 ! 6th arch mesenchyme + +[Term] +id: UBERON:0010359 +name: pharyngeal arch mesenchyme from neural crest +namespace: uberon +def: "Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme." [OBOL:automatic] +comment: Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme +synonym: "arch mesenchyme from neural crest" EXACT [] +synonym: "branchial arch mesenchyme from neural crest" EXACT [] +synonym: "neural crest derived arch mesenchyme" EXACT [] +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0014387 ! mesenchyme derived from neural crest +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0002342 ! neural crest +intersection_of: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme +relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme + +[Term] +id: UBERON:0010360 +name: pharyngeal arch mesenchyme from head mesenchyme +namespace: uberon +def: "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme." [OBOL:automatic] +comment: Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme +synonym: "arch mesenchyme from head mesenchyme" EXACT [] +synonym: "branchial arch mesenchyme from head mesenchyme" EXACT [] +synonym: "head mesenchyme derived arch mesenchyme" EXACT [] +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm +intersection_of: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme +relationship: develops_from UBERON:0006904 ! head mesenchyme from mesoderm +relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme + +[Term] +id: UBERON:0010371 +name: ecto-epithelium +namespace: uberon +def: "Epithelium composed of cells that develops from the ectoderm[FMA,modified]." [FMA:69064] +synonym: "ectoderm-derived epithelium" EXACT [] +xref: FMA:69064 +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000483 ! epithelium +intersection_of: develops_from UBERON:0000924 ! ectoderm + +[Term] +id: UBERON:0010378 +name: mesenchyme from splanchnopleure +namespace: uberon +def: "Mesenchyme that develops_from a splanchnopleure." [OBOL:automatic] +xref: EHDAA2:0001122 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0004873 ! splanchnopleure +intersection_of: part_of UBERON:0000922 ! embryo +relationship: develops_from UBERON:0004873 ! splanchnopleure +relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme + +[Term] +id: UBERON:0010498 +name: pseudostratified columnar epithelium +namespace: uberon +def: "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels." [http://en.wikipedia.org/wiki/Pseudostratified_columnar_epithelium, http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium] +xref: FMA:45572 +xref: http://en.wikipedia.org/wiki/Pseudostratified_columnar_epithelium +xref: http://linkedlifedata.com/resource/umls/id/C0836138 +xref: http://linkedlifedata.com/resource/umls/id/C1514590 +xref: NCIT:C33419 +xref: NCIT:C49316 +xref: UMLS:C0836138 {source="ncithesaurus:Pseudostratified_Columnar_Epithelium"} +xref: UMLS:C1514590 {source="ncithesaurus:Pseudostratified_Epithelium"} +is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium +property_value: UBPROP:0000009 "Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia." xsd:string +property_value: UBPROP:0000012 "glandular in NCIT; we consider the two NCIT terms synonymous" xsd:string {external_ontology="NCIT"} + +[Term] +id: UBERON:0010499 +name: pseudostratified ciliated columnar epithelium +namespace: uberon +def: "Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile." [NCIT:NCIT] +synonym: "epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)" EXACT [FMA:13146] +xref: FMA:13146 +xref: http://linkedlifedata.com/resource/umls/id/C0506992 +xref: NCIT:C13181 +xref: UMLS:C0506992 {source="ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium"} +is_a: UBERON:0007592 ! ciliated columnar epithelium +is_a: UBERON:0010498 ! pseudostratified columnar epithelium + +[Term] +id: UBERON:0010523 +name: microcirculatory vessel +namespace: uberon +def: "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses." [http://orcid.org/0000-0002-6601-2165, MESH:A07.231.432, ZFA:0005251] +synonym: "microcirculatory vessels" RELATED PLURAL [TAO:0005251] +xref: MESH:A07.231.432 +xref: TAO:0005251 +xref: ZFA:0005251 +is_a: UBERON:0000055 ! vessel +relationship: part_of UBERON:0002049 {source="ZFA"} ! vasculature + +[Term] +id: UBERON:0010912 +name: subdivision of skeleton +namespace: uberon +def: "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] +subset: non_informative +synonym: "skeletal subdivision" EXACT [VSAO:0000042] +synonym: "subdivision of skeleton (in vivo)" RELATED [FMA:23879] +xref: FMA:23879 +xref: http://www.snomedbrowser.com/Codes/Details/129140006 +xref: VSAO:0000042 +is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision +relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system +relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton +property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} + +[Term] +id: UBERON:0011134 +name: nonsynovial joint +namespace: uberon +def: "Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis." [FMA:7491] +synonym: "solid joint" EXACT [FMA:7491] +xref: FMA:7491 +is_a: UBERON:0000982 {source="FMA"} ! skeletal joint + +[Term] +id: UBERON:0011137 +name: axial skeletal system +namespace: uberon +def: "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] +xref: FMA:7483 +is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system +relationship: has_part UBERON:0000982 ! skeletal joint +relationship: has_part UBERON:0005944 ! axial skeleton plus cranial skeleton +property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI + +[Term] +id: UBERON:0011138 +name: postcranial axial skeletal system +namespace: uberon +def: "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints." [https://github.com/obophenotype/uberon/issues/44, https://orcid.org/0000-0002-6601-2165] +synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/wiki/The-axial-skeleton] +synonym: "post-cranial axial skeletal system" EXACT [] +xref: FMA:302077 +is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system +relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: seeAlso http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton xsd:anyURI + +[Term] +id: UBERON:0011215 +name: central nervous system cell part cluster +namespace: uberon +def: "A multi cell part structure that is part of a central nervous system." [OBOL:automatic] +subset: upper_level +synonym: "cell part cluster of neuraxis" EXACT [FMA:83143] +synonym: "neuraxis layer" EXACT [FMA:83143] +xref: FMA:83143 +is_a: UBERON:0005162 ! multi cell part structure +intersection_of: UBERON:0005162 ! multi cell part structure +intersection_of: part_of UBERON:0001017 ! central nervous system +relationship: part_of UBERON:0001017 ! central nervous system + +[Term] +id: UBERON:0011216 +name: organ system subdivision +namespace: uberon +def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2165] +subset: upper_level +xref: FBbt:00007330 +xref: FMA:67509 +xref: http://www.snomedbrowser.com/Codes/Details/91690000 +is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure +relationship: part_of UBERON:0000467 ! anatomical system + +[Term] +id: UBERON:0011270 +name: dorsal trunk +namespace: uberon +def: "The part of the trunk that is in the dorsum[cjm]." [http://en.wikipedia.org/wiki/Human_back, UBERONREF:0000006] +synonym: "back of trunk" EXACT [FMA:25056] +synonym: "dorsal part of trunk" EXACT [] +synonym: "dorsum of trunk" EXACT [FMA:25056] +synonym: "trunk back" EXACT [FMA:25056] +xref: EMAPA:35162 +xref: FMA:25056 +xref: Human:back +xref: MA:0000020 +is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk +relationship: part_of UBERON:0001137 {source="FMA"} ! dorsum +property_value: UBPROP:0000008 "In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]" xsd:string + +[Term] +id: UBERON:0011272 +name: embryonic skin basal layer +namespace: uberon +synonym: "basal cell layer of skin" RELATED [] +synonym: "outer epithelium of body" RELATED [Wikipathways:WP2062] +xref: EHDAA2:0001845 +is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0010371 ! ecto-epithelium +relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm +relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument +property_value: IAO:0000116 "compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'" xsd:string + +[Term] +id: UBERON:0011362 +name: cranial blood vasculature +namespace: uberon +def: "A blood vasculature that is part of a head." [OBOL:automatic] +synonym: "cranial blood vessel" EXACT [ZFA:0005297] +synonym: "cranial blood vessels" RELATED PLURAL [TAO:0005297] +synonym: "set of blood vessels of head" EXACT [] +xref: TAO:0005297 +xref: ZFA:0005297 +is_a: UBERON:0002200 ! vasculature of head +is_a: UBERON:0004537 ! blood vasculature +intersection_of: UBERON:0004537 ! blood vasculature +intersection_of: part_of UBERON:0000033 ! head +property_value: UBPROP:0000001 "Blood vessel part of cranial vasculature.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005297", ontology="TAO", source="ZFIN:curator"} + +[Term] +id: UBERON:0011585 +name: cell condensation +namespace: uberon +def: "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." [GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070, PSPUB:0000170, VSAO:0000006] +xref: VSAO:0000006 +xref: XAO:0004021 +is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string + +[Term] +id: UBERON:0011642 +name: oral epithelium from ectoderm +namespace: uberon +def: "An epithelium that develops_from a ectoderm and is part of a oral epithelium." [OBOL:automatic] +xref: EHDAA2:0004137 +is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0002424 ! oral epithelium +is_a: UBERON:0010371 ! ecto-epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: develops_from UBERON:0000924 ! ectoderm +intersection_of: part_of UBERON:0002424 ! oral epithelium +relationship: develops_from UBERON:0009479 {source="EHDAA2"} ! ectoderm of buccopharyngeal membrane + +[Term] +id: UBERON:0011676 +name: subdivision of organism along main body axis +namespace: uberon +def: "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column." [https://orcid.org/0000-0002-6601-2165] +subset: upper_level +synonym: "axial subdivision of organism" EXACT [] +synonym: "body segment" RELATED [] +synonym: "main body segment" RELATED [] +is_a: UBERON:0000475 ! organism subdivision +relationship: part_of UBERON:0013701 ! main body axis +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string + +[Term] +id: UBERON:0011695 +name: embryonic cardiovascular system +namespace: uberon +def: "A cardiovascular system that is part of a conceptus." [OBOL:automatic] +synonym: "conceptus cardiovascular system" EXACT [] +synonym: "embryonic circulatory system" RELATED [] +synonym: "fetal circulatory system" RELATED [] +xref: EHDAA2:0000216 +xref: FMA:305965 +xref: NCIT:C34148 +is_a: UBERON:0004535 ! cardiovascular system +intersection_of: UBERON:0004535 ! cardiovascular system +intersection_of: part_of UBERON:0004716 ! conceptus +relationship: part_of UBERON:0004716 ! conceptus + +[Term] +id: UBERON:0011821 +name: irregular connective tissue +namespace: uberon +def: "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20107] +xref: FMA:20107 +is_a: UBERON:0002384 {source="FMA"} ! connective tissue + +[Term] +id: UBERON:0011822 +name: dense irregular connective tissue +namespace: uberon +def: "Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium." [FMA:20109, http://en.wikipedia.org/wiki/Dense_irregular_connective_tissue] +synonym: "irregular dense connective tissue" EXACT [] +synonym: "typus irregularis (textus connectivus collagenosus compactus)" EXACT [FMA:20109] +xref: FMA:20109 +xref: http://en.wikipedia.org/wiki/Dense_irregular_connective_tissue +xref: http://linkedlifedata.com/resource/umls/id/C0738366 +xref: NCIT:C32882 +xref: UMLS:C0738366 {source="ncithesaurus:Irregular_Dense_Connective_Tissue"} +is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue +is_a: UBERON:0011823 ! dense connective tissue +property_value: UBPROP:0000001 "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Irregular_Dense_Connective_Tissue", ontology="NCIT"} + +[Term] +id: UBERON:0011823 +name: dense connective tissue +namespace: uberon +def: "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets" [http://en.wikipedia.org/wiki/Dense_connective_tissue] +xref: AAO:0000121 +xref: http://en.wikipedia.org/wiki/Dense_connective_tissue +xref: http://linkedlifedata.com/resource/umls/id/C1511770 +xref: NCIT:C32450 +xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} +is_a: UBERON:0002384 ! connective tissue +intersection_of: UBERON:0002384 ! connective tissue +intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils +disjoint_from: UBERON:0011825 ! loose connective tissue +relationship: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils +property_value: IAO:0000116 "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string +property_value: UBPROP:0000001 "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Dense_Connective_Tissue", ontology="NCIT"} + +[Term] +id: UBERON:0011824 +name: fibrous connective tissue +namespace: uberon +xref: FMA:75634 +xref: http://www.snomedbrowser.com/Codes/Details/363130003 +is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue + +[Term] +id: UBERON:0011825 +name: loose connective tissue +namespace: uberon +def: "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue." [FMA:19783] +synonym: "textus connectivus collagenosus laxus" EXACT LATIN [FMA:19783, FMA:TA] +synonym: "textus connectivus laxus" EXACT LATIN [FMA:19783, FMA:TA] +xref: FMA:19783 +xref: http://en.wikipedia.org/wiki/Loose_connective_tissue +xref: http://linkedlifedata.com/resource/umls/id/C1253917 +xref: NCIT:C33007 +xref: UMLS:C1253917 {source="ncithesaurus:Loose_Connective_Tissue"} +is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue + +[Term] +id: UBERON:0011858 +name: acinus of exocrine gland +namespace: uberon +def: "An acinus that is part of a exocrine gland." [OBOL:automatic] +synonym: "exocrine gland acinus" EXACT [] +is_a: UBERON:0009842 ! glandular acinus +intersection_of: UBERON:0009842 ! glandular acinus +intersection_of: part_of UBERON:0002365 ! exocrine gland +relationship: part_of UBERON:0002365 ! exocrine gland + +[Term] +id: UBERON:0011860 +name: collection of collagen fibrils +namespace: uberon +xref: FMA:63212 +xref: MESH:D024022 +xref: NCIT:C32339 +xref: NIF_Subcellular:sao7547390221 +is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure +property_value: seeAlso UBERON:0007377 +property_value: UBPROP:0000012 "the FMA class specifically refers to ureter" xsd:string {external_ontology="FMA"} + +[Term] +id: UBERON:0011862 +name: pulmonary collagen fibril +namespace: uberon +def: "The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity" [MP:0011641] +subset: pheno_slim +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0011860 ! collection of collagen fibrils +intersection_of: UBERON:0011860 ! collection of collagen fibrils +intersection_of: part_of UBERON:0002048 ! lung +relationship: contributes_to_morphology_of UBERON:0002048 ! lung +relationship: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0011997 +name: coelom +namespace: uberon +def: "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen." [http://en.wikipedia.org/wiki/Body_cavity, http://en.wikipedia.org/wiki/Coelom, UBERON:cjm] +synonym: "coelem" RELATED [] +synonym: "coelomic cavity" RELATED [EHDAA2:0004731] +synonym: "enterocoelom" NARROW [NCBITaxon:33511] +synonym: "haemocoelom" NARROW [] +synonym: "schizocoelom" NARROW [] +xref: EHDAA2:0004731 +xref: http://en.wikipedia.org/wiki/Coelom +is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: UBPROP:0000007 "coelomic" xsd:string + +[Term] +id: UBERON:0012125 +name: dermatological-muscosal system +namespace: uberon +def: "Anatomical system that consists of the integumental system plus all mucosae and submucosae." [https://github.com/obophenotype/uberon/issues/53] +synonym: "dermatological system" RELATED [OBI:MC] +is_a: UBERON:0000467 ! anatomical system +relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: has_part UBERON:0000009 ! submucosa +relationship: has_part UBERON:0000344 ! mucosa +relationship: has_part UBERON:0002072 ! hypodermis +relationship: has_part UBERON:0002097 ! skin of body +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/mcourtot + +[Term] +id: UBERON:0012180 +name: head or neck skin +namespace: uberon +def: "A zone of skin that is part of a craniocervical region." [OBOL:automatic] +xref: EMAPA:37276 {source="MA:th"} +xref: http://linkedlifedata.com/resource/umls/id/C1522650 +xref: MA:0000574 +xref: NCIT:C12294 +xref: UMLS:C1522650 {source="ncithesaurus:Skin_of_the_Scalp_and_Neck"} +is_a: UBERON:0000014 ! zone of skin +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0007811 ! craniocervical region +relationship: part_of UBERON:0007811 ! craniocervical region + +[Term] +id: UBERON:0012274 +name: columnar epithelium +namespace: uberon +def: "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]" [http://en.wikipedia.org/wiki/Columnar_epithelium] +xref: Columnar:epithelium +is_a: UBERON:0000483 ! epithelium + +[Term] +id: UBERON:0012275 +name: meso-epithelium +namespace: uberon +def: "Epithelium that derives from the mesoderm. [Automatically generated definition]." [OBOL:automatic] +synonym: "mesoderm-derived epithelium" EXACT [] +synonym: "mesoepithelium" EXACT [] +xref: FMA:86452 +is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000483 ! epithelium +intersection_of: develops_from UBERON:0000926 ! mesoderm + +[Term] +id: UBERON:0012320 +name: cervical artery +namespace: uberon +def: "An artery of the neck" [https://orcid.org/0000-0002-6601-2165] +xref: EMAPA:37075 {source="MA:th"} +xref: http://linkedlifedata.com/resource/umls/id/C1707349 +xref: NCIT:C52850 +xref: UMLS:C1707349 {source="ncithesaurus:Cervical_Artery"} +is_a: UBERON:0001637 ! artery +is_a: UBERON:0003502 ! neck blood vessel +intersection_of: UBERON:0001637 ! artery +intersection_of: part_of UBERON:0000974 ! neck + +[Term] +id: UBERON:0012321 +name: deep cervical artery +namespace: uberon +def: "The deep cervical artery (Profunda cervicalis) is an artery of the neck." [http://en.wikipedia.org/wiki/Deep_cervical_artery] +synonym: "profunda cervicalis" RELATED [http://en.wikipedia.org/wiki/Deep_cervical_artery] +xref: FMA:10659 +xref: http://en.wikipedia.org/wiki/Deep_cervical_artery +xref: http://www.snomedbrowser.com/Codes/Details/244223002 +is_a: UBERON:0012320 ! cervical artery +intersection_of: UBERON:0012320 ! cervical artery +intersection_of: part_of UBERON:0035551 ! deep vasculature +relationship: branching_part_of UBERON:0004688 {source="FMA"} ! costo-cervical trunk +relationship: part_of UBERON:0004688 ! costo-cervical trunk +relationship: part_of UBERON:0035551 ! deep vasculature + +[Term] +id: UBERON:0012416 +name: respiratory system arterial smooth muscle +namespace: uberon +xref: EMAPA:37567 {source="MA:th"} +xref: MA:0001802 +is_a: UBERON:0004297 ! respiratory system blood vessel smooth muscle +is_a: UBERON:0004695 ! arterial system smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0003643 ! respiratory system arterial blood vessel +relationship: part_of UBERON:0003643 ! respiratory system arterial blood vessel + +[Term] +id: UBERON:0012418 +name: respiratory system venous smooth muscle +namespace: uberon +def: "A smooth muscle tissue that is part of a respiratory system venous blood vessel." [OBOL:automatic] +xref: EMAPA:37586 {source="MA:th"} +xref: MA:0001812 +is_a: UBERON:0004696 ! venous system smooth muscle +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0003476 ! respiratory system venous blood vessel +relationship: part_of UBERON:0003476 ! respiratory system venous blood vessel + +[Term] +id: UBERON:0012466 +name: extraembryonic cavity +namespace: uberon +synonym: "extraembryonic cavities" RELATED PLURAL [EHDAA2:0000472] +xref: EHDAA2:0000472 +xref: EMAPA:16054 +xref: VHOG:0000767 +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: part_of UBERON:0016887 ! entire extraembryonic component +relationship: part_of UBERON:0016887 ! entire extraembryonic component + +[Term] +id: UBERON:0012467 +name: enclosed anatomical space +namespace: uberon +def: "An anatomical space with no opening to another space or to the exterior." [AEO:0000222] +synonym: "closed anatomical space" EXACT [] +xref: AEO:0000222 +is_a: UBERON:0000464 ! anatomical space + +[Term] +id: UBERON:0013136 +name: vein of lip +namespace: uberon +def: "A vein that drains a lip." [OBOL:automatic] +synonym: "labial vein" RELATED [] +synonym: "labial vein of face" EXACT [] +synonym: "lip vein" EXACT [OBOL:automatic] +synonym: "vena labialis" EXACT LATIN [] +xref: http://www.snomedbrowser.com/Codes/Details/367664002 +is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0003502 ! neck blood vessel +is_a: UBERON:0009141 ! craniocervical region vein +intersection_of: UBERON:0001638 ! vein +intersection_of: drains UBERON:0001833 ! lip +relationship: drains UBERON:0001833 ! lip +relationship: part_of UBERON:0001653 ! facial vein +relationship: tributary_of UBERON:0001653 {source="FMA"} ! facial vein + +[Term] +id: UBERON:0013140 +name: systemic vein +namespace: uberon +def: "Any vein within the general circulation that transports blood back to the right atrium of the heart." [ncithesaurus:Systemic_Vein] +synonym: "systemic venous tree organ part" EXACT [FMA:66644] +xref: FMA:66644 +xref: http://linkedlifedata.com/resource/umls/id/C0447117 +xref: http://www.snomedbrowser.com/Codes/Details/244389004 +xref: NCIT:C33719 +xref: UMLS:C0447117 {source="ncithesaurus:Systemic_Vein"} +is_a: UBERON:0001638 ! vein +intersection_of: UBERON:0001638 ! vein +intersection_of: part_of UBERON:0004581 ! systemic venous system +relationship: part_of UBERON:0004581 ! systemic venous system + +[Term] +id: UBERON:0013232 +name: serous acinus +namespace: uberon +def: "The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells." [http://orcid.org/0000-0002-6601-2165, http://www.siumed.edu/~dking2/intro/glands.htm] +synonym: "acinus of serous gland" EXACT [] +xref: FMA:86279 +is_a: UBERON:0011858 ! acinus of exocrine gland +intersection_of: UBERON:0009842 ! glandular acinus +intersection_of: part_of UBERON:0000409 ! serous gland +relationship: part_of UBERON:0000409 ! serous gland + +[Term] +id: UBERON:0013479 +name: lung endothelium +namespace: uberon +def: "A blood vessel endothelium that is part of a lung [Automatically generated definition]." [OBOL:automatic] +synonym: "respiratory endothelium" RELATED [BTO:0004128] +xref: BTO:0004128 +xref: CALOHA:TS-0573 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0000115 ! lung epithelium +is_a: UBERON:0004702 ! respiratory system blood vessel endothelium +intersection_of: UBERON:0004638 ! blood vessel endothelium +intersection_of: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0013514 +name: space surrounding organism +namespace: uberon +def: "The space that surrounds an organism." [https://orcid.org/0000-0002-6601-2165] +synonym: "external to organism" EXACT [] +synonym: "outside of body" EXACT [] +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: surrounds UBERON:0000468 ! multicellular organism +relationship: surrounds UBERON:0000468 ! multicellular organism + +[Term] +id: UBERON:0013522 +name: subdivision of tube +namespace: uberon +is_a: UBERON:0000064 ! organ part +relationship: has_part UBERON:0000060 ! anatomical wall +relationship: has_part UBERON:0000464 ! anatomical space +relationship: part_of UBERON:0000025 ! tube +relationship: subdivision_of UBERON:0000025 ! tube + +[Term] +id: UBERON:0013686 +name: anatomical conduit space +namespace: uberon +def: "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]." [FMA:9338, http://orcid.org/0000-0002-6601-2165] +synonym: "foramen space" NARROW [] +xref: FMA:9338 +is_a: UBERON:0000464 {source="FMA"} ! anatomical space +relationship: connects UBERON:0000464 {minCardinality="2", maxCardinality="2"} ! anatomical space +relationship: luminal_space_of UBERON:0004111 ! anatomical conduit +relationship: part_of UBERON:0004111 ! anatomical conduit + +[Term] +id: UBERON:0013694 +name: brain endothelium +namespace: uberon +def: "Vascular endothelium found in blood vessels of the blood-brain-barrier." [CALOHA:TS-0092] +synonym: "cerebromicrovascular endothelium" RELATED [CALOHA:TS-0092] +xref: BTO:0001852 +xref: BTO:0003248 +xref: CALOHA:TS-0092 +is_a: UBERON:0001986 ! endothelium +is_a: UBERON:0010371 ! ecto-epithelium +intersection_of: UBERON:0001986 ! endothelium +intersection_of: part_of UBERON:0000955 ! brain +relationship: part_of UBERON:0000955 ! brain + +[Term] +id: UBERON:0013701 +name: main body axis +namespace: uberon +def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] +subset: non_informative +is_a: UBERON:0000475 ! organism subdivision + +[Term] +id: UBERON:0013702 +name: body proper +namespace: uberon +def: "The region of the organism associated with the visceral organs." [AEO:0000103] +subset: non_informative +synonym: "body" RELATED [AEO:0000103] +synonym: "whole body" RELATED [BTO:0001489] +xref: AEO:0000103 +xref: BTO:0001489 +xref: EMAPA:36031 +xref: FMA:231424 +is_a: UBERON:0000475 {source="AEO"} ! organism subdivision +relationship: part_of UBERON:0013701 ! main body axis +property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} + +[Term] +id: UBERON:0013704 +name: notochordal canal +namespace: uberon +def: "A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily." [http://medical-dictionary.thefreedictionary.com/notochordal+canal] +synonym: "chordal canal" RELATED [] +xref: FMA:293127 +xref: http://linkedlifedata.com/resource/umls/id/C1518428 +xref: NCIT:C34230 +xref: UMLS:C1518428 {source="ncithesaurus:Notochordal_Canal"} +is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0004111 ! anatomical conduit +intersection_of: part_of UBERON:0006268 ! notochordal process +relationship: part_of UBERON:0006268 ! notochordal process + +[Term] +id: UBERON:0013727 +name: notochordal fluid +namespace: uberon +def: "Fluid contained within the notochordal canal" [http://animaldiversity.org/accounts/Latimeria_chalumnae/, http://orcid.org/0000-0002-6601-2165] +comment: Distinct feature of coelocanths +synonym: "notochord fluid" EXACT [] +synonym: "portion of notochordal fluid" EXACT [] +is_a: UBERON:0006314 ! bodily fluid +intersection_of: UBERON:0006314 ! bodily fluid +intersection_of: located_in UBERON:0013704 ! notochordal canal +intersection_of: part_of UBERON:0036242 ! post-embryonic notochord +relationship: located_in UBERON:0013704 ! notochordal canal +relationship: part_of UBERON:0036242 ! post-embryonic notochord + +[Term] +id: UBERON:0013754 +name: integumentary system layer +namespace: uberon +def: "A organ component layer that is part of a integumental system." [OBOL:automatic] +subset: non_informative +synonym: "layer of skin" NARROW [] +synonym: "skin layer" NARROW [] +xref: http://www.snomedbrowser.com/Codes/Details/314820002 +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: part_of UBERON:0002416 ! integumental system +relationship: part_of UBERON:0002416 ! integumental system + +[Term] +id: UBERON:0013755 +name: arterial blood +namespace: uberon +def: "A blood that is part of a artery." [OBOL:automatic] +subset: pheno_slim +synonym: "arterial blood" EXACT [FMA:83066] +synonym: "blood in artery" EXACT [FMA:83066] +synonym: "portion of arterial blood" EXACT [FMA:83066] +xref: FMA:83066 +is_a: UBERON:0000178 ! blood +intersection_of: UBERON:0000178 ! blood +intersection_of: part_of UBERON:0001637 ! artery +relationship: part_of UBERON:0001637 ! artery + +[Term] +id: UBERON:0013756 +name: venous blood +namespace: uberon +def: "A blood that is part of a vein." [OBOL:automatic] +synonym: "blood in vein" EXACT [FMA:83067] +synonym: "portion of venous blood" EXACT [FMA:83067] +synonym: "venous blood" EXACT [FMA:83067] +xref: FMA:83067 +is_a: UBERON:0000178 ! blood +intersection_of: UBERON:0000178 ! blood +intersection_of: part_of UBERON:0001638 ! vein +relationship: part_of UBERON:0001638 ! vein + +[Term] +id: UBERON:0013757 +name: capillary blood +namespace: uberon +def: "A blood that is part of a capillary." [OBOL:automatic] +synonym: "blood in capillary" EXACT [] +synonym: "portion of blood in capillary" EXACT [FMA:263901] +synonym: "portion of capillary blood" EXACT [] +xref: FMA:263901 +xref: NCIT:C32212 +is_a: UBERON:0000178 ! blood +intersection_of: UBERON:0000178 ! blood +intersection_of: part_of UBERON:0001982 ! capillary +relationship: part_of UBERON:0001982 ! capillary + +[Term] +id: UBERON:0013765 +name: digestive system element +namespace: uberon +def: "Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +subset: pheno_slim +synonym: "digestive organ" EXACT [] +synonym: "digestive system organ" EXACT [] +xref: EMAPA:37843 {source="MA:th"} +xref: http://www.snomedbrowser.com/Codes/Details/272627002 +is_a: UBERON:0000062 ! organ +intersection_of: UBERON:0000062 ! organ +intersection_of: part_of UBERON:0001007 ! digestive system +relationship: part_of UBERON:0001007 ! digestive system + +[Term] +id: UBERON:0013768 +name: great vessel of heart +namespace: uberon +def: "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart." [http://en.wikipedia.org/wiki/Great_vessels] +comment: Groupings may vary - typically pulmonary vessels and aorta and vena cavae +subset: grouping_class +synonym: "great vessel" BROAD [] +synonym: "great vessel of thorax" EXACT [] +xref: EMAPA:36460 +xref: Great:vessels +xref: http://www.snomedbrowser.com/Codes/Details/304066000 +is_a: UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0014387 +name: mesenchyme derived from neural crest +namespace: uberon +def: "Mesenchyme that develops_from the neural crest[Automatically generated definition]." [https://github.com/obophenotype/uberon/issues/248, OBOL:automatic] +synonym: "mesenchyme from neural crest" EXACT [] +synonym: "neural crest derived mesenchyme" EXACT [] +synonym: "neural crest mesenchyme" EXACT [] +xref: EMAPA:32735 +xref: FMA:293883 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0010313 ! neural crest-derived structure +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: develops_from UBERON:0002342 ! neural crest + +[Term] +id: UBERON:0014477 +name: thoracic skeleton +namespace: uberon +def: "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum." [http://en.wikipedia.org/wiki/Rib_cage, https://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "skeleton of thorax" EXACT [] +synonym: "thoracic part of axial skeleton" EXACT [] +synonym: "thoracic skeleton" EXACT [EHDAA2:0002013] +xref: EHDAA2:0002013 +xref: FMA:77169 +xref: Thoracic:skeleton +is_a: UBERON:0010912 ! subdivision of skeleton +relationship: part_of UBERON:0000915 ! thoracic segment of trunk +relationship: part_of UBERON:0002090 ! postcranial axial skeleton + +[Term] +id: UBERON:0014776 +name: midbrain neuromere +namespace: uberon +def: "A neuromere that is part of the presumptive midbrain" [http://orcid.org/0000-0002-6601-2165] +synonym: "future mesencephalon" RELATED [] +synonym: "mesomere" BROAD [] +synonym: "mesomere group" RELATED [EHDAA2:0004352] +synonym: "mesomere of nervous system" EXACT [] +synonym: "midbrain segment" BROAD [] +synonym: "neuromere of mesomere group" EXACT [] +synonym: "segment of midbrain" BROAD [] +xref: EHDAA2:0004352 +xref: FMA:61997 +is_a: UBERON:0004731 ! neuromere +intersection_of: UBERON:0004731 ! neuromere +intersection_of: part_of UBERON:0009616 ! presumptive midbrain +relationship: part_of UBERON:0009616 ! presumptive midbrain + +[Term] +id: UBERON:0014777 +name: spinal neuromere +namespace: uberon +def: "A neuromere that is part of the presumptive spinal cord" [http://orcid.org/0000-0002-6601-2165] +synonym: "spinal cord metameric segment" EXACT [] +synonym: "spinal cord segment" RELATED [TAO:0001332] +synonym: "spinal neuromeres" EXACT PLURAL [TAO:0001332] +xref: TAO:0001332 +xref: ZFA:0001332 +is_a: UBERON:0004731 ! neuromere +intersection_of: UBERON:0004731 ! neuromere +intersection_of: part_of UBERON:0006241 ! future spinal cord +relationship: part_of UBERON:0006241 ! future spinal cord + +[Term] +id: UBERON:0014903 +name: primordial vasculature +namespace: uberon +def: "A portion of tissue that will develop into vasculature." [ZFA:0005076, ZFA:curator] +xref: EFO:0003708 +xref: TAO:0005076 +xref: ZFA:0005076 +is_a: UBERON:0001048 ! primordium +intersection_of: UBERON:0001048 ! primordium +intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature +relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +relationship: part_of UBERON:0011695 ! embryonic cardiovascular system + +[Term] +id: UBERON:0015178 +name: somite border +namespace: uberon +def: "A region of somite adjacent to presomitic mesoderm." [http://orcid.org/0000-0002-6601-2165] +subset: pheno_slim +synonym: "inter-somited border" RELATED [] +synonym: "intersomitic boundary" RELATED [] +synonym: "intersomitic fissure" RELATED [] +synonym: "intersomitic junction" RELATED [XAO:0004074] +synonym: "segmental border" RELATED [] +synonym: "somite boundary" RELATED [ZFA:0001462] +xref: TAO:0001462 +xref: XAO:0004074 +xref: ZFA:0001462 +is_a: UBERON:0007651 ! anatomical junction +intersection_of: UBERON:0007651 ! anatomical junction +intersection_of: adjacent_to UBERON:0003059 ! presomitic mesoderm +intersection_of: part_of UBERON:0002329 ! somite +relationship: adjacent_to UBERON:0003059 ! presomitic mesoderm +relationship: part_of UBERON:0002329 ! somite + +[Term] +id: UBERON:0015179 +name: somite boundary epithelium +namespace: uberon +def: "Epithelium located in the intersomitic region." [XAO:0004077, XAO:EJS] +synonym: "intersomitic epithelium" EXACT [XAO:0004077] +synonym: "intersomitic membrane" EXACT [XAO:0004077] +xref: XAO:0004077 +is_a: UBERON:0000483 ! epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0015178 ! somite border +relationship: part_of UBERON:0015178 ! somite border + +[Term] +id: UBERON:0015212 +name: lateral structure +namespace: uberon +def: "Any structure that is placed on one side of the left-right axis of a bilaterian." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +subset: non_informative +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity +relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity +property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string + +[Term] +id: UBERON:0015228 +name: circulatory organ +namespace: uberon +def: "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile." [http://orcid.org/0000-0002-6601-2165] +subset: grouping_class +synonym: "cardiac pump" EXACT [] +synonym: "cardiac structure" RELATED [] +synonym: "circulatory vessel" NARROW [] +synonym: "heart" BROAD [] +synonym: "heart or heart like organ" EXACT [] +xref: SPD:0000130 +is_a: UBERON:0003103 ! compound organ +relationship: part_of UBERON:0001009 ! circulatory system + +[Term] +id: UBERON:0015329 +name: respiratory system basement membrane +namespace: uberon +def: "A basement membrane of epithelium that is part of a respiratory system." [OBOL:automatic] +xref: EMAPA:37570 {source="MA:th"} +xref: MA:0001815 +is_a: UBERON:0005769 ! basement membrane of epithelium +intersection_of: UBERON:0005769 ! basement membrane of epithelium +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0003570 {source="MA"} ! respiratory system connective tissue + +[Term] +id: UBERON:0015410 +name: heart plus pericardium +namespace: uberon +synonym: "heart/pericardium" EXACT [MA:0002449] +xref: EMAPA:37597 {source="MA:th"} +xref: MA:0002449 +is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element +relationship: part_of UBERON:0004535 ! cardiovascular system + +[Term] +id: UBERON:0015783 +name: smooth muscle layer in fatty layer of subcutaneous tissue +namespace: uberon +def: "A smooth muscle tissue that is part of a hypodermis." [OBOL:automatic] +synonym: "muscle layer in fatty layer of subcutaneous tissue" EXACT [FMA:77862] +synonym: "stratum musculosum panniculi adiposi telae subcutaneae" EXACT LATIN [FMA:77862, FMA:TA] +xref: FMA:77862 +is_a: UBERON:0001135 ! smooth muscle tissue +intersection_of: UBERON:0001135 ! smooth muscle tissue +intersection_of: part_of UBERON:0002072 ! hypodermis +relationship: part_of UBERON:0002072 ! hypodermis + +[Term] +id: UBERON:0015833 +name: foregut epithelium +namespace: uberon +def: "A epithelium that is part of a foregut." [OBOL:automatic] +xref: EMAPA:32922 +xref: MA:0003204 +is_a: UBERON:0003929 ! digestive tract epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001041 ! foregut +relationship: part_of UBERON:0001041 ! foregut + +[Term] +id: UBERON:0016405 +name: pulmonary capillary +namespace: uberon +def: "A capillary that is part of a lung." [OBOL:automatic] +subset: pheno_slim +synonym: "capillary of lung" EXACT [FMA:14121] +xref: FMA:14121 +is_a: UBERON:0003512 ! lung blood vessel +is_a: UBERON:0003526 ! respiratory system capillary +intersection_of: UBERON:0001982 ! capillary +intersection_of: part_of UBERON:0002048 ! lung + +[Term] +id: UBERON:0016545 +name: pharyngeal ectoderm +namespace: uberon +alt_id: UBERON:2001379 +def: "The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches." [http://orcid.org/0000-0002-6601-2165, http://www.ncbi.nlm.nih.gov/pubmed/23020903] +xref: TAO:0001379 +xref: ZFA:0001379 +is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0003351 ! pharyngeal epithelium +is_a: UBERON:0005291 ! embryonic tissue +intersection_of: UBERON:0000490 ! unilaminar epithelium +intersection_of: part_of UBERON:0000076 ! external ectoderm +intersection_of: part_of UBERON:0001042 ! chordate pharynx +relationship: part_of UBERON:0000076 ! external ectoderm + +[Term] +id: UBERON:0016879 +name: future central nervous system +namespace: uberon +alt_id: UBERON:3000469 +def: "Primordium that develops into the central nervous system" [http://orcid.org/0000-0002-6601-2165] +synonym: "future CNS" EXACT [] +synonym: "presumptive central nervous system" EXACT [] +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system +relationship: develops_from UBERON:0000924 ! ectoderm +relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +relationship: part_of UBERON:0016880 ! future nervous system + +[Term] +id: UBERON:0016880 +name: future nervous system +namespace: uberon +alt_id: UBERON:3000477 +def: "Primordium that develops into the nervous system" [http://orcid.org/0000-0002-6601-2165] +synonym: "presumptive nervous system" EXACT [AAO:0000477] +xref: AAO:0000477 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system +relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage +relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system + +[Term] +id: UBERON:0016887 +name: entire extraembryonic component +namespace: uberon +def: "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism." [AEO:0000195, AEO:JB] +synonym: "extra-embryonic component" EXACT [] +synonym: "extraembryonic component" EXACT [AEO:0000195] +xref: AEO:0000195 +xref: EHDAA2:0000003 +xref: EMAPA:16042 +is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure +relationship: adjacent_to UBERON:0002050 ! embryonic structure +relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage +relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus + +[Term] +id: UBERON:0016888 +name: transitional anatomical structure +namespace: uberon +def: "An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development." [AEO:0000132, AEO:JB] +xref: AEO:0000132 +is_a: UBERON:0005423 {source="AEO"} ! developing anatomical structure + +[Term] +id: UBERON:0017650 +name: developing mesenchymal structure +namespace: uberon +def: "A mesenchyme-derived anatomical entity undergoing a transtion to become another structure." [AEO:0001016, AEO:JB] +xref: AEO:0001016 +is_a: UBERON:0005423 ! developing anatomical structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: composed_primarily_of UBERON:0003104 ! mesenchyme +relationship: composed_primarily_of UBERON:0003104 ! mesenchyme + +[Term] +id: UBERON:0018239 +name: rhombomere boundary +namespace: uberon +def: "A boundary delimiting a rhombomere." [GO:0021654] +synonym: "rhombomere junction" EXACT [] +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0007651 ! anatomical junction +intersection_of: UBERON:0007651 ! anatomical junction +intersection_of: connects UBERON:0001892 ! rhombomere +relationship: connects UBERON:0001892 ! rhombomere +relationship: part_of UBERON:0007277 ! presumptive hindbrain + +[Term] +id: UBERON:0018257 +name: submucosa of digestive tract +namespace: uberon +def: "Any portion of submucosa that lines the digestive tract." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000009 ! submucosa +intersection_of: UBERON:0000009 ! submucosa +intersection_of: part_of UBERON:0001555 ! digestive tract +relationship: part_of UBERON:0001555 ! digestive tract + +[Term] +id: UBERON:0018260 +name: layer of muscle tissue +namespace: uberon +def: "Any organ component layer that consists of muscle tissue." [http://orcid.org/0000-0002-6601-2165] +xref: FMA:45634 +xref: http://linkedlifedata.com/resource/umls/id/C0225358 +xref: NCIT:C75444 +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue +relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +property_value: UBPROP:0000012 "NCITA class may refer to smooth muscle only" xsd:string {external_ontology="NCIT"} + +[Term] +id: UBERON:0018674 +name: heart vasculature +namespace: uberon +def: "An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart." [ZFA:0005811, ZFA:CVS] +synonym: "cardiac vasculature" EXACT [FMA:73747] +xref: FMA:73747 +xref: ZFA:0005811 +is_a: UBERON:0002201 ! vasculature of trunk +is_a: UBERON:0006876 ! vasculature of organ +intersection_of: UBERON:0002049 ! vasculature +intersection_of: part_of UBERON:0000948 ! heart +relationship: part_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0019204 +name: skin epithelium +namespace: uberon +def: "Any region of epithelium that is part of a skin region." [http://orcid.org/0000-0002-6601-2165] +xref: BTO:0004382 +is_a: UBERON:0010371 ! ecto-epithelium +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0000014 ! zone of skin +relationship: part_of UBERON:0000014 ! zone of skin + +[Term] +id: UBERON:0019263 +name: gray matter of hindbrain +namespace: uberon +synonym: "gray matter of the hindbrain" EXACT [DHBA:HGM] +xref: DHBA:10654 +xref: FMA:268630 +is_a: UBERON:0003528 ! brain gray matter +intersection_of: UBERON:0002020 ! gray matter +intersection_of: part_of UBERON:0002028 ! hindbrain +relationship: part_of UBERON:0002028 ! hindbrain + +[Term] +id: UBERON:0019267 +name: gray matter of midbrain +namespace: uberon +xref: DHBA:10649 +xref: FMA:83913 +is_a: UBERON:0003528 ! brain gray matter +intersection_of: UBERON:0002020 ! gray matter +intersection_of: part_of UBERON:0001891 ! midbrain +relationship: part_of UBERON:0001891 ! midbrain + +[Term] +id: UBERON:0019319 +name: exocrine gland of integumental system +namespace: uberon +def: "An exocrine gland that is part of a integumental system." [GOC:dos, http://orcid.org/0000-0002-6601-2165] +synonym: "integumental exocrine gland" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "integumental system exocrine gland" EXACT [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0002365 ! exocrine gland +is_a: UBERON:0003297 ! gland of integumental system +intersection_of: UBERON:0002365 ! exocrine gland +intersection_of: part_of UBERON:0002416 ! integumental system + +[Term] +id: UBERON:0022350 +name: visceral serous membrane +namespace: uberon +def: "Serous membrane layer that is adjacent to and lines an organ." [http://orcid.org/0000-0002-6601-2165] +synonym: "visceral wall of serous membrane" EXACT [FMA:15860] +xref: FMA:15860 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: adjacent_to UBERON:0000062 ! organ +intersection_of: part_of UBERON:0000042 ! serous membrane +relationship: adjacent_to UBERON:0000062 ! organ +relationship: part_of UBERON:0000042 ! serous membrane + +[Term] +id: UBERON:0022351 +name: parietal serous membrane +namespace: uberon +def: "Serous membrane layer that lines to a body cavity." [http://orcid.org/0000-0002-6601-2165] +synonym: "cavity lining" BROAD [MA:0002448] +synonym: "parietal wall of serous membrane" EXACT [FMA:15859] +xref: FMA:15859 +xref: MA:0002448 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004923 ! organ component layer +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: adjacent_to UBERON:0002553 ! anatomical cavity +intersection_of: part_of UBERON:0000042 ! serous membrane +relationship: adjacent_to UBERON:0002553 ! anatomical cavity +relationship: part_of UBERON:0000042 ! serous membrane + +[Term] +id: UBERON:0022361 +name: lung field +namespace: uberon +def: "A specific region of the foregut into the area in which the lung will develop." [GOC:dph, GOC:mtg_lung] +synonym: "lung field" EXACT [] +xref: http://www.snomedbrowser.com/Codes/Details/34922002 +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0007688 ! anlage +intersection_of: UBERON:0007688 ! anlage +intersection_of: has_potential_to_develop_into UBERON:0002048 ! lung +relationship: has_potential_to_develop_into UBERON:0002048 ! lung +relationship: part_of UBERON:0003258 ! endoderm of foregut + +[Term] +id: UBERON:0034705 +name: developing neuroepithelium +namespace: uberon +def: "An embryonic or larval epithelium that is committed to form part of the nervous system." [AEO:0001008, AEO:JB] +synonym: "embryonic neuroepithelium" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "neurepithelium" BROAD [BTO:0000314] +synonym: "neuroepithelium" EXACT [AEO:0001008] +xref: AEO:0001008 +xref: BTO:0000314 +xref: EHDAA2_RETIRED:0004654 +xref: FMA:64807 +is_a: UBERON:0000483 ! epithelium +relationship: part_of UBERON:0001016 ! nervous system + +[Term] +id: UBERON:0034706 +name: proliferating neuroepithelium +namespace: uberon +def: "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells." [AEO:0001009] +xref: AEO:0001009 +is_a: UBERON:0034705 {source="AEO"} ! developing neuroepithelium + +[Term] +id: UBERON:0034707 +name: differentiating neuroepithelium +namespace: uberon +def: "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells." [AEO:0001010] +xref: AEO:0001010 +is_a: UBERON:0034705 {source="AEO"} ! developing neuroepithelium + +[Term] +id: UBERON:0034709 +name: hindbrain marginal layer +namespace: uberon +synonym: "marginal zone of hindbrain" EXACT [DHBA:12694] +synonym: "MZH" RELATED ABBREVIATION [DHBA:12694] +xref: DHBA:12694 +xref: EMAPA:32916 +is_a: UBERON:0004062 ! neural tube marginal layer +is_a: UBERON:0011215 ! central nervous system cell part cluster +intersection_of: UBERON:0004062 ! neural tube marginal layer +intersection_of: part_of UBERON:0002028 ! hindbrain +relationship: part_of UBERON:0002028 ! hindbrain + +[Term] +id: UBERON:0034710 +name: spinal cord ventricular layer +namespace: uberon +synonym: "spinal cord lateral wall ventricular layer" EXACT [EHDAA2:0001267] +xref: EHDAA2:0001267 +xref: EMAPA:17585 +is_a: UBERON:0004060 ! neural tube ventricular layer +intersection_of: UBERON:0004060 ! neural tube ventricular layer +intersection_of: part_of UBERON:0006241 ! future spinal cord +relationship: part_of UBERON:0005496 {source="EHDAA2"} ! neural tube lateral wall +relationship: part_of UBERON:0006241 ! future spinal cord + +[Term] +id: UBERON:0034873 +name: bodily gas +namespace: uberon +def: "Any substance in the body or expelled from the body that is in a gaseous state." [http://orcid.org/0000-0002-6601-2165] +synonym: "gas in anatomical space" EXACT [] +synonym: "portion of gas in anatomical space" EXACT [FMA:84580] +xref: FMA:84580 +is_a: UBERON:0000463 ! organism substance + +[Term] +id: UBERON:0034874 +name: air in respiratory system +namespace: uberon +def: "Any portion of gas located in a part of the respiratory system that is composed primarily of air." [http://orcid.org/0000-0002-6601-2165] +synonym: "respiratory air" EXACT [FMA:84581] +synonym: "respiratory system air" EXACT [] +xref: FMA:84581 +is_a: UBERON:0034947 ! gas in respiratory system + +[Term] +id: UBERON:0034878 +name: prechordal mesoderm +namespace: uberon +def: "the area of axial mesoderm that develops into the prechordal plate" [MGI:anna] +synonym: "prechordal mesenchyme" EXACT [] +is_a: UBERON:0002050 ! embryonic structure +intersection_of: UBERON:0005423 ! developing anatomical structure +intersection_of: has_potential_to_develop_into UBERON:0003063 ! prechordal plate +intersection_of: part_of UBERON:0003068 ! axial mesoderm +relationship: has_potential_to_develop_into UBERON:0003063 ! prechordal plate +relationship: part_of UBERON:0003068 ! axial mesoderm + +[Term] +id: UBERON:0034905 +name: gland lumen +namespace: uberon +synonym: "lumen of gland" EXACT [] +is_a: UBERON:0000464 ! anatomical space +intersection_of: UBERON:0000464 ! anatomical space +intersection_of: luminal_space_of UBERON:0002530 ! gland +relationship: luminal_space_of UBERON:0002530 ! gland +relationship: part_of UBERON:0002530 ! gland + +[Term] +id: UBERON:0034921 +name: multi organ part structure +namespace: uberon +def: "An multicellular anatomical structure that has subparts of multiple organs as a part." [CARO:0020001] +synonym: "anatomical cluster" RELATED [CARO:0020001] +xref: CARO:0020001 +is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure +relationship: composed_primarily_of UBERON:0000064 ! organ part + +[Term] +id: UBERON:0034922 +name: cell cluster +namespace: uberon +def: "A cluster of cells, largely surrounded by a morphological boundary." [CARO:0020002] +xref: CARO:0020002 +xref: FMA:62807 +is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure +relationship: surrounded_by UBERON:0000015 ! non-material anatomical boundary + +[Term] +id: UBERON:0034925 +name: anatomical collection +namespace: uberon +def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000465 ! material anatomical entity +relationship: has_member UBERON:0000061 ! anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string + +[Term] +id: UBERON:0034933 +name: layer of smooth muscle tissue +namespace: uberon +def: "Any organ component layer that consists of smooth muscle tissue." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0018260 ! layer of muscle tissue +intersection_of: UBERON:0004923 ! organ component layer +intersection_of: composed_primarily_of UBERON:0001135 ! smooth muscle tissue +relationship: composed_primarily_of UBERON:0001135 ! smooth muscle tissue + +[Term] +id: UBERON:0034944 +name: zone of organ +namespace: uberon +synonym: "organ region with floating fiat boundary" RELATED [FMA:55268] +synonym: "organ sector" EXACT [FMA:55268] +synonym: "organ zonal region" EXACT [] +synonym: "organ zone" EXACT [FMA:55268] +xref: FMA:55268 +is_a: UBERON:0000064 ! organ part + +[Term] +id: UBERON:0034947 +name: gas in respiratory system +namespace: uberon +def: "Any portion of gas located in a part of the respiratory system." [http://orcid.org/0000-0002-6601-2165] +synonym: "respiratory gas" EXACT [] +synonym: "respiratory system gas" EXACT [] +is_a: UBERON:0034873 ! bodily gas +intersection_of: UBERON:0034873 ! bodily gas +intersection_of: located_in UBERON:0001004 ! respiratory system +relationship: located_in UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0034969 +name: epithelial layer of duct +namespace: uberon +synonym: "duct epithelium" RELATED [] +synonym: "ductal epithelium" RELATED [] +xref: http://linkedlifedata.com/resource/umls/id/C1512086 +xref: NCIT:C25787 +is_a: UBERON:0003914 ! epithelial tube +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0000058 ! duct +relationship: part_of UBERON:0000058 ! duct + +[Term] +id: UBERON:0035118 +name: material entity in digestive tract +namespace: uberon +def: "Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included." [https://github.com/EnvironmentOntology/envo/issues/110] +synonym: "digestive tract contents" EXACT PLURAL [] +synonym: "ingested material entity" RELATED [] +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: located_in UBERON:0006909 ! lumen of digestive tract +relationship: located_in UBERON:0006909 ! lumen of digestive tract +property_value: IAO:0000116 "Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat" xsd:string + +[Term] +id: UBERON:0035159 +name: entire surface of organism +namespace: uberon +def: "Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface." [FMA:61695] +synonym: "surface of body" EXACT [FMA:61695] +xref: FMA:61695 +xref: http://linkedlifedata.com/resource/umls/id/C0489451 +xref: http://www.snomedbrowser.com/Codes/Details/261060002 +xref: NCIT:C29667 +is_a: UBERON:0006984 ! anatomical surface +intersection_of: UBERON:0006984 ! anatomical surface +intersection_of: surrounds UBERON:0000468 ! multicellular organism +relationship: surrounds UBERON:0000468 ! multicellular organism + +[Term] +id: UBERON:0035549 +name: vasculature of integument +namespace: uberon +def: "The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin." [http://orcid.org/0000-0002-6601-2165] +synonym: "dermis vasculature" NARROW [] +synonym: "hypodermis vasculature" NARROW [] +synonym: "skin vasculature" RELATED [] +synonym: "subcutaneous vasculature" RELATED [] +synonym: "superficial part of circulatory system" EXACT [] +synonym: "superficial vasculature" EXACT [] +synonym: "vasculature of skin" RELATED [FMA:225275] +xref: FMA:225275 +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: located_in UBERON:0002199 ! integument +relationship: located_in UBERON:0002199 ! integument + +[Term] +id: UBERON:0035550 +name: superficial vein +namespace: uberon +def: "Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers." [ncithesaurus:Superficial_Vein] +synonym: "superfical vein" RELATED [http://en.wikipedia.org/wiki/Superficial_vein] +synonym: "superficial veins" RELATED [http://en.wikipedia.org/wiki/Superficial_vein] +synonym: "superficial vessels" RELATED [http://en.wikipedia.org/wiki/Superficial_vein] +xref: FMA:76719 +xref: http://linkedlifedata.com/resource/umls/id/C0226513 +xref: http://www.snomedbrowser.com/Codes/Details/341382008 +xref: NCIT:C33666 +xref: Superficial:vein +is_a: UBERON:0001638 ! vein +intersection_of: UBERON:0001638 ! vein +intersection_of: part_of UBERON:0035549 ! vasculature of integument +relationship: part_of UBERON:0035549 ! vasculature of integument + +[Term] +id: UBERON:0035551 +name: deep vasculature +namespace: uberon +def: "The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin." [http://orcid.org/0000-0002-6601-2165] +synonym: "deep part of circulatory system" EXACT [] +is_a: UBERON:0002049 ! vasculature +intersection_of: UBERON:0002049 ! vasculature +intersection_of: deep_to UBERON:0002199 ! integument +relationship: deep_to UBERON:0002199 ! integument + +[Term] +id: UBERON:0035552 +name: deep vein +namespace: uberon +def: "A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery." [ncithesaurus:Deep_Vein] +synonym: "deep veins" RELATED [http://en.wikipedia.org/wiki/Deep_vein] +synonym: "deep vessels" RELATED [http://en.wikipedia.org/wiki/Deep_vein] +xref: Deep:vein +xref: FMA:76718 +xref: http://linkedlifedata.com/resource/umls/id/C0226514 +xref: http://www.snomedbrowser.com/Codes/Details/341484008 +xref: NCIT:C32444 +is_a: UBERON:0001638 ! vein +intersection_of: UBERON:0001638 ! vein +intersection_of: part_of UBERON:0035551 ! deep vasculature +relationship: part_of UBERON:0035551 ! deep vasculature + +[Term] +id: UBERON:0035553 +name: left cardiac chamber +namespace: uberon +def: "Any chamber of the left side of the heart" [http://orcid.org/0000-0002-6601-2165] +xref: FMA:7166 +xref: http://www.snomedbrowser.com/Codes/Details/362008007 +is_a: UBERON:0004151 ! cardiac chamber +is_a: UBERON:0015212 ! lateral structure +intersection_of: UBERON:0004151 ! cardiac chamber +intersection_of: in_left_side_of UBERON:0000948 ! heart +relationship: in_left_side_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0035554 +name: right cardiac chamber +namespace: uberon +def: "Any chamber of the right side of the heart" [http://orcid.org/0000-0002-6601-2165] +xref: FMA:7165 +xref: http://www.snomedbrowser.com/Codes/Details/362007002 +is_a: UBERON:0004151 ! cardiac chamber +is_a: UBERON:0015212 ! lateral structure +intersection_of: UBERON:0004151 ! cardiac chamber +intersection_of: in_right_side_of UBERON:0000948 ! heart +relationship: in_right_side_of UBERON:0000948 ! heart + +[Term] +id: UBERON:0035763 +name: cavity of cardiac chamber +namespace: uberon +synonym: "cardiac chamber cavity" EXACT [FMA:9464] +synonym: "heart cavity" EXACT [FMA:9464] +synonym: "heart lumen" EXACT [EHDAA2:0004181] +xref: EHDAA2:0004181 +xref: FMA:9464 +is_a: UBERON:0002553 ! anatomical cavity +intersection_of: UBERON:0002553 ! anatomical cavity +intersection_of: luminal_space_of UBERON:0004151 ! cardiac chamber +relationship: luminal_space_of UBERON:0004151 ! cardiac chamber +relationship: part_of UBERON:0004151 ! cardiac chamber +relationship: surrounded_by UBERON:0002165 {source="FMA"} ! endocardium + +[Term] +id: UBERON:0035804 +name: future mouth +namespace: uberon +def: "The primordial mouth region of the developing head." [MP:0003119] +synonym: "primitive mouth" EXACT [FMA:293105] +synonym: "primordial mouth" EXACT [] +xref: FMA:293105 +is_a: UBERON:0013522 ! subdivision of tube +relationship: has_part UBERON:0000925 ! endoderm +relationship: has_part UBERON:0000930 ! stomodeum +relationship: part_of UBERON:0007026 ! presumptive gut + +[Term] +id: UBERON:0035809 +name: serous cavity +namespace: uberon +xref: FMA:12241 +xref: http://www.snomedbrowser.com/Codes/Details/304404008 +is_a: UBERON:0002553 ! anatomical cavity +intersection_of: UBERON:0002553 ! anatomical cavity +intersection_of: luminal_space_of UBERON:0005906 ! serous sac +relationship: luminal_space_of UBERON:0005906 ! serous sac +relationship: part_of UBERON:0005906 ! serous sac + +[Term] +id: UBERON:0035814 +name: pericardial fat +namespace: uberon +def: "The sum of epicardial and paracardial fat deposits." [http://dx.doi.org/10.5935/abc.20130138] +xref: http://www.snomedbrowser.com/Codes/Details/42267001 +xref: ZFA:0005765 +is_a: UBERON:0035818 ! visceral fat +intersection_of: UBERON:0001013 ! adipose tissue +intersection_of: surrounds UBERON:0000948 ! heart +relationship: surrounds UBERON:0000948 ! heart + +[Term] +id: UBERON:0035818 +name: visceral fat +namespace: uberon +def: "Any fat deposit surrounding a visceral organ." [UBERON:cjm] +is_a: UBERON:0001013 ! adipose tissue +intersection_of: UBERON:0001013 ! adipose tissue +intersection_of: surrounds UBERON:0000062 ! organ +relationship: surrounds UBERON:0000062 ! organ + +[Term] +id: UBERON:0035965 +name: wall of blood vessel +namespace: uberon +synonym: "blood vessel wall" EXACT [FMA:67473] +synonym: "vascular wall" RELATED [BTO:0004378] +xref: BTO:0004378 +xref: EMAPA:37987 {source="MA:th"} +xref: FMA:67473 +is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure +intersection_of: UBERON:0000060 ! anatomical wall +intersection_of: part_of UBERON:0001981 ! blood vessel +relationship: composed_primarily_of UBERON:0004797 ! blood vessel layer +relationship: part_of UBERON:0001981 ! blood vessel + +[Term] +id: UBERON:0036072 +name: respiratory primordium epithelium +namespace: uberon +xref: EHDAA2:0004070 +is_a: UBERON:0004185 ! endodermal part of digestive tract +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0007499 ! epithelial sac +is_a: UBERON:0009854 ! digestive tract diverticulum +is_a: UBERON:0015833 ! foregut epithelium +intersection_of: UBERON:0007499 ! epithelial sac +intersection_of: part_of UBERON:0008947 ! respiratory primordium +relationship: develops_from UBERON:0007690 {source="EHDAA2"} ! early pharyngeal endoderm +relationship: part_of UBERON:0008947 ! respiratory primordium + +[Term] +id: UBERON:0036073 +name: respiratory primordium mesenchyme +namespace: uberon +synonym: "respiratory primordium associated mesenchyme" EXACT [EHDAA2:0004071] +xref: EHDAA2:0004071 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0003104 ! mesenchyme +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: part_of UBERON:0008947 ! respiratory primordium +relationship: develops_from UBERON:0004873 {source="EHDAA2"} ! splanchnopleure +relationship: part_of UBERON:0008947 ! respiratory primordium + +[Term] +id: UBERON:0036146 +name: cardiopharyngeal field +namespace: uberon +def: "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles." [BGEE:ann, http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1] +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007688 ! anlage + +[Term] +id: UBERON:0036217 +name: coelomic fluid +namespace: uberon +def: "A bodily fluid that is located in the coelom." [http://www.ncbi.nlm.nih.gov/pubmed/10874572, https://github.com/obophenotype/uberon/issues/1326] +xref: BTO:0001708 +is_a: UBERON:0006314 ! bodily fluid +intersection_of: UBERON:0006314 ! bodily fluid +intersection_of: located_in UBERON:0011997 ! coelom +relationship: located_in UBERON:0011997 ! coelom +property_value: UBPROP:0000009 "he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste[https://en.wikipedia.org/wiki/Coelom#Coelomic_fluid]" xsd:string + +[Term] +id: UBERON:0036225 +name: respiratory system gland +namespace: uberon +def: "Any gland that is part os the respiratory system." [UBERON:cjm] +is_a: UBERON:0002530 ! gland +intersection_of: UBERON:0002530 ! gland +intersection_of: part_of UBERON:0001004 ! respiratory system +relationship: part_of UBERON:0001004 ! respiratory system + +[Term] +id: UBERON:0036242 +name: post-embryonic notochord +namespace: uberon +def: "A notochord that has persisted beyond the embryonic stage." [UBERON:cjm] +is_a: UBERON:0002328 ! notochord +intersection_of: UBERON:0002328 ! notochord +intersection_of: part_of UBERON:0009953 ! post-embryonic organism +relationship: part_of UBERON:0009953 ! post-embryonic organism +property_value: RO:0002175 NCBITaxon:118072 +property_value: RO:0002175 NCBITaxon:7737 +property_value: RO:0002175 NCBITaxon:7746 +property_value: RO:0002175 NCBITaxon:7878 +property_value: RO:0002175 NCBITaxon:8292 + +[Term] +id: UBERON:0036244 +name: secretion of serous membrane +namespace: uberon +def: "A transudate found in the serous sac." [FMA:20932] +synonym: "serous fluid" BROAD [FMA:20932] +synonym: "serous sac fluid" EXACT [] +xref: FMA:20932 +is_a: UBERON:0007779 ! transudate +intersection_of: UBERON:0007779 ! transudate +intersection_of: filtered_through UBERON:0000042 ! serous membrane +relationship: filtered_through UBERON:0000042 ! serous membrane +relationship: located_in UBERON:0005906 ! serous sac + +[Term] +id: UBERON:1000021 +name: skin of face +namespace: uberon +def: "A zone of skin that is part of the face." [https://github.com/obophenotype/uberon/issues/34, UBERON:EJS] +subset: pheno_slim +subset: phenotype_rcn +synonym: "face skin" EXACT [EMAPA:36657, FMA:24758] +synonym: "facial skin" RELATED [] +xref: EMAPA:36657 +xref: FMA:24758 +xref: http://linkedlifedata.com/resource/umls/id/C0222084 +xref: http://www.snomedbrowser.com/Codes/Details/361703006 +xref: NCIT:C33561 +xref: UMLS:C0222084 {source="ncithesaurus:Skin_of_the_Face"} +is_a: UBERON:0001084 ! skin of head +intersection_of: UBERON:0000014 ! zone of skin +intersection_of: part_of UBERON:0001456 ! face +relationship: part_of UBERON:0001456 ! face +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/cmungall +property_value: http://purl.org/dc/elements/1.1/contributor https://github.com/seger +created_by: eriks +creation_date: 2012-02-05T05:23:01Z + +[Term] +id: UBERON:3000961 +name: external integument structure +namespace: uberon/phenoscape-anatomy +def: "Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument." [AAO:EJS] +comment: Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 +is_a: UBERON:0003102 ! surface structure +intersection_of: UBERON:0003102 ! surface structure +intersection_of: part_of UBERON:0002199 ! integument +relationship: part_of UBERON:0002199 ! integument +property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string +created_by: amphibian_anatomy_curators + +[Term] +id: UBERON:3000972 +name: head external integument structure +namespace: uberon/phenoscape-anatomy +def: "Dermal, epidermal, glandular and pigment structures of the external head integument." [AAO:EJS] +is_a: UBERON:3000961 ! external integument structure +intersection_of: UBERON:3000961 ! external integument structure +intersection_of: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0000033 ! head +property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string +created_by: amphibian_anatomy_curators + +[Term] +id: UBERON:3000977 +name: body external integument structure +namespace: uberon/phenoscape-anatomy +def: "Dermal, epidermal, glandular and pigment structures of the body integument." [AAO:EJS] +is_a: UBERON:3000961 ! external integument structure +intersection_of: UBERON:3000961 ! external integument structure +intersection_of: part_of UBERON:0002100 ! trunk +relationship: part_of UBERON:0002100 ! trunk +property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string +created_by: amphibian_anatomy_curators + +[Term] +id: UBERON:3010200 +name: vasculature of respiratory integument +namespace: uberon/phenoscape-anatomy +def: "Blood vessels in respiratory skin." [AAO:EJS] +is_a: UBERON:0003504 ! respiratory system blood vessel +intersection_of: UBERON:0001981 ! blood vessel +intersection_of: part_of UBERON:0001004 ! respiratory system +intersection_of: part_of UBERON:0002199 ! integument +relationship: part_of UBERON:0002199 ! integument +property_value: IAO:0000116 "Modified from the original AAO source" xsd:string +created_by: amphibian_anatomy_curators + +[Typedef] +id: adjacent_to +name: adjacent_to +namespace: uberon +def: "x adjacent_to y iff: x and y share a boundary" [] +xref: RO:0002220 +is_symmetric: true + +[Typedef] +id: anterior_to +name: anterior_to +namespace: uberon +def: "x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer" [http://orcid.org/0000-0002-6601-2165] +xref: BSPO:0000096 +is_transitive: true +created_by: cjm +creation_date: 2009-07-31T02:15:46Z + +[Typedef] +id: anteriorly_connected_to +name: anteriorly connected to +namespace: uberon +def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] +is_a: connected_to ! connected to +is_a: posterior_to ! posterior_to +is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to + +[Typedef] +id: bounding_layer_of +name: bounding layer of +namespace: uberon +comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. +xref: RO:0002007 +is_a: part_of ! part of + +[Typedef] +id: branching_part_of +name: branching_part_of +namespace: uberon +xref: RO:0002380 +property_value: IAO:0000116 "we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve" xsd:string +property_value: seeAlso FMA:85994 +is_a: part_of ! part of +inverse_of: has_branching_part ! has branching part + +[Typedef] +id: channel_for +name: channel for +namespace: uberon +synonym: "carries" BROAD [] +domain: UBERON:0004111 ! anatomical conduit +range: UBERON:0000463 ! organism substance + +[Typedef] +id: channels_from +name: channels_from +namespace: uberon +is_transitive: true + +[Typedef] +id: channels_into +name: channels_into +namespace: uberon +is_transitive: true + +[Typedef] +id: composed_primarily_of +name: composed primarily of +namespace: uberon +def: "x composed_primarily_of y iff: more than half of the mass of x is made from parts of y" [] +xref: RO:0002473 +is_a: has_part ! has part + +[Typedef] +id: conduit_for +name: conduit for +namespace: uberon +def: "x is a conduit for y iff y passes through the lumen of x." [] + +[Typedef] +id: connected_to +name: connected to +namespace: uberon +def: "Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] +comment: Connection does not imply overlaps. +xref: RO:0002170 +property_value: seeAlso SIO:000652 +is_a: transitively_connected_to ! transitively_connected to + +[Typedef] +id: connects +name: connects +namespace: uberon +def: "Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] +xref: RO:0002176 +property_value: IAO:0000116 "this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)" xsd:string + +[Typedef] +id: continuous_with +name: continuous_with +namespace: uberon +xref: RO:0002150 +is_symmetric: true + +[Typedef] +id: contributes_to_morphology_of +name: contributes to morphology of +namespace: uberon +xref: RO:0002433 + +[Typedef] +id: deep_to +name: deep_to +namespace: uberon +def: "Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines." [http://orcid.org/0000-0002-6601-2165] +xref: BSPO:0000107 +is_transitive: true + +[Typedef] +id: developmentally_contributes_to +name: developmentally_contributes_to +namespace: uberon +xref: RO:0002255 +holds_over_chain: develops_into part_of +is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to + +[Typedef] +id: developmentally_induced_by +name: developmentally_induced_by +namespace: uberon +def: "t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T." [GO:0001759] +comment: sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) +xref: RO:0002256 + +[Typedef] +id: developmentally_replaces +name: developmentally_replaces +namespace: uberon +xref: RO:0002285 + +[Typedef] +id: develops_from +name: develops_from +namespace: uberon +xref: RO:0002202 +holds_over_chain: part_of develops_from +is_transitive: true +is_a: has_developmental_contribution_from ! has developmental contribution from +inverse_of: develops_into ! develops_into +transitive_over: part_of ! part of + +[Typedef] +id: develops_into +name: develops_into +namespace: uberon +xref: RO:0002203 +is_a: has_potential_to_develop_into ! has potential to develop into + +[Typedef] +id: dorsal_to +name: dorsal_to +namespace: uberon +def: "x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly)." [http://orcid.org/0000-0002-6601-2165] +xref: BSPO:0000098 +is_transitive: true +inverse_of: ventral_to ! ventral_to + +[Typedef] +id: drains +name: drains +namespace: uberon +comment: source: Wikipedia +synonym: "drains blood from" EXACT [] +synonym: "drains from" EXACT [] +xref: RO:0002179 +domain: UBERON:0001638 ! vein +is_a: connected_to ! connected to + +[Typedef] +id: ends +name: ends +namespace: uberon +def: "Relation between occurrents, shares an end boundary with." [Allen:starts, https://orcid.org/0000-0002-6601-2165, ZFS:finishes] +synonym: "finishes" EXACT [] +xref: RO:0002229 +is_a: part_of ! part of + +[Typedef] +id: ends_with +name: ends with +namespace: uberon +xref: RO:0002230 +is_transitive: true +is_a: has_part ! has part + +[Typedef] +id: existence_ends_during +name: existence ends during +namespace: uberon +def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] +synonym: "ceases_to_exist_during" EXACT [] +xref: RO:0002492 +is_a: existence_ends_during_or_before ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: existence_ends_during_or_before +name: existence ends during or before +namespace: uberon +xref: RO:0002497 +holds_over_chain: part_of existence_ends_during_or_before +transitive_over: part_of ! part of +transitive_over: precedes ! precedes + +[Typedef] +id: existence_ends_with +name: existence ends with +namespace: uberon +def: "Relation between continuant and occurrent, such that c ceases to exist at the end of p." [https://orcid.org/0000-0002-6601-2165] +xref: RO:0002493 +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0000105 ! life cycle stage +is_a: existence_ends_during ! existence ends during + +[Typedef] +id: existence_starts_and_ends_during +name: existence starts and ends during +namespace: uberon +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0000105 ! life cycle stage +is_a: existence_ends_during ! existence ends during +is_a: existence_starts_during ! existence starts during + +[Typedef] +id: existence_starts_during +name: existence starts during +namespace: uberon +def: "Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s." [https://orcid.org/0000-0002-6601-2165] +synonym: "begins_to_exist_during" EXACT [] +xref: RO:0002488 +is_a: existence_starts_during_or_after ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: existence_starts_during_or_after +name: existence starts during or after +namespace: uberon +xref: RO:0002496 +holds_over_chain: part_of existence_starts_during_or_after +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded_by + +[Typedef] +id: existence_starts_with +name: existence starts with +namespace: uberon +def: "Relation between continuant and occurrent, such that c comes into existence at the start of p." [https://orcid.org/0000-0002-6601-2165] +xref: RO:0002489 +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0000105 ! life cycle stage +is_a: existence_starts_during ! existence starts during + +[Typedef] +id: filtered_through +name: filtered through +namespace: uberon +def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] +comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed + +[Typedef] +id: has_boundary +name: has boundary +namespace: uberon +xref: RO:0002002 + +[Typedef] +id: has_branching_part +name: has branching part +namespace: uberon +xref: RO:0002569 +is_transitive: true + +[Typedef] +id: has_developmental_contribution_from +name: has developmental contribution from +namespace: uberon +xref: RO:0002254 +holds_over_chain: has_part develops_from +is_transitive: true + +[Typedef] +id: has_member +name: has member +namespace: uberon +xref: RO:0002351 +is_a: has_part ! has part + +[Typedef] +id: has_part +name: has part +namespace: uberon +xref: BFO:0000051 +is_transitive: true + +[Typedef] +id: has_potential_to_develop_into +name: has potential to develop into +namespace: uberon +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] +xref: RO:0002387 + +[Typedef] +id: has_potential_to_developmentally_contribute_to +name: has potential to developmentally contribute to +namespace: uberon +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +xref: RO:0002385 + +[Typedef] +id: has_skeleton +name: has skeleton +namespace: uberon +def: "A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision." [http://orcid.org/0000-0002-6601-2165] +synonym: "has sekeletal support" RELATED [] +synonym: "has supporting framework" RELATED [] +xref: RO:0002551 +domain: UBERON:0000475 ! organism subdivision +range: UBERON:0010912 ! subdivision of skeleton +is_a: has_part ! has part +inverse_of: skeleton_of ! skeleton of + +[Typedef] +id: immediate_transformation_of +name: immediate transformation of +namespace: uberon +synonym: "direct_transformation_of" EXACT [https://orcid.org/0000-0002-6601-2165] +synonym: "immediately transforms from" EXACT [SIO:000658] +xref: RO:0002495 +property_value: seeAlso SIO:000658 +is_a: transformation_of ! transformation of + +[Typedef] +id: immediately_deep_to +name: immediately_deep_to +namespace: uberon +def: "This relation holds when both the deep_to and ajdacent_to relationship similarly hold." [http://orcid.org/0000-0002-6601-2165] +xref: BSPO:0001107 +is_a: adjacent_to ! adjacent_to +is_a: deep_to ! deep_to + +[Typedef] +id: immediately_preceded_by +name: immediately_preceded_by +namespace: uberon +def: "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" [] +synonym: "directly preceded by" EXACT [] +synonym: "is directly preceded by" EXACT [] +synonym: "is immediately preceded by" EXACT [SIO:000251] +synonym: "starts_at_end_of" EXACT [] +xref: RO:0002087 +property_value: seeAlso SIO:000251 +property_value: UBPROP:0000001 "A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]." xsd:string {source="SIO:000251"} +is_a: preceded_by ! preceded_by + +[Typedef] +id: in_anterior_side_of +name: in_anterior_side_of +namespace: uberon +def: "X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion." [BSPO:PATO_mtg_2009] +xref: BSPO:0000123 +is_a: part_of ! part of + +[Typedef] +id: in_distal_side_of +name: in_distal_side_of +namespace: uberon +def: "X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion." [BSPO:PATO_mtg_2009] +xref: BSPO:0000125 +is_a: part_of ! part of + +[Typedef] +id: in_lateral_side_of +name: in_lateral_side_of +namespace: uberon +def: "X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure" [https://orcid.org/0000-0002-6601-2165] +xref: BSPO:0000126 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI +is_a: part_of ! part of + +[Typedef] +id: in_left_side_of +name: in_left_side_of +namespace: uberon +def: "X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion." [BSPO:PATO_mtg_2009] +xref: BSPO:0000120 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI +is_a: in_lateral_side_of ! in_lateral_side_of + +[Typedef] +id: in_proximal_side_of +name: in_proximal_side_of +namespace: uberon +def: "X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion." [BSPO:PATO_mtg_2009] +xref: BSPO:0000124 +is_a: part_of ! part of +inverse_of: in_distal_side_of ! in_distal_side_of + +[Typedef] +id: in_right_side_of +name: in_right_side_of +namespace: uberon +def: "X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion." [BSPO:PATO_mtg_2009] +xref: BSPO:0000121 +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern xsd:anyURI +is_a: in_lateral_side_of ! in_lateral_side_of + +[Typedef] +id: indirectly_supplies +name: indirectly_supplies +namespace: uberon +def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s" [] +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: has_branching_part indirectly_supplies +holds_over_chain: has_branching_part supplies +is_transitive: true + +[Typedef] +id: located_in +name: located_in +namespace: uberon +xref: RO:0001025 + +[Typedef] +id: location_of +name: location_of +namespace: uberon +xref: RO:0001015 + +[Typedef] +id: luminal_space_of +name: luminal space of +namespace: uberon +xref: RO:0002572 +is_a: part_of ! part of + +[Typedef] +id: member_of +name: member of +namespace: uberon +xref: RO:0002350 +is_a: part_of ! part of +inverse_of: has_member ! has member + +[Typedef] +id: part_of +name: part of +namespace: uberon +xref: BFO:0000050 +is_transitive: true +inverse_of: has_part ! has part + +[Typedef] +id: posterior_to +name: posterior_to +namespace: uberon +def: "x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail." [http://orcid.org/0000-0002-6601-2165] +synonym: "caudal_to" NARROW [] +xref: BSPO:0000099 +is_transitive: true + +[Typedef] +id: posteriorly_connected_to +name: posteriorly connected to +namespace: uberon +def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] +is_a: anterior_to ! anterior_to +is_a: connected_to ! connected to + +[Typedef] +id: preceded_by +name: preceded_by +namespace: uberon +def: "X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)" [] +synonym: "is preceded by" EXACT [SIO:000249] +synonym: "takes place after" EXACT [Allen:precedes] +xref: BFO:0000062 +is_transitive: true + +[Typedef] +id: precedes +name: precedes +namespace: uberon +xref: BFO:0000063 +is_transitive: true + +[Typedef] +id: produced_by +name: produced_by +namespace: uberon +xref: RO:0003001 + +[Typedef] +id: produces +name: produces +namespace: uberon +xref: RO:0003000 + +[Typedef] +id: proximalmost_part_of +name: proximalmost_part_of +namespace: uberon +def: "X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y" [https://orcid.org/0000-0002-6601-2165] +xref: BSPO:0001106 +is_a: in_proximal_side_of ! in_proximal_side_of + +[Typedef] +id: skeleton_of +name: skeleton of +namespace: uberon +xref: RO:0002576 +is_a: part_of ! part of + +[Typedef] +id: starts +name: starts +namespace: uberon +def: "Relation between occurrents, shares a start boundary with." [Allen:starts, https://orcid.org/0000-0002-6601-2165] +xref: RO:0002223 +is_a: part_of ! part of +inverse_of: starts_with ! starts with + +[Typedef] +id: starts_with +name: starts with +namespace: uberon +xref: RO:0002224 +is_transitive: true +is_a: has_part ! has part + +[Typedef] +id: subdivision_of +name: subdivision of +namespace: uberon +comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B + +[Typedef] +id: superficial_to +name: superficial_to +namespace: uberon +def: "Near the outer surface of the organism. Thus, skin is superficial to the muscle layer." [http://orcid.org/0000-0002-6601-2165] +xref: BSPO:0000108 + +[Typedef] +id: supplies +name: supplies +namespace: uberon +def: "relation between an artery and the structure is supplies with blood." [] +comment: source: FMA +synonym: "arterial supply of" EXACT [FMA:86003] +xref: RO:0002178 +property_value: seeAlso FMA:86003 +domain: UBERON:0001637 ! artery +is_a: connected_to ! connected to + +[Typedef] +id: surrounded_by +name: surrounded_by +namespace: uberon +def: "x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y" [https://orcid.org/0000-0002-6601-2165] +xref: RO:0002219 +inverse_of: surrounds ! surrounds + +[Typedef] +id: surrounds +name: surrounds +namespace: uberon +def: "inverse of surrounded_by" [https://orcid.org/0000-0002-6601-2165] +xref: RO:0002221 + +[Typedef] +id: transformation_of +name: transformation of +namespace: uberon +synonym: "transforms from" EXACT [SIO:000657] +xref: RO:0002494 +property_value: seeAlso SIO:000657 +is_transitive: true +is_a: develops_from ! develops_from + +[Typedef] +id: transitively_anteriorly_connected_to +name: transitively anteriorly connected to +namespace: uberon +def: "." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] +is_transitive: true + +[Typedef] +id: transitively_connected_to +name: transitively_connected to +namespace: uberon +is_transitive: true + +[Typedef] +id: tributary_of +name: tributary_of +namespace: uberon +synonym: "drains into" RELATED [dbpowl:drainsTo] +xref: RO:0002376 + +[Typedef] +id: ventral_to +name: ventral_to +namespace: uberon +def: "x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly)." [http://orcid.org/0000-0002-6601-2165] +xref: BSPO:0000102 +is_transitive: true + diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl new file mode 100644 index 00000000..e2180b96 --- /dev/null +++ b/src/ontology/imports/uberon_import.owl @@ -0,0 +1,46890 @@ + + + + + + + + + + + + + + + definition + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has_exact_synonym + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BFO:0000050 + uberon + part_of + part_of + part of + + + + + + + + + BFO:0000051 + uberon + has_part + has_part + has part + + + + + + + + + X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) + BFO:0000062 + is preceded by + takes place after + uberon + preceded_by + preceded_by + preceded_by + + + + + is preceded by + SIO:000249 + + + + + takes place after + Allen:precedes + + + + + + + + + BFO:0000063 + uberon + precedes + precedes + precedes + + + + + + + + + x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer + cjm + 2009-07-31T02:15:46Z + BSPO:0000096 + uberon + anterior_to + anterior_to + anterior_to + + + + + x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer + + + + + + + + + + + x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). + BSPO:0000098 + uberon + dorsal_to + dorsal_to + dorsal_to + + + + + x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). + + + + + + + + + + x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. + BSPO:0000099 + caudal_to + uberon + posterior_to + posterior_to + posterior_to + + + + + x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. + + + + + + + + + + x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). + BSPO:0000102 + uberon + ventral_to + ventral_to + ventral_to + + + + + x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). + + + + + + + + + + Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. + BSPO:0000107 + uberon + deep_to + deep_to + deep_to + + + + + Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. + + + + + + + + + Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. + BSPO:0000108 + uberon + superficial_to + superficial_to + superficial_to + + + + + Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. + + + + + + + + + + X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. + BSPO:0000120 + uberon + in_left_side_of + in_left_side_of + in_left_side_of + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + + X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. + BSPO:PATO_mtg_2009 + + + + + + + + + X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. + BSPO:0000121 + uberon + in_right_side_of + in_right_side_of + in_right_side_of + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + + X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. + BSPO:PATO_mtg_2009 + + + + + + + + + X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. + BSPO:0000123 + uberon + in_anterior_side_of + in_anterior_side_of + in_anterior_side_of + + + + + X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. + BSPO:PATO_mtg_2009 + + + + + + + + + + X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. + BSPO:0000124 + uberon + in_proximal_side_of + in_proximal_side_of + in_proximal_side_of + + + + + X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. + BSPO:PATO_mtg_2009 + + + + + + + + + X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. + BSPO:0000125 + uberon + in_distal_side_of + in_distal_side_of + in_distal_side_of + + + + + X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. + BSPO:PATO_mtg_2009 + + + + + + + + + X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure + BSPO:0000126 + uberon + in_lateral_side_of + in_lateral_side_of + in_lateral_side_of + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + + X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure + + + + + + + + + + X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y + BSPO:0001106 + uberon + proximalmost_part_of + proximalmost_part_of + proximalmost_part_of + + + + + X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y + + + + + + + + + + + This relation holds when both the deep_to and ajdacent_to relationship similarly hold. + BSPO:0001107 + uberon + immediately_deep_to + immediately_deep_to + immediately_deep_to + + + + + This relation holds when both the deep_to and ajdacent_to relationship similarly hold. + + + + + + + + + RO:0001015 + uberon + location_of + location_of + location_of + + + + + + + + RO:0001025 + uberon + located_in + located_in + located_in + + + + + + + + RO:0002002 + uberon + has_boundary + has_boundary + has boundary + + + + + + + + + RO:0002007 + uberon + bounding_layer_of + bounding_layer_of + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. + bounding layer of + + + + + + + + + X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) + A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. + RO:0002087 + directly preceded by + is directly preceded by + is immediately preceded by + starts_at_end_of + uberon + immediately_preceded_by + immediately_preceded_by + immediately_preceded_by + + + + + + A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. + SIO:000251 + + + + + is immediately preceded by + SIO:000251 + + + + + + + + + RO:0002150 + uberon + continuous_with + continuous_with + continuous_with + + + + + + + + + Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. + RO:0002170 + uberon + connected_to + connected_to + Connection does not imply overlaps. + connected to + + + + + + Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. + + + + + + + + + Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. + this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) + RO:0002176 + uberon + connects + connects + connects + + + + + Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. + + + + + + + + + + + relation between an artery and the structure is supplies with blood. + RO:0002178 + arterial supply of + uberon + supplies + supplies + source: FMA + supplies + + + + + + arterial supply of + FMA:86003 + + + + + + + + + + RO:0002179 + drains blood from + drains from + uberon + drains + drains + source: Wikipedia + drains + + + + + + + + + + + + + + + + + + + RO:0002202 + uberon + develops_from + develops_from + develops_from + + + + + + + + + RO:0002203 + uberon + develops_into + develops_into + develops_into + + + + + + + + + x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y + RO:0002219 + uberon + surrounded_by + surrounded_by + surrounded_by + + + + + x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y + + + + + + + + + + x adjacent_to y iff: x and y share a boundary + RO:0002220 + uberon + adjacent_to + adjacent_to + adjacent_to + + + + + + + + inverse of surrounded_by + RO:0002221 + uberon + surrounds + surrounds + surrounds + + + + + inverse of surrounded_by + + + + + + + + + + + Relation between occurrents, shares a start boundary with. + RO:0002223 + uberon + starts + starts + starts + + + + + Relation between occurrents, shares a start boundary with. + + Allen:starts + + + + + + + + + + RO:0002224 + uberon + starts_with + starts_with + starts with + + + + + + + + + Relation between occurrents, shares an end boundary with. + RO:0002229 + finishes + uberon + ends + ends + ends + + + + + Relation between occurrents, shares an end boundary with. + + Allen:starts + ZFS:finishes + + + + + + + + + + RO:0002230 + uberon + ends_with + ends_with + ends with + + + + + + + + + + + + + RO:0002254 + uberon + has_developmental_contribution_from + has_developmental_contribution_from + has developmental contribution from + + + + + + + + + + + + + RO:0002255 + uberon + developmentally_contributes_to + developmentally_contributes_to + developmentally_contributes_to + + + + + + + + t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. + RO:0002256 + uberon + developmentally_induced_by + developmentally_induced_by + sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) + developmentally_induced_by + + + + + t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. + GO:0001759 + + + + + + + + RO:0002285 + uberon + developmentally_replaces + developmentally_replaces + developmentally_replaces + + + + + + + + + + RO:0002350 + uberon + member_of + member_of + member of + + + + + + + + + RO:0002351 + uberon + has_member + has_member + has member + + + + + + + + RO:0002376 + uberon + drains into + tributary_of + tributary_of + tributary_of + + + + + drains into + dbpowl:drainsTo + + + + + + + + + + we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve + RO:0002380 + uberon + branching_part_of + branching_part_of + branching_part_of + + + + + + + + + x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y + RO:0002385 + uberon + has_potential_to_developmentally_contribute_to + has_potential_to_developmentally_contribute_to + has potential to developmentally contribute to + + + + + + + + x has the potential to develop into y iff x develops into y or if x is capable of developing into y + RO:0002387 + uberon + has_potential_to_develop_into + has_potential_to_develop_into + has potential to develop into + + + + + + + + RO:0002433 + uberon + contributes_to_morphology_of + contributes_to_morphology_of + contributes to morphology of + + + + + + + + + x composed_primarily_of y iff: more than half of the mass of x is made from parts of y + RO:0002473 + uberon + composed_primarily_of + composed_primarily_of + composed primarily of + + + + + + + + + + + + + Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. + RO:0002488 + begins_to_exist_during + uberon + existence_starts_during + existence_starts_during + existence starts during + + + + + Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. + + + + + + + + + + + + Relation between continuant and occurrent, such that c comes into existence at the start of p. + RO:0002489 + uberon + existence_starts_with + existence_starts_with + existence starts with + + + + + Relation between continuant and occurrent, such that c comes into existence at the start of p. + + + + + + + + + + + + + + Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. + RO:0002492 + ceases_to_exist_during + uberon + existence_ends_during + existence_ends_during + existence ends during + + + + + Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. + + + + + + + + + + + + Relation between continuant and occurrent, such that c ceases to exist at the end of p. + RO:0002493 + uberon + existence_ends_with + existence_ends_with + existence ends with + + + + + Relation between continuant and occurrent, such that c ceases to exist at the end of p. + + + + + + + + + + + RO:0002494 + transforms from + uberon + transformation_of + transformation_of + transformation of + + + + + + transforms from + SIO:000657 + + + + + + + + + RO:0002495 + direct_transformation_of + immediately transforms from + uberon + immediate_transformation_of + immediate_transformation_of + immediate transformation of + + + + + + direct_transformation_of + + + + + + immediately transforms from + SIO:000658 + + + + + + + + + + + + + + + + + + + + RO:0002496 + uberon + existence_starts_during_or_after + existence_starts_during_or_after + existence starts during or after + + + + + + + + + + + + + + + + + + + + RO:0002497 + uberon + existence_ends_during_or_before + existence_ends_during_or_before + existence ends during or before + + + + + + + + + + + + A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. + RO:0002551 + uberon + has sekeletal support + has supporting framework + has_skeleton + has_skeleton + has skeleton + + + + + A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. + + + + + + + + + + RO:0002569 + uberon + has_branching_part + has_branching_part + has branching part + + + + + + + + + RO:0002572 + uberon + luminal_space_of + luminal_space_of + luminal space of + + + + + + + + + RO:0002576 + uberon + skeleton_of + skeleton_of + skeleton of + + + + + + + + RO:0003000 + uberon + produces + produces + produces + + + + + + + + RO:0003001 + uberon + produced_by + produced_by + produced_by + + + + + + + + + + + x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. + uberon + anteriorly_connected_to + anteriorly connected to + + + + + x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. + + + + + + + + + + + carries + uberon + channel_for + channel for + + + + + + + + + uberon + channels_from + channels_from + + + + + + + + + uberon + channels_into + channels_into + + + + + + + + x is a conduit for y iff y passes through the lumen of x. + uberon + conduit_for + conduit for + + + + + + + + + + + + uberon + existence_starts_and_ends_during + existence starts and ends during + + + + + + + + Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. + uberon + filtered_through + Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed + filtered through + + + + + + + + + + + + + + + + + a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s + add to RO + uberon + indirectly_supplies + indirectly_supplies + + + + + + + + + + x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. + uberon + posteriorly_connected_to + posteriorly connected to + + + + + x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. + + + + + + + + + uberon + subdivision_of + placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B + subdivision of + + + + + + + + + . + uberon + transitively_anteriorly_connected_to + transitively anteriorly connected to + + + + + . + + + + + + + + + + uberon + transitively_connected_to + transitively_connected to + + + + + + + + + + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + uberon + UBERON:0000000 + + processual entity + + + + + An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. + span:ProcessualEntity + + + + + + + + + + + + + + + + + + + + + A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. + submucosal + + + + BTO:0002107 + FMA:85391 + FMA:85392 + NCIT:C13167 + UMLS:C0225344 + organ submucosa + region of submucosa + submucosa of organ + submucosa of region of organ + uberon + submucous layer + tela submucosa + tunica submucosa + UBERON:0000009 + + + submucosa + + + + + + + A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. + + + + + + UMLS:C0225344 + ncithesaurus:Submucosa + + + + + organ submucosa + FMA:85391 + + + + + region of submucosa + FMA:85392 + + + + + submucosa of organ + FMA:85391 + + + + + submucosa of region of organ + FMA:85392 + + + + + submucous layer + BTO:0002107 + + + + + tela submucosa + BTO:0002107 + + + + + + + + + + + + + + + A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. + Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] + Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] + The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) + (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] + PNS + + + + + + + AAO:0000429 + BAMS:PNS + BILA:0000081 + BTO:0001028 + CALOHA:TS-0808 + EFO:0000891 + EHDAA2:0001445 + EHDAA:2893 + EMAPA:16665 + EV:0100335 + FBbt:00005098 + FMA:9903 + GAID:715 + MA:0000218 + MAT:0000338 + MESH:D017933 + MIAA:0000338 + NCIT:C12465 + TAO:0000142 + UMLS:C0206417 + UMLS:C1305921 + VHOG:0000399 + XAO:0000178 + ZFA:0000142 + pars peripherica + systema nervosum periphericum + uberon + UBERON:0000010 + + + + + + peripheral nervous system + + + + + + + cjm + + + + + A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. + GO:0007422 + + + + + Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000142 + TAO + ZFIN:curator + + + + + Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] + 2012-06-20 + AAO:0000429 + AAO + AAO:BJB + + + + + The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) + + + + + + (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] + 2012-09-17 + VHOG:0000399 + VHOG + + DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) + + + + + PNS + + + + + + UMLS:C0206417 + NIFSTD:birnlex_1111 + + + + + UMLS:C0206417 + ncithesaurus:Peripheral_Nervous_System + + + + + UMLS:C1305921 + NIFSTD:birnlex_1111 + + + + + pars peripherica + + FMA:9903 + FMA:TA + + + + + + systema nervosum periphericum + + FMA:9903 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. + Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee + (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] + we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive + + + EHDAA2:0001844 + EHDAA:6530 + EMAPA:17525 + EV:0100152 + FMA:86166 + GAID:933 + MA:0000151 + MAT:0000284 + MESH:D012867 + MIAA:0000284 + OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA + VHOG:0000860 + portion of skin + region of skin + skin + skin region + skin zone + uberon + UBERON:0000014 + + zone of skin + + + + + + + + FMA + + + + + Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. + + + + + + + (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] + 2012-09-17 + VHOG:0000860 + VHOG + + DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) + + + + + skin + MA:0000151 + + + + + + + + + A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. + AEO:0000192 + CARO:0000010 + FMA:50705 + anatomical boundary + uberon + UBERON:0000015 + + Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. + non-material anatomical boundary + + + + + anatomical boundary + CARO:0000010 + + + + + + CARO + + + + + A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. + CARO:0000010 + + + + + + + + + + + + + + + Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. + not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) + tubular + galen:Tube + anatomical tube + duct + uberon + UBERON:0000025 + tube + + + + + Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. + + + + + + + + + + + + + + + + The head is the anterior-most division of the body [GO]. + Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] + Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] + Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] + + + + + AAO:0010335 + AEO:0000106 + BILA:0000115 + BTO:0000282 + CALOHA:TS-0436 + EFO:0000964 + EHDAA2:0003106 + EMAPA:31858 + FBbt:00000004 + FMA:7154 + GAID:61 + HAO:0000397 + MA:0000023 + MAT:0000294 + MESH:D006257 + MIAA:0000294 + NCIT:C12419 + OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg + OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA + SPD:0000016 + TAO:0001114 + TGMA:0000002 + UMLS:C0018670 + VHOG:0001644 + WBbt:0005739 + XAO:0003024 + ZFA:0001114 + galen:Head + head (volume) + adult head + uberon + cephalic area + UBERON:0000033 + + + + + head + + + + + The head is the anterior-most division of the body [GO]. + + GO:0060322 + + + + + Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] + 2012-06-20 + AAO:0010335 + AAO + AAO:BJB + + + + + Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] + 2012-08-14 + TAO:0001114 + TAO + ZFIN:curator + + + + + Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] + 2012-09-17 + VHOG:0001644 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 + + + + + UMLS:C0018670 + NIFSTD:birnlex_1230 + + + + + UMLS:C0018670 + ncithesaurus:Head + + + + + head (volume) + FMA:7154 + + + + + cephalic area + SPD:0000016 + + + + + + + + + + + + + + + + + + + + + + + + + + + + multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. + A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] + a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] + in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. + + + + + FMA:9581 + GAID:19 + MESH:D012704 + NCIT:C13169 + TAO:0005425 + UMLS:C0036760 + ZFA:0005425 + tunica serosa + wall of serous sac + uberon + serosa + UBERON:0000042 + + + serous membrane + + + + + + + multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. + + + + + + + A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] + 2012-08-14 + TAO:0005425 + TAO + + + + + + a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] + + + + + + in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. + FMA + + + + + UMLS:C0036760 + ncithesaurus:Serosa + + + + + tunica serosa + FMA:9581 + + + + + + wall of serous sac + FMA:9581 + + + + + serosa + + + + + + + + + + + + + + + + A tubular structure that contains, conveys body fluid, such as blood or lymph. + uberon + UBERON:0000055 + + + vessel + + + + + A tubular structure that contains, conveys body fluid, such as blood or lymph. + + + + + + + + + + + + + + + + + + + + + + A tubular structure that transports secreted or excreted substances. + A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. + Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. + + + + AAO:0011123 + FBbt:00100314 + FMA:30320 + NCIT:C12948 + TAO:0005171 + UMLS:C0687028 + XAO:0004000 + ZFA:0005171 + galen:Duct + anatomical duct + exocrine duct + exocrine gland duct + uberon + ducts + UBERON:0000058 + + duct + + + + + A tubular structure that transports secreted or excreted substances. + + + + + + + A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. + ZFA:0005171 + + + + + UMLS:C0687028 + ncithesaurus:Duct + + + + + ducts + XAO:0004000 + + + + + + + + + + + + + + + + + + + + + + Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. + in FMA, serosa is a wall + UBERON:0009915 + wall + EMAPA:25036 + FMA:82482 + galen:Wall + wall of organ + uberon + organ wall + UBERON:0000060 + + anatomical wall + + + + + Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. + FMA:82482 + + + + + in FMA, serosa is a wall + FMA + + + + + wall of organ + FMA:82482 + + + + + organ wall + FMA:82482 + + + + + + + + + + + + + + + + + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + + + AAO:0010825 + AEO:0000003 + BILA:0000003 + CARO:0000003 + EHDAA2:0003003 + EMAPA:0 + FBbt:00007001 + FMA:305751 + FMA:67135 + GAID:781 + HAO:0000003 + MA:0003000 + MESH:D000825 + TAO:0000037 + TGMA:0001823 + VHOG:0001759 + XAO:0003000 + ZFA:0000037 + biological structure + connected biological structure + uberon + UBERON:0000061 + + anatomical structure + + + + + Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. + CARO:0000003 + + + + + connected biological structure + CARO:0000003 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 + + + + + CARO:0020004 + EFO:0000634 + EMAPA:35949 + ENVO:01000162 + FMA:67498 + MA:0003001 + NCIT:C13018 + OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA + OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA + UMLS:C0178784 + WBbt:0003760 + uberon + anatomical unit + body organ + element + UBERON:0000062 + + organ + + + + + Anatomical structure that performs a specific function or group of functions [WP]. + + + + + + Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. + GO:0048513 + + + + + UMLS:C0178784 + ncithesaurus:Organ + + + + + element + + + + + + + + + + A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. + FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction + Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. + Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. + FMA:86140 + uberon + organ region with fixed fiat boundary + organ segment + segment of organ + UBERON:0000063 + + organ subunit + + + + + A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. + + + + + + Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. + FMA:86140 + 3 + + + + + Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. + FMA:86140 + 1 + + + + + organ region with fixed fiat boundary + FMA:86140 + + + + + organ segment + FMA:86140 + + + + + segment of organ + FMA:86140 + + + + + + + + + + + + + + + A multicellular structure that is a part of an organ. + currently defined in a very broad sense, may be replaced by more specific classes in the future + + + + AAO:0011124 + EFO:0000635 + FMA:82472 + cardinal organ part + uberon + regional part of organ + UBERON:0000064 + + + + organ part + + + + + A multicellular structure that is a part of an organ. + + + + + + cardinal organ part + FMA:82472 + + + + + regional part of organ + NIFSTD:birnlex_16 + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts + + EHDAA2:0001606 + EHDAA:1568 + EHDAA:2219 + EMAPA:16737 + FMA:265130 + OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA + VHOG:0000393 + uberon + UBERON:0000065 + respiratory tract + + + + + + + + + + + NCBIBook:NBK10107 + + + + + Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts + + + + + + + + + + + + + + + + + + + + + + + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + adult stage + BTO:0001043 + BilaDO:0000004 + EFO:0001272 + FBdv:00005369 + WBls:0000041 + XtroDO:0000084 + fully formed animal stage + juvenile-adult stage + uberon + UBERON:0000066 + + fully formed stage + + + + + + The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. + + + + + + + + + + + + + + + + + + + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + BilaDO:0000002 + EV:0300001 + FBdv:00005289 + FMA:72652 + HsapDv:0000002 + MmusDv:0000002 + OGES:000000 + OGES:000022 + WBls:0000003 + WBls:0000092 + WBls:0000102 + XAO:1000012 + embryonic stage + uberon + embryogenesis + UBERON:0000068 + embryo stage + + + + + A life cycle stage that starts with fertilization and ends with the fully formed embryo. + + + + + + + + + + + + + + + + End of the life of an organism. + ncit:Death is an outcome + XAO:0000437 + XtroDO:0000085 + uberon + death + UBERON:0000071 + death stage + + + + + End of the life of an organism. + XAO:0000437 + + + + + ncit:Death is an outcome + ncit + + + + + + + + + + + + + + + + + + + + + + + + + + + An section of a respiratory tract. + MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole + EMAPA:16737 + FMA:45660 + MA:0000434 + uberon + respiratory tract + subdivision of respiratory tract + UBERON:0000072 + + proximo-distal subdivision of respiratory tract + + + + + An section of a respiratory tract. + + + + + + MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole + MA + + + + + respiratory tract + MA:0000434 + + + + + + + + + + + + + + + + + + + + + + + + + + Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. + Melissa Haendel + 2009-06-18T09:00:04Z + + + + NCIT:C13040 + UMLS:C1518256 + part of nervous system + uberon + UBERON:0000073 + + + regional part of nervous system + + + + + Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. + NIFSTD:birnlex_1157 + + + + + UMLS:C1518256 + ncithesaurus:Nervous_System_Part + + + + + part of nervous system + NIFSTD:birnlex_1157 + + + + + + + + + + + + + + + + + + + + + Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. + UBERON:0010322 + + + FMA:85544 + NCIT:C34076 + UMLS:C1519343 + galen:ComplexSkeletalStructure + skeletal system subdivision + uberon + skeletal system part + UBERON:0000075 + + subdivision of skeletal system + + + + + + cjm + + + + + Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. + + UBERONREF:0000003 + + + + + UMLS:C1519343 + ncithesaurus:Skeletal_System_Part + + + + + skeletal system subdivision + FMA:85544 + + + + + + + + + + + + + + + + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. + merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) + (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis + + + EHDAA2:0001968 + EHDAA:1494 + EHDAA:350 + EHDAA:4784 + EHDAA:4790 + EHDAA:4796 + EHDAA:7860 + EMAPA:16096 + FMA:87656 + NCIT:C34309 + UMLS:C1515087 + surface (external) ectoderm + surface ectoderm + uberon + UBERON:0000076 + + external ectoderm + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. + MGI:anna + MP:0012532 + + + + + UMLS:C1515087 + ncithesaurus:Surface_Ectoderm + + + + + surface ectoderm + MP:0012532 + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the endoderm and the mesoderm. + Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple + uberon + UBERON:0000077 + + mixed endoderm/mesoderm-derived structure + + + + + An anatomical structure that develops from the endoderm and the mesoderm. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the ectoderm, mesoderm and endoderm. + Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple + uberon + UBERON:0000078 + + mixed ectoderm/mesoderm/endoderm-derived structure + + + + + An anatomical structure that develops from the ectoderm, mesoderm and endoderm. + + + + + + + + + + + + + + + + stage succeeding embryo, including mature structure + In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) + BilaDO:0000003 + OGES:000010 + OGES:000014 + OGES:000024 + WBls:0000022 + WBls:0000093 + WBls:0000103 + postembryonic stage + post-hatching stage + uberon + postembryonic + UBERON:0000092 + post-embryonic stage + + + + + + stage succeeding embryo, including mature structure + + + + + + + + + + + + + + + + Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] + cjm + 2009-07-30T05:19:13Z + membrane + FMA:7145 + membrane of organ + uberon + UBERON:0000094 + membrane organ + + + + + + + + + + + FMA-def + + + + + Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] + FMA:7145 + + + + + + + + + + + + + + + + + + + + + + + + + + + The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. + FMA:73750 + lung vascular network + pulmonary vasculature + vascular network of lung + vasculature of lung + uberon + UBERON:0000102 + + lung vasculature + + + + + The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. + GOC:GO + + + + + lung vascular network + OBOL:automatic + + + + + pulmonary vasculature + FMA:73750 + + + + + vascular network of lung + OBOL:automatic + + + + + vasculature of lung + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + FBdv:00000000 + HsapDv:0000001 + MmusDv:0000001 + OGES:000011 + ncithesaurus:Life + entire life cycle + entire lifespan + life + lifespan + uberon + UBERON:0000104 + + life cycle + + + + + + An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. + + + + + + + + + + + + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here + the WBls class 'all stages' belongs here as it is the superclass of other WBls stages + we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage + BILS:0000105 + EFO:0000399 + FBdv:00007012 + FMA:24120 + HsapDv:0000000 + MmusDv:0000000 + OlatDv:0000010 + PdumDv:0000090 + WBls:0000002 + XAO:1000000 + ZFS:0000000 + ZFS:0100000 + ncithesaurus:Developmental_Stage + developmental stage + stage + uberon + UBERON:0000105 + + + life cycle stage + + + + + A spatiotemporal region encompassing some part of the life cycle of an organism. + + + + + + + + + + + + + + + + + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + + BILS:0000106 + BilaDO:0000005 + EFO:0001322 + EHDAA:27 + FBdv:00005288 + HsapDv:0000001 + NCIT:C12601 + PdumDv:0000100 + VHOG:0000745 + XAO:1000001 + ZFS:0000001 + 1-cell stage + fertilized egg stage + one cell stage + uberon + fertilized egg stage + one-cell stage + zygote + zygotum + UBERON:0000106 + + zygote stage + + + + + + A stage at which the organism is a single cell produced by means of sexual reproduction. + + + + + + As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] + 2012-09-17 + VHOG:0000745 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 + + + + + fertilized egg stage + BTO:0000854 + + + + + one-cell stage + VHOG:0000745 + + + + + zygote + VHOG:0000745 + + + + + zygotum + + + + + + + + + + + + + + + + + + + + + + + The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. + + BILS:0000107 + BilaDO:0000006 + EFO:0001290 + FBdv:00000054 + MESH:A16.254.270 + MmusDv:0000004 + OGES:000015 + OGES:000020 + PdumDv:0000200 + XAO:1000004 + ZFS:0000046 + uberon + UBERON:0000107 + + cleavage stage + + + + + The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. + + GO:0040016 + + + + + + + + + + + + + + + + + + + + + An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + consider adding a preceding stage 'morula stage' as part of cleavage + + BILS:0000108 + BilaDO:0000007 + EFO:0001282 + HsapDv:0000006 + MmusDv:0000007 + OGES:000003 + OGES:000016 + OGES:000021 + OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg + WBls:0000005 + XAO:1000003 + ZFS:0000045 + uberon + UBERON:0000108 + + blastula stage + + + + + + An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + + + + + + + + + + + + + + + + + + + + + + A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. + BILS:0000109 + BilaDO:0000008 + EFO:0001296 + FBdv:00005317 + HsapDv:0000010 + MmusDv:0000013 + OGES:000004 + OGES:000019 + WBls:0000010 + XAO:1000005 + ZFS:0000047 + uberon + blastocystis trilaminaris stage + trilaminar blastocyst stage + trilaminar blastoderm stage + trilaminar disk stage + trilaminar germ stage + trilaminar stage + UBERON:0000109 + + gastrula stage + + + + + + + + + + + BILS + + + + + A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. + GO:0007369 + + + + + blastocystis trilaminaris stage + + + + + + trilaminar blastocyst stage + + + + + + trilaminar blastoderm stage + + + + + + trilaminar disk stage + + + + + + trilaminar germ stage + + + + + + trilaminar stage + + + + + + + + + + + + + + + + + + + + + + Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. + BILS:0000110 + BilaDO:0000009 + HsapDv:0000012 + MmusDv:0000017 + XAO:1000006 + uberon + UBERON:0000110 + neurula stage + + + + + + Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. + GO:0001841 + + + + + + + + + + + + + + + + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + + BILS:0000111 + BilaDO:0000010 + HsapDv:0000015 + MmusDv:0000018 + OGES:000005 + OGES:000032 + uberon + segmentation stage + UBERON:0000111 + organogenesis stage + + + + + + A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin + it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces + + EMAPA:35521 + FMA:27533 + MA:0001782 + connective tissue of lung + pulmonary interstitium + uberon + lung interstitial tissue + lung interstitium + pulmonary connective tissue + pulmonary interstitial tissue + UBERON:0000114 + + lung connective tissue + + + + + the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin + + ISBN:0-683-40008-8 + MGI:anna + MP:0002276 + + + + + connective tissue of lung + OBOL:automatic + + + + + pulmonary interstitium + FMA:27533 + + + + + lung interstitial tissue + MA:0001782 + + + + + pulmonary connective tissue + EMAPA:35521 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The epithelial layer of the lung. + A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[doi:10.1242/dev.115469] + BTO:0001653 + EMAPA:32860 + MA:0001783 + epithelial tissue of lung + epithelium of lung + lung epithelial tissue + uberon + pulmonary epithelium + UBERON:0000115 + + lung epithelium + + + + + The epithelial layer of the lung. + MP:0006382 + + + + + epithelial tissue of lung + OBOL:automatic + + + + + epithelium of lung + OBOL:automatic + + + + + lung epithelial tissue + OBOL:automatic + + + + + pulmonary epithelium + BTO:0001653 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. + in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) + EMAPA:37946 + FMA:12224 + segment of tracheobronchial tree + respiratory conducting tube + segment of tracheobronchial tree + tracheobronchial tree segment + uberon + airway + UBERON:0000117 + respiratory tube + + + + + A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. + + GO:0030323 + + + + + in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) + GO + + + + + EMAPA:37946 + MA:th + + + + + segment of tracheobronchial tree + FMA:12224 + + + + + respiratory conducting tube + MP:0004391 + + + + + segment of tracheobronchial tree + FMA:12224 + + + + + tracheobronchial tree segment + FMA:12224 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Structure derived from foregut that becomes a lung[GO]. + clarify successors - include bronchi? + + + + + BTO:0001643 + EHDAA2:0004089 + NCIT:C34260 + NCIT:C34282 + UMLS:C1514420 + UMLS:C1514897 + uberon + gemma pulmonalis + gemma respiratoria + lung bud + primary lung bud + respiratory diverticulum + UBERON:0000118 + + lung bud + + + + + + + GO:0060441 + + + + + + + + + + + EHDAA2 + + + + + Structure derived from foregut that becomes a lung[GO]. + + GO:0060431 + + + + + UMLS:C1514420 + ncithesaurus:Primary_Bronchial_Bud + + + + + UMLS:C1514897 + ncithesaurus:Respiratory_Diverticulum + + + + + gemma pulmonalis + + + + + + + gemma respiratoria + + + + + + + lung bud + + + + + + primary lung bud + GO:0060572 + + + + + respiratory diverticulum + + + + + + + + + + + + + + + + + uberon + UBERON:0000153 + anterior region of body + + + + + + lexical + + + + + + + + + uberon + UBERON:0000154 + posterior region of body + + + + + + lexical + + + + + + + + + Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. + in FMA, this is an anatomical conduit *space*, rather than anatomical conduit + anatomical ostium + ostium + + FMA:3724 + anatomical orifice + hilum + uberon + UBERON:0000161 + orifice + + + + + Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. + FMA:3724 + + + + + in FMA, this is an anatomical conduit *space*, rather than anatomical conduit + FMA + + + + + anatomical ostium + FMA:3724 + + + + + anatomical orifice + FMA:3724 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] + Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] + oral + some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives + in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips + + + + AAO:0010355 + BTO:0001090 + BTO:0004698 + CALOHA:TS-1315 + EFO:0000825 + EHDAA2:0001326 + EHDAA:542 + EMAPA:16262 + FBbt:00003126 + FMA:49184 + GAID:75 + MA:0000341 + MA:0002474 + MAT:0000038 + MESH:D009055 + MIAA:0000038 + OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA + TADS:0000040 + TAO:0000547 + TAO:0000590 + TGMA:0000131 + VHOG:0000280 + VHOG:0000812 + XAO:0003029 + ZFA:0000547 + ZFA:0000590 + galen:Mouth + regio oralis + adult mouth + uberon + cavital oralis + cavitas oris + cavum oris + mouth cavity + oral region + oral vestibule + rima oris + stoma + stomatodaeum + trophic apparatus + vestibule of mouth + vestibulum oris + UBERON:0000165 + + + + + + mouth + + + + + + + + the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts + + + + + + + + + + + + + + + + exceptions in some taxa + + + + + The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). + + + + + + + Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] + 2012-06-20 + AAO:0010355 + AAO + AAO:BJB + + + + + Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] + 2012-09-17 + VHOG:0000812 + VHOG + + DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) + + + + + in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips + FMA + + + + + regio oralis + BTO:0004698 + + + + + regio oralis + FMA:49184 + FMA:TA + + + + + + cavital oralis + + + + + + + cavitas oris + BTO:0001090 + + + + + cavum oris + BTO:0001090 + + + + + mouth cavity + BTO:0001090 + + + + + oral region + EHDAA2:0001326 + + + + + oral vestibule + BTO:0001090 + + + + + rima oris + BTO:0001090 + + + + + stomatodaeum + VHOG:0000812 + + + + + trophic apparatus + + + + + + vestibule of mouth + BTO:0001090 + + + + + vestibulum oris + BTO:0001090 + + + + + + + + + + + + + + + The orifice that connects the mouth to the exterior of the body. + (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] + FMA:59806 + oral fissure + oral orifice + uberon + mouth + oral part of face + UBERON:0000166 + + + oral opening + + + + + + FMA + + + + + The orifice that connects the mouth to the exterior of the body. + + + + + + (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] + 2012-09-17 + VHOG:0000280 + VHOG + + DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007) + + + + + oral fissure + FMA:59806 + + + + + oral orifice + FMA:59806 + + + + + mouth + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) + Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] + The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] + Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] + + + AAO:0000053 + AAO:0000960 + BSA:0000107 + CALOHA:TS-1315 + EFO:0001975 + EHDAA2:0001324 + EHDAA:6970 + EMAPA:17411 + EMAPA:18399 + EV:0100057 + FMA:20292 + HAO:0000669 + NCIT:C12421 + TAO:0001027 + TGMA:0000102 + UMLS:C0226896 + VHOG:0000188 + WBbt:0005255 + XAO:0000126 + ZFA:0001027 + buccal cavity + cavity of mouth + uberon + bucca + UBERON:0000167 + + + + oral cavity + + + + + Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) + + + ISBN10:0073040584 + + + + + Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] + 2012-06-20 + AAO:0000960 + AAO + AAO:EJS + + + + + The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] + 2012-09-17 + VHOG:0000188 + VHOG + + + + + + + Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] + 2012-09-17 + VHOG:0000188 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32 + + + + + UMLS:C0226896 + ncithesaurus:Oral_Cavity + + + + + buccal cavity + FMA:20292 + ISBN10:0073040584 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + + + 1 + + + + + + + + + + + 1 + + + + + 1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The pair of anatomical structures comprised of a left lung and right lung. + FMA:68877 + OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA + lungs + lungs pair + pulmones + set of lungs + uberon + UBERON:0000170 + + pair of lungs + + + + + + + + + + + FMA-abduced + + + + + The pair of anatomical structures comprised of a left lung and right lung. + + + + + + pulmones + FMA:68877 + FMA:TA + + + + + + + + + + + + + + + + Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. + + EMAPA:17607 + SPD:0000428 + TGMA:0001247 + apparatus respiratorius organ + breathing organ + organ of apparatus respiratorius + organ of respiratory system + respiratory organ + respiratory system organ + uberon + gas exchange organ + UBERON:0000171 + + + respiration organ + + + + + Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. + GO:0007585 + + + + + apparatus respiratorius organ + OBOL:automatic + + + + + organ of apparatus respiratorius + OBOL:automatic + + + + + organ of respiratory system + OBOL:automatic + + + + + respiratory system organ + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fluid that is composed of blood plasma and erythrocytes. + This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. + A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] + Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] + relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] + Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] + + + + + AAO:0000046 + BTO:0000089 + CALOHA:TS-0079 + EFO:0000296 + EHDAA2:0000176 + EHDAA:418 + EMAPA:16332 + ENVO:02000027 + EV:0100047 + FMA:9670 + GAID:965 + MA:0000059 + MESH:D001769 + MIAA:0000315 + NCIT:C12434 + OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA + TAO:0000007 + UMLS:C0005767 + VHOG:0000224 + XAO:0000124 + ZFA:0000007 + galen:Blood + portion of blood + vertebrate blood + uberon + whole blood + UBERON:0000178 + + + + + blood + + + + + + + + + + + + + + + + + + + + + + Bgee:AN + + + + + A fluid that is composed of blood plasma and erythrocytes. + + + + FMA:9670 + + + + + A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] + 2012-08-14 + TAO:0000007 + TAO + ZFIN:curator + + + + + Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] + 2012-06-20 + AAO:0000046 + AAO + AAO:LAP + + + + + relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] + 2012-06-20 + AAO:0000046 + AAO + + + + + Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] + 2012-09-17 + VHOG:0000224 + VHOG + + DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) + + + + + UMLS:C0005767 + ncithesaurus:Blood + + + + + whole blood + BTO:0000089 + + + + + + + + + + + + + + + + + + + + + + + + + + Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. + cjm + 2009-04-08T04:38:19Z + CARO:0000081 + uberon + blood or blood analog + circulating fluid + UBERON:0000179 + haemolymphatic fluid + + + + + Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula + UBERON:0007011 + + BILA:0000059 + BTO:0000128 + GAID:1294 + MESH:A16.254.270.274 + OGEM:000006 + OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg + blastula embryo + uberon + blastosphere + UBERON:0000307 + + blastula + + + + + + Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. + + + + + + blastula embryo + BILA:0000059 + + + + + blastosphere + + + + + + + + + + + + + + + + + + + + + + + + + + + The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). + We model the digestive tract as consisting of two parts: the wall and the lumen. + BTO:0000547 + FMA:45653 + digestive tract wall + wall of digestive tract + wall of gut + uberon + wall of alimentary tract + UBERON:0000328 + gut wall + + + + + The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). + + + + + + wall of gut + FMA:45653 + + + + + + + + + + + + + + + + + + + + + A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] + mucosal + FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately + + + + AEO:0000199 + BTO:0000886 + CALOHA:TS-2031 + EHDAA2_RETIRED:0003234 + EV:0100382 + FMA:85355 + FMA:85358 + GAID:297 + MESH:D009092 + NCIT:C13166 + OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA + UMLS:C0026724 + galen:Mucosa + mucosa of organ + mucosa of organ part + mucosal region + mucous membrane + organ mucosa + uberon + region of mucosa + tunica mucosa + UBERON:0000344 + + mucosa + + + + + + + A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] + + + + + + FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately + FMA + + + + + UMLS:C0026724 + ncithesaurus:Mucosa + + + + + mucosa of organ + FMA:85355 + + + + + mucosa of organ part + FMA:85358 + + + + + mucosal region + FMA:85358 + + + + + mucous membrane + FMA:85355 + + + + + organ mucosa + FMA:85355 + + + + + region of mucosa + FMA:85358 + + + + + tunica mucosa + + + + + + + tunica mucosa + BTO:0000886 + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a pharynx [Automatically generated definition]. + UBERON:0003344 + + BTO:0001047 + EMAPA:26957 + FMA:55031 + MA:0003143 + mucosa of organ of pharynx + mucosa of pharynx + mucous membrane of pharynx + organ mucosa of pharynx + pharynx mucosa + pharynx mucosa of organ + pharynx mucous membrane + pharynx organ mucosa + tunica mucosa pharyngea + tunica mucosa pharyngis + uberon + mucous membrane of the pharynx + UBERON:0000355 + pharyngeal mucosa + + + + + A mucosa that is part of a pharynx [Automatically generated definition]. + OBOL:automatic + + + + + mucosa of organ of pharynx + OBOL:automatic + + + + + mucosa of pharynx + OBOL:automatic + + + + + mucous membrane of pharynx + FMA:55031 + + + + + mucous membrane of pharynx + OBOL:automatic + + + + + organ mucosa of pharynx + OBOL:automatic + + + + + pharynx mucosa + OBOL:automatic + + + + + pharynx mucosa of organ + OBOL:automatic + + + + + pharynx mucous membrane + OBOL:automatic + + + + + pharynx organ mucosa + OBOL:automatic + + + + + tunica mucosa pharyngea + FMA:55031 + FMA:TA + + + + + + mucous membrane of the pharynx + BTO:0001047 + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a respiratory airway. + + BTO:0001390 + FMA:7471 + mucosa of organ of trachea + mucosa of organ of windpipe + mucosa of trachea + mucosa of windpipe + mucous membrane of trachea + mucous membrane of windpipe + organ mucosa of trachea + organ mucosa of windpipe + trachea mucosa + trachea mucosa of organ + trachea mucous membrane + trachea organ mucosa + tracheal mucous membrane + tunica mucosa (tracheae) + tunica mucosa tracheae + windpipe mucosa + windpipe mucosa of organ + windpipe mucous membrane + windpipe organ mucosa + uberon + UBERON:0000379 + tracheal mucosa + + + + + A mucosa that is part of a respiratory airway. + OBOL:automatic + + + + + mucosa of organ of trachea + OBOL:automatic + + + + + mucosa of organ of windpipe + OBOL:automatic + + + + + mucosa of trachea + OBOL:automatic + + + + + mucosa of windpipe + OBOL:automatic + + + + + mucous membrane of trachea + FMA:7471 + + + + + mucous membrane of trachea + OBOL:automatic + + + + + mucous membrane of windpipe + OBOL:automatic + + + + + organ mucosa of trachea + OBOL:automatic + + + + + organ mucosa of windpipe + OBOL:automatic + + + + + trachea mucosa + OBOL:automatic + + + + + trachea mucosa of organ + OBOL:automatic + + + + + trachea mucous membrane + OBOL:automatic + + + + + trachea organ mucosa + OBOL:automatic + + + + + tracheal mucous membrane + FMA:7471 + + + + + tunica mucosa (tracheae) + FMA:7471 + + + + + tunica mucosa tracheae + FMA:7471 + FMA:TA + + + + + + windpipe mucosa + OBOL:automatic + + + + + windpipe mucosa of organ + OBOL:automatic + + + + + windpipe mucous membrane + OBOL:automatic + + + + + windpipe organ mucosa + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. + consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 + Anatomical system that consists of the muscles of the body.[VSAO] + we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA + AAO:0000307 + BILA:0000088 + BTO:0001369 + BTO:0001485 + EFO:0000801 + EMAPA:35578 + FBbt:00005069 + FMA:72954 + MA:0002888 + MAT:0000025 + MIAA:0000025 + VSAO:0000033 + XAO:0004042 + muscle system + muscle system of body + muscular system + musculature system + set of all muscles + set of muscles of body + vertebrate muscular system + uberon + muskelsystem + UBERON:0000383 + + + musculature of body + + + + + The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. + VSAO:0000033 + + + + + Anatomical system that consists of the muscles of the body.[VSAO] + 2012-08-14 + VSAO:0000033 + VSAO + VSAO:curator + + + + + we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA + MA + + + + + muscular system + FMA:72954 + + + + + musculature system + BILA:0000088 + + + + + set of all muscles + FMA:72954 + + + + + set of muscles of body + FMA:72954 + + + + + vertebrate muscular system + BTO:0001369 + + + + + muskelsystem + BTO:0001485 + + + + + + + + + + + + + + + + + + + + + A gland in which the principal secretory cells are serous secreting cells. + glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. + + BTO:0001837 + EMAPA:37950 + FMA:62889 + uberon + UBERON:0000409 + + + serous gland + + + + + + A gland in which the principal secretory cells are serous secreting cells. + + + + + + + glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. + MP:0008052 + + + + + EMAPA:37950 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical wall that is part of an artery [Automatically generated definition]. + BTO:0002009 + FMA:14155 + galen:ArterialWall + arterial wall + wall of artery + uberon + UBERON:0000415 + artery wall + + + + + An anatomical wall that is part of an artery [Automatically generated definition]. + OBOL:automatic + + + + + arterial wall + FMA:14155 + + + + + wall of artery + FMA:14155 + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of organism substance that is produced by exocrine glands. + BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions + UBERON:0006540 + secretion + + AEO:0001005 + BTO:0002977 + BTO:0002979 + EMAPA:36535 + FMA:9675 + MA:0002504 + MESH:D012634 + NCIT:C34062 + UMLS:C1516992 + galen:Secretion + bodily secretion + exocrine gland fluid/secretion + secreted substance + uberon + exocrine gland fluid + exocrine gland fluid or secretion + exocrine gland secretion + external secretion + UBERON:0000456 + secretion of exocrine gland + + + + + A portion of organism substance that is produced by exocrine glands. + + + + + + BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions + BTO + + + + + secretion + FMA:9675 + + + + + UMLS:C1516992 + ncithesaurus:Exocrine_Gland_Fluid_or_Secretion + + + + + bodily secretion + MESH:D012634 + + + + + exocrine gland fluid/secretion + MA:0002504 + + + + + external secretion + BTO:0002977 + + + + + + + + + + + + + + + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. + AAO:0010839 + AEO:0000004 + BILA:0000004 + CALOHA:TS-2101 + CARO:0000004 + EHDAA2:0003004 + EMAPA:35178 + FBbt:00007019 + FMA:9669 + HAO:0000004 + MA:0002450 + NCIT:C13236 + SPD:0000008 + TAO:0001487 + TGMA:0001824 + VHOG:0001726 + XAO:0004001 + ZFA:0001487 + galen:BodySubstance + body fluid or substance + body substance + organism substance + portion of body substance + portion of organism substance + uberon + UBERON:0000463 + + + organism substance + + + + + + + + + + + this relationship may be too strong and may be weakened in future + + + + + Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. + + + + + + body fluid or substance + MA:0002450 + + + + + body substance + FMA:9669 + + + + + organism substance + CARO:0000004 + + + + + portion of body substance + FMA:9669 + + + + + portion of organism substance + ZFA:0001487 + + + + + + + + + + + + + + + Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. + lumen + space + + AAO:0010110 + AEO:0000005 + BILA:0000005 + CARO:0000005 + EHDAA2:0003005 + FBbt:00007017 + FMA:5897 + HAO:0000005 + NCIT:C94478 + TAO:0001668 + TGMA:0001825 + UMLS:C0524461 + VHOG:0001728 + XAO:0003190 + ZFA:0001643 + lumen space + uberon + anatomical spaces + UBERON:0000464 + + anatomical space + + + + + Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. + + + + + + UMLS:C0524461 + ncithesaurus:Lumen_Space + + + + + anatomical spaces + ZFA:0001643 + + + + + + + + + + Anatomical entity that has mass. + AAO:0010264 + AEO:0000006 + BILA:0000006 + CARO:0000006 + EHDAA2:0003006 + FBbt:00007016 + FMA:67165 + HAO:0000006 + TAO:0001836 + TGMA:0001826 + VHOG:0001721 + uberon + UBERON:0000465 + + material anatomical entity + + + + + Anatomical entity that has mass. + + + + + + + + + + Anatomical entity that has no mass. + AAO:0010265 + AEO:0000007 + BILA:0000007 + CARO:0000007 + EHDAA2:0003007 + FBbt:00007015 + FMA:67112 + HAO:0000007 + TAO:0001835 + TGMA:0001827 + VHOG:0001727 + immaterial physical anatomical entity + uberon + UBERON:0000466 + + immaterial anatomical entity + + + + + Anatomical entity that has no mass. + + + + + + immaterial physical anatomical entity + FMA:67112 + + + + + + + + + + + + + + + + + + + + + + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + system + + + + + AAO:0000007 + AEO:0000011 + BILA:0000011 + BSA:0000049 + CALOHA:TS-2088 + CARO:0000011 + EHDAA2:0003011 + EHDAA:392 + EMAPA:16103 + EV:0100000 + FBbt:00004856 + FMA:7149 + HAO:0000011 + MA:0000003 + NCIT:C12919 + OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ + TAO:0001439 + TGMA:0001831 + UMLS:C0460002 + VHOG:0001725 + WBbt:0005746 + WBbt:0005763 + XAO:0003002 + ZFA:0001439 + galen:AnatomicalSystem + body system + connected anatomical system + organ system + uberon + anatomical systems + UBERON:0000467 + + + + anatomical system + + + + + + Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. + CARO:0000011 + + + + + system + GO:0048731 + + + + + UMLS:C0460002 + ncithesaurus:Organ_System + + + + + body system + NIFSTD:birnlex_14 + + + + + connected anatomical system + CARO:0000011 + + + + + anatomical systems + ZFA:0001439 + + + + + + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + TODO - split body and mc organism? body continues after death stage + organismal + organism + + + + AAO:0010026 + AEO:0000191 + BILA:0000012 + BSA:0000038 + BTO:0000042 + CARO:0000012 + EFO:0002906 + EHDAA2:0003103 + EHDAA2:0003191 + EHDAA:1 + EMAPA:25765 + EV:0100016 + FBbt:00000001 + FMA:256135 + HAO:0000012 + NCIT:C13041 + TADS:0000001 + TAO:0001094 + TGMA:0001832 + VHOG:0000671 + WBbt:0007833 + XAO:0003004 + ZFA:0001094 + galen:Organism + ncithesaurus:Whole_Organism + multi-cellular organism + animal + uberon + Koerper + body + whole body + whole organism + UBERON:0000468 + + + + + multicellular organism + + + + + Anatomical structure that is an individual member of a species and consists of more than one cell. + + + CARO:0000012 + + + + + organism + FBbt:00000001 + VHOG:0000671 + WBbt:0007833 + + + + + multi-cellular organism + CARO:0000012 + + + + + animal + BTO:0000042 + + + + + Koerper + BTO:0001489 + + + + + body + + AEO:0000103 + FMA:256135 + NCIT:C13041 + + + + + whole body + BTO:0001489 + + + + + whole organism + FBbt:00000001 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency + + + + AAO:0010053 + AEO:0000032 + BILA:0000032 + CALOHA:TS-2084 + CARO:0000032 + EFO:0000808 + EHDAA2:0003032 + EMAPA:36031 + FBbt:00007009 + FMA:7153 + HAO:0000032 + MA:0002433 + MAT:0000293 + MESH:D001829 + MIAA:0000293 + NCIT:C32221 + OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA + TAO:0001308 + TGMA:0001840 + UMLS:C0229962 + VHOG:0001758 + XAO:0003013 + ZFA:0001308 + galen:BodyPart + anatomic region + uberon + body part + body region + cardinal body part + UBERON:0000475 + + + + + organism subdivision + + + + + + CARO + + + + + Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. + + CARO:0000032 + CARO:DOS + + + + + UMLS:C0229962 + ncithesaurus:Body_Part + + + + + anatomic region + MA:0002433 + + + + + body region + FMA:7153 + + + + + cardinal body part + FMA:7153 + + + + + + + + + + Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. + AAO:0010268 + AEO:0000040 + BILA:0000040 + CARO:0000040 + EHDAA2:0003040 + FBbt:00007013 + FMA:63863 + HAO:0000040 + TAO:0000382 + TGMA:0001841 + XAO:0003162 + ZFA:0000382 + uberon + acellular anatomical structures + UBERON:0000476 + + acellular anatomical structure + + + + + + CARO + + + + + Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. + + + + + + acellular anatomical structures + ZFA:0000382 + + + + + + + + + + Anatomical group that has its parts adjacent to one another. + Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] + AAO:0010009 + AEO:0000041 + BILA:0000041 + CARO:0000041 + EHDAA2:0003041 + FBbt:00007277 + FMA:49443 + HAO:0000041 + TADS:0000605 + TAO:0001478 + TGMA:0001842 + VHOG:0001737 + XAO:0003160 + ZFA:0001478 + uberon + UBERON:0000477 + + anatomical cluster + + + + + Anatomical group that has its parts adjacent to one another. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. + + + AAO:0010020 + AEO:0000042 + BILA:0000042 + CALOHA:TS-2119 + CARO:0000042 + EHDAA2:0003042 + EHDAA:46 + FBbt:00005835 + FMA:85537 + HAO:0000042 + NCIT:C34055 + TAO:0000020 + TGMA:0001843 + UMLS:C1282438 + VHOG:0000292 + XAO:0004005 + ZFA:0000020 + extra-embryonic structure + uberon + extraembryonic structures + extraembryonic tissue + UBERON:0000478 + + + + see also conceptus extraembryonic component in EHDAA2. + extraembryonic structure + + + + + A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. + + + CARO:DOS + + + + + UMLS:C1282438 + ncithesaurus:Extraembryonic_Structure + + + + + extraembryonic structures + ZFA:0000020 + + + + + + + + + + + + + + + + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + changed label and definition to reflect CARO2 + + + AAO:0000607 + AAO:0010054 + AEO:0000043 + BILA:0000043 + CALOHA:TS-2090 + CARO:0000043 + EHDAA2:0003043 + EMAPA:35868 + FBbt:00007003 + FMA:9637 + HAO:0000043 + MA:0003002 + MESH:D014024 + NCIT:C12801 + TAO:0001477 + TGMA:0001844 + UMLS:C0040300 + VHOG:0001757 + WBbt:0005729 + XAO:0003040 + ZFA:0001477 + galen:Tissue + portion of tissue + tissue portion + simple tissue + uberon + UBERON:0000479 + + + tissue + + + + + + CARO + + + + + Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. + CARO:0000043 + + + + + UMLS:C0040300 + ncithesaurus:Tissue + + + + + portion of tissue + CARO:0000043 + + + + + simple tissue + AEO:0000043 + + + + + + + + + + + + + + + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. + AAO:0010048 + AEO:0000055 + BILA:0000055 + CARO:0000055 + EHDAA2:0003055 + FBbt:00007010 + HAO:0000055 + TAO:0001488 + TGMA:0001847 + VHOG:0001762 + XAO:0003037 + ZFA:0001488 + uberon + multi-tissue structures + UBERON:0000481 + + multi-tissue structure + + + + + + CARO + + + + + Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. + + CARO:0000055 + + + + + multi-tissue structures + ZFA:0001488 + + + + + + + + + + + + + + + + + + + + + + + + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. + The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] + epithelial + + + + AAO:0000144 + AAO:0010055 + AEO:0000066 + BILA:0000066 + BTO:0000416 + CALOHA:TS-0288 + CARO:0000066 + EHDAA2:0003066 + EMAPA:32738 + FBbt:00007005 + FMA:9639 + GAID:402 + HAO:0000066 + MA:0003060 + MESH:D004848 + NCIT:C12710 + TAO:0001486 + UMLS:C0014609 + VHOG:0000387 + XAO:0003045 + ZFA:0001486 + epithelial tissue + portion of epithelium + uberon + UBERON:0000483 + + + + epithelium + + + + + + Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. + + + + + + + The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] + 2012-09-17 + VHOG:0000387 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 + + + + + UMLS:C0014609 + ncithesaurus:Epithelium + + + + + portion of epithelium + FMA:9639 + + + + + + + + + + Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] + columnar epithelium + columnar epithlium + + + + AAO:0010063 + AEO:0000068 + BILA:0000068 + CARO:0000068 + EHDAA2_RETIRED:0003068 + FBbt:00007027 + FMA:45567 + HAO:0000068 + NCIT:C33552 + TAO:0001496 + UMLS:C0836135 + XAO:0004008 + ZFA:0001496 + epithelium simplex columnare + simple columnar epithelium + uberon + simple columnar epithelia + UBERON:0000485 + + + simple columnar epithelium + + + + + + Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] + + + FMA:FMA + + + + + columnar epithelium + EHDAA2:0003068 + + + + + columnar epithlium + AEO:0000068 + + + + + UMLS:C0836135 + ncithesaurus:Simple_Columnar_Epithelium + + + + + simple columnar epithelia + ZFA:0001496 + + + + + + + + + + Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] + Epithelium that consists of more than one layer of epithelial cells.[CARO] + + + + AAO:0010059 + AEO:0000069 + BILA:0000069 + BTO:0002074 + CARO:0000069 + EHDAA2:0003069 + FMA:45562 + HAO:0000069 + NCIT:C33622 + TAO:0001494 + UMLS:C0682575 + XAO:0004006 + ZFA:0001494 + stratified epithelium + uberon + laminated epithelium + UBERON:0000486 + + + multilaminar epithelium + + + + + Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] + + + FMA:FMA + + + + + Epithelium that consists of more than one layer of epithelial cells.[CARO] + 2012-06-20 + CARO:0000069 + CARO + + FMA:45562 + + + + + UMLS:C0682575 + ncithesaurus:Stratified_Epithelium + + + + + laminated epithelium + BTO:0002074 + + + + + + + + + + Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] + Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] + + + AAO:0010066 + AEO:0000070 + BILA:0000070 + BTO:0002073 + CARO:0000070 + EHDAA2:0003070 + FMA:45565 + HAO:0000070 + NCIT:C13178 + TAO:0001498 + UMLS:C0836133 + XAO:0004010 + ZFA:0001498 + epithelium simplex squamosum + uberon + simple squamous epithelia + UBERON:0000487 + + + simple squamous epithelium + + + + + + Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] + + + FMA:45565 + + + + + Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] + 2012-06-20 + CARO:0000070 + CARO + + FMA:45565 + + + + + UMLS:C0836133 + ncithesaurus:Simple_Squamous_Epithelium + + + + + simple squamous epithelia + ZFA:0001498 + + + + + + + + + + + + + + + + + + + + + + + + + + + Compound organ that contains one or more macroscopic anatomical spaces. + this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future + AAO:0010016 + AEO:0000072 + BILA:0000072 + CARO:0000072 + EHDAA2:0003072 + FMA:55671 + HAO:0000072 + TAO:0001490 + TGMA:0001857 + VHOG:0001730 + XAO:0003165 + ZFA:0001490 + cavitated organ + uberon + cavitated compound organs + UBERON:0000489 + + + cavitated compound organ + + + + + Compound organ that contains one or more macroscopic anatomical spaces. + + + + + + cavitated organ + FMA:55671 + + + + + cavitated compound organs + ZFA:0001490 + + + + + + + + + + Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] + consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable + Epithelium that consists of a single layer of epithelial cells.[CARO] + + + AAO:0010062 + AEO:0000073 + BILA:0000073 + BTO:0002073 + CARO:0000073 + EHDAA2:0003073 + FMA:45561 + HAO:0000073 + NCIT:C33554 + TAO:0001495 + UMLS:C0682574 + XAO:0004007 + ZFA:0001495 + simple epithelium + uberon + unilaminar epithelia + UBERON:0000490 + + unilaminar epithelium + + + + + Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] + + FMA:45561 + + + + + Epithelium that consists of a single layer of epithelial cells.[CARO] + 2012-06-20 + CARO:0000073 + CARO + + FMA:45561 + + + + + UMLS:C0682574 + ncithesaurus:Simple_Epithelium + + + + + simple epithelium + FMA:45561 + + + + + unilaminar epithelia + ZFA:0001495 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Subdivision of trunk that lies between the head and the abdomen. + note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest + + + EMAPA:35862 + FMA:259209 + MA:0000022 + thorax + uberon + anterior subdivision of trunk + upper body + upper trunk + UBERON:0000915 + + thoracic segment of trunk + + + + + + FMA + + + + + Subdivision of trunk that lies between the head and the abdomen. + + + + + + thorax + MA:0000022 + + + + + upper trunk + FMA:259209 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + embryonic + Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo + + + + + AAO:0011035 + AEO:0000169 + BILA:0000056 + BSA:0000039 + BTO:0000379 + CALOHA:TS-0229 + EFO:0001367 + EHDAA2:0000002 + EHDAA2_RETIRED:0003236 + EHDAA:38 + EMAPA:16039 + FBbt:00000052 + FMA:69068 + GAID:963 + MAT:0000226 + MESH:D004622 + MIAA:0000019 + NCIT:C28147 + OGEM:000001 + OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA + UMLS:C0013935 + VHOG:0001766 + XAO:0000113 + ZFA:0000103 + embryonic organism + uberon + developing organism + developmental tissue + UBERON:0000922 + + + + + embryo + + + + + + + Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. + + BTO:0000379 + FB:FBrf0039741 + FB:FBrf0041814 + GO:0009790 + + + + + Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo + ZFA + + + + + UMLS:C0013935 + ncithesaurus:Embryo + + + + + embryonic organism + BILA:0000056 + + + + + developing organism + BILA:0000056 + + + + + + + + + A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + embryonic tissue + + + + AAO:0000480 + BILA:0000035 + BTO:0000556 + EMAPA:36033 + FBbt:00000110 + FMA:69069 + GAID:1303 + MESH:A16.254.425 + NCIT:C12950 + NCIT:C54105 + TAO:0001122 + UMLS:C0920502 + UMLS:C1708239 + VHOG:0001223 + XAO:0003011 + ZFA:0001122 + germinal layer + primary germ layer + uberon + embryonic germ layer + embryonic germ layers + UBERON:0000923 + + + Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] + germ layer + + + + + A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. + + + + + + + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + 2012-09-17 + VHOG:0001223 + VHOG + + ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 + + + + + embryonic tissue + FMA:69069 + + + + + UMLS:C0920502 + ncithesaurus:Embryonic_Tissue + + + + + UMLS:C1708239 + ncithesaurus:Germinal_Layer + + + + + germinal layer + ncithesaurus:Germinal_Layer + + + + + primary germ layer + GO:0001704 + ZFA:0001122 + + + + + + + + + + + + + + + + + + + + + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. + Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + ectodermal + + + + AAO:0000137 + BILA:0000036 + BTO:0000315 + CALOHA:TS-0216 + EFO:0000414 + EHDAA2:0000428 + EMAPA:16069 + EV:0100003 + FBbt:00000111 + FMA:69070 + GAID:1304 + MAT:0000155 + MAT:0000173 + MESH:A16.254.425.273 + MIAA:0000173 + NCIT:C12703 + TAO:0000016 + UMLS:C0013574 + VHOG:0000153 + XAO:0000001 + ZFA:0000016 + embryonic ectoderm + uberon + UBERON:0000924 + + + + + ectoderm + + + + + + + + + + + + Bgee:AN + + + + + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. + + + + + + Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] + 2012-06-20 + AAO:0000137 + AAO + AAO:EJS + + + + + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + 2012-09-17 + VHOG:0000153 + VHOG + + ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 + + + + + UMLS:C0013574 + ncithesaurus:Ectoderm + + + + + embryonic ectoderm + VHOG:0000153 + + + + + + + + + + + + + + + + + + + + + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + endodermal + + + + AAO:0000139 + BILA:0000038 + BTO:0000800 + CALOHA:TS-0273 + EFO:0002545 + EHDAA2:0000436 + EMAPA:16062 + EV:0100005 + FBbt:00000125 + FMA:69071 + GAID:1305 + MAT:0000175 + MESH:A16.254.425.407 + MIAA:0000175 + NCIT:C12706 + TAO:0000017 + UMLS:C0014144 + VHOG:0000154 + XAO:0000090 + ZFA:0000017 + uberon + entoderm + UBERON:0000925 + + + + + endoderm + + + + + + + + + + + + + Bgee:AN + + + + + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. + + + + + + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + 2012-09-17 + VHOG:0000154 + VHOG + + ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 + + + + + UMLS:C0014144 + ncithesaurus:Endoderm + + + + + entoderm + + + + + + + + + + + + + + + + + + + + + + + The middle germ layer of the embryo, between the endoderm and ectoderm. + Primary germ layer that is the middle of the embryonic germ layers.[AAO] + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + mesodermal + sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates + UBERON:0003263 + + + + AAO:0000304 + BILA:0000037 + BTO:0000839 + CALOHA:TS-0623 + EFO:0001981 + EHDAA2:0001128 + EHDAA:124 + EHDAA:160 + EHDAA:183 + EMAPA:16083 + EV:0100006 + FBbt:00000126 + FMA:69072 + GAID:522 + MAT:0000174 + MESH:A16.254.425.660 + MIAA:0000174 + NCIT:C12750 + TAO:0000041 + UMLS:C0025485 + VHOG:0000152 + XAO:0000050 + ZFA:0000041 + uberon + embryonic mesoderm + entire mesoderm + mesodermal mantle + UBERON:0000926 + + + + + mesoderm + + + + + + + sometimes not considered primary + + + + + + + + + + + Bgee:AN + + + + + The middle germ layer of the embryo, between the endoderm and ectoderm. + + + + + + Primary germ layer that is the middle of the embryonic germ layers.[AAO] + 2012-06-20 + AAO:0000304 + AAO + AAO:EJS + + + + + The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] + 2012-09-17 + VHOG:0000152 + VHOG + + ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 + + + + + sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates + + + + + + UMLS:C0025485 + ncithesaurus:Mesoderm + + + + + embryonic mesoderm + VHOG:0000152 + + + + + entire mesoderm + + + + + + + + + + + + + + + + + + + + + + + Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. + consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence + Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] + the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx + stomodeal + This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. + stomodeal-hypophyseal primordium + + + BTO:0004224 + EHDAA2:0001929 + EMAPA:16263 + FBbt:00000439 + FMA:295846 + NCIT:C34306 + TAO:0001290 + TGMA:0000135 + UMLS:C1514977 + XAO:0000269 + ZFA:0001290 + mouth primordium + primitive oral cavity + stomatodeum + stomodaeum + uberon + mouth pit + oral ectoderm + oral pit + UBERON:0000930 + + + + + stomodeum + + + + + + Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. + + + + + + + + Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] + 2012-08-14 + TAO:0001290 + TAO + ZFIN:curator + + + + + the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx + MP:0012522 + NCBITaxon:40674 + + + + + stomodeal-hypophyseal primordium + XAO:0000269 + + + + + UMLS:C1514977 + ncithesaurus:Stomodeum + + + + + mouth primordium + XAO:0000269 + + + + + primitive oral cavity + + + + + + stomatodeum + + + + + + mouth pit + EMAPA:16263 + + + + + oral ectoderm + ZFA:0001290,ZFIN:ZDB-PUB-100726-23 + + + + + oral pit + EMAPA:16263 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. + Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] + Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] + relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] + As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] + cardiac + + + + AAO:0010210 + BILA:0000020 + BTO:0000562 + CALOHA:TS-0445 + EFO:0000815 + EHDAA2:0000738 + EHDAA:420 + EMAPA:16105 + EV:0100018 + FMA:7088 + GAID:174 + MA:0000072 + MAT:0000036 + MESH:D006321 + MIAA:0000036 + NCIT:C12727 + OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA + TAO:0000114 + UMLS:C0018787 + VHOG:0000276 + XAO:0000064 + ZFA:0000114 + galen:Heart + chambered heart + vertebrate heart + branchial heart + uberon + Herz@de + cardium + UBERON:0000948 + + + + + + + Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" http://dx.doi.org/10.1101/gad.1485706 + heart + + + + + + + + + + + MA + + + + + A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. + + + + + + + Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] + 2012-08-14 + TAO:0000114 + TAO + ZFIN:curator + + + + + Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] + 2012-06-20 + AAO:0010210 + AAO + AAO:BJB + + + + + relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] + 2012-06-20 + AAO:0010210 + AAO + + + + + As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] + 2012-09-17 + VHOG:0000276 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 + + + + + UMLS:C0018787 + ncithesaurus:Heart + + + + + chambered heart + + + + + + branchial heart + + + + + + Herz@de + BTO:0000562 + + + + + cardium + EMAPA:16105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. + requires review for applicability to invertebrate structures, e.g. synganglion + Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] + Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] + The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] + + + + + + + + AAO:0010478 + ABA:Brain + BAMS:Br + BAMS:Brain + BILA:0000135 + BTO:0000142 + CALOHA:TS-0095 + DHBA:10155 + EFO:0000302 + EHDAA2:0000183 + EHDAA:2641 + EHDAA:6485 + EMAPA:16894 + EV:0100164 + FBbt:00005095 + FMA:50801 + GAID:571 + HBA:4005 + MA:0000168 + MAT:0000098 + MBA:8 + MBA:997 + MESH:D001921 + MIAA:0000098 + NCIT:C12439 + OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA + PBA:3999 + TAO:0000008 + UMLS:C0006104 + UMLS:C1269537 + VHOG:0000157 + XAO:0000010 + ZFA:0000008 + galen:Brain + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 + uberon + encephalon + suprasegmental levels of nervous system + suprasegmental structures + synganglion + the brain + UBERON:0000955 + + + + + + + brain + + + + + + GO + + + + + + + + + + + FMA + + + + + + + + + + + Bgee:AN + + + + + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. + + + + + + + Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] + 2012-08-14 + TAO:0000008 + TAO + ZFIN:curator + + + + + Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] + 2012-06-20 + AAO:0010478 + AAO + AAO:BJB + + + + + The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) + + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000157 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 + + + + + UMLS:C0006104 + NIFSTD:birnlex_796 + + + + + UMLS:C0006104 + ncithesaurus:Brain + + + + + UMLS:C1269537 + NIFSTD:birnlex_796 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 + NIFSTD:birnlex_796 + + + + + encephalon + BTO:0000142 + + + + + suprasegmental levels of nervous system + NeuroNames:21 + + + + + suprasegmental structures + NeuroNames:21 + + + + + the brain + NeuroNames:21 + + + + + + + + + + + + + + + + + + + + + + + + + + + An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. + true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. + + cervical + + + + AEO:0000108 + BTO:0000420 + CALOHA:TS-2045 + EFO:0000967 + EHDAA2:0003108 + EMAPA:35587 + FMA:7155 + GAID:86 + MA:0000024 + MAT:0000297 + MESH:D009333 + MIAA:0000297 + NCIT:C13063 + OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA + UMLS:C0027530 + galen:Neck + uberon + collum + neck (volume) + UBERON:0000974 + + + + neck + + + + + + An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. + + + + + + + ISBN:9780674021839 + + + + + UMLS:C0027530 + ncithesaurus:Neck + + + + + collum + + + + + + + neck (volume) + FMA:7155 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. + Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] + Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] + articulation + joint + + + + AEO:0000182 + BTO:0001686 + CALOHA:TS-2023 + EFO:0000948 + EMAPA:35456 + FMA:7490 + GAID:102 + MA:0000319 + MAT:0000188 + MESH:D007596 + MIAA:0000188 + NCIT:C13044 + OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA + RETIRED_EHDAA2:0003182 + TAO:0000367 + UMLS:C0022417 + VHOG:0001276 + VSAO:0000101 + XAO:0000171 + ZFA:0001596 + galen:Joint + uberon + articular joint + joints + UBERON:0000982 + + + + + + skeletal joint + + + + + Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. + + + GO_REF:0000034 + VSAO:0000101 + + + + + Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] + 2012-08-14 + VSAO:0000101 + VSAO + PSPUB:0000170 + + + + + Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] + 2012-08-14 + TAO:0000367 + TAO + TAO:pem + + + + + articulation + VSAO:0000101 + + + + + joint + FMA:7490 + VSAO:0000101 + + + + + UMLS:C0022417 + ncithesaurus:Joint + + + + + articular joint + BTO:0001686 + + + + + joints + ZFA:0001596 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The outer epithelial layer of the skin that is superficial to the dermis. + A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] + The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] + relationship loss: subclass external integument structures (AAO:0000961)[AAO] + (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] + epidermal + Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). + epidermis + skin + + + + AAO:0000143 + BTO:0000404 + CALOHA:TS-0283 + EFO:0000954 + EMAPA:17528 + EV:0100153 + FMA:70596 + GAID:932 + MA:0000153 + MAT:0000154 + MESH:D004817 + MIAA:0000154 + NCIT:C12708 + TAO:0000105 + UMLS:C0014520 + VHOG:0000077 + XAO:0000028 + ZFA:0000105 + vertebrate epidermis + uberon + UBERON:0001003 + + + + + skin epidermis + + + + + The outer epithelial layer of the skin that is superficial to the dermis. + + ISBN10:0073040584 + + + + + A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] + 2012-08-14 + TAO:0000105 + TAO + ZFIN:curator + + + + + The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] + 2012-06-20 + AAO:0000143 + AAO + AAO:BJB + + + + + relationship loss: subclass external integument structures (AAO:0000961)[AAO] + 2012-06-20 + AAO:0000143 + AAO + + + + + (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] + 2012-09-17 + VHOG:0000077 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72 + + + + + UMLS:C0014520 + ncithesaurus:Epidermis + + + + + + + + + + + + + + + + + + + + + + + Functional system which consists of structures involved in respiration. + The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] + There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] + + + + AAO:0000541 + BTO:0000203 + CALOHA:TS-1319 + EFO:0000804 + EHDAA2:0001604 + EHDAA:2203 + EMAPA:16727 + EV:0100036 + FMA:7158 + GAID:78 + MA:0000327 + MAT:0000030 + MESH:D012137 + MIAA:0000030 + NCIT:C12779 + OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA + TAO:0000272 + UMLS:C0035237 + VHOG:0000202 + XAO:0000117 + ZFA:0000272 + apparatus respiratorius + respiratory system + uberon + Atmungssystem + apparatus respiratorius + systema respiratorium + UBERON:0001004 + + + + + + respiratory system + + + + + + Functional system which consists of structures involved in respiration. + + + + + + + The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] + 2012-06-20 + AAO:0000541 + AAO + AAO:BJB + + + + + There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] + 2012-09-17 + VHOG:0000202 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23 + + + + + UMLS:C0035237 + ncithesaurus:Respiratory_System + + + + + Atmungssystem + BTO:0000203 + + + + + apparatus respiratorius + BTO:0000203 + + + + + systema respiratorium + + + + + + + + + + + + + + + + + + + + + + + + An airway through which respiratory air passes in organisms. + This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends + airway + airways + + + FMA:265130 + uberon + UBERON:0001005 + + + respiratory airway + + + + + An airway through which respiratory air passes in organisms. + + + + + + airway + + + + + + airways + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. + An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] + digestive + many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class + + + AAO:0000129 + BILA:0000082 + BTO:0000058 + CALOHA:TS-1293 + EFO:0000793 + EV:0100056 + FBbt:00005055 + FMA:7152 + GAID:278 + MA:0002431 + MAT:0000018 + MESH:D004064 + MIAA:0000018 + TADS:0000170 + TAO:0000339 + WBbt:0005748 + XAO:0000125 + ZFA:0000339 + galen:DigestiveSystem + ncithesaurus:Digestive_System + uberon + alimentary system + alimentary tract + gastrointestinal system + gut + UBERON:0001007 + + + + + digestive system + + + + + Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. + + FB:gg + NLM:alimentary+system + + + + + An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] + 2012-06-20 + AAO:0000129 + AAO + AAO:BJB + + + + + many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class + MA + + + + + + + + + + + + + + + + + + + + + organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. + the cardiovascular system and the lymphatic system are parts of the circulatory system + + Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] + We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] + + AAO:0000959 + CALOHA:TS-2103 + FBbt:00005057 + OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA + VHOG:0001248 + uberon + systema cardiovasculare + UBERON:0001009 + + circulatory system + + + + + + organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. + + + + + + + WBbt coelomocyte currently classified as circulating cell + + + + + Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] + 2012-06-20 + AAO:0000959 + AAO + AAO:BJB + + + + + We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] + 2012-09-17 + VHOG:0001248 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 + + + + + systema cardiovasculare + + + + + + + + + + + + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue + Connective tissue in which fat is stored.[TAO] + Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] + relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] + Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] + adipose + In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. + in FMA this is dense irregular connective tissue + + + + AAO:0000001 + AEO:000020 + BTO:0001487 + CALOHA:TS-0013 + EFO:0000790 + EHDAA2:0003120 + EMAPA:35112 + EV:0100381 + FMA:20110 + GAID:920 + MA:0000009 + MAT:0000015 + MESH:D000273 + MIAA:0000015 + NCIT:C12472 + OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA + TAO:0002134 + UMLS:C0001527 + VHOG:0001284 + XAO:0003049 + ZFA:0005345 + galen:FattyTissue + fat + fat tissue + fatty tissue + uberon + adipose + bodyfat + fatty depot + UBERON:0001013 + + + + + adipose tissue + + + + + + FMA + + + + + Portion of connective tissue composed of adipocytes enmeshed in areolar tissue + + + MESH:A10.165.114 + MGI:cwg + MP:0000003 + + + + + Connective tissue in which fat is stored.[TAO] + 2012-08-14 + TAO:0002134 + TAO + ZFIN:curator + + + + + Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] + 2012-06-20 + AAO:0000001 + AAO + AAO:LAP + + + + + relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] + 2012-06-20 + AAO:0000001 + AAO + + + + + Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] + 2012-09-17 + VHOG:0001284 + VHOG + + DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007) + + + + + in FMA this is dense irregular connective tissue + FMA + + + + + UMLS:C0001527 + ncithesaurus:Adipose_Tissue + + + + + fat + MA:0000009 + + + + + adipose + BTO:0001487 + + + + + bodyfat + BTO:0001487 + + + + + + + + + + + + + + + + + + + + + A subdivision of the muscular system corresponding to a subdisivision of an organism. + In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. + + + AAO:0011066 + BTO:0000887 + EFO:0001949 + EMAPA:32715 + EMAPA:35577 + FMA:32558 + MA:0000165 + NCIT:C13056 + OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA + TAO:0000548 + UMLS:C0026845 + VSAO:0005038 + WBbt:0005737 + ZFA:0000548 + muscle group + muscles set + musculature + musculi + set of muscles + set of skeletal muscles + uberon + muscle system + muscles + musculature system + UBERON:0001015 + + + + + musculature + + + + + + A subdivision of the muscular system corresponding to a subdisivision of an organism. + + + + + + + In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. + FMA + + + + + UMLS:C0026845 + ncithesaurus:Muscle + + + + + musculi + FMA:32558 + FMA:TA + + + + + + set of muscles + FMA:32558 + + + + + set of skeletal muscles + MA:0000165 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. + A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] + Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] + Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] + nervous + neural + + + + + + AAO:0000324 + BILA:0000079 + BTO:0001484 + CALOHA:TS-1313 + EFO:0000802 + EHDAA2:0001246 + EHDAA:826 + EMAPA:16469 + EV:0100162 + FBbt:00005093 + FMA:7157 + GAID:466 + MA:0000016 + MAT:0000026 + MESH:D009420 + MIAA:0000026 + NCIT:C12755 + OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA + TAO:0000396 + UMLS:C0027763 + VHOG:0000402 + WBbt:0005735 + XAO:0000177 + ZFA:0000396 + neurological system + nerve net + uberon + systema nervosum + UBERON:0001016 + + + + + + nervous system + + + + + + + + + + + + + Bgee:AN + + + + + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. + + + ISBN:0-14-051288-8 + ISBN:3110148986 + NLM:nervous+system + WB:rynl + ZFIN:curator + + + + + A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] + 2012-08-14 + TAO:0000396 + TAO + ZFIN:curator + + + + + Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] + 2012-06-20 + AAO:0000324 + AAO + AAO:BJB + + + + + Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] + 2012-09-17 + VHOG:0000402 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 + + + + + UMLS:C0027763 + ncithesaurus:Nervous_System + + + + + neurological system + GO:0050877 + + + + + nerve net + + + + + + systema nervosum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. + Part of the nervous system which includes the brain and spinal cord.[AAO] + The brain and spinal cord. Kimmel et al, 1995.[TAO] + The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] + + + + + + AAO:0000090 + BAMS:CNS + BILA:0000080 + BTO:0000227 + CALOHA:TS-0150 + EFO:0000908 + EHDAA2:0000225 + EHDAA:828 + EMAPA:16470 + EMAPA:16754 + EV:0100163 + FBbt:00005094 + FMA:55675 + GAID:570 + MA:0000167 + MAT:0000457 + MESH:D002490 + NCIT:C12438 + OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA + TAO:0000012 + UMLS:C0927232 + VHOG:0000293 + XAO:0000215 + ZFA:0000012 + CNS + systema nervosum centrale + cerebrospinal axis + uberon + neuraxis + UBERON:0001017 + + + + + + central nervous system + + + + + + FBbt + cjm + + + + + + + + + + + Bgee:AN + + + + + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. + + + GO:0021551 + + + + + Part of the nervous system which includes the brain and spinal cord.[AAO] + 2012-06-20 + AAO:0000090 + AAO + AAO:BJB + + + + + The brain and spinal cord. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000012 + TAO + ZFIN:curator + + + + + The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). + NIFSTD:birnlex_1099 + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] + 2012-09-17 + VHOG:0000293 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) + + + + + UMLS:C0927232 + NIFSTD:birnlex_1099 + + + + + UMLS:C0927232 + ncithesaurus:Central_Nervous_System + + + + + CNS + + + + + + systema nervosum centrale + FMA:55675 + FMA:TA + + + + + + cerebrospinal axis + FMA:55675 + + + + + neuraxis + FMA:55675 + + + + + + + + + Anterior subdivision of a digestive tract. + Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure + The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. + The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] + + + + AAO:0011042 + BILA:0000085 + BTO:0000507 + EHDAA2:0000557 + EHDAA:520 + EMAPA:16548 + FBbt:00005379 + FMA:45616 + MA:0001526 + NCIT:C34180 + TGMA:0001014 + UMLS:C0231051 + VHOG:0000285 + XAO:0000232 + uberon + praeenteron + proenteron + UBERON:0001041 + + + + foregut + + + + + + Anterior subdivision of a digestive tract. + + + + + + The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. + MP:0000474 + + + + + The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000285 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 + + + + + UMLS:C0231051 + ncithesaurus:Foregut + + + + + praeenteron + + + + + + + proenteron + + + + + + + + + + + + + + + + + + + + + + + A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. + A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. + Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] + Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] + Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. + The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] + relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] + (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] + MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme + pharynx + + + + AAO:0000967 + BTO:0001049 + CALOHA:TS-0785 + EFO:0000836 + EHDAA2:0001458 + EHDAA:2947 + EMAPA:16706 + EV:0100065 + FMA:46688 + GAID:155 + MA:0000432 + MESH:A03.867 + NCIT:C12425 + OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA + TAO:0000056 + UMLS:C0031354 + VHOG:0000462 + XAO:0003227 + ZFA:0000056 + galen:Pharynx + uberon + UBERON:0001042 + + + + + Consider generalizing to deuterostome pharynx + chordate pharynx + + + + + + + + + + + EHDAA2 + + + + + A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. + + + + + + A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. + MESH:A03.867 + + + + + Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] + 2012-06-20 + AAO:0000967 + AAO + AAO:EJS + + + + + Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000056 + TAO + ZFIN:curator + + + + + Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. + ZFIN:ZDB-PUB-961014-576 + + + + + The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] + 2012-09-17 + VHOG:0000462 + VHOG + + + + + + relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] + 2012-06-20 + AAO:0000967 + AAO + + + + + relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] + 2012-06-20 + AAO:0000967 + AAO + + + + + (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] + 2012-09-17 + VHOG:0000462 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503 + + + + + MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme + MA + + + + + pharynx + FMA:46688 + + + + + + UMLS:C0031354 + ncithesaurus:Pharynx + + + + + + + + + + + + + + + Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. + + + AEO:0000171 + BTO:0001886 + EFO:0001652 + EHDAA2:0003171 + FBbt:00005495 + FMA:86589 + MAT:0000482 + NCIT:C34275 + UMLS:C0678727 + XAO:0003043 + uberon + bud + future organ + placode + primordia + rudiment + UBERON:0001048 + + + + primordium + + + + + + EHDAA2 + + + + + Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. + + BTO:0001886 + FB:DJS + FB:FBrf0089570 + + + + + UMLS:C0678727 + ncithesaurus:Primordium + + + + + placode + FBbt:00005495 + + + + + primordia + XAO:0003043 + + + + + + + + + + + + + + + + + + + In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. + Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] + The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium + + + + + AAO:0010617 + BTO:0001057 + CALOHA:TS-2371 + DHBA:10154 + EHDAA2:0001254 + EHDAA:2869 + EHDAA:908 + EMAPA:16164 + EMAPA:16757 + FMA:293882 + MAT:0000069 + MIAA:0000069 + NCIT:C34226 + TAO:0001135 + UMLS:C0231024 + VHOG:0000307 + XAO:0003204 + ZFA:0001135 + uberon + neural primordium + presumptive central nervous system + tubus neuralis + UBERON:0001049 + + + + neural tube + + + + + + + EHDAA2 + + + + + In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. + + + + + + Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] + 2012-06-20 + AAO:0010617 + AAO + AAO:JOR + + + + + The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] + 2012-09-17 + VHOG:0000307 + VHOG + + + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0000307 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium + GO:0021915 + + + + + UMLS:C0231024 + ncithesaurus:Neural_Tube + + + + + tubus neuralis + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + + AAO:0010841 + AEO:0000000 + BILA:0000000 + CARO:0000000 + EHDAA2:0002229 + FBbt:10000000 + FBbt_root:00000000 + FMA:62955 + HAO:0000000 + MA:0000001 + NCIT:C12219 + TAO:0100000 + TGMA:0001822 + UMLS:C1515976 + WBbt:0000100 + XAO:0000000 + ZFA:0100000 + uberon + UBERON:0001062 + + anatomical entity + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + + FMA:62955 + + + + + UMLS:C1515976 + ncithesaurus:Anatomic_Structure_System_or_Substance + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a back [Automatically generated definition]. + TODO - distinguish between entire skin of region and arbitrary zone of skin on region + + EMAPA:36392 + FMA:10462 + FMA:22985 + MA:0000498 + back skin + back zone of skin + skin, dorsal region + zone of skin of back + uberon + UBERON:0001068 + + skin of back + + + + + + MA + + + + + + + + + + + MA + + + + + A zone of skin that is part of a back [Automatically generated definition]. + OBOL:automatic + + + + + back zone of skin + OBOL:automatic + + + + + skin, dorsal region + + + + + + zone of skin of back + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. + + + + EMAPA:37117 + FMA:10665 + MA:0002052 + NCIT:C53005 + UMLS:C0226271 + superficial branch of transverse cervical artery + uberon + UBERON:0001071 + + The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] + superficial cervical artery + + + + + It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. + + + + + + EMAPA:37117 + MA:th + + + + + UMLS:C0226271 + ncithesaurus:Superficial_Cervical_Artery + + + + + superficial branch of transverse cervical artery + + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a head [Automatically generated definition]. + TODO - distinguish between entire skin of region and arbitrary zone of skin on region + + + FMA:12166 + FMA:24756 + MA:0000582 + NCIT:C52757 + UMLS:C0205029 + adult head zone of skin + head skin + head zone of skin + zone of skin of adult head + zone of skin of head + uberon + UBERON:0001084 + skin of head + + + + + A zone of skin that is part of a head [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C0205029 + ncithesaurus:Head_Skin + + + + + adult head zone of skin + OBOL:automatic + + + + + head zone of skin + OBOL:automatic + + + + + zone of skin of adult head + OBOL:automatic + + + + + zone of skin of head + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a trunk [Automatically generated definition]. + TODO - distinguish between entire skin of region and arbitrary zone of skin on region + + + EMAPA:37278 + FMA:12167 + FMA:23093 + MA:0000517 + NCIT:C12295 + UMLS:C0205031 + torso zone of skin + trunk skin + trunk zone of skin + zone of skin of torso + zone of skin of trunk + uberon + UBERON:0001085 + skin of trunk + + + + + A zone of skin that is part of a trunk [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37278 + MA:th + + + + + UMLS:C0205031 + ncithesaurus:Skin_of_the_Trunk + + + + + torso zone of skin + OBOL:automatic + + + + + trunk zone of skin + OBOL:automatic + + + + + zone of skin of torso + OBOL:automatic + + + + + zone of skin of trunk + OBOL:automatic + + + + + + + + + + + + + + + + Joint fluid is a transudate of plasma that is actively secreted by synovial cells. + Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] + It provides nutrients and lubrication for articular cartilage + The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma + + + BTO:0001339 + CALOHA:TS-0996 + ENVO:02000039 + FMA:12277 + GAID:265 + MA:0002544 + MESH:D013582 + NCIT:C33718 + TAO:0005154 + UMLS:C0039097 + ZFA:0005154 + galen:SynovialFluid + joint fluid + uberon + UBERON:0001090 + + + synovial fluid + + + + + + FMA + + + + + Joint fluid is a transudate of plasma that is actively secreted by synovial cells. + + + + + + Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] + 2012-08-14 + TAO:0005154 + TAO + ZFIN:curator + + + + + UMLS:C0039097 + ncithesaurus:Synovial_Fluid + + + + + joint fluid + + + + + + + + + + Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. + A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] + Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] + (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] + GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. + + + AAO:0010244 + AEO:0000141 + BTO:0001260 + CALOHA:TS-0943 + EFO:0000889 + EHDAA2:0003141 + EMAPA:32717 + EV:0100378 + FBbt:00003525 + FMA:14070 + GAID:167 + MA:0000166 + MAT:0000303 + MESH:D009130 + MIAA:0000303 + NCIT:C12437 + OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA + TAO:0005274 + UMLS:C1267092 + VHOG:0001246 + WBbt:0005781 + XAO:0000175 + ZFA:0005274 + galen:SmoothMuscle + galen:SmoothMuscleTissue + involuntary muscle + non-striated muscle + smooth muscle + textus muscularis nonstriatus + visceral muscle + visceral muscle tissue + uberon + textus muscularis levis; textus muscularis nonstriatus + UBERON:0001135 + + + + + smooth muscle tissue + + + + + + Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. + + GO:0006939 + + + + + A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] + 2012-08-14 + TAO:0005274 + TAO + ZFIN:curator + + + + + Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] + 2012-06-20 + AAO:0010244 + AAO + AAO:CAM + + + + + (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] + 2012-09-17 + VHOG:0001246 + VHOG + + DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) + + + + + UMLS:C1267092 + ncithesaurus:Smooth_Muscle_Tissue + + + + + textus muscularis nonstriatus + FMA:14070 + FMA:TA + + + + + + visceral muscle + + + + + + visceral muscle tissue + + + + + + textus muscularis levis; textus muscularis nonstriatus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). + + + + AEO:0000111 + BTO:0002422 + CALOHA:TS-1183 + EHDAA2_RETIRED:0003111 + EHDAA:2331 + EHDAA:2349 + EHDAA:295 + EHDAA:6073 + EHDAA:640 + EHDAA:646 + EMAPA:32856 + FMA:14074 + MA:0000565 + NCIT:C33105 + UMLS:C0086610 + uberon + UBERON:0001136 + + mesothelium + + + + + + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). + + FMA:14074 + + + + + UMLS:C0086610 + ncithesaurus:Mesothelium + + + + + + + + + A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. + dorsal + In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body + + + + BTO:0001713 + CALOHA:TS-2223 + EFO:0001405 + FMA:14181 + GAID:30 + MESH:A01.176 + NCIT:C13062 + OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA + UMLS:C0004600 + galen:Back + back + back of body proper + dorsal part of organism + uberon + UBERON:0001137 + + + dorsum + + + + + + A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. + + BSPO:0000063 + UBERONREF:0000006 + + + + + UMLS:C0004600 + ncithesaurus:Back + + + + + back + FMA:14181 + + + + + back of body proper + FMA:14181 + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a neck [Automatically generated definition]. + + + EMAPA:37277 + FMA:23021 + FMA:23022 + MA:0000590 + NCIT:C52756 + UMLS:C0205030 + neck (volume) zone of skin + neck skin + neck zone of skin + zone of skin of neck + zone of skin of neck (volume) + uberon + UBERON:0001417 + skin of neck + + + + + A zone of skin that is part of a neck [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37277 + MA:th + + + + + UMLS:C0205030 + ncithesaurus:Neck_Skin + + + + + neck (volume) zone of skin + OBOL:automatic + + + + + neck zone of skin + OBOL:automatic + + + + + zone of skin of neck + OBOL:automatic + + + + + zone of skin of neck (volume) + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a thorax [Automatically generated definition]. + + EMAPA:37765 + FMA:23028 + FMA:23029 + MA:0000564 + thoracic skin + thorax skin + thorax zone of skin + zone of skin of thorax + uberon + upper body skin + UBERON:0001418 + skin of thorax + + + + + A zone of skin that is part of a thorax [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37765 + MA:th + + + + + thorax zone of skin + OBOL:automatic + + + + + zone of skin of thorax + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] + System that provides physical support to the organism.[AAO] + By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] + skeletal + GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates + + AAO:0000566 + BTO:0001486 + CALOHA:TS-1320 + EFO:0000806 + EHDAA2:0003168 + EMAPA:35773 + FMA:23881 + MA:0000018 + NCIT:C12788 + OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA + TAO:0000434 + UMLS:C0037253 + VHOG:0001254 + VSAO:0000027 + XAO:0003060 + ZFA:0000434 + skeleton system + set of all bones and joints + uberon + Skelettsystem + UBERON:0001434 + + + + + skeletal system + https://github.com/obophenotype/uberon/wiki/The-skeletal-system + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. + + GO_REF:0000034 + VSAO:0000027 + + + + + Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] + 2012-08-14 + TAO:0000434 + TAO + TAO:wd + + + + + Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] + 2012-08-14 + VSAO:0000027 + VSAO + GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 + PSPUB:0000170 + + + + + System that provides physical support to the organism.[AAO] + 2012-06-20 + AAO:0000566 + AAO + AAO:LAP + + + + + By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] + 2012-09-17 + VHOG:0001254 + VHOG + + DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) + + + + + GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates + GO + + + + + UMLS:C0037253 + ncithesaurus:Skeletal_System + + + + + set of all bones and joints + + + + + + Skelettsystem + BTO:0001486 + + + + + + + + + + + + + + + + FMA:24218 + XAO:0000040 + head subdivision + uberon + head region + region of head + UBERON:0001444 + + subdivision of head + + + + + + + + + + + + + + + + + + + + + A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). + Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. + The area that extends from the median ocellus to the oral foramen[HAO]. + facial + The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) + + + + BTO:0003369 + CALOHA:TS-2216 + EMAPA:32763 + FMA:24728 + GAID:64 + HAO:0000316 + MA:0002473 + MESH:D005145 + NCIT:C13071 + OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA + UMLS:C0015450 + galen:Face + uberon + facia/facies + visage + UBERON:0001456 + + + face + + + + + + A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). + + + + + + Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. + FMA:24728 + + + + + The area that extends from the median ocellus to the oral foramen[HAO]. + + HAO:0000316 + NCBITaxon:7399 + + + + + The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) + vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf + + + + + UMLS:C0015450 + ncithesaurus:Face + + + + + facia/facies + + + + + + + visage + BTO:0003369 + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a lip [Automatically generated definition]. + + + EMAPA:37643 + FMA:24764 + MA:0001579 + NCIT:C12291 + UMLS:C0222101 + lip skin + lip zone of skin + zone of skin of lip + uberon + skin of lips + UBERON:0001458 + skin of lip + + + + + A zone of skin that is part of a lip [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37643 + MA:th + + + + + UMLS:C0222101 + ncithesaurus:Skin_of_the_Lip + + + + + lip zone of skin + OBOL:automatic + + + + + zone of skin of lip + OBOL:automatic + + + + + skin of lips + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. + check ncita + + + + EMAPA:37621 + FMA:34836 + GAID:263 + MA:0001519 + MESH:D017746 + NCIT:C32259 + NCIT:C84388 + UMLS:C0206207 + galen:JointCapsule + capsula articularis + fibrous capsule of joint + joint capsule + joint fibrous capsule + uberon + capsulae articulares + UBERON:0001484 + + + articular capsule + + + + + + + An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. + + + + + + check ncita + ncit + + + + + EMAPA:37621 + MA:th + + + + + UMLS:C0206207 + ncithesaurus:Joint_Capsule + + + + + capsula articularis + FMA:34836 + FMA:TA + + + + + + capsulae articulares + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tube extending from the mouth to the anus. + The alimentary or digestive tract, and associated organs.[TAO] + The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] + FMA also has a term 'gastrointestinal tract', but this includes the liver. + we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 + we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this + gut + + AAO:0010023 + BILA:0000083 + BTO:0000511 + BTO:0000545 + EHDAA2:0000726 + EHDAA:518 + EMAPA:16247 + FBbt:00003125 + FMA:45615 + MA:0000917 + NCIT:C34082 + OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA + TAO:0000112 + TGMA:0001819 + UMLS:C0017189 + VHOG:0000309 + WBbt:0005743 + ZFA:0000112 + galen:AlimentaryTract + digestive tube + enteric tract + alimentary canal + alimentary tract + uberon + digestive canal + gut tube + UBERON:0001555 + + + digestive tract + + + + + + + + + + + NCBIBook:NBK10107 + + + + + A tube extending from the mouth to the anus. + + + + + + + The alimentary or digestive tract, and associated organs.[TAO] + 2012-08-14 + TAO:0000112 + TAO + ZFIN:curator + + + + + The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000309 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 + + + + + FMA also has a term 'gastrointestinal tract', but this includes the liver. + FMA + + + + + we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 + MA + + + + + UMLS:C0017189 + ncithesaurus:Gastrointestinal_Tract + + + + + enteric tract + ZFA:0000112 + + + + + digestive canal + BTO:0000058 + + + + + + + + + + + + + + + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] + + + EHDAA2:0001036 + EMAPA:16738 + FMA:45662 + MA:0000435 + OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g + VHOG:0000382 + lower respiratory system + uberon + UBERON:0001558 + + + lower respiratory tract + + + + + + + The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] + + + + + + + + + + + + + + + + + + + + + + + One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. + Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] + + + + AAO:0010236 + EHDAA2:0000877 + EHDAA:5407 + EMAPA:17620 + FMA:4724 + MA:0002157 + NCIT:C32849 + OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA + RETIRED_EHDAA2:0000878 + UMLS:C0226550 + XAO:0000382 + galen:InternalJugularVein + internal jugular + internal jugular venous tree + uberon + vena jugularis interna + UBERON:0001586 + + internal jugular vein + + + + + + One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. + + + + + + Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] + 2012-06-20 + AAO:0010236 + AAO + AAO:BJB + + + + + UMLS:C0226550 + ncithesaurus:Internal_Jugular_Vein + + + + + internal jugular + EHDAA2:0000877 + + + + + vena jugularis interna + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. + Portion of tissue composed of contractile fibers.[TAO] + It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] + muscular + muscle + + AAO:0011066 + EMAPA:32715 + EMAPA:37474 + EV:0100146 + FMA:5022 + GAID:131 + MA:0000015 + OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA + TAO:0005145 + VHOG:0001245 + XAO:0000172 + ZFA:0005145 + galen:Muscle + uberon + UBERON:0001630 + + + + + muscle organ + + + + + Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. + GO:0007517 + + + + + Portion of tissue composed of contractile fibers.[TAO] + 2012-08-14 + TAO:0005145 + TAO + ZFIN:curator + + + + + It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] + 2012-09-17 + VHOG:0001245 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 + + + + + muscle + ZFA:0005145 + + + + + EMAPA:37474 + MA:th + + + + + + + + + + + + + + + An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. + Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. + Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + arterial + + + + + AAO:0010211 + AEO:0000208 + BTO:0000573 + CALOHA:TS-0054 + EFO:0000814 + EHDAA2:0000143 + EHDAA2:0003253 + EMAPA:35147 + EV:0100026 + FMA:50720 + GAID:468 + MA:0000064 + MAT:0000034 + MESH:D001158 + MIAA:0000034 + NCIT:C12372 + OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA + TAO:0000005 + UMLS:C0003842 + VHOG:0001251 + XAO:0000114 + ZFA:0000005 + galen:Artery + arterial subtree + arterial tree organ part + arteries + uberon + arterial system + arterial vessel + UBERON:0001637 + + + + + artery + + + + + An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. + AEO:JB + + + + + Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] + 2012-06-20 + AAO:0010211 + AAO + AAO:BJB + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0001251 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) + + + + + UMLS:C0003842 + ncithesaurus:Artery + + + + + arteries + TAO:0000005 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. + TODO - check with MA - vein vs venous blood vessel + Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + venous + + venous subtree + venous vessel + + + + AAO:0010212 + AEO:0000209 + BTO:0000234 + CALOHA:TS-1108 + EFO:0000816 + EHDAA2:0003254 + EMAPA:35906 + EV:0100031 + FMA:50723 + GAID:492 + MA:0000067 + MAT:0000037 + MESH:D014680 + MIAA:0000037 + NCIT:C12814 + OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA + TAO:0000082 + UMLS:C0042449 + VHOG:0001743 + XAO:0000115 + ZFA:0000082 + galen:Vein + venous tree organ part + uberon + vascular element + vena + venae + UBERON:0001638 + + + + + vein + + + + + + Any of the tubular branching vessels that carry blood from the capillaries toward the heart. + + + + + + Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] + 2012-06-20 + AAO:0010212 + AAO + AAO:BJB + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0001743 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) + + + + + UMLS:C0042449 + ncithesaurus:Vein + + + + + vascular element + EMAPA:th + + + + + vena + + + + + + + venae + VHOG:0001743 + + + + + + + + + + + + + + + + + + + + + + + + + + + The pulmonary artery that supplies the right lung. + TODO - add class 'pulmonary artery tree organ' + + + + EMAPA:37378 + FMA:50872 + MA:0002500 + NCIT:C33489 + UMLS:C0923924 + galen:RightPulmonaryArtery + right main pulmonary artery + right pulmonary arterial tree + uberon + arteria pulmonalis dextra + UBERON:0001651 + + right pulmonary artery + + + + + + + The pulmonary artery that supplies the right lung. + UBERON:cjm + + + + + EMAPA:37378 + MA:th + + + + + UMLS:C0923924 + ncithesaurus:Right_Pulmonary_Artery + + + + + arteria pulmonalis dextra + + + + + + + + + + + + + + + + + + + + + + + + + + + + The pulmonary artery that supplies the left lung. + TODO - add class 'pulmonary artery tree organ' + + + + EMAPA:37097 + FMA:50873 + MA:0002032 + NCIT:C32971 + UMLS:C0923925 + galen:LeftPulmonaryArtery + left main pulmonary artery + left pulmonary arterial tree + uberon + arteria pulmonalis sinistra + UBERON:0001652 + + left pulmonary artery + + + + + + + The pulmonary artery that supplies the left lung. + UBERON:cjm + + + + + EMAPA:37097 + MA:th + + + + + UMLS:C0923925 + ncithesaurus:Left_Pulmonary_Artery + + + + + arteria pulmonalis sinistra + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. + Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] + MA and NCITA also has 'anterior facial vein' + + + + AAO:0010513 + EMAPA:19220 + FMA:50874 + MA:0002115 + NCIT:C32579 + OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA + UMLS:C0226532 + face vein + vein of face + uberon + anterior facial vein + vena facialis anterior + UBERON:0001653 + + facial vein + + + + + + + + + + + + FMA + + + + + The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. + + + + + + Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] + 2012-06-20 + AAO:0010513 + AAO + AAO:BJB + + + + + MA and NCITA also has 'anterior facial vein' + MA + + + + + UMLS:C0226532 + ncithesaurus:Facial_Vein + + + + + face vein + OBOL:automatic + + + + + vein of face + OBOL:automatic + + + + + anterior facial vein + + + + + + + vena facialis anterior + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A anatomical space that is enclosed by a pharynx. + See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship + TOODO check + + AAO:0010435 + BSA:0000113 + BTO:0002097 + EMAPA:18381 + FMA:54935 + XAO:0000105 + lumen of pharynx + pharyngeal cavity + uberon + cavitas pharyngealis + cavitas pharyngis + UBERON:0001731 + cavity of pharynx + + + + + + + + + + + XAO + + + + + A anatomical space that is enclosed by a pharynx. + OBOL:automatic + + + + + cavitas pharyngealis + + + + + + cavitas pharyngis + BTO:0002097 + + + + + + + + + + + + + + + + + + + + + + + + + + + One of the two fleshy folds which surround the opening of the mouth. + Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] + labial + + + + + BTO:0001647 + CALOHA:TS-0558 + EMAPA:32839 + FMA:59816 + GAID:76 + MA:0000343 + MESH:D008046 + NCIT:C12220 + OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA + TAO:0007006 + UMLS:C0023759 + VHOG:0000677 + ZFA:0007006 + galen:Lip + uberon + labia oris + lips + UBERON:0001833 + + + + lip + + + + + + + + ZFA + + + + + + + + + + + BTO + FMA-implicit + VHOG + ZFA + + + + + + + + + + + cjm + + + + + One of the two fleshy folds which surround the opening of the mouth. + + + + + + + Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] + 2012-08-14 + TAO:0007006 + TAO + + ZFIN:curator + + + + + UMLS:C0023759 + ncithesaurus:Lip + + + + + labia oris + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. + developmental relationships need revised + Middle part of the brain composed of the optic tectum and penducular region.[AAO] + The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] + Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] + mesencephalic + part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships + MB + + + + + + AAO:0010149 + BAMS:MES + BM:MB + BTO:0000138 + CALOHA:TS-0630 + DHBA:10648 + DMBA:16649 + EFO:0000919 + EHDAA2:0001162 + EHDAA:3694 + EMAPA:16974 + EV:0100242 + FMA:61993 + HBA:9001 + MA:0000207 + MAT:0000106 + MBA:313 + MESH:D008636 + MIAA:0000106 + NCIT:C12510 + OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA + RETIRED_EHDAA2:0001104 + TAO:0000128 + UMLS:C0025462 + VHOG:0000069 + XAO:0000014 + ZFA:0000128 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 + uberon + mesencephalon + UBERON:0001891 + + + + + midbrain + + + + + + + + + + + + definitional + + + + + + + + + + + Bgee:AN + + + + + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. + GO:0030901 + + + + + Middle part of the brain composed of the optic tectum and penducular region.[AAO] + 2012-06-20 + AAO:0010149 + AAO + AAO:BJB + + + + + The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000128 + TAO + ZFIN:curator + + + + + Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] + 2012-09-17 + VHOG:0000069 + VHOG + + DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) + + + + + part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships + ABA + + + + + MB + + NIFSTD:NeuroNames_abbrevSource + + + + + + UMLS:C0025462 + NIFSTD:birnlex_1667 + + + + + UMLS:C0025462 + ncithesaurus:Mesencephalon + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 + NIFSTD:birnlex_1667 + + + + + mesencephalon + + + + + + + + + + + + + + + + + + + + + + + + + + + + A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. + A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] + Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] + In human embryonic development, the rhombomeres are present by day 29 + DHBA divides this into A(1-3),B(4),C(5-7) and D(8) + hindbrain segment + segment of hindbrain + + DHBA:12664 + EFO:0003617 + EMAPA:16148 + FMA:295666 + MAT:0000272 + MIAA:0000272 + RETIRED_EHDAA2:0000669 + TAO:0001064 + VHOG:0000672 + XAO:0004079 + ZFA:0001064 + hindbrain neuromere + hindbrain neuromeres + rhombomere + uberon + future rhombencephalon + rhombomeres + UBERON:0001892 + + + + + rhombomere + + + + + A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. + + ZFIN:curator + + + + + A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0001064 + TAO + ZFIN:curator + + + + + Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] + 2012-09-17 + VHOG:0000672 + VHOG + + DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002) + + + + + hindbrain segment + ZFA:0001064 + + + + + segment of hindbrain + ZFA:0001064 + + + + + hindbrain neuromeres + DHBA:HNM + + + + + + future rhombencephalon + MIAA:0000272 + + + + + rhombomeres + VHOG:0000672 + + + + + + + + + + + + + + + + + + + + + + + + Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. + Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] + The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] + Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] + bulb + medulla + + + + + + + AAO:0010486 + BAMS:MY + BAMS:Md + BM:Me + BTO:0000041 + CALOHA:TS-0607 + DMBA:17352 + EFO:0000924 + EHDAA2:0001088 + EHDAA:7588 + EMAPA:17550 + EV:0100275 + FMA:62004 + GAID:590 + MA:0000206 + MAT:0000111 + MAT:0000367 + MBA:354 + MESH:D008526 + MIAA:0000111 + NCIT:C12442 + OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA + OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA + TAO:0000545 + UMLS:C0025148 + UMLS:C1269575 + VHOG:0000181 + XAO:0003100 + ZFA:0000545 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 + bulbus + uberon + medulla oblonzata + metepencephalon + UBERON:0001896 + + + + + medulla oblongata + + + + + + Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. + + FMA:62004 + GO:0021550 + + + + + Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] + 2012-06-20 + AAO:0010486 + AAO + AAO:BJB + + + + + The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] + 2012-09-17 + VHOG:0000181 + VHOG + + + + + + Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] + 2012-09-17 + VHOG:0000181 + VHOG + + DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) + + + + + medulla + ABA:MY + + + + + UMLS:C0025148 + NIFSTD:birnlex_957 + + + + + UMLS:C0025148 + ncithesaurus:Medulla_Oblongata + + + + + UMLS:C1269575 + NIFSTD:birnlex_957 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 + NIFSTD:birnlex_957 + + + + + bulbus + FMA:62004 + FMA:TA + + + + + + medulla oblonzata + + + + + + + metepencephalon + FMA:62004 + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + + BTO:0004954 + CALOHA:TS-0112 + EMAPA:36292 + FMA:62114 + MA:0000711 + NCIT:C49215 + UMLS:C0006904 + blood capillary endothelium + capillary endothelium + capillary vessel endothelium + endothelium of blood capillary + endothelium of capillary vessel + uberon + UBERON:0001915 + endothelium of capillary + + + + + An endothelium that is part of a capillary [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C0006904 + ncithesaurus:Capillary_Endothelium + + + + + blood capillary endothelium + OBOL:automatic + + + + + capillary vessel endothelium + OBOL:automatic + + + + + endothelium of blood capillary + OBOL:automatic + + + + + endothelium of capillary vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of an arteriole [Automatically generated definition]. + + EMAPA:36286 + FMA:62115 + MA:0000705 + NCIT:C49192 + UMLS:C1179024 + arteriole endothelium + uberon + UBERON:0001916 + endothelium of arteriole + + + + + An endothelium that is part of an arteriole [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1179024 + ncithesaurus:Arteriole_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of an artery [Automatically generated definition]. + The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + + AAO:0011013 + BTO:0004757 + EMAPA:35148 + FMA:62116 + MA:0000707 + NCIT:C49194 + UMLS:C1179025 + VHOG:0001215 + XAO:0000357 + arterial endothelium + artery endothelium + uberon + UBERON:0001917 + endothelium of artery + + + + + An endothelium that is part of an artery [Automatically generated definition]. + OBOL:automatic + + + + + The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] + 2012-06-20 + AAO:0011013 + AAO + XAO:curator + + + + + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + 2012-09-17 + VHOG:0001215 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 + + + + + UMLS:C1179025 + ncithesaurus:Artery_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a venule [Automatically generated definition]. + + EMAPA:36290 + FMA:62117 + MA:0000716 + NCIT:C49319 + UMLS:C1179026 + venule endothelium + uberon + UBERON:0001918 + endothelium of venule + + + + + An endothelium that is part of a venule [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1179026 + ncithesaurus:Venule_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a vein [Automatically generated definition]. + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + + AAO:0011110 + BTO:0004756 + EMAPA:36288 + FMA:62118 + MA:0000712 + NCIT:C49317 + UMLS:C1179027 + VHOG:0001216 + XAO:0000358 + vein endothelium + venous endothelium + uberon + veinous endothelium + UBERON:0001919 + endothelium of vein + + + + + An endothelium that is part of a vein [Automatically generated definition]. + OBOL:automatic + + + + + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + 2012-09-17 + VHOG:0001216 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 + + + + + UMLS:C1179027 + ncithesaurus:Vein_Endothelium + + + + + veinous endothelium + VHOG:0001216 + + + + + + + + + + + + + + + + + + + + + + + + + + + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. + Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] + MTg + tegmentum + + + + + + BAMS:MTg + BTO:0003388 + DHBA:12195 + EFO:0000921 + EHDAA2:0004475 + EMAPA:18215 + FMA:62393 + HBA:9002 + MA:0000212 + MAT:0000452 + TAO:0000160 + UMLS:C0039441 + VHOG:0001367 + XAO:0004271 + ZFA:0000160 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 + tegmentum mesencephali + tegmentum of midbrain + uberon + mesencephalic tegmentum + tegmentum mesencephalicum + UBERON:0001943 + + + + + 'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum + midbrain tegmentum + + + + + + + + + + + + ZFA + + + + + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. + + FMA:FMA + ISBN10:0471888893 + + + + + Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] + 2012-09-17 + VHOG:0001367 + VHOG + + DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) + + + + + MTg + + NIFSTD:NeuroNames_abbrevSource + + + + + + tegmentum + ISBN10:0471888893 + + + + + UMLS:C0039441 + NIFSTD:birnlex_1200 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 + NIFSTD:birnlex_1200 + + + + + tegmentum mesencephali + + + + + + + mesencephalic tegmentum + VHOG:0001367 + + + + + tegmentum mesencephalicum + NeuroNames:491 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A multi-tissue structure that is part of a spinal cord. + + + + NCIT:C33969 + UMLS:C1268166 + uberon + spinal cord part + UBERON:0001948 + + regional part of spinal cord + + + + + A multi-tissue structure that is part of a spinal cord. + OBOL:automatic + + + + + UMLS:C1268166 + ncithesaurus:Spinal_Cord_Part + + + + + + + + + + + + + + + The liquid component of blood, in which erythrocytes are suspended. + plasma + portion of plasma + + + BTO:0000131 + CALOHA:TS-0800 + EFO:0001905 + EMAPA:35690 + FMA:62970 + GAID:1178 + MA:0002501 + MAT:0000052 + MESH:D010949 + MIAA:0000052 + NCIT:C13356 + OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw + UMLS:C0032105 + blood plasm + portion of blood plasma + uberon + UBERON:0001969 + + + + blood plasma + + + + + The liquid component of blood, in which erythrocytes are suspended. + + + + + + plasma + MA:0002501 + + + + + portion of plasma + FMA:62970 + + + + + UMLS:C0032105 + ncithesaurus:Plasma + + + + + + + + + + + + + + + + + + + + + One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins + Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] + + + + BTO:0002626 + EMAPA:35917 + FMA:63130 + MA:0000071 + MESH:A07.231.432.952 + NCIT:C12818 + TAO:0005315 + UMLS:C0042520 + VHOG:0001765 + ZFA:0005315 + uberon + venula + UBERON:0001979 + + + + venule + + + + + + One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins + MESH:A07.231.432.952 + MP:0004125 + + + + + Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] + 2012-08-14 + TAO:0005315 + TAO + ZFIN:curator + + + + + UMLS:C0042520 + ncithesaurus:Venule + + + + + venula + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The smallest division of the artery located between the muscular arteries and the capillaries[GO]. + Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] + Small, terminal branch of an artery which generally connects to capillaries.[AAO] + + + + AAO:0010253 + BTO:0001997 + EMAPA:35146 + FMA:63182 + MA:0000063 + MESH:D001160 + NCIT:C12672 + TAO:0002138 + UMLS:C0003847 + VHOG:0001763 + ZFA:0005255 + uberon + arteriola + UBERON:0001980 + + + + arteriole + + + + + + + MA + + + + + The smallest division of the artery located between the muscular arteries and the capillaries[GO]. + GO:0014830 + + + + + Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] + 2012-08-14 + TAO:0002138 + TAO + ZFIN:curator + + + + + Small, terminal branch of an artery which generally connects to capillaries.[AAO] + 2012-06-20 + AAO:0010253 + AAO + AAO:BJB + + + + + UMLS:C0003847 + ncithesaurus:Arteriole + + + + + arteriola + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A vessel through which blood circulates in the body. + consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus + Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] + Any of the vessels through which blood circulates in the body.[AAO] + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + annelids have blood vessels, but this class is not applicable to annelids. + FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX + vascular element + + + + + AAO:0011004 + AEO:0000207 + BTO:0001102 + CALOHA:TS-0080 + EFO:0000817 + EHDAA2:0003252 + EHDAA:240 + EMAPA:32743 + EMAPA:35993 + FMA:50722 + FMA:63183 + GAID:169 + MA:0000060 + MAT:0000393 + MESH:D001808 + NCIT:C12679 + OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA + TAO:0002137 + UMLS:C0005847 + VHOG:0001250 + XAO:0001011 + ZFA:0005314 + region of vascular tree organ + vascular tree organ region + uberon + vas sanguineum + UBERON:0001981 + + + + + blood vessel + + + + + + + + + + + + EHDAA2 + + + + + + + + + + + GO:0072360 + + + + + A vessel through which blood circulates in the body. + + BTO:0001102 + + + + + Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] + 2012-09-17 + VHOG:0001250 + VHOG + + + + + + Any of the vessels through which blood circulates in the body.[AAO] + 2012-06-20 + AAO:0011004 + AAO + AAO:EJS + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0001250 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) + + + + + FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX + FMA + + + + + vascular element + EMAPA:35993 + + + + + UMLS:C0005847 + ncithesaurus:Blood_Vessel + + + + + region of vascular tree organ + FMA:50722 + + + + + vascular tree organ region + FMA:50722 + + + + + vas sanguineum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the smallest blood vessels connecting arterioles with venules. + not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element + Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs + + + + AAO:0010252 + BTO:0002045 + CALOHA:TS-2006 + EFO:0001906 + EMAPA:35198 + EV:0100035 + FMA:63194 + MA:0000065 + MESH:A07.231.432.410 + NCIT:C12685 + OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA + TAO:0005250 + UMLS:C0935624 + VHOG:0001253 + XAO:0000116 + ZFA:0005250 + blood capillary + capillary vessel + uberon + UBERON:0001982 + + + + + capillary + + + + + + + FMA + MA + XAO + + + + + + ZFA + + + + + Any of the smallest blood vessels connecting arterioles with venules. + + + ISBN10:0073040584 + + + + + Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] + 2012-06-20 + AAO:0010252 + AAO + AAO:BJB + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0001253 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) + + + + + UMLS:C0935624 + ncithesaurus:Capillary + + + + + + + + + + A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] + endothelial + + + BTO:0000393 + CALOHA:TS-0278 + EFO:0002548 + FMA:63916 + GAID:520 + MESH:D004727 + NCIT:C12481 + UMLS:C0014257 + galen:Endothelium + uberon + UBERON:0001986 + + + The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) + endothelium + + + + + + + FMA-text-def + + + + + A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] + + FMA:63916 + MESH:A10.272.491 + + + + + UMLS:C0014257 + ncithesaurus:Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. + Major artery which supplies blood to the lungs.[AAO] + One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] + On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] + In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP] + + + + AAO:0010221 + BTO:0000778 + CALOHA:TS-0839 + EFO:0001399 + EHDAA2:0001575 + EHDAA:4351 + EMAPA:17008 + FMA:66326 + GAID:505 + MA:0002031 + MESH:D011651 + NCIT:C12774 + OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA + UMLS:C0034052 + VHOG:0000982 + XAO:0004162 + galen:PulmonaryArtery + pulmonary arterial tree + pulmonary arterial tree organ part + uberon + arteria pulmonalis + pulmonary arterial subtree + truncus pulmonalis + UBERON:0002012 + + + + pulmonary artery + + + + + + + + + + + + Wikipedia + + + + + + + + + + + EHDAA2 + XAO + + + + + + + + + + + EHDAA2 + + + + + An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. + + + + + + + Major artery which supplies blood to the lungs.[AAO] + 2012-06-20 + AAO:0010221 + AAO + AAO:BJB + + + + + One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] + 2012-09-17 + VHOG:0000982 + VHOG + + + + + + + On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] + 2012-09-17 + VHOG:0000982 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 + + + + + UMLS:C0034052 + ncithesaurus:Pulmonary_Artery + + + + + pulmonary arterial tree + FMA:66326 + + + + + pulmonary arterial tree organ part + FMA:66326 + + + + + arteria pulmonalis + + + + + + + pulmonary arterial subtree + FMA:66326 + + + + + truncus pulmonalis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. + Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] + One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] + the veins that return oxygenated blood from the lungs to the left atrium of the heart + On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] + + + + + AAO:0010521 + BTO:0001799 + CALOHA:TS-0840 + EHDAA2:0001579 + EHDAA:2629 + EMAPA:18645 + FMA:66643 + GAID:543 + MA:0002206 + MESH:D011667 + NCIT:C12776 + UMLS:C0034090 + VHOG:0001133 + XAO:0000394 + galen:PulmonaryVein + pulmonary venous tree organ part + uberon + venae pulmonales + UBERON:0002016 + + + pulmonary vein + + + + + + Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. + GO:0060577 + + + + + Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] + 2012-06-20 + AAO:0010521 + AAO + AAO:BJB + + + + + One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] + 2012-09-17 + VHOG:0001133 + VHOG + + + + + + + the veins that return oxygenated blood from the lungs to the left atrium of the heart + MP:0002726,MGI:cwg + + + + + On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] + 2012-09-17 + VHOG:0001133 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 + + + + + UMLS:C0034090 + ncithesaurus:Pulmonary_Vein + + + + + venae pulmonales + + + + + + + + + + + A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. + Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] + + + + AEO:0001012 + EHDAA2:0003136 + EHDAA2_RETIRED:0004658 + EMAPA:37596 + FMA:67242 + HBA:4006 + MA:0001112 + NCIT:C32695 + OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA + TAO:0002197 + UMLS:C0018220 + VHOG:0001768 + ZFA:0001681 + gray matter + gray matter of neuraxis + grey matter + grey matter of neuraxis + grey substance + neuronal grey matter + substantia grisea + uberon + gray mater + grisea + UBERON:0002020 + + + + gray matter + + + + + + A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. + + + + + + + Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] + 2012-08-14 + TAO:0002197 + TAO + ZFIN:curator + + + + + EMAPA:37596 + MA:th + + + + + UMLS:C0018220 + ncithesaurus:Gray_Matter + + + + + gray matter of neuraxis + FMA:67242 + + + + + neuronal grey matter + AEO:0001012 + + + + + substantia grisea + FMA:67242 + FMA:TA + + + + + + gray mater + ZFA:0001681 + + + + + grisea + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. + + Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] + The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] + relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] + Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] + rhombencephalic + in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps + + + + + + + AAO:0010150 + BAMS:HB + BTO:0000672 + CALOHA:TS-0457 + DHBA:10653 + DMBA:16808 + EFO:0000923 + EHDAA2:0000746 + EHDAA:3514 + EHDAA:6487 + EMAPA:16916 + FMA:67687 + MA:0000195 + MAT:0000107 + MBA:1065 + MESH:D012249 + MIAA:0000107 + NCIT:C40336 + TAO:0000029 + UMLS:C0035507 + UMLS:C1522180 + VHOG:0000070 + XAO:0000015 + ZFA:0000029 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 + uberon + rhombencephalon + UBERON:0002028 + + + + + hindbrain + + + + + + + + + + + + + + + + + modified-source-relation + ABA + + + + + + + + + + + Bgee:AN + + + + + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. + + ZFA:0000029 + ZFIN:curator + + + + + + + + + + + Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] + 2012-06-20 + AAO:0010150 + AAO + AAO:BJB + + + + + The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000029 + TAO + ZFIN:curator + + + + + relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] + 2012-08-14 + TAO:0000029 + TAO + + + + + Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] + 2012-09-17 + VHOG:0000070 + VHOG + + DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) + + + + + in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps + MA + + + + + UMLS:C0035507 + NIFSTD:birnlex_942 + + + + + UMLS:C0035507 + ncithesaurus:Hind-Brain + + + + + UMLS:C1522180 + NIFSTD:birnlex_942 + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 + NIFSTD:birnlex_942 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A systemic artery that supplies the lung with with oxygenated blood. + + + + EMAPA:18608 + FMA:68109 + GAID:477 + MA:0001923 + MESH:D001981 + NCIT:C32230 + OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg + UMLS:C0006257 + bronchial arterial tree + uberon + arteriae bronchiales + rami bronchiales partis thoracicae aortae + UBERON:0002040 + + Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. + bronchial artery + + + + + + A systemic artery that supplies the lung with with oxygenated blood. + + UBERON:cjm + + + + + UMLS:C0006257 + ncithesaurus:Bronchial_Artery + + + + + arteriae bronchiales + + + + + + + rami bronchiales partis thoracicae aortae + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Respiration organ that develops as an oupocketing of the esophagus. + Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] + pulmonary + respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi + + + + AAO:0000275 + AAO:0010567 + BTO:0000763 + CALOHA:TS-0568 + EFO:0000934 + EHDAA2:0001042 + EHDAA:1554 + EHDAA:2205 + EMAPA:16728 + EV:0100042 + FMA:7195 + GAID:345 + MA:0000415 + MAT:0000135 + MESH:D008168 + MIAA:0000135 + NCIT:C12468 + OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA + UMLS:C0024109 + VHOG:0000310 + XAO:0000119 + galen:Lung + pulmo + uberon + UBERON:0002048 + + + + + + Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] + lung + + + + + + + + + + + + some species only have a single lung + + + + + Respiration organ that develops as an oupocketing of the esophagus. + + + + + + Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] + 2012-06-20 + AAO:0010567 + AAO + AAO:SBH + + + + + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000310 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) + + + + + UMLS:C0024109 + ncithesaurus:Lung + + + + + pulmo + + + + + + + + + + + + + + + + + + + + + + + + + + + + An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. + see also: vascular system. Consider merging? + vascular + BTO:0003718 + FMA:69050 + TAO:0005249 + ZFA:0005249 + vascular network + uberon + UBERON:0002049 + + + + vasculature + + + + + + + FMA + + + + + An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. + ZFA:0005249 + + + + + vascular network + FMA:69050 + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that is part of an embryo. + Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] + Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] + Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] + in FMA embryo is_a embryonic structure + + + AAO:0000138 + BILA:0000034 + BTO:0000174 + CALOHA:TS-2110 + EFO:0000461 + FBbt:00004208 + FMA:69067 + GAID:407 + MESH:D004628 + NCIT:C13229 + RETIRED_EHDAA2:0003169 + TAO:0001105 + UMLS:C0013948 + VSAO:0000178 + XAO:0003042 + ZFA:0001105 + developing embryonic structure + embryonic anatomical structure + uberon + developing structure + embryonale Struktur + embryonic structures + UBERON:0002050 + + + + embryonic structure + + + + + Anatomical structure that is part of an embryo. + BTO:0000174 + ZFIN:curator + + + + + Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] + 2012-06-20 + AAO:0000138 + AAO + AAO:BJB + + + + + Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] + 2012-08-14 + TAO:0001105 + TAO + ZFIN:curator + + + + + Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] + 2012-08-14 + VSAO:0000178 + VSAO + ZFIN:curator + + + + + in FMA embryo is_a embryonic structure + FMA + + + + + UMLS:C0013948 + ncithesaurus:Embryonic_Structure + + + + + developing embryonic structure + FBbt:00004208 + + + + + embryonic anatomical structure + RETIRED_EHDAA2:0003169 + + + + + embryonale Struktur + BTO:0000174 + + + + + embryonic structures + ZFA:0001105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. + assume spelling error for ncit + + + + EHDAA2:0004143 + EMAPA:35887 + FMA:70301 + GAID:554 + MA:0000103 + MESH:D014338 + NCIT:C34317 + OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw + UMLS:C1519589 + uberon + UBERON:0002061 + + truncus arteriosus + + + + + + EHDAA2 + + + + + + FMA + + + + + + + + + + + MA + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. + + + + + + assume spelling error for ncit + ncit + + + + + UMLS:C1519589 + ncithesaurus:Trancus_Arteriosus + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. + Consider adding a layer-of-skin grouping class for all skin layers + A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] + When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] + dermal + + + + AAO:0000128 + BTO:0000294 + CALOHA:TS-2076 + EFO:0000953 + EMAPA:17527 + EV:0100154 + FMA:70323 + GAID:1321 + MA:0000152 + MAT:0000153 + MESH:D020405 + MIAA:0000153 + NCIT:C12701 + TAO:0001119 + UMLS:C0011646 + VHOG:0000108 + XAO:0000217 + ZFA:0001119 + vertebrate dermis + uberon + corium + cutis + UBERON:0002067 + + + + + dermis + + + + + + + + + + + + FMA + + + + + + + + + + + definitional + + + + + The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. + + ZFIN:curator + + + + + A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] + 2012-08-14 + TAO:0001119 + TAO + ZFIN:curator + + + + + When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] + 2012-09-17 + VHOG:0000108 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 + + + + + UMLS:C0011646 + ncithesaurus:Dermis + + + + + corium + + + + + + + corium + BTO:0000294 + + + + + cutis + BTO:0000294 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. + A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] + A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. + hypodermal + subcutaneous + subcutaneus + BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. + + + BTO:0001314 + CALOHA:TS-2366 + EMAPA:37505 + FMA:70544 + NCIT:C33645 + TAO:0001136 + UMLS:C0278403 + ZFA:0001136 + hypoderm + vertebrate hypodermis + uberon + sub-tegumental tissue + subcutaneous tissue + subcutis + subtegumental tissue + superficial fascia + tela subcutanea + UBERON:0002072 + + + + hypodermis + + + + + + + + + + + + ZFA + + + + + + + + + + + FMA-modified + + + + + Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. + + + + + + A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] + 2012-08-14 + TAO:0001136 + TAO + ZFIN:curator + + + + + A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. + FMA:70544 + + + + + BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. + BTO + + + + + EMAPA:37505 + MA:th + + + + + UMLS:C0278403 + ncithesaurus:Subcutis + + + + + sub-tegumental tissue + BTO:0004525 + + + + + subcutaneous tissue + + + + + + subtegumental tissue + BTO:0004525 + + + + + superficial fascia + + + + + + tela subcutanea + + + + + + + + + + + + + + + + + + + + + + + + + + + + An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. + An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] + general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. + + + + AAO:0010386 + BTO:0001491 + EHDAA:512 + EMAPA:16245 + FMA:7085 + MA:0000019 + MESH:D014781 + NCIT:C28287 + RETIRED_EHDAA2:0002201 + UMLS:C0042779 + XAO:0003034 + visceral organ + visceral organ system + uberon + Organsystem@de + splanchnic tissue + viscera + visceral tissue + UBERON:0002075 + + + + + viscus + + + + + An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. + + + BTO:0001491 + + + + + An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] + 2012-06-20 + AAO:0010386 + AAO + BTO:0001491 + + + + + general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. + FMA + + + + + UMLS:C0042779 + ncithesaurus:Viscera + + + + + visceral organ + RETIRED_EHDAA2:0002201 + + + + + visceral organ system + MA:0000019 + + + + + Organsystem@de + BTO:0001491 + + + + + splanchnic tissue + BTO:0001491 + + + + + visceral tissue + BTO:0001491 + + + + + + + + + + + + + + + + + + + + + + + + + + + The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. + Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] + The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] + The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] + The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] + axial skeleton + AAO:0000034 + EFO:0000942 + EHDAA2:0000161 + EHDAA:5049 + EMAPA:17214 + EMAPA:37721 + FMA:71221 + MA:0002986 + MAT:0000148 + MIAA:0000148 + TAO:0000317 + VHOG:0000317 + VSAO:0000093 + XAO:0003073 + ZFA:0000317 + post-cranial axial skeleton + uberon + UBERON:0002090 + + + + + previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. + postcranial axial skeleton + http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + + + + + The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. + + + ZFA:0000317 + + + + + Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] + 2012-08-14 + VSAO:0000093 + VSAO + PSPUB:0000170 + + + + + The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] + 2012-06-20 + AAO:0000034 + AAO + AAO:LAP + + + + + The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] + 2012-08-14 + TAO:0000317 + TAO + ZFIN:curator + + + + + The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] + 2012-09-17 + VHOG:0000317 + VHOG + + DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) + + + + + axial skeleton + + FMA:71221 + + + + + EMAPA:37721 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + + + The organ covering the body that consists of the dermis and epidermis. + consider 'integumentary system' for invertebrates + MA uses the term skin to refer to what is called here: zone of skin + + + + BTO:0001253 + CALOHA:TS-0934 + EFO:0000962 + EHDAA2:0001844 + EMAPA:17525 + FMA:7163 + MESH:D012867 + MFMO:0000099 + NCIT:C12470 + OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA + UMLS:C1123023 + XAO:0000023 + galen:Skin + entire skin + skin organ + uberon + entire integument + integument + integumental organ + pelt + skin + UBERON:0002097 + + + + + skin of body + + + + + + + + + + + + Wikipathways:WP2062 + + + + + The organ covering the body that consists of the dermis and epidermis. + UBERON:cjm + + + + + MA uses the term skin to refer to what is called here: zone of skin + FMA + + + + + UMLS:C1123023 + ncithesaurus:Skin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. + 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' + in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this + + + EMAPA:35400 + FMA:7180 + GAID:562 + MA:0000083 + MESH:D006346 + NCIT:C49485 + UMLS:C0018819 + XAO:0004141 + cardiac septa + heart septa + heart septum + septum of heart + uberon + spiral septa + UBERON:0002099 + + + cardiac septum + + + + + The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. + MESH:A07.541.459 + + + + + in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this + GO + + + + + UMLS:C0018819 + ncithesaurus:Heart_Septum + + + + + cardiac septa + + + + + + heart septa + + + + + + spiral septa + XAO:0004141 + + + + + + + + + + + + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + + + + AAO:0010339 + BILA:0000116 + BTO:0001493 + CALOHA:TS-1071 + EFO:0000966 + EMAPA:31857 + FMA:7181 + MA:0000004 + MAT:0000296 + MIAA:0000296 + NCIT:C33816 + OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA + TAO:0001115 + UMLS:C0460005 + XAO:0000054 + XAO:0003025 + ZFA:0001115 + galen:Trunk + thoracolumbar region + torso + trunk region + uberon + Rumpf + UBERON:0002100 + + + + + trunk + + + + + Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. + + TAO:0001115 + UBERONREF:0000006 + + + + + Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] + 2012-06-20 + AAO:0010339 + AAO + AAO:BJB + + + + + Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] + 2012-08-14 + TAO:0001115 + TAO + ZFIN:curator + + + + + UMLS:C0460005 + ncithesaurus:Trunk + + + + + trunk region + XAO:0000054 + + + + + Rumpf + BTO:0001493 + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. + + BTO:0000087 + CALOHA:TS-1198 + EMAPA:36285 + FMA:72024 + MA:0000708 + NCIT:C49195 + UMLS:C1706851 + arterial smooth muscle + artery smooth muscle + artery smooth muscle tissue + smooth muscle of artery + uberon + arterial smooth muscle cell + UBERON:0002111 + artery smooth muscle tissue + + + + + A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1706851 + ncithesaurus:Artery_Smooth_Muscle_Tissue + + + + + arterial smooth muscle + BTO:0000087 + + + + + smooth muscle of artery + FMA:72024 + + + + + arterial smooth muscle cell + BTO:0000087 + + + + + + + + + + + + + + + + + + + + + + + + + + + + The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. + Layer that lines the lumen of the heart.[TAO] + Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] + Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. + UBERON:0006225 + + + + AAO:0010408 + BTO:0000387 + CALOHA:TS-2075 + EFO:0000821 + EHDAA2:0004153 + EMAPA:17868 + EMAPA:32686 + EV:0100021 + FMA:7280 + GAID:550 + MA:0000076 + MAT:0000455 + MESH:D004699 + NCIT:C13004 + OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw + TAO:0001320 + UMLS:C0014124 + VHOG:0000084 + XAO:0000066 + ZFA:0001320 + galen:Endocardium + endocardial lining + endocardial tissue + heart endocardium + uberon + heart endocardial tissue + UBERON:0002165 + + + + + fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 + endocardium + + + + + + + + + + + + Bgee:AN + + + + + The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. + GO:0003157 + + + + + Layer that lines the lumen of the heart.[TAO] + 2012-08-14 + TAO:0001320 + TAO + ZFIN:curator + + + + + Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] + 2012-06-20 + AAO:0010408 + AAO + AAO:BJB + + + + + Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. + FMA:7280 + + + + + UMLS:C0014124 + ncithesaurus:Endocardium + + + + + endocardial lining + EMAPA:32686 + + + + + endocardial tissue + EMAPA:17868 + + + + + heart endocardial tissue + VHOG:0000084 + + + + + + + + + + + + + + + + + + + + + + + + + + Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + EHDAA2:0001730 + EHDAA:4969 + EMAPA:17661 + FMA:7309 + MA:0000426 + NCIT:C33483 + OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA + UMLS:C0225706 + VHOG:0000301 + uberon + UBERON:0002167 + + + right lung + + + + + + Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] + + FMA:FMA + + + + + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] + 2012-09-17 + VHOG:0000301 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 + + + + + UMLS:C0225706 + ncithesaurus:Right_Lung + + + + + + + + + + + + + + + + + + + + + + + + + + Lung which consists of the left upper lobe and left lower lobe.[FMA] + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] + https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern + + + + EHDAA2:0000943 + EHDAA:4947 + EMAPA:17653 + FMA:7310 + MA:0000425 + NCIT:C32967 + OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA + UMLS:C0225730 + VHOG:0000618 + uberon + UBERON:0002168 + + + left lung + + + + + + Lung which consists of the left upper lobe and left lower lobe.[FMA] + + FMA:FMA + + + + + Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] + 2012-09-17 + VHOG:0000618 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 + + + + + UMLS:C0225730 + ncithesaurus:Left_Lung + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of adipose tissue that is part of the hypodermis, beneath the dermis. + the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] + UBERON:0008875 + panniculus adiposus + BTO:0004042 + EMAPA:35829 + FMA:74315 + MA:0000473 + fatty layer of subcutaneous tissue + hypodermis fat layer + panniculus adiposus (tela subcutanea) + panniculus adiposus telae subcutaneae + subcutaneous fat layer + uberon + fatty layer of superficial fascia + subcutaneous fat + UBERON:0002190 + + subcutaneous adipose tissue + + + + + A portion of adipose tissue that is part of the hypodermis, beneath the dermis. + + + + + + the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] + MP:0011156 + + + + + panniculus adiposus + MP:0011156 + + + + + fatty layer of subcutaneous tissue + FMA:74315 + + + + + hypodermis fat layer + MP:0011156 + + + + + panniculus adiposus (tela subcutanea) + FMA:74315 + FMA:TA + + + + + + panniculus adiposus telae subcutaneae + FMA:74315 + FMA:TA + + + + + + subcutaneous fat layer + MP:0011156 + + + + + fatty layer of superficial fascia + FMA:74315 + + + + + subcutaneous fat + BTO:0004042 + + + + + + + + + Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. + CALOHA:TS-2018 + EHDAA2:0004615 + EMAPA:18765 + FMA:74562 + MA:0000013 + hematolymphoid system + lymphomyeloid complex + uberon + haemolymphoid system + UBERON:0002193 + hemolymphoid system + + + + + + MA + + + + + Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The dermis, epidermis and hypodermis. + in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. + Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] + Surface structure that is the outer protective covering of the body.[VSAO] + The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] + integumental + integumentary + + AAO:0000239 + BTO:0000634 + EMAPA:37504 + FMA:74657 + TAO:0000368 + VSAO:0000029 + ZFA:0000368 + galen:Integument + dermis plus epidermis plus hypodermis + integumentum commune + skin and subcutaneous tissue + skin plus hypodermis + the integument + uberon + Hautsystem@de + dermal system + dermoid system + skin + tegument + vertebrate integument + UBERON:0002199 + + + + integument + + + + + + FMA + + + + + + + + + + + FMA + + + + + The dermis, epidermis and hypodermis. + + + + + + Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] + 2012-06-20 + AAO:0000239 + AAO + AAO:EJS + + + + + Surface structure that is the outer protective covering of the body.[VSAO] + 2012-08-14 + VSAO:0000029 + VSAO + PSPUB:0000170 + + + + + The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] + 2012-08-14 + TAO:0000368 + TAO + ZFIN:curator + + + + + EMAPA:37504 + MA:th + + + + + integumentum commune + FMA:74657 + FMA:TA + + + + + + the integument + FMA:74657 + + + + + Hautsystem@de + BTO:0000634 + + + + + dermal system + BTO:0000634 + + + + + dermoid system + BTO:0000634 + + + + + tegument + BTO:0000634 + + + + + + + + + + + + + + + + + + + + + + + + + + Vasculature that is part of a head [Automatically generated definition]. + EFO:0003656 + FMA:74710 + TAO:0001267 + XAO:0004152 + ZFA:0001267 + adult head vascular network + adult head vasculature + cranial vasculature + head vascular network + vascular network of adult head + vascular network of head + vasculature of adult head + uberon + head vasculature + UBERON:0002200 + + + vasculature of head + + + + + Vasculature that is part of a head [Automatically generated definition]. + OBOL:automatic + + + + + adult head vascular network + OBOL:automatic + + + + + adult head vasculature + OBOL:automatic + + + + + head vascular network + OBOL:automatic + + + + + vascular network of adult head + OBOL:automatic + + + + + vascular network of head + OBOL:automatic + + + + + vasculature of adult head + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a trunk [Automatically generated definition]. + FMA:74712 + TAO:0005024 + ZFA:0005024 + torso vascular network + torso vasculature + trunk vascular network + trunk vasculature + vascular network of torso + vascular network of trunk + vasculature of torso + uberon + UBERON:0002201 + + vasculature of trunk + + + + + A vasculature that is part of a trunk [Automatically generated definition]. + OBOL:automatic + + + + + torso vascular network + OBOL:automatic + + + + + torso vasculature + OBOL:automatic + + + + + trunk vascular network + OBOL:automatic + + + + + vascular network of torso + OBOL:automatic + + + + + vascular network of trunk + OBOL:automatic + + + + + vasculature of torso + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of the muscular and skeletal systems. + Anatomical system that provides locomotion and physical support to the organism.[AAO] + There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] + musculoskeletal + + + + + AAO:0010546 + CALOHA:TS-1311 + EMAPA:32714 + EV:0100139 + FMA:7482 + GAID:98 + MA:0002418 + MESH:D009141 + NCIT:C12754 + OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g + UMLS:C0026860 + VHOG:0001275 + VSAO:0000031 + XAO:0000168 + musculo-skeletal system + uberon + UBERON:0002204 + + musculoskeletal system + + + + + + + + + + + check ctenophore + + + + + Anatomical system that consists of the muscular and skeletal systems. + + VSAO:0000031 + VSAO:curator + + + + + Anatomical system that provides locomotion and physical support to the organism.[AAO] + 2012-06-20 + AAO:0010546 + AAO + AAO:EJS + + + + + There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] + 2012-09-17 + VHOG:0001275 + VHOG + + DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) + + + + + UMLS:C0026860 + ncithesaurus:Musculoskeletal_System + + + + + + + + + + + + + + + + + + + + + + + + + + + Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] + Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] + + + AEO:0000183 + CALOHA:TS-2138 + EHDAA2:0003183 + FMA:7501 + MA:0000322 + NCIT:C32461 + OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA + TAO:0005153 + ZFA:0005153 + galen:SynovialJoint + articulatio synoviale + diarthroses + diarthrosis + diarthrosis joint + uberon + diarthrodial joints + UBERON:0002217 + + + + synovial joint + + + + + Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] + + FMA:7501 + + + + + Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] + 2012-08-14 + TAO:0005153 + TAO + ZFIN:Curator + + + + + diarthroses + ZFA:0005153 + + + + + + diarthrodial joints + ZFA:0005153 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. + In many species, the diaphragm separates thoracic and abdominal cavities + + + + EMAPA:36497 + FMA:7565 + GAID:93 + MA:0000032 + MESH:A01.911.800 + NCIT:C12905 + OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg + OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA + UMLS:C0230139 + cavitas thoracis + cavity of chest + cavity of thorax + chest cavity + pectoral cavity + space of thoracic compartment + thoracic lumen + uberon + UBERON:0002224 + + + thoracic cavity + + + + + + + The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. + + UBERON:cjm + + + + + UMLS:C0230139 + ncithesaurus:Thoracic_Cavity + + + + + cavitas thoracis + + + + + + + space of thoracic compartment + FMA:7565 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) + TODO - add superclass to unify with VNC? + Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] + + + + + + AAO:0010151 + BAMS:SP + BAMS:Spinal + BM:SpC + BTO:0001279 + CALOHA:TS-0953 + DHBA:12890 + DMBA:17651 + EFO:0000110 + EHDAA2:0001255 + EHDAA:2863 + EMAPA:17577 + EV:0100316 + FMA:7647 + GAID:695 + MA:0000216 + MAT:0000183 + MESH:D013116 + MIAA:0000183 + NCIT:C12464 + OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA + TAO:0000075 + UMLS:C0037925 + VHOG:0000601 + XAO:0000020 + ZFA:0000075 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 + uberon + SpC + cerebro-cerebellar fissure + cerebrocerebellar fissure + fissura cerebro-cerebellaris + fissura cerebrocerebellaris + medulla spinalis + spinal cord structure + spinal medulla + UBERON:0002240 + + + + + + + + spinal cord + + + + + + + + + + + + definitional + + + + + + + + + + + definitional + + + + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) + NIFSTD:birnlex_1709 + + + + + Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] + 2012-06-20 + AAO:0010151 + AAO + AAO:BJB + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000601 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 + + + + + UMLS:C0037925 + NIFSTD:birnlex_1709 + + + + + UMLS:C0037925 + ncithesaurus:Spinal_Cord + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 + NIFSTD:birnlex_1709 + + + + + SpC + + + + + + cerebro-cerebellar fissure + NeuroNames:22 + + + + + cerebrocerebellar fissure + NeuroNames:22 + + + + + fissura cerebro-cerebellaris + NeuroNames:22 + + + + + + fissura cerebrocerebellaris + NeuroNames:22 + + + + + + medulla spinalis + + + + + + + medulla spinalis + BTO:0001279 + + + + + spinal cord structure + ZFA:0000075 + + + + + spinal medulla + BTO:0001279 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. + Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] + Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. + the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] + + + + + + BAMS:BS + BTO:0000146 + CALOHA:TS-0093 + EFO:0001962 + EMAPA:32678 + EV:0100241 + FMA:79876 + MA:0000169 + MBA:343 + MESH:D001933 + NCIT:C12441 + TAO:0002156 + UMLS:C0006121 + VHOG:0001457 + ZFA:0001707 + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 + brain stem + truncus encephali + uberon + accessory medullary lamina of pallidum + lamella pallidi incompleta + lamina medullaris accessoria + lamina medullaris incompleta pallidi + lamina pallidi incompleta + truncus encephalicus + UBERON:0002298 + + + + + 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN10:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). + brainstem + + + + + + Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. + + ISBN10:0471888893 + MP:0005277 + ZFA:0001707 + + + + + Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] + 2012-08-14 + TAO:0002156 + TAO + ISBN:3764351209 + + + + + Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. + ZFA:0001707 + + + + + the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] + MP:0005277 + + + + + UMLS:C0006121 + NIFSTD:birnlex_1565 + + + + + UMLS:C0006121 + ncithesaurus:Brain_Stem + + + + + http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 + NIFSTD:birnlex_1565 + + + + + brain stem + ABA:BS + + + + + truncus encephali + + + + + + + accessory medullary lamina of pallidum + NeuroNames:236 + + + + + lamella pallidi incompleta + NeuroNames:236 + + + + + + lamina medullaris accessoria + NeuroNames:236 + + + + + + lamina medullaris incompleta pallidi + NeuroNames:236 + + + + + + lamina pallidi incompleta + NeuroNames:236 + + + + + + truncus encephalicus + BTO:0000146 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. + + + + + BAMS:Scgrey + DHBA:146035048 + EMAPA:35792 + FMA:256580 + MA:0000002 + NCIT:C32696 + UMLS:C0475853 + gray matter of spinal cord + gray substance of spinal cord + grey matter of spinal cord + grey substance of spinal cord + spinal cord gray matter + spinal cord grey matter + spinal cord grey substance + substantia grisea medullae spinalis + uberon + UBERON:0002315 + + gray matter of spinal cord + + + + + The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. + MP:0008503 + + + + + UMLS:C0475853 + ncithesaurus:Gray_Matter_of_the_Spinal_Cord + + + + + gray matter of spinal cord + OBOL:automatic + + + + + gray substance of spinal cord + FMA:256580 + + + + + spinal cord gray matter + OBOL:automatic + + + + + spinal cord grey substance + OBOL:automatic + + + + + substantia grisea medullae spinalis + FMA:256580 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. + check the FMA placement here; ncit placement of body cavity here probably not correct + Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. + In mammals it forms the peritoneal, pleural, and pericardial cavities + UBERON:0000169 + body cavity + + + AEO:0000186 + BTO:0001707 + EHDAA2:0000267 + FBbt:00005060 + FMA:85006 + NCIT:C25444 + RETIRED_EHDAA2:0003186 + TAO:0001438 + UMLS:C0333343 + ZFA:0001438 + galen:BodyCavity + coelomic cavity + coelomic cavity lumen + main body cavity + space of body compartment + ventral body cavity + uberon + celom + coelom + coelome + hemocoel + UBERON:0002323 + + + coelemic cavity lumen + + + + + + + + + + + definitional + + + + + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. + BTO:0001707 + + + + + Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. + 2012-09-12 + ZFA:0001438 + ZFA + ZFIN:curator + + + + + The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. + 2012-09-12 + BTO:0001707 + BTO + BTO + + + + + body cavity + BTO:0001707 + + + + + UMLS:C0333343 + ncithesaurus:Cavity + + + + + coelomic cavity + EHDAA2:0000267 + + + + + coelomic cavity lumen + EHDAA2:0000267 + + + + + space of body compartment + FMA:85006 + + + + + ventral body cavity + NCBITaxon:7742 + + + + + celom + BTO:0001707 + + + + + coelome + BTO:0001707 + + + + + hemocoel + FBbt:00005060 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. + Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] + Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] + Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] + relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] + notochordal + In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. + + + + + + + AAO:0000327 + BTO:0001768 + CALOHA:TS-0690 + EHDAA2:0001277 + EHDAA:1241 + EHDAA:6021 + EMAPA:16191 + EV:0100002 + FMA:85521 + GAID:1311 + MAT:0000281 + MESH:A16.254.610 + NCIT:C12463 + TAO:0000135 + UMLS:C0028439 + VHOG:0000199 + VSAO:0000032 + XAO:0000055 + ZFA:0000135 + embryonic notocord + notocord + uberon + notochorda + UBERON:0002328 + + + + The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] + notochord + + + + + + + VSAO + + + + + + + + + + + ZFA + + + + + + + + + + + EHDAA2 + + + + + A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. + + + + + ISBN:0815318960 + + + + + Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] + 2012-08-14 + VSAO:0000032 + VSAO + PSPUB:0000170 + + + + + Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000135 + TAO + ZFIN:curator + + + + + Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] + 2012-06-20 + AAO:0000327 + AAO + AAO:LAP + + + + + relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] + 2012-06-20 + AAO:0000327 + AAO + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0000199 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + UMLS:C0028439 + ncithesaurus:Notochord + + + + + notocord + ZFA:0000135 + + + + + notochorda + + + + + + + + + + + + + + + + + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. + currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk + Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] + Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] + relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] + relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] + relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] + (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] + somitic + mesodermal cluster + + + AAO:0010569 + AEO:0001015 + BTO:0001558 + EHDAA2:0003436 + EHDAA:366 + EHDAA:699 + EMAPA:31169 + FMA:85522 + GAID:1306 + MAT:0000068 + MESH:A16.254.425.660.750 + MIAA:0000068 + NCIT:C34302 + TAO:0000155 + UMLS:C0376449 + VHOG:0000191 + XAO:0000058 + ZFA:0000155 + uberon + epimere + epimere mesoderm + epithelial somite + somites + somitic mesoderm + somitus + UBERON:0002329 + + + + When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] + somite + + + + + + + EHDAA2 + + + + + + + + + + + ZFA + + + + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. + + + + + + + Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] + 2012-06-20 + AAO:0010569 + AAO + AAO:EJS + + + + + Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000155 + TAO + ZFIN:curator + + + + + relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] + 2012-08-14 + TAO:0000155 + TAO + + + + + relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] + 2012-08-14 + TAO:0000155 + TAO + + + + + relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] + 2012-06-20 + AAO:0010569 + AAO + + + + + (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000191 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) + + + + + mesodermal cluster + GO:0001756 + + + + + UMLS:C0376449 + ncithesaurus:Somite + + + + + epimere + ISBN10:0073040584 + + + + + epithelial somite + + + + + + somites + + + + + + somitus + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. + + + CALOHA:TS-2057 + EHDAA2:0002225 + EMAPA:35329 + FMA:85539 + MA:0002411 + NCIT:C12957 + UMLS:C1516995 + WikipediaCategory:Exocrine_system + exocrine glandular system + uberon + UBERON:0002330 + + + exocrine system + + + + + Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. + + + + + + UMLS:C1516995 + ncithesaurus:Exocrine_System + + + + + exocrine glandular system + EHDAA2:0002225 + + + + + + + + + + + + + + + + + + + + + An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. + An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] + As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] + EHDAA2:0001576 + EHDAA:9831 + EMAPA:17015 + FMA:8612 + MA:0002033 + NCIT:C116918 + OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA + VHOG:0001134 + galen:PulmonaryTrunk + pulmonary artery (trunk) + trunk of pulmonary arterial tree + uberon + main pulmonary artery + UBERON:0002333 + + + + pulmonary trunk + + + + + + + MA + + + + + An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. + + + + + + An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] + 2012-09-17 + VHOG:0001134 + VHOG + + + + + + + As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] + 2012-09-17 + VHOG:0001134 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 + + + + + main pulmonary artery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. + consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). + + A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] + Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] + A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] + We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] + + + + + AAO:0010578 + BTO:0001764 + CALOHA:TS-0676 + EHDAA2:0004419 + EMAPA:32737 + FMA:86666 + GAID:1310 + MAT:0000066 + MESH:A16.254.600 + MIAA:0000066 + NCIT:C34222 + TAO:0000045 + UMLS:C0027789 + VHOG:0000057 + XAO:0000048 + ZFA:0000045 + NC + uberon + crista neuralis + neural crest material + UBERON:0002342 + + + + Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. + neural crest + + + + + + + + + + + + + + XAO + + + + + + + + + + + BTO + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. + MP:0009846 + + + + + + + ISBN10:0073040584 + + + + + A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000045 + TAO + ZFIN:curator + + + + + Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] + 2012-06-20 + AAO:0010578 + AAO + AAO:EJS + + + + + A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] + + + + + + We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] + 2012-09-17 + VHOG:0000057 + VHOG + + DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) + + + + + UMLS:C0027789 + ncithesaurus:Neural_Crest + + + + + NC + XAO:0000048 + + + + + + crista neuralis + + + + + + + neural crest material + VHOG:0000057 + + + + + + + + + + Embryonic ectoderm that gives rise to nervous tissue. + (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] + neurectodermal + we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here + + + AAO:0011074 + BILA:0000039 + CALOHA:TS-1212 + EHDAA2:0001248 + EHDAA:1498 + EHDAA:255 + EMAPA:16073 + EV:0100004 + FBbt:00001061 + FMA:87657 + MAT:0000176 + MIAA:0000176 + NCIT:C34228 + TAO:0001120 + UMLS:C1518271 + VHOG:0000150 + XAO:0000042 + ZFA:0001120 + neural ectoderm + neuroectoderm + uberon + epithelium tubi neuralis; neuroectoderma + neuaral ectoderm + presumptive central nervous system + ventral neurogenic region + UBERON:0002346 + + + neurectoderm + + + + + Embryonic ectoderm that gives rise to nervous tissue. + + + + + + (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] + 2012-09-17 + VHOG:0000150 + VHOG + + DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) + + + + + UMLS:C1518271 + ncithesaurus:Neuroectoderm + + + + + epithelium tubi neuralis; neuroectoderma + + + + + + + ventral neurogenic region + VHOG:0000150 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas + Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses + + + + AEO:0000097 + BTO:0000765 + CALOHA:TS-2012 + EHDAA2:0003097 + EMAPA:35327 + FMA:9596 + GAID:34 + MA:0002564 + MESH:D005088 + NCIT:C12712 + UMLS:C0015282 + ducted gland + glandula exocrina + uberon + UBERON:0002365 + + + + exocrine gland + + + + + A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas + + + + + + UMLS:C0015282 + ncithesaurus:Exocrine_Gland + + + + + ducted gland + AEO:0000097 + + + + + glandula exocrina + + + + + + + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] + Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] + MA also has set of connective tissues + + + + + AAO:0000098 + BTO:0000421 + CALOHA:TS-2009 + EFO:0000952 + EMAPA:35251 + FMA:9640 + GAID:100 + MA:0000011 + MAT:0000301 + MESH:D003238 + MIAA:0000301 + NCIT:C12374 + OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA + TAO:0001641 + UMLS:C0009780 + VSAO:0000017 + XAO:0001017 + ZFA:0001632 + galen:ConnectiveTissue + portion of connective tissue + textus connectivus + uberon + Bindegewebe + UBERON:0002384 + + + + connective tissue + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. + + + GO_REF:0000034 + PSPUB:0000170 + VSAO:0000017 + + + + + One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] + 2012-06-20 + AAO:0000098 + AAO + AAO:LAP + + + + + Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] + 2012-08-14 + TAO:0001641 + TAO + TAO:wd + + + + + Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] + 2012-08-14 + VSAO:0000017 + VSAO + GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 + PSPUB:0000170 + + + + + MA also has set of connective tissues + MA + + + + + UMLS:C0009780 + ncithesaurus:Connective_Tissue + + + + + portion of connective tissue + FMA:9640 + + + + + Bindegewebe + BTO:0000421 + + + + + + + + + + + + + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] + + + + AAO:0000306 + AEO:0000122 + CALOHA:TS-0642 + EHDAA2:0003122 + EMAPA:32715 + FMA:9641 + MA:0002437 + MESH:D009132 + NCIT:C12435 + UMLS:C2328219 + galen:MuscleTissue + muscular tissue + portion of muscle tissue + textus muscularis + uberon + UBERON:0002385 + + Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. + muscle tissue + + + + + Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. + + + GO:0060537 + + + + + One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] + 2012-06-20 + AAO:0000306 + AAO + AAO:LAP + + + + + UMLS:C2328219 + ncithesaurus:Muscle_Tissue + + + + + muscular tissue + + + + + + portion of muscle tissue + FMA:9641 + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that is involved in the production of hematopoietic cells. + Anatomical system that consists of the blood and blood forming tissues.[AAO] + Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] + hematopoietic + In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes + + + + AAO:0011002 + BTO:0000570 + CALOHA:TS-0449 + EFO:0000798 + EMAPA:35402 + EV:0100045 + FMA:9667 + GAID:1008 + MA:0002434 + MAT:0000022 + MESH:D006413 + MIAA:0000022 + NCIT:C12909 + TAO:0005023 + UMLS:C0018957 + VHOG:0001624 + XAO:0000122 + ZFA:0005023 + haematological system + haemopoietic system + organa haemopoietica + uberon + Blutbildungssystem + haematopoietic system + hematological system + hematolymphoid system + hemopoietic system + UBERON:0002390 + + + + + hematopoietic system + + + + + + + + + + + FMA + + + + + + + + + + + definitional + + + + + Anatomical system that is involved in the production of hematopoietic cells. + + + + + + Anatomical system that consists of the blood and blood forming tissues.[AAO] + 2012-06-20 + AAO:0011002 + AAO + AAO:EJS + + + + + Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] + 2012-09-17 + VHOG:0001624 + VHOG + + DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) + + + + + In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes + WP + + + + + UMLS:C0018957 + ncithesaurus:Hematopoietic_System + + + + + Blutbildungssystem + BTO:0000570 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. + (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] + + + UBERON:0007029 + + + + AEO:0000154 + BILA:0000118 + CALOHA:TS-1299 + CARO:0002001 + EFO:0000807 + EHDAA2:0000836 + EHDAA2_RETIRED:0003154 + EHDAA:6520 + EMAPA:17524 + EV:0100151 + FBbt:00004969 + FMA:72979 + HAO:0000421 + MA:0000014 + MAT:0000033 + MESH:D034582 + MIAA:0000033 + NCIT:C12907 + TADS:0000108 + UMLS:C0037267 + VHOG:0000403 + XAO:0000176 + galen:Surface + integumentary system + uberon + body surface + dermal system + external covering of organism + integumentum commune + organism surface + surface + UBERON:0002416 + + + + integumental system + + + + + Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. + + + CARO:0002001 + + + + + (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] + 2012-09-17 + VHOG:0000403 + VHOG + + DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) + + + + + UMLS:C0037267 + ncithesaurus:Integumentary_System + + + + + integumentary system + FMA:72979 + + + + + dermal system + MIAA:0000033 + + + + + integumentum commune + + + + + + + organism surface + EHDAA2:0003154 + + + + + surface + BILA:0000118 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a skin of body [Automatically generated definition]. + check FMA, use plural for now as general class not there + + EMAPA:35774 + FMA:71878 + MA:0000146 + glandulae cutis + uberon + set of skin glands + skin glands + skin glands set + UBERON:0002419 + + skin gland + + + + + A gland that is part of a skin of body [Automatically generated definition]. + OBOL:automatic + + + + + glandulae cutis + FMA:71878 + FMA:TA + + + + + + set of skin glands + FMA:71878 + + + + + skin glands + + + + + + skin glands set + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues + consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) + The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. + the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme + + AAO:0010357 + BTO:0001775 + CALOHA:TS-0715 + EHDAA2:0001325 + EHDAA:2187 + EMAPA:16839 + EMAPA:26942 + FMA:265152 + MA:0000344 + NCIT:C49595 + TAO:0000816 + UMLS:C1709332 + VHOG:0000187 + XAO:0003201 + ZFA:0000816 + epithelium of mucosa of mouth + epithelium of oral mucosa + uberon + UBERON:0002424 + + oral epithelium + + + + + + + + + + + AAO-modified + + + + + An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues + + + + + + The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. + ZFA:0000816 + + + + + the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme + + + + + + UMLS:C1709332 + ncithesaurus:Oral_Cavity_Epithelium + + + + + epithelium of mucosa of mouth + FMA:265152 + + + + + epithelium of oral mucosa + FMA:265152 + + + + + + + + + + + + + + + + + + + + + + + + + + Arteries that supply the spinal cord. + + + + EHDAA2:0001890 + EHDAA:4355 + EMAPA:18241 + MA:0002043 + NCIT:C33587 + TAO:0000682 + UMLS:C0447043 + ZFA:0000682 + spinal arteries + uberon + UBERON:0002458 + + + spinal artery + + + + + Arteries that supply the spinal cord. + + + + + + + UMLS:C0447043 + ncithesaurus:Spinal_Artery + + + + + spinal arteries + ZFA:0000682 + + + + + + + + + + Connective tissue composed of elastic fibers. + + + FMA:20113 + GAID:926 + MA:0002853 + MESH:D004547 + NCIT:C32495 + elastic connective tissue + textus connectivus elasticus + elastic fiber + uberon + UBERON:0002521 + + elastic tissue + + + + + + Connective tissue composed of elastic fibers. + + + + + + textus connectivus elasticus + + + + + + + + + + + + + + + + + + + + + + + + + + + + The middle layer of an artery or vein. [WP,unvetted]. + + + + BTO:0002011 + EMAPA:36298 + FMA:55590 + GAID:170 + MA:0002855 + MESH:D017540 + NCIT:C33821 + UMLS:C0162867 + uberon + tunica media vasorum + UBERON:0002522 + + May be composed of smooth muscle and elastic tissue + tunica media + + + + + + + MA + + + + + + + + + + + cjm + + + + + + + + + + + cjm + + + + + The middle layer of an artery or vein. [WP,unvetted]. + + + + + + UMLS:C0162867 + ncithesaurus:Tunica_Media + + + + + tunica media vasorum + + + + + + + tunica media vasorum + BTO:0002011 + + + + + + + + + + + + + + + + + + + + + + + + + + + The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. + the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure + the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts + The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] + + + + + BTO:0002012 + EMAPA:36297 + FMA:55589 + GAID:523 + MA:0002861 + MESH:D017539 + NCIT:C33820 + UMLS:C0162864 + uberon + Bichat's tunic + intima + tunica intima vasorum + UBERON:0002523 + + tunica intima + + + + + + + FMA + + + + + + + + + + + check for exceptions, e.g. capillaries + + + + + + + + + + + ISBN10:0073040584 + + + + + The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. + + ISBN10:0073040584 + NCIT:C33820 + + + + + The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] + Wikipedia + + + + + + UMLS:C0162864 + ncithesaurus:Tunica_Intima + + + + + Bichat's tunic + BTO:0002012 + + + + + intima + BTO:0002012 + + + + + tunica intima vasorum + BTO:0002012 + + + + + + + + + + + + + + + an organ that functions as a secretory or excretory organ + glandular + UBERON:MIAA_0000021 + + + + AAO:0000212 + AEO:0000096 + BTO:0000522 + EFO:0000797 + EHDAA2:0003096 + EHDAA:2161 + EHDAA:4475 + EHDAA:6522 + EMAPA:18425 + FBbt:00100317 + FMA:7146 + FMA:86294 + HAO:0000375 + MA:0003038 + MAT:0000021 + MIAA:0000021 + NCIT:C13319 + OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA + UMLS:C1285092 + WikipediaCategory:Glands + galen:Gland + glandular organ + uberon + Druese + glandula + UBERON:0002530 + + + + gland + + + + + + an organ that functions as a secretory or excretory organ + MGI:csmith + MP:0002163 + + + + + UMLS:C1285092 + ncithesaurus:Gland + + + + + glandular organ + + + + + + Druese + BTO:0000522 + + + + + glandula + + + + + + + glandula + BTO:0000522 + + + + + + + + + In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] + MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class + In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] + + BTO:0004593 + FMA:296704 + MAT:0000067 + MIAA:0000067 + VHOG:0000243 + epiblast + uberon + blastocyst + ectoblast + epiblastus + primitive ectoderm + UBERON:0002532 + + + + + epiblast (generic) + + + + + + In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] + + ZFIN:curator + + + + + In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] + 2012-09-17 + VHOG:0000243 + VHOG + + DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) + + + + + epiblast + VHOG:0000243 + + + + + ectoblast + MP:0003886 + + + + + epiblastus + + + + + + + primitive ectoderm + VHOG:0000243 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. + One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] + A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] + Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering + + + + AAO:0010359 + BTO:0001785 + EFO:0000959 + EHDAA:571 + EMAPA:16117 + FMA:293015 + GAID:1292 + MAT:0000242 + MESH:A16.254.160 + MIAA:0000242 + NCIT:C34249 + TAO:0001306 + UMLS:C0080322 + VHOG:0000155 + XAO:0000096 + ZFA:0001306 + pharyngeal arches + branchial arch + uberon + arcus pharyngei + visceral arch + UBERON:0002539 + + + + + pharyngeal arch + + + + + + + EHDAA2 + + + + + + + + + + + + + + + + + + + + + + + + + + + One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. + + + ZFA:yb + + + + + One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] + 2012-06-20 + AAO:0010359 + AAO + NLM:branchial+arch + + + + + A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] + 2012-09-17 + VHOG:0000155 + VHOG + + DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) + + + + + UMLS:C0080322 + ncithesaurus:Pharyngeal_Arch + + + + + pharyngeal arches + + + + + + branchial arch + BTO:0001785 + MP:0002884 + + + + + arcus pharyngei + + + + + + + + + + + + + + + + + Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. + cavity + + EMAPA:37442 + FMA:67552 + MA:0002447 + NCIT:C34007 + galen:Cavity + uberon + UBERON:0002553 + + anatomical cavity + + + + + Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. + FMA:67552 + + + + + EMAPA:37442 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. + + + + FMA:55676 + NCIT:C13031 + UMLS:C0445620 + anatomical structure of brain + biological structure of brain + brain anatomical structure + brain biological structure + brain part + neuraxis segment + neuroanatomical region + segment of brain + uberon + UBERON:0002616 + + regional part of brain + + + + + Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. + NIFSTD:birnlex_1167 + + + + + UMLS:C0445620 + ncithesaurus:Brain_Part + + + + + anatomical structure of brain + OBOL:automatic + + + + + biological structure of brain + OBOL:automatic + + + + + brain anatomical structure + OBOL:automatic + + + + + brain biological structure + OBOL:automatic + + + + + neuraxis segment + FMA:55676 + + + + + segment of brain + NIFSTD:birnlex_1167 + + + + + + + + + + + + + + + A wall, dividing a cavity or structure into smaller ones[WP]. + septal + + AAO:0011127 + FMA:86461 + OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ + septa + uberon + UBERON:0003037 + + general anatomical term in FMA + septum + + + + + A wall, dividing a cavity or structure into smaller ones[WP]. + + + + + + septa + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. + consider adding class for organizer. Consider adding separate class for isthmus as a structure + Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] + + AAO:0011064 + DMBA:16810 + EHDAA2:0004395 + EHDAA:5789 + EMAPA:32857 + NCIT:C93172 + TAO:0000042 + VHOG:0000649 + XAO:0000016 + ZFA:0000042 + MHB + mid-hindbrain boundary + mid-hindbrain junction + midbrain hindbrain boundary + uberon + isthmic organizer territory + isthmo-cerebellar region + isthmus + isthmus/MHB + UBERON:0003052 + + + + midbrain-hindbrain boundary + + + + + + ZFA + + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. + GO:0021555 + + + + + Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] + 2012-09-17 + VHOG:0000649 + VHOG + + DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) + + + + + isthmic organizer territory + XAO:0000016 + + + + + isthmo-cerebellar region + VHOG:0000649 + + + + + isthmus/MHB + Geisha:syn + NCBITaxon:8782 + + + + + + + + + + + + + + + + + + + + + + A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. + The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] + relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] + In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] + In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis + Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) + + EHDAA2:0001846 + EHDAA:6538 + FMA:295662 + NCIT:C34247 + TAO:0001185 + UMLS:C1518973 + VHOG:0001680 + XAO:0000029 + ZFA:0001185 + skin periderm + uberon + EVL + epidermis epithelial layer + epidermis outer layer + epitrichium + periderm + UBERON:0003055 + + + periderm + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + ZFA + + + + + A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. + ISBN:9780878932504 + + + + + The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] + 2012-08-14 + TAO:0001185 + TAO + ZFIN:curator + + + + + relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] + 2012-08-14 + TAO:0001185 + TAO + + + + + UMLS:C1518973 + ncithesaurus:Periderm + + + + + skin periderm + EHDAA2:0001846 + + + + + EVL + ZFA:0001185 + + + + + epitrichium + MP:0013530 + + + + + + + + + + + + + + + + + + + + + + The portion of neural plate anterior to the mid-hindbrain junction. + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + AAO:0011084 + TAO:0007016 + VHOG:0001200 + XAO:0000045 + ZFA:0007016 + uberon + anterior neural plate + UBERON:0003056 + pre-chordal neural plate + + + + + The portion of neural plate anterior to the mid-hindbrain junction. + XB:curator + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0001200 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + + + + + + + + + + + + + + + + + The portion of neural plate posterior to the mid-hindbrain junction. + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + TAO:0007017 + VHOG:0001201 + XAO:0000046 + ZFA:0007017 + uberon + posterior neural plate + UBERON:0003057 + chordal neural plate + + + + + The portion of neural plate posterior to the mid-hindbrain junction. + XB:curator + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0001201 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] + It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] + AAO:0011086 + EFO:0001982 + EMAPA:16189 + EMAPA:16752 + TAO:0000279 + VHOG:0000559 + XAO:0000057 + ZFA:0000279 + segmental plate + unsegmented paraxial mesoderm + uberon + PSM + presumptive somite mesoderm + somitogenic mesoderm + somitomeric mesoderm + unsegmented mesenchyme + UBERON:0003059 + + + presomitic mesoderm + + + + + + + + + + + Bgee:AN + + + + + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. + ZFIN:curator + + + + + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000279 + TAO + ZFIN:curator + + + + + It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] + 2012-09-17 + VHOG:0000559 + VHOG + + DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) + + + + + unsegmented paraxial mesoderm + + + + + + somitomeric mesoderm + GO:0002075 + + + + + unsegmented mesenchyme + VHOG:0000559 + + + + + + + + + + + + + + + + + + + + + Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. + Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] + Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] + relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] + Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] + EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac + ventral lateral plate mesoderm + + + AAO:0011006 + EFO:0003489 + EHDAA:207 + NCIT:C34113 + TAO:0000094 + TE:E5.11.2.0.0.0.4 + UMLS:C1511224 + VHOG:0000085 + XAO:0000067 + ZFA:0000094 + blood islands + uberon + VBI + caudal hematopoietic tissue + posterior ICM + posterior blood island + ventral blood island + UBERON:0003061 + + + + + blood island + + + + + Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. + + + + + + Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000094 + TAO + ZFIN:curator + + + + + Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] + 2012-06-20 + AAO:0011006 + AAO + AAO:EJS + + + + + relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] + 2012-08-14 + TAO:0000094 + TAO + + + + + Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000085 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) + + + + + EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac + EHDAA2 + + + + + UMLS:C1511224 + ncithesaurus:Blood_Island + + + + + blood islands + + + + + + + + + + + + + + + + + + + + + + + + + + + + A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue + TODO - check; developmental relationship to anterior hypoblast in ZFA? + Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] + Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] + There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] + UBERON:0004881 + head mesenchyme + head mesoderm + + AAO:0011085 + EHDAA2:0001493 + EHDAA:181 + FMA:295532 + TAO:0000060 + VHOG:0000086 + XAO:0000079 + ZFA:0000060 + uberon + UBERON:0003063 + + + + prechordal plate + + + + + + + + + + + ZFA + + + + + + + + + + + PMID:16313393 + + + + + A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue + ISBN:0838580343 + MP:0004387 + + + + + Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000060 + TAO + ZFIN:curator + + + + + Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] + 2012-09-17 + VHOG:0000086 + VHOG + + + + + + There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] + 2012-09-17 + VHOG:0000086 + VHOG + + DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008) + + + + + head mesenchyme + XAO:0000079 + + + + + head mesoderm + XAO:0000079 + + + + + + + + + + + + + + + + + + + + + The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. + The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] + + AAO:0011017 + EFO:0003647 + TAO:0001204 + VHOG:0000107 + XAO:0000205 + ZFA:0001204 + uberon + chordamesoderm + UBERON:0003068 + + + axial mesoderm + + + + + + The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. + + GO:0048318 + + + + + The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] + 2012-09-17 + VHOG:0000107 + VHOG + + + + + + chordamesoderm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] + The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + + + + AAO:0011072 + BTO:0001765 + DHBA:10153 + DMBA:15565 + EHDAA:346 + EHDAA:902 + EMAPA:35593 + FMA:293879 + NCIT:C34225 + RETIRED_EHDAA2:0001252 + TAO:0000132 + UMLS:C0920623 + VHOG:0000068 + XAO:0000249 + ZFA:0000132 + uberon + lamina neuralis + presumptive central nervous system + UBERON:0003075 + + + + neural plate + + + + + + + + + + + + Wikipedia + + + + + + + + + + + Bgee:AN + + + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] + + ISBN:0815318960 + OMD:neural+plate + ZFIN:curator + + + + + The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000132 + TAO + ZFIN:curator + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0000068 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + UMLS:C0920623 + ncithesaurus:Neural_Plate + + + + + lamina neuralis + + + + + + + + + + + + + + + + + + + + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + AAO:0011082 + TAO:0007037 + VHOG:0001383 + XAO:0000250 + ZFA:0007037 + uberon + UBERON:0003076 + posterior neural tube + + + + + + lexical + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0001383 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] + Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] + Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] + note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) + + + + AAO:0010568 + EFO:0003515 + EMAPA:16183 + EMAPA:16751 + FMA:293145 + NCIT:C34244 + TAO:0000255 + UMLS:C1284009 + VHOG:0000114 + XAO:0000259 + ZFA:0000255 + paraxial mesenchyme + somitic mesoderm + uberon + mesoderma paraxiale + UBERON:0003077 + + + + paraxial mesoderm + + + + + + + EHDAA2 + + + + + + + + + + + Bgee:AN + + + + + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] + + GO:0048339 + + + + + Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] + 2012-06-20 + AAO:0010568 + AAO + AAO:EJS + + + + + Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] + 2012-09-17 + VHOG:0000114 + VHOG + + DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) + + + + + note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) + ZFA + + + + + UMLS:C1284009 + ncithesaurus:Paraxial_Mesoderm + + + + + paraxial mesenchyme + + + ZFA:0000255 + + + + + somitic mesoderm + ISBN:9780878932504 + + + + + mesoderma paraxiale + + + + + + + + + + + + + + + + + + + + + + + TODO - add grouping class for the anterior end of the neural tube at all stages + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + AAO:0011012 + TAO:0007038 + VHOG:0001384 + XAO:0000307 + ZFA:0007038 + uberon + UBERON:0003080 + anterior neural tube + + + + + + lexical + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0001384 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + + + + + + + + + + + + + + + + + + + + Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. + Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] + The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] + A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] + subclass of mesoderm in ZFA. + UBERON:0006258 + + + + AAO:0010574 + EHDAA2:0000919 + EHDAA:379 + EMAPA:16179 + FMA:293149 + NCIT:C34199 + TAO:0000121 + UMLS:C1517749 + VHOG:0000118 + XAO:0000311 + ZFA:0000121 + LPM + lateral mesoderm + uberon + lateral plate + lateral plate mesenchyme + mesoderma laminae lateralis + UBERON:0003081 + + + lateral plate mesoderm + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + VHOG + + + + + Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. + + MP:0010117 + + + + + Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] + 2012-06-20 + AAO:0010574 + AAO + AAO:EJS + + + + + The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] + 2012-09-17 + VHOG:0000118 + VHOG + + + + + + A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] + 2012-09-17 + VHOG:0000118 + VHOG + + DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) + + + + + subclass of mesoderm in ZFA. + ZFA + + + + + UMLS:C1517749 + ncithesaurus:Lateral_Mesoderm + + + + + LPM + ZFA:0000121 + + + + + + lateral mesoderm + GO:0048368 + + + + + lateral plate mesenchyme + EHDAA2:0000919 + + + + + mesoderma laminae lateralis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. + should probably be merged with heart rudiment. + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] + The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] + relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] + + AAO:0011044 + BTO:0001887 + NCIT:C34276 + TAO:0000028 + UMLS:C1514450 + XAO:0000336 + ZFA:0000028 + uberon + cardiac field + fused heart primordium + UBERON:0003084 + + heart primordium + + + + + + Obol + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + + + + + + + XAO + + + + + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. + ZFIN:curator + + + + + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] + 2012-08-14 + TAO:0000028 + TAO + ZFIN:curator + + + + + The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] + 2012-06-20 + AAO:0011044 + AAO + XAO:curator + + + + + relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] + 2012-08-14 + TAO:0000028 + TAO + + + + + UMLS:C1514450 + ncithesaurus:Primordium_of_the_Heart + + + + + cardiac field + ZFA:0000028 + + + + + + + + + + + + + + + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. + Skeletogenic portion of somites.[AAO] + The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] + part_of somite in XAO + + + AAO:0010571 + AEO:0000212 + EHDAA2:0003439 + EMAPA:31159 + FMA:295652 + NCIT:C34287 + TAO:0001080 + UMLS:C0183176 + VHOG:0000680 + XAO:0000397 + ZFA:0001080 + sclerotomes + uberon + sclerotomus + UBERON:0003089 + + + + sclerotome + + + + + + + EHDAA2 + + + + + + EHDAA2 + + + + + + + + + + + ZFA + + + + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. + + + XB:curator + + + + + Skeletogenic portion of somites.[AAO] + 2012-06-20 + AAO:0010571 + AAO + AAO:EJS + + + + + The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] + 2012-09-17 + VHOG:0000680 + VHOG + + DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) + + + + + part_of somite in XAO + XAO + + + + + UMLS:C0183176 + ncithesaurus:Sclerotome + + + + + sclerotomes + TAO:0001080 + + + + + + sclerotomus + + + + + + + + + + + + + + + + + + + neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. + Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] + Neural crest that is part of the head.[TAO] + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] + + AAO:0010580 + EFO:0003645 + EHDAA2:0004420 + EMAPA:16091 + TAO:0001194 + VHOG:0000063 + XAO:0001001 + ZFA:0001194 + CNC + cephalic neural crest + cranial NCC population + head NCC population + uberon + crista neuralis cranialis + head crest + head neural crest + UBERON:0003099 + + + + cranial neural crest + + + + + neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. + MGI:anna + + + + + Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] + 2012-06-20 + AAO:0010580 + AAO + AAO:EJS + + + + + Neural crest that is part of the head.[TAO] + 2012-08-14 + TAO:0001194 + TAO + ZFIN:curator + + + + + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] + 2012-09-17 + VHOG:0000063 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + + + + + CNC + XAO:0001001 + + + + + + cephalic neural crest + EMAPA:16091 + + + + + crista neuralis cranialis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + consider obsoleting. See issue/1305 + Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] + + + + AAO:0010337 + AEO_RETIRED:0000010 + EHDAA2_RETIRED:0003010 + TAO:0000292 + VSAO:0000001 + XAO:0003028 + ZFA:0000292 + galen:SurfaceRegion + anatomical surface feature + uberon + surface feature + surface region + surface structures + UBERON:0003102 + + surface structure + + + + + Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. + + + + + + + Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] + 2012-08-14 + TAO:0000292 + TAO + ZFIN:curator + + + + + anatomical surface feature + EHDAA2:0003010 + + + + + surface structures + ZFA:0000292 + + + + + + + + + + Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. + this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs + AAO:0010015 + AEO:0000024 + BILA:0000024 + CARO:0000024 + EHDAA2:0003024 + HAO:0000024 + TADS:0000598 + TAO:0000496 + TGMA:0001837 + VHOG:0001723 + XAO:0003041 + ZFA:0000496 + uberon + organ + UBERON:0003103 + + + compound organ + + + + + Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. + CARO:0000024 + + + + + + + + + + + + + + + Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. + the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense + A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] + Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] + mesenchymal + + + AAO:0010427 + AEO:0000145 + BTO:0001393 + CALOHA:TS-0620 + EHDAA2:0003145 + EV:0100007 + NCIT:C13301 + TAO:0000393 + UMLS:C0162415 + VHOG:0000170 + XAO:0003046 + ZFA:0000393 + mesenchymal tissue + mesenchyme tissue + portion of mesenchymal tissue + portion of mesenchyme tissue + uberon + mesenchyma + UBERON:0003104 + + + + mesenchyme + + + + + + Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. + + BTO:0001393 + ZFIN:curator + + + + + A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000393 + TAO + ZFIN:curator + + + + + Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] + 2012-06-20 + AAO:0010427 + AAO + AAO:EJS + + + + + UMLS:C0162415 + ncithesaurus:Mesenchyme + + + + + mesenchyma + + + + + + + + + + + The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles + The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] + A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] + 6 + UBERON:0004349 + + AAO:0010368 + EHDAA2:0004075 + EMAPA:32766 + FMA:293047 + TAO:0001601 + VHOG:0001205 + XAO:0000453 + ZFA:0001609 + 6th arch + gill arch 4 + sixth branchial arch + visceral arch 6 + uberon + 6th pharyngeal arch + 6th visceral arch + branchial arch 4 + fourth branchial arch + sixth pharyngeal arch + sixth visceral arch + UBERON:0003117 + + pharyngeal arch 6 + + + + + The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles + MP:0006347 + + + + + The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] + 2012-06-20 + AAO:0010368 + AAO + ISBN:0-02-377110-0 + + + + + A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] + 2012-09-17 + VHOG:0001205 + VHOG + + DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) + + + + + 6th arch + EHDAA2:0004075 + + + + + gill arch 4 + ZFA:0001609 + + + + + visceral arch 6 + ZFA:0001609 + + + + + 6th pharyngeal arch + VHOG:0001205 + + + + + 6th visceral arch + VHOG:0001205 + + + + + branchial arch 4 + AAO:0010368 + ZFA:0001609 + + + + + + fourth branchial arch + + + + + + sixth pharyngeal arch + VHOG:0001205 + + + + + sixth visceral arch + XAO:0000453 + + + + + + + + + + + + + + + + + + + + + + + + + + The vessels formed within the sixth pair of branchial arches in embryogenesis + The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] + The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] + The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. + the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries + UBERON:0004351 + + + AAO:0010422 + EHDAA2:0000102 + EMAPA:17005 + TAO:0005016 + VHOG:0000144 + XAO:0000353 + ZFA:0005016 + 6th arch artery + AA6 + aortic arch 6 + sixth aortic arch + sixth branchial arch artery + uberon + 6th aortic arch artery + 6th branchial arch artery + 6th pharyngeal arch artery + pulmonary arch + UBERON:0003123 + + + pharyngeal arch artery 6 + + + + + The vessels formed within the sixth pair of branchial arches in embryogenesis + MP:0006355 + + + + + The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] + 2012-08-14 + TAO:0005016 + TAO + ZFIN:curator + + + + + The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] + 2012-06-20 + AAO:0010422 + AAO + ISBN:0-02-377110-0 + + + + + The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. + + + + + + the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries + + + + + + 6th arch artery + EMAPA:17005 + + + + + AA6 + ZFA:0005016 + + + + + aortic arch 6 + ZFA:0005016 + + + + + sixth aortic arch + XAO:0000353 + + + + + 6th aortic arch artery + EMAPA:17005 + + + + + 6th branchial arch artery + EMAPA:17005 + + + + + 6th pharyngeal arch artery + EMAPA:17005 + + + + + pulmonary arch + ISBN10:0073040584 + + + + + + + + + + + + + + + + + + + + + + + + + + An endoderm that is part of a foregut [Automatically generated definition]. + TODO - check + EHDAA2:0004568 + EHDAA:524 + foregut endoderm + uberon + UBERON:0003258 + endoderm of foregut + + + + + An endoderm that is part of a foregut [Automatically generated definition]. + OBOL:automatic + + + + + foregut endoderm + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a foregut [Automatically generated definition]. + EHDAA2:0000567 + EHDAA:950 + EMAPA:16557 + VHOG:0000650 + foregut gland + uberon + UBERON:0003294 + gland of foregut + + + + + A gland that is part of a foregut [Automatically generated definition]. + OBOL:automatic + + + + + foregut gland + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + Racemose mucous glands beneath the mucous membrane of the pharynx. + BTO:0004849 + EHDAA2:0001461 + EHDAA:2967 + FMA:55075 + pharynx gland + uberon + glandulae pharyngeae + UBERON:0003295 + + pharyngeal gland + + + + + + + + + + + BTO + + + + + Racemose mucous glands beneath the mucous membrane of the pharynx. + Biology-Online_Dictionary:http://www.biology-online.org/dictionary/ + + + + + pharynx gland + EHDAA2:0001461 + + + + + glandulae pharyngeae + BTO:0004849 + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a integumental system [Automatically generated definition]. + EHDAA2:0000837 + EHDAA:6522 + EMAPA:17758 + MA:0000144 + VHOG:0000654 + integumental gland + integumental system gland + integumentary gland + uberon + UBERON:0003297 + gland of integumental system + + + + + A gland that is part of a integumental system [Automatically generated definition]. + OBOL:automatic + + + + + integumental gland + + + + + + integumental system gland + + + + + + integumentary gland + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood island that is part of a mesoderm. + in EHDAA2, gives rise to blood and dorsal aorta + UBERON:0003305 + EHDAA2:0003241 + EHDAA:170 + EMAPA:16115 + mesoderm blood islands + uberon + mesenchyme blood island + UBERON:0003304 + mesoderm blood island + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + A blood island that is part of a mesoderm. + OBOL:automatic + + + + + in EHDAA2, gives rise to blood and dorsal aorta + EHDAA2 + + + + + mesoderm blood islands + EHDAA2:0003241 + + + + + + mesenchyme blood island + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A mucosa that is part of a oral opening [Automatically generated definition]. + + EMAPA:26937 + mucosa of oral opening + mucosa of oral part of face + mucosa of organ of oral opening + mucosa of organ of oral part of face + mucosa of organ of oral region + mucosa of organ of subdivision of mouth + mucosa of subdivision of mouth + mucous membrane of oral opening + mucous membrane of oral part of face + mucous membrane of oral region + mucous membrane of subdivision of mouth + oral opening mucosa + oral opening mucosa of organ + oral opening mucous membrane + oral opening organ mucosa + oral part of face mucosa + oral part of face mucosa of organ + oral part of face mucous membrane + oral part of face organ mucosa + oral region mucosa + oral region mucosa of organ + oral region mucous membrane + oral region organ mucosa + organ mucosa of oral opening + organ mucosa of oral part of face + organ mucosa of oral region + organ mucosa of subdivision of mouth + subdivision of mouth mucosa + subdivision of mouth mucosa of organ + subdivision of mouth mucous membrane + subdivision of mouth organ mucosa + uberon + UBERON:0003343 + mucosa of oral region + + + + + A mucosa that is part of a oral opening [Automatically generated definition]. + OBOL:automatic + + + + + mucosa of oral opening + OBOL:automatic + + + + + mucosa of oral part of face + OBOL:automatic + + + + + mucosa of organ of oral opening + OBOL:automatic + + + + + mucosa of organ of oral part of face + OBOL:automatic + + + + + mucosa of organ of oral region + OBOL:automatic + + + + + mucosa of organ of subdivision of mouth + OBOL:automatic + + + + + mucosa of subdivision of mouth + OBOL:automatic + + + + + mucous membrane of oral opening + OBOL:automatic + + + + + mucous membrane of oral part of face + OBOL:automatic + + + + + mucous membrane of oral region + OBOL:automatic + + + + + mucous membrane of subdivision of mouth + OBOL:automatic + + + + + oral opening mucosa + OBOL:automatic + + + + + oral opening mucosa of organ + OBOL:automatic + + + + + oral opening mucous membrane + OBOL:automatic + + + + + oral opening organ mucosa + OBOL:automatic + + + + + oral part of face mucosa + OBOL:automatic + + + + + oral part of face mucosa of organ + OBOL:automatic + + + + + oral part of face mucous membrane + OBOL:automatic + + + + + oral part of face organ mucosa + OBOL:automatic + + + + + oral region mucosa + OBOL:automatic + + + + + oral region mucosa of organ + OBOL:automatic + + + + + oral region mucous membrane + OBOL:automatic + + + + + oral region organ mucosa + OBOL:automatic + + + + + organ mucosa of oral opening + OBOL:automatic + + + + + organ mucosa of oral part of face + OBOL:automatic + + + + + organ mucosa of oral region + OBOL:automatic + + + + + organ mucosa of subdivision of mouth + OBOL:automatic + + + + + subdivision of mouth mucosa + OBOL:automatic + + + + + subdivision of mouth mucosa of organ + OBOL:automatic + + + + + subdivision of mouth mucous membrane + OBOL:automatic + + + + + subdivision of mouth organ mucosa + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A layer of epithelial cells on the surface of the mucosa. + BTO:0003752 + uberon + lamina epithelialis mucosa + lamina epithelialis mucosae + UBERON:0003350 + lies on top of lamina propria + epithelium of mucosa + + + + + A layer of epithelial cells on the surface of the mucosa. + BTO:0003752 + + + + + lamina epithelialis mucosa + BTO:0003752 + + + + + lamina epithelialis mucosae + BTO:0003752 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a pharynx [Automatically generated definition]. + Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] + BSA:0000112 + BTO:0005240 + EMAPA:16708 + MA:0002725 + RETIRED_EHDAA2:0001460 + TAO:0001174 + XAO:0003202 + ZFA:0001174 + epithelial tissue of pharynx + epithelium of pharynx + pharynx epithelial tissue + pharynx epithelium + uberon + UBERON:0003351 + + pharyngeal epithelium + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + An epithelium that is part of a pharynx [Automatically generated definition]. + OBOL:automatic + + + + + Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] + 2012-08-14 + TAO:0001174 + TAO + ZFIN:curator + + + + + epithelial tissue of pharynx + OBOL:automatic + + + + + epithelium of pharynx + OBOL:automatic + + + + + pharynx epithelial tissue + OBOL:automatic + + + + + pharynx epithelium + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a right lung [Automatically generated definition]. + EMAPA:17663 + MA:0003132 + epithelial tissue of right lung + right lung epithelial tissue + right lung epithelium + uberon + UBERON:0003364 + epithelium of right lung + + + + + An epithelium that is part of a right lung [Automatically generated definition]. + OBOL:automatic + + + + + epithelial tissue of right lung + OBOL:automatic + + + + + right lung epithelial tissue + OBOL:automatic + + + + + right lung epithelium + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a left lung [Automatically generated definition]. + EMAPA:17655 + MA:0003131 + epithelial tissue of left lung + left lung epithelial tissue + left lung epithelium + uberon + UBERON:0003365 + epithelium of left lung + + + + + An epithelium that is part of a left lung [Automatically generated definition]. + OBOL:automatic + + + + + epithelial tissue of left lung + OBOL:automatic + + + + + left lung epithelial tissue + OBOL:automatic + + + + + left lung epithelium + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a digestive tract [Automatically generated definition]. + EMAPA:18815 + MA:0003202 + digestive tract gland + gland of digestive tract + gland of lower gastrointestinal tract + gut gland + lower gastrointestinal tract gland + uberon + UBERON:0003408 + gland of digestive tract + + + + + A gland that is part of a digestive tract [Automatically generated definition]. + OBOL:automatic + + + + + digestive tract gland + OBOL:automatic + + + + + gland of digestive tract + OBOL:automatic + + + + + gland of lower gastrointestinal tract + OBOL:automatic + + + + + gut gland + MA:0003202 + + + + + lower gastrointestinal tract gland + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + An adipose tissue that is part of a dermis [Automatically generated definition]. + MA:0000798 + adipose tissue of dermis + dermis fat tissue + dermis fatty tissue + fat tissue of dermis + fatty tissue of dermis + uberon + UBERON:0003426 + + dermis adipose tissue + + + + + An adipose tissue that is part of a dermis [Automatically generated definition]. + OBOL:automatic + + + + + adipose tissue of dermis + OBOL:automatic + + + + + dermis fat tissue + OBOL:automatic + + + + + dermis fatty tissue + OBOL:automatic + + + + + fat tissue of dermis + OBOL:automatic + + + + + fatty tissue of dermis + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + An artery that is part of a respiratory system [Automatically generated definition]. + EMAPA:37569 + MA:0001804 + uberon + UBERON:0003469 + respiratory system artery + + + + + An artery that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37569 + MA:th + + + + + + + + + + + + + + + + + + + + + An artery that is part of a thoracic cavity[cjm]. + in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity + EMAPA:37241 + MA:0001902 + MESH:D013895 + uberon + thoracic artery + UBERON:0003473 + thoracic cavity artery + + + + + An artery that is part of a thoracic cavity[cjm]. + + + + + + in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity + MA + + + + + EMAPA:37241 + MA:th + + + + + thoracic artery + MESH:A07.231.114.891 + + + + + + + + + + + + + + + + + + + + + + + + + + A vein that is part of a respiratory system [Automatically generated definition]. + EMAPA:37584 + MA:0001809 + MA:0001810 + apparatus respiratorius vein + respiratory system vein + vein of apparatus respiratorius + vein of respiratory system + uberon + UBERON:0003476 + respiratory system venous blood vessel + + + + + A vein that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37584 + MA:th + + + + + apparatus respiratorius vein + OBOL:automatic + + + + + respiratory system vein + OBOL:automatic + + + + + vein of apparatus respiratorius + OBOL:automatic + + + + + vein of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + A vein that is part of a thoracic cavity [Automatically generated definition]. + EMAPA:37242 + MA:0001903 + cavity of chest vein + cavity of thorax vein + chest cavity vein + pectoral cavity vein + vein of cavity of chest + vein of cavity of thorax + vein of chest cavity + vein of pectoral cavity + vein of thoracic cavity + uberon + UBERON:0003479 + thoracic cavity vein + + + + + A vein that is part of a thoracic cavity [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37242 + MA:th + + + + + cavity of chest vein + OBOL:automatic + + + + + cavity of thorax vein + OBOL:automatic + + + + + chest cavity vein + OBOL:automatic + + + + + pectoral cavity vein + OBOL:automatic + + + + + vein of cavity of chest + OBOL:automatic + + + + + vein of cavity of thorax + OBOL:automatic + + + + + vein of chest cavity + OBOL:automatic + + + + + vein of pectoral cavity + OBOL:automatic + + + + + vein of thoracic cavity + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. + EMAPA:37575 + MA:0001808 + apparatus respiratorius blood capillary endothelium + apparatus respiratorius capillary endothelium + apparatus respiratorius capillary vessel endothelium + apparatus respiratorius endothelium of blood capillary + apparatus respiratorius endothelium of capillary + apparatus respiratorius endothelium of capillary vessel + blood capillary endothelium of apparatus respiratorius + blood capillary endothelium of respiratory system + capillary endothelium of apparatus respiratorius + capillary endothelium of respiratory system + capillary vessel endothelium of apparatus respiratorius + capillary vessel endothelium of respiratory system + endothelium of blood capillary of apparatus respiratorius + endothelium of blood capillary of respiratory system + endothelium of capillary of apparatus respiratorius + endothelium of capillary of respiratory system + endothelium of capillary vessel of apparatus respiratorius + endothelium of capillary vessel of respiratory system + respiratory system blood capillary endothelium + respiratory system capillary vessel endothelium + respiratory system endothelium of blood capillary + respiratory system endothelium of capillary + respiratory system endothelium of capillary vessel + uberon + UBERON:0003489 + respiratory system capillary endothelium + + + + + + + + + + + true + + + + + + An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37575 + MA:th + + + + + apparatus respiratorius blood capillary endothelium + OBOL:automatic + + + + + apparatus respiratorius capillary endothelium + OBOL:automatic + + + + + apparatus respiratorius capillary vessel endothelium + OBOL:automatic + + + + + apparatus respiratorius endothelium of blood capillary + OBOL:automatic + + + + + apparatus respiratorius endothelium of capillary + OBOL:automatic + + + + + apparatus respiratorius endothelium of capillary vessel + OBOL:automatic + + + + + blood capillary endothelium of apparatus respiratorius + OBOL:automatic + + + + + blood capillary endothelium of respiratory system + OBOL:automatic + + + + + capillary endothelium of apparatus respiratorius + OBOL:automatic + + + + + capillary endothelium of respiratory system + OBOL:automatic + + + + + capillary vessel endothelium of apparatus respiratorius + OBOL:automatic + + + + + capillary vessel endothelium of respiratory system + OBOL:automatic + + + + + endothelium of blood capillary of apparatus respiratorius + OBOL:automatic + + + + + endothelium of blood capillary of respiratory system + OBOL:automatic + + + + + endothelium of capillary of apparatus respiratorius + OBOL:automatic + + + + + endothelium of capillary of respiratory system + OBOL:automatic + + + + + endothelium of capillary vessel of apparatus respiratorius + OBOL:automatic + + + + + endothelium of capillary vessel of respiratory system + OBOL:automatic + + + + + respiratory system blood capillary endothelium + OBOL:automatic + + + + + respiratory system capillary vessel endothelium + OBOL:automatic + + + + + respiratory system endothelium of blood capillary + OBOL:automatic + + + + + respiratory system endothelium of capillary + OBOL:automatic + + + + + respiratory system endothelium of capillary vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + A venule that is part of a respiratory system [Automatically generated definition]. + EMAPA:37587 + MA:0001813 + apparatus respiratorius venule + venule of apparatus respiratorius + venule of respiratory system + uberon + UBERON:0003494 + respiratory system venule + + + + + A venule that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37587 + MA:th + + + + + apparatus respiratorius venule + OBOL:automatic + + + + + venule of apparatus respiratorius + OBOL:automatic + + + + + venule of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An arteriole that is part of a respiratory system [Automatically generated definition]. + EMAPA:37568 + MA:0001803 + uberon + UBERON:0003495 + respiratory system arteriole + + + + + + + + + + + true + + + + + + An arteriole that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37568 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a head [Automatically generated definition]. + + EMAPA:36610 + MA:0000575 + adult head blood vessel + blood vessel of adult head + blood vessel of head + uberon + UBERON:0003496 + head blood vessel + + + + + + + + + + + true + + + + + + A blood vessel that is part of a head [Automatically generated definition]. + OBOL:automatic + + + + + adult head blood vessel + OBOL:automatic + + + + + blood vessel of adult head + OBOL:automatic + + + + + blood vessel of head + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a heart [Automatically generated definition]. + EMAPA:35397 + MA:0002483 + blood vessel of heart + uberon + cardiac blood vessel + UBERON:0003498 + + heart blood vessel + + + + + A blood vessel that is part of a heart [Automatically generated definition]. + OBOL:automatic + + + + + blood vessel of heart + OBOL:automatic + + + + + cardiac blood vessel + EMAPA:35397 + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a brain [Automatically generated definition]. + EMAPA:35182 + MA:0002769 + blood vessel of brain + uberon + UBERON:0003499 + + brain blood vessel + + + + + A blood vessel that is part of a brain [Automatically generated definition]. + OBOL:automatic + + + + + blood vessel of brain + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a neck [Automatically generated definition]. + EMAPA:37236 + MA:0000583 + blood vessel of neck + blood vessel of neck (volume) + neck (volume) blood vessel + uberon + UBERON:0003502 + neck blood vessel + + + + + A blood vessel that is part of a neck [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37236 + MA:th + + + + + blood vessel of neck + OBOL:automatic + + + + + blood vessel of neck (volume) + OBOL:automatic + + + + + neck (volume) blood vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a respiratory system [Automatically generated definition]. + EMAPA:35731 + EMAPA:35995 + MA:0001799 + apparatus respiratorius blood vessel + blood vessel of apparatus respiratorius + blood vessel of respiratory system + uberon + UBERON:0003504 + respiratory system blood vessel + + + + + A blood vessel that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + apparatus respiratorius blood vessel + OBOL:automatic + + + + + blood vessel of apparatus respiratorius + OBOL:automatic + + + + + blood vessel of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. + EMAPA:35144 + MA:0000061 + uberon + UBERON:0003509 + + only in MA - supertype of artery, arteriole, aorta. + arterial blood vessel + + + + + A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a lung [Automatically generated definition]. + EMAPA:32867 + MA:0002457 + blood vessel of lung + uberon + pulmonary vascular element + UBERON:0003512 + + lung blood vessel + + + + + A blood vessel that is part of a lung [Automatically generated definition]. + OBOL:automatic + + + + + blood vessel of lung + OBOL:automatic + + + + + pulmonary vascular element + EMAPA:32867 + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a trunk [Automatically generated definition]. + EMAPA:37237 + MA:0000511 + blood vessel of torso + blood vessel of trunk + torso blood vessel + uberon + UBERON:0003513 + trunk blood vessel + + + + + A blood vessel that is part of a trunk [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37237 + MA:th + + + + + blood vessel of torso + OBOL:automatic + + + + + blood vessel of trunk + OBOL:automatic + + + + + torso blood vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a thoracic cavity [Automatically generated definition]. + EMAPA:37240 + MA:0000554 + blood vessel of cavity of chest + blood vessel of cavity of thorax + blood vessel of chest cavity + blood vessel of pectoral cavity + blood vessel of thoracic cavity + cavity of chest blood vessel + cavity of thorax blood vessel + chest cavity blood vessel + pectoral cavity blood vessel + uberon + UBERON:0003519 + thoracic cavity blood vessel + + + + + A blood vessel that is part of a thoracic cavity [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37240 + MA:th + + + + + blood vessel of cavity of chest + OBOL:automatic + + + + + blood vessel of cavity of thorax + OBOL:automatic + + + + + blood vessel of chest cavity + OBOL:automatic + + + + + blood vessel of pectoral cavity + OBOL:automatic + + + + + blood vessel of thoracic cavity + OBOL:automatic + + + + + cavity of chest blood vessel + OBOL:automatic + + + + + cavity of thorax blood vessel + OBOL:automatic + + + + + chest cavity blood vessel + OBOL:automatic + + + + + pectoral cavity blood vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + A capillary that is part of a respiratory system [Automatically generated definition]. + EMAPA:37574 + MA:0001807 + apparatus respiratorius blood capillary + apparatus respiratorius capillary + apparatus respiratorius capillary vessel + blood capillary of apparatus respiratorius + blood capillary of respiratory system + capillary of apparatus respiratorius + capillary of respiratory system + capillary vessel of apparatus respiratorius + capillary vessel of respiratory system + respiratory system blood capillary + respiratory system capillary vessel + uberon + UBERON:0003526 + respiratory system capillary + + + + + A capillary that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37574 + MA:th + + + + + apparatus respiratorius blood capillary + OBOL:automatic + + + + + apparatus respiratorius capillary + OBOL:automatic + + + + + apparatus respiratorius capillary vessel + OBOL:automatic + + + + + blood capillary of apparatus respiratorius + OBOL:automatic + + + + + blood capillary of respiratory system + OBOL:automatic + + + + + capillary of apparatus respiratorius + OBOL:automatic + + + + + capillary of respiratory system + OBOL:automatic + + + + + capillary vessel of apparatus respiratorius + OBOL:automatic + + + + + capillary vessel of respiratory system + OBOL:automatic + + + + + respiratory system blood capillary + OBOL:automatic + + + + + respiratory system capillary vessel + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A gray matter that is part of a brain [Automatically generated definition]. + + EMAPA:35184 + MA:0000810 + NCIT:C49333 + UMLS:C1707348 + brain grey matter + brain grey substance + gray matter of brain + grey matter of brain + grey substance of brain + uberon + UBERON:0003528 + brain gray matter + + + + + A gray matter that is part of a brain [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1707348 + ncithesaurus:Cerebral_Gray_Matter + + + + + brain grey matter + MA:0000810 + + + + + brain grey substance + OBOL:automatic + + + + + gray matter of brain + OBOL:automatic + + + + + grey matter of brain + OBOL:automatic + + + + + grey substance of brain + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a head [Automatically generated definition]. + EMAPA:16098 + MA:0000577 + adult head connective tissue + adult head portion of connective tissue + adult head textus connectivus + connective tissue of adult head + connective tissue of head + head portion of connective tissue + head textus connectivus + portion of connective tissue of adult head + portion of connective tissue of head + textus connectivus of adult head + textus connectivus of head + uberon + UBERON:0003566 + head connective tissue + + + + + A portion of connective tissue that is part of a head [Automatically generated definition]. + OBOL:automatic + + + + + adult head connective tissue + OBOL:automatic + + + + + adult head portion of connective tissue + OBOL:automatic + + + + + adult head textus connectivus + OBOL:automatic + + + + + connective tissue of adult head + OBOL:automatic + + + + + connective tissue of head + OBOL:automatic + + + + + head portion of connective tissue + OBOL:automatic + + + + + head textus connectivus + OBOL:automatic + + + + + portion of connective tissue of adult head + OBOL:automatic + + + + + portion of connective tissue of head + OBOL:automatic + + + + + textus connectivus of adult head + OBOL:automatic + + + + + textus connectivus of head + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a neck [Automatically generated definition]. + EMAPA:37250 + MA:0000585 + connective tissue of neck + connective tissue of neck (volume) + neck (volume) connective tissue + neck (volume) portion of connective tissue + neck (volume) textus connectivus + neck portion of connective tissue + neck textus connectivus + portion of connective tissue of neck + portion of connective tissue of neck (volume) + textus connectivus of neck + textus connectivus of neck (volume) + uberon + UBERON:0003568 + neck connective tissue + + + + + A portion of connective tissue that is part of a neck [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37250 + MA:th + + + + + connective tissue of neck + OBOL:automatic + + + + + connective tissue of neck (volume) + OBOL:automatic + + + + + neck (volume) connective tissue + OBOL:automatic + + + + + neck (volume) portion of connective tissue + OBOL:automatic + + + + + neck (volume) textus connectivus + OBOL:automatic + + + + + neck portion of connective tissue + OBOL:automatic + + + + + neck textus connectivus + OBOL:automatic + + + + + portion of connective tissue of neck + OBOL:automatic + + + + + portion of connective tissue of neck (volume) + OBOL:automatic + + + + + textus connectivus of neck + OBOL:automatic + + + + + textus connectivus of neck (volume) + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. + EMAPA:35968 + EMAPA:35977 + MA:0001814 + apparatus respiratorius connective tissue + apparatus respiratorius portion of connective tissue + apparatus respiratorius textus connectivus + connective tissue of apparatus respiratorius + connective tissue of respiratory system + portion of connective tissue of apparatus respiratorius + portion of connective tissue of respiratory system + respiratory system portion of connective tissue + respiratory system textus connectivus + textus connectivus of apparatus respiratorius + textus connectivus of respiratory system + uberon + UBERON:0003570 + respiratory system connective tissue + + + + + A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + apparatus respiratorius connective tissue + OBOL:automatic + + + + + apparatus respiratorius portion of connective tissue + OBOL:automatic + + + + + apparatus respiratorius textus connectivus + OBOL:automatic + + + + + connective tissue of apparatus respiratorius + OBOL:automatic + + + + + connective tissue of respiratory system + OBOL:automatic + + + + + portion of connective tissue of apparatus respiratorius + OBOL:automatic + + + + + portion of connective tissue of respiratory system + OBOL:automatic + + + + + respiratory system portion of connective tissue + OBOL:automatic + + + + + respiratory system textus connectivus + OBOL:automatic + + + + + textus connectivus of apparatus respiratorius + OBOL:automatic + + + + + textus connectivus of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. + EMAPA:37548 + MA:0002409 + connective tissue of lower respiratory tract + lower respiratory tract portion of connective tissue + lower respiratory tract textus connectivus + portion of connective tissue of lower respiratory tract + textus connectivus of lower respiratory tract + uberon + UBERON:0003580 + lower respiratory tract connective tissue + + + + + A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37548 + MA:th + + + + + connective tissue of lower respiratory tract + OBOL:automatic + + + + + lower respiratory tract portion of connective tissue + OBOL:automatic + + + + + lower respiratory tract textus connectivus + OBOL:automatic + + + + + portion of connective tissue of lower respiratory tract + OBOL:automatic + + + + + textus connectivus of lower respiratory tract + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a dermis [Automatically generated definition]. + EMAPA:36509 + MA:0000799 + connective tissue of dermis + dermis portion of connective tissue + dermis textus connectivus + portion of connective tissue of dermis + textus connectivus of dermis + uberon + UBERON:0003585 + + dermis connective tissue + + + + + A portion of connective tissue that is part of a dermis [Automatically generated definition]. + OBOL:automatic + + + + + connective tissue of dermis + OBOL:automatic + + + + + dermis portion of connective tissue + OBOL:automatic + + + + + dermis textus connectivus + OBOL:automatic + + + + + portion of connective tissue of dermis + OBOL:automatic + + + + + textus connectivus of dermis + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a trunk [Automatically generated definition]. + EMAPA:37252 + MA:0000513 + connective tissue of torso + connective tissue of trunk + portion of connective tissue of torso + portion of connective tissue of trunk + textus connectivus of torso + textus connectivus of trunk + torso connective tissue + torso portion of connective tissue + torso textus connectivus + trunk portion of connective tissue + trunk textus connectivus + uberon + UBERON:0003586 + trunk connective tissue + + + + + A portion of connective tissue that is part of a trunk [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37252 + MA:th + + + + + connective tissue of torso + OBOL:automatic + + + + + connective tissue of trunk + OBOL:automatic + + + + + portion of connective tissue of torso + OBOL:automatic + + + + + portion of connective tissue of trunk + OBOL:automatic + + + + + textus connectivus of torso + OBOL:automatic + + + + + textus connectivus of trunk + OBOL:automatic + + + + + torso connective tissue + OBOL:automatic + + + + + torso portion of connective tissue + OBOL:automatic + + + + + torso textus connectivus + OBOL:automatic + + + + + trunk portion of connective tissue + OBOL:automatic + + + + + trunk textus connectivus + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. + EMAPA:37255 + MA:0000555 + cavity of chest connective tissue + cavity of chest portion of connective tissue + cavity of chest textus connectivus + cavity of thorax connective tissue + cavity of thorax portion of connective tissue + cavity of thorax textus connectivus + chest cavity connective tissue + chest cavity portion of connective tissue + chest cavity textus connectivus + connective tissue of cavity of chest + connective tissue of cavity of thorax + connective tissue of chest cavity + connective tissue of pectoral cavity + connective tissue of thoracic cavity + pectoral cavity connective tissue + pectoral cavity portion of connective tissue + pectoral cavity textus connectivus + portion of connective tissue of cavity of chest + portion of connective tissue of cavity of thorax + portion of connective tissue of chest cavity + portion of connective tissue of pectoral cavity + portion of connective tissue of thoracic cavity + textus connectivus of cavity of chest + textus connectivus of cavity of thorax + textus connectivus of chest cavity + textus connectivus of pectoral cavity + textus connectivus of thoracic cavity + thoracic cavity portion of connective tissue + thoracic cavity textus connectivus + uberon + UBERON:0003593 + thoracic cavity connective tissue + + + + + A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37255 + MA:th + + + + + cavity of chest connective tissue + OBOL:automatic + + + + + cavity of chest portion of connective tissue + OBOL:automatic + + + + + cavity of chest textus connectivus + OBOL:automatic + + + + + cavity of thorax connective tissue + OBOL:automatic + + + + + cavity of thorax portion of connective tissue + OBOL:automatic + + + + + cavity of thorax textus connectivus + OBOL:automatic + + + + + chest cavity connective tissue + OBOL:automatic + + + + + chest cavity portion of connective tissue + OBOL:automatic + + + + + chest cavity textus connectivus + OBOL:automatic + + + + + connective tissue of cavity of chest + OBOL:automatic + + + + + connective tissue of cavity of thorax + OBOL:automatic + + + + + connective tissue of chest cavity + OBOL:automatic + + + + + connective tissue of pectoral cavity + OBOL:automatic + + + + + connective tissue of thoracic cavity + OBOL:automatic + + + + + pectoral cavity connective tissue + OBOL:automatic + + + + + pectoral cavity portion of connective tissue + OBOL:automatic + + + + + pectoral cavity textus connectivus + OBOL:automatic + + + + + portion of connective tissue of cavity of chest + OBOL:automatic + + + + + portion of connective tissue of cavity of thorax + OBOL:automatic + + + + + portion of connective tissue of chest cavity + OBOL:automatic + + + + + portion of connective tissue of pectoral cavity + OBOL:automatic + + + + + portion of connective tissue of thoracic cavity + OBOL:automatic + + + + + textus connectivus of cavity of chest + OBOL:automatic + + + + + textus connectivus of cavity of thorax + OBOL:automatic + + + + + textus connectivus of chest cavity + OBOL:automatic + + + + + textus connectivus of pectoral cavity + OBOL:automatic + + + + + textus connectivus of thoracic cavity + OBOL:automatic + + + + + thoracic cavity portion of connective tissue + OBOL:automatic + + + + + thoracic cavity textus connectivus + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. + MA:0002858 + cardiac elastic tissue + elastic connective tissue of heart + elastic tissue of heart + heart elastic connective tissue + heart textus connectivus elasticus + textus connectivus elasticus of heart + uberon + UBERON:0003610 + + heart elastic tissue + + + + + The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. + MP:0009863 + + + + + cardiac elastic tissue + MP:0009863 + + + + + elastic connective tissue of heart + OBOL:automatic + + + + + elastic tissue of heart + OBOL:automatic + + + + + heart elastic connective tissue + OBOL:automatic + + + + + heart textus connectivus elasticus + OBOL:automatic + + + + + textus connectivus elasticus of heart + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An elastic tissue that is part of a respiratory system [Automatically generated definition]. + EMAPA:37579 + MA:0001820 + apparatus respiratorius elastic connective tissue + apparatus respiratorius elastic tissue + apparatus respiratorius textus connectivus elasticus + elastic connective tissue of apparatus respiratorius + elastic connective tissue of respiratory system + elastic tissue of apparatus respiratorius + elastic tissue of respiratory system + respiratory system elastic connective tissue + respiratory system textus connectivus elasticus + textus connectivus elasticus of apparatus respiratorius + textus connectivus elasticus of respiratory system + uberon + UBERON:0003611 + respiratory system elastic tissue + + + + + An elastic tissue that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37579 + MA:th + + + + + apparatus respiratorius elastic connective tissue + OBOL:automatic + + + + + apparatus respiratorius elastic tissue + OBOL:automatic + + + + + apparatus respiratorius textus connectivus elasticus + OBOL:automatic + + + + + elastic connective tissue of apparatus respiratorius + OBOL:automatic + + + + + elastic connective tissue of respiratory system + OBOL:automatic + + + + + elastic tissue of apparatus respiratorius + OBOL:automatic + + + + + elastic tissue of respiratory system + OBOL:automatic + + + + + respiratory system elastic connective tissue + OBOL:automatic + + + + + respiratory system textus connectivus elasticus + OBOL:automatic + + + + + textus connectivus elasticus of apparatus respiratorius + OBOL:automatic + + + + + textus connectivus elasticus of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An elastic tissue that is part of a circulatory system [Automatically generated definition]. + MA:0002857 + cardiovascular system elastic connective tissue + cardiovascular system textus connectivus elasticus + circulatory system elastic connective tissue + circulatory system elastic tissue + circulatory system textus connectivus elasticus + elastic connective tissue of cardiovascular system + elastic connective tissue of circulatory system + elastic tissue of cardiovascular system + elastic tissue of circulatory system + textus connectivus elasticus of cardiovascular system + textus connectivus elasticus of circulatory system + uberon + UBERON:0003613 + cardiovascular system elastic tissue + + + + + An elastic tissue that is part of a circulatory system [Automatically generated definition]. + OBOL:automatic + + + + + cardiovascular system elastic connective tissue + OBOL:automatic + + + + + cardiovascular system textus connectivus elasticus + OBOL:automatic + + + + + circulatory system elastic connective tissue + OBOL:automatic + + + + + circulatory system elastic tissue + OBOL:automatic + + + + + circulatory system textus connectivus elasticus + OBOL:automatic + + + + + elastic connective tissue of cardiovascular system + OBOL:automatic + + + + + elastic connective tissue of circulatory system + OBOL:automatic + + + + + elastic tissue of cardiovascular system + OBOL:automatic + + + + + elastic tissue of circulatory system + OBOL:automatic + + + + + textus connectivus elasticus of cardiovascular system + OBOL:automatic + + + + + textus connectivus elasticus of circulatory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + Elastic tissue layer that lines a blood vessel layer. + elastic lamina + elastic laminae + EMAPA:36300 + MA:0002856 + blood vessel elastic connective tissue + blood vessel textus connectivus elasticus + elastic connective tissue of blood vessel + elastic tissue of blood vessel + textus connectivus elasticus of blood vessel + vascular elastic lamina + vascular elastic laminae + vascular elastic tissue + uberon + UBERON:0003614 + + blood vessel elastic tissue + + + + + Elastic tissue layer that lines a blood vessel layer. + + + + + + + elastic lamina + MP:0006083 + + + + + elastic laminae + MP:0006083 + + + + + + blood vessel elastic connective tissue + OBOL:automatic + + + + + blood vessel textus connectivus elasticus + OBOL:automatic + + + + + elastic connective tissue of blood vessel + OBOL:automatic + + + + + elastic tissue of blood vessel + OBOL:automatic + + + + + textus connectivus elasticus of blood vessel + OBOL:automatic + + + + + vascular elastic lamina + + + + + + vascular elastic laminae + + + + + + + vascular elastic tissue + MP:0006083 + + + + + + + + + + + + + + + + + + + + + Elastic tissue that is part of a lung [Automatically generated definition]. + MA:0002860 + elastic connective tissue of lung + elastic tissue of lung + lung elastic connective tissue + lung textus connectivus elasticus + textus connectivus elasticus of lung + pulmonary elastic fiber + uberon + UBERON:0003615 + lung elastic tissue + + + + + Elastic tissue that is part of a lung [Automatically generated definition]. + OBOL:automatic + + + + + elastic connective tissue of lung + OBOL:automatic + + + + + elastic tissue of lung + OBOL:automatic + + + + + lung elastic connective tissue + OBOL:automatic + + + + + lung textus connectivus elasticus + OBOL:automatic + + + + + textus connectivus elasticus of lung + OBOL:automatic + + + + + pulmonary elastic fiber + + + + + + + + + + + + + + + + + + + + + + An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. + EMAPA:37565 + MA:0001800 + uberon + UBERON:0003643 + respiratory system arterial blood vessel + + + + + An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37565 + MA:th + + + + + + + + + + + + + + + Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. + One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] + FMA definition includes vasculature + + + AAO:0000325 + AEO:0000123 + EHDAA2:0003123 + FMA:9642 + GAID:609 + MESH:D009417 + NCIT:C13052 + OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ + UMLS:C0027757 + nerve tissue + nervous tissue + portion of neural tissue + uberon + UBERON:0003714 + neural tissue + + + + + Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. + FMA:9642 + + + + + One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] + 2012-06-20 + AAO:0000325 + AAO + AAO:LAP + + + + + FMA definition includes vasculature + FMA + + + + + UMLS:C0027757 + ncithesaurus:Nervous_Tissue + + + + + nerve tissue + FMA:9642 + + + + + nervous tissue + FMA:9642 + + + + + portion of neural tissue + FMA:9642 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mucous membrane that lines the mouth. + this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) + the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. + + + BTO:0002860 + CALOHA:TS-0716 + EMAPA:26937 + FMA:59660 + GAID:951 + MA:0002794 + MESH:D009061 + NCIT:C77637 + UMLS:C0026639 + mouth mucosa + mouth mucous membrane + mouth organ mucosa + mucosa of mouth + mucous membrane of mouth + oral mucous membrane + oral part of viscerocranial mucosa + tunica mucosa oris + uberon + buccal mucosa + mucosal lining of mouth + oral mucosa + tunica mucosa oris + UBERON:0003729 + + mouth mucosa + + + + + A mucous membrane that lines the mouth. + + + + + + the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. + + + + + + UMLS:C0026639 + ncithesaurus:Oral_Mucosa + + + + + mouth mucosa + FMA:59660 + + + + + mouth mucous membrane + OBOL:accepted + + + + + mouth organ mucosa + OBOL:accepted + + + + + mucosa of mouth + OBOL:accepted + + + + + mucous membrane of mouth + FMA:59660 + + + + + oral part of viscerocranial mucosa + FMA:59660 + + + + + tunica mucosa oris + FMA:59660 + FMA:TA + + + + + + buccal mucosa + GAID:951 + + + + + mucosal lining of mouth + MA:0002794 + + + + + oral mucosa + GAID:951 + + + + + tunica mucosa oris + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any muscle organ that is part of a respiratory system [Automatically generated definition]. + EMAPA:35733 + MA:0001828 + apparatus respiratorius muscle organ + muscle organ of apparatus respiratorius + muscle organ of respiratory system + respiratory system muscle organ + uberon + UBERON:0003831 + respiratory system muscle + + + + + Any muscle organ that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + apparatus respiratorius muscle organ + OBOL:automatic + + + + + muscle organ of apparatus respiratorius + OBOL:automatic + + + + + muscle organ of respiratory system + OBOL:automatic + + + + + respiratory system muscle organ + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a thorax [Automatically generated definition]. + EMAPA:37238 + MA:0000558 + blood vessel of thorax + thorax blood vessel + uberon + upper body blood vessel + UBERON:0003834 + thoracic segment blood vessel + + + + + A blood vessel that is part of a thorax [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37238 + MA:th + + + + + blood vessel of thorax + OBOL:automatic + + + + + thorax blood vessel + OBOL:automatic + + + + + upper body blood vessel + MA:0000558 + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a thorax [Automatically generated definition]. + EMAPA:37253 + MA:0000560 + connective tissue of thorax + portion of connective tissue of thorax + textus connectivus of thorax + thorax connective tissue + thorax portion of connective tissue + thorax textus connectivus + uberon + upper body connective tissue + UBERON:0003837 + thoracic segment connective tissue + + + + + A portion of connective tissue that is part of a thorax [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37253 + MA:th + + + + + connective tissue of thorax + OBOL:automatic + + + + + portion of connective tissue of thorax + OBOL:automatic + + + + + textus connectivus of thorax + OBOL:automatic + + + + + thorax connective tissue + OBOL:automatic + + + + + thorax portion of connective tissue + OBOL:automatic + + + + + thorax textus connectivus + OBOL:automatic + + + + + upper body connective tissue + MA:0000560 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical space that surrounded_by a neural tube. + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + UBERON:0005713 + AAO:0011073 + EHDAA2:0001269 + EHDAA:2889 + EHDAA:914 + EMAPA:16167 + VHOG:0001119 + XAO:0000252 + cavity of neural tube + lumen of neural tube + neural tube neural lumen + prosencoel + uberon + central lumen + neural lumen + neurocoel + UBERON:0003842 + neural tube lumen + + + + + An anatomical space that surrounded_by a neural tube. + OBOL:automatic + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] + 2012-09-17 + VHOG:0001119 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + cavity of neural tube + + + + + + lumen of neural tube + + + + + + neural tube neural lumen + EHDAA2:0001269 + + + + + neural lumen + EHDAA:2889 + + + + + neurocoel + VHOG:0001119 + + + + + + + + + + + + + + + + + + + + + + + + + + + A neural crest that has_potential_to_developmentally_contribute_to a midbrain. + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] + EFO:0003591 + EHDAA2:0001101 + EHDAA:360 + TAO:0000935 + VHOG:0000796 + ZFA:0000935 + mesencephalic neural crest + neural crest midbrain + uberon + UBERON:0003849 + + + mesencephalic neural crest + + + + + + ZFA + + + + + A neural crest that has_potential_to_developmentally_contribute_to a midbrain. + OBOL:automatic + + + + + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] + 2012-09-17 + VHOG:0000796 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + + + + + mesencephalic neural crest + ZFA:0000935 + + + + + neural crest midbrain + ZFA:0000935 + + + + + + + + + + + + + + + + + + + + + + + + + + + A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. + Cranial neural crest that is part of the hindbrain.[TAO] + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] + EHDAA2:0001628 + EHDAA:362 + EMAPA:35747 + TAO:0007063 + VHOG:0001210 + ZFA:0007063 + neural crest hindbrain + rhombencephalic neural crest + uberon + rhombomere neural crest + UBERON:0003852 + + rhombencephalon neural crest + + + + + + ZFA + + + + + A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. + OBOL:automatic + + + + + Cranial neural crest that is part of the hindbrain.[TAO] + 2012-08-14 + TAO:0007063 + TAO + ZFIN:curator + + + + + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] + 2012-09-17 + VHOG:0001210 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + + + + + neural crest hindbrain + ZFA:0007063 + + + + + rhombencephalic neural crest + ZFA:0007063 + + + + + rhombomere neural crest + EMAPA:35747 + + + + + + + + + + + + + + + + + + + + + + + + + + A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] + EHDAA:696 + EMAPA:16163 + EMAPA:16881 + VHOG:0001006 + neural crest spinal cord + uberon + spinal neural crest + UBERON:0003853 + spinal cord neural crest + + + + + A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. + OBOL:automatic + + + + + We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] + 2012-09-17 + VHOG:0001006 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 + + + + + neural crest spinal cord + VHOG:0001006 + + + + + spinal neural crest + VHOG:0001006 + + + + + + + + + + + + + + + + + + + + + + + + + + A neural plate that develops_from a future spinal cord. + Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] + FMA:312957 + TAO:0007021 + VHOG:0000439 + ZFA:0007021 + neural plate of spinal cord + uberon + UBERON:0003854 + spinal cord neural plate + + + + + + + + + + + ZFA + + + + + A neural plate that develops_from a future spinal cord. + OBOL:automatic + + + + + Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] + 2012-09-17 + VHOG:0000439 + VHOG + + + + + + (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] + 2012-09-17 + VHOG:0000439 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 + + + + + neural plate of spinal cord + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical cavity that has the potential to develop into a coelemic cavity lumen. + uberon + body cavity precursor + UBERON:0003886 + + + future coelemic cavity lumen + + + + + An anatomical cavity that has the potential to develop into a coelemic cavity lumen. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom + consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults + (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] + + + EHDAA:251 + EMAPA:16088 + NCIT:C34195 + UMLS:C1512940 + VHOG:0000316 + somatic coelom + uberon + UBERON:0003887 + + intraembryonic coelom + + + + + + + + + + + Wikipedia + + + + + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom + MGI:anna + MP:0012187 + + + + + (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] + 2012-09-17 + VHOG:0000316 + VHOG + + ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 + + + + + UMLS:C1512940 + ncithesaurus:Intraembryonic_Coelom + + + + + somatic coelom + + + + + + + + + + + Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. + contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers + AEO:0000114 + EHDAA2:0003114 + FBbt:00007474 + epithelial or endothelial tube + uberon + UBERON:0003914 + epithelial tube + + + + + Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. + + GO:0060562 + + + + + + + + + + Any endothelium that has the quality of being cylindrical [Automatically generated definition]. + uberon + UBERON:0003915 + endothelial tube + + + + + Any endothelium that has the quality of being cylindrical [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that carries blood from the capillaries toward the heart + EMAPA:35932 + FMA:86188 + MA:0000066 + segment of venous tree organ + venous tree organ segment + uberon + UBERON:0003920 + Compare to: vein + venous blood vessel + + + + + A blood vessel that carries blood from the capillaries toward the heart + + + + + + segment of venous tree organ + FMA:86188 + + + + + venous tree organ segment + FMA:86188 + + + + + + + + + + + + + + + + + + + + + + + + + + A duct that is part of a digestive system [Automatically generated definition]. + TAO:0005162 + ZFA:0005162 + duct of digestive system + duct of gastrointestinal system + gastrointestinal system duct + uberon + UBERON:0003928 + digestive system duct + + + + + A duct that is part of a digestive system [Automatically generated definition]. + OBOL:automatic + + + + + duct of digestive system + OBOL:automatic + + + + + duct of gastrointestinal system + OBOL:automatic + + + + + gastrointestinal system duct + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that lines the lumen of the digestive tract. + Epithelium lining the lumen of the gut.[TAO] + + + BTO:0000956 + EHDAA2:0004567 + EMAPA:32928 + MA:0003201 + NCIT:C12963 + TAO:0005123 + UMLS:C0836205 + XAO:0003200 + ZFA:0005123 + digestive tract epithelial tissue + epithelial tissue of digestive tract + epithelial tissue of gut + epithelium of digestive tract + epithelium of gut + gastrodermis + gut epithelial tissue + gut epithelium + uberon + alimentary tract epithelium + UBERON:0003929 + digestive tract epithelium + + + + + An epithelium that lines the lumen of the digestive tract. + + + + + + Epithelium lining the lumen of the gut.[TAO] + 2012-08-14 + TAO:0005123 + TAO + ZFIN:curator + + + + + UMLS:C0836205 + ncithesaurus:Gut_Epithelium + + + + + digestive tract epithelial tissue + OBOL:automatic + + + + + epithelial tissue of digestive tract + OBOL:automatic + + + + + epithelial tissue of gut + OBOL:automatic + + + + + epithelium of digestive tract + OBOL:automatic + + + + + epithelium of gut + OBOL:automatic + + + + + gastrodermis + BGEE:ANN + NCBITaxon:6073 + + + + + + gut epithelial tissue + OBOL:automatic + + + + + gut epithelium + EHDAA2:0004567 + MA:0003201 + ZFA:0005123 + + + + + alimentary tract epithelium + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity + EMAPA:37841 + cutaneous elastic fiber + dermal elastic fiber + uberon + UBERON:0003967 + + cutaneous elastic tissue + + + + + The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity + MP:0008418 + + + + + EMAPA:37841 + MA:th + + + + + cutaneous elastic fiber + MP:0008418 + + + + + dermal elastic fiber + MP:0008418 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The connection between the embryo proper and extraembryonic tissues + uberon + UBERON:0004015 + + embryonic-extraembryonic boundary + + + + + The connection between the embryo proper and extraembryonic tissues + MP:0003890 + + + + + + + + + + + + + + + A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. + Not to be confused with 'dermatome segment of skin'. + + + AAO:0011028 + AEO:0001017 + EHDAA2_RETIRED:0003428 + EHDAA:1719 + EHDAA:1725 + EHDAA:1731 + EHDAA:1737 + EMAPA:32838 + FMA:295656 + NCIT:C61572 + UMLS:C0180383 + XAO:0000220 + cutis plate + dermatomal mesenchyme + uberon + epimere mesoderm + mesenchyma dermatomiale + UBERON:0004016 + + dermatome + + + + + + + AEO + + + + + + + + + + + EHDAA2-abduced + + + + + A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. + AEO:0001017 + AEO:JB + + + + + UMLS:C0180383 + ncithesaurus:Dermatome + + + + + cutis plate + + + + + + dermatomal mesenchyme + + + + + + mesenchyma dermatomiale + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells + As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] + germinal neuroepithelial layer + germinal neuroepithelium + original neural tube + uberon + UBERON:0004022 + + germinal neuroepithelium + + + + + + NCBIBook:NBK10047 + + + + + The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells + + MP:0004261 + + + + + germinal neuroepithelial layer + + + + + + germinal neuroepithelium + NCBIBook:NBK10047 + + + + + original neural tube + NCBIBook:NBK10047 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium + consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure + The layer of undifferentiated, proliferating cells that line the neural tube lumen + ependymal layer + EMAPA:17152 + EMAPA:35362 + EMAPA_RETIRED:16783 + MA:0003193 + neural tube ependymal layer + neural tube ventricular germinal zone + neural tube ventricular zone + neural tube ependymal zone + uberon + UBERON:0004060 + + neural tube ventricular layer + + + + + + NCBIBook:NBK10047 + + + + + + + + + + + NCBIBook:NBK10047 + + + + + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium + + MP:0009689 + + + + + The layer of undifferentiated, proliferating cells that line the neural tube lumen + MP:0009689 + + + + + ependymal layer + NCBIBook:NBK10047 + + + + + neural tube ependymal layer + NCBIBook:NBK10047 + + + + + neural tube ventricular germinal zone + NCBIBook:NBK10047 + + + + + neural tube ventricular zone + MP:0009689 + + + + + neural tube ependymal zone + MP:0009689 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. + + EMAPA:17148 + EMAPA:35360 + neural tube intermediate zone + uberon + future brain marginal layer + UBERON:0004061 + + neural tube mantle layer + + + + + + NCBIBook:NBK10047 + + + + + + + + + + + by division + NCBIBook:NBK10047 + + + + + The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. + + MP:0009690 + + + + + neural tube intermediate zone + + MP:0009690 + + + + + future brain marginal layer + EMAPA:35360 + + + + + + + + + + + + + + + + + + + + + + + + + + + The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter + + EMAPA:17151 + neural tube marginal zone + uberon + brain marginal zone + UBERON:0004062 + + neural tube marginal layer + + + + + + + + + + + forms from axons + + + + + The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter + + MP:0009691 + + + + + neural tube marginal zone + MP:0009691 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + + 2 + + + + + + + + + + + + + + + + + + Any tube, opening or passage that connects two distinct anatomical spaces. + FMA has both conduit and conduit space. In EHDAA2 this is a surface feature + + + AEO:0000080 + EHDAA2:0003080 + FMA:242873 + foramen + foramina + uberon + opening + ostia + ostium + UBERON:0004111 + anatomical conduit + + + + + Any tube, opening or passage that connects two distinct anatomical spaces. + + + + + + FMA has both conduit and conduit space. In EHDAA2 this is a surface feature + FMA + + + + + foramen + EHDAA2:0003080 + + + + + foramina + + + + + + + ostia + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the endoderm. + Grouping term for query purposes + uberon + UBERON:0004119 + + endoderm-derived structure + + + + + An anatomical structure that develops (entirely or partially) from the endoderm. + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the mesoderm. + Grouping term for query purposes + FBbt:00025998 + mesodermal derivative + uberon + UBERON:0004120 + + mesoderm-derived structure + + + + + An anatomical structure that develops (entirely or partially) from the mesoderm. + + + + + + mesodermal derivative + FBbt:00025998 + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops (entirely or partially) from the ectoderm. + Grouping term for query purposes + FBbt:00025990 + ectodermal deriviative + uberon + UBERON:0004121 + + ectoderm-derived structure + + + + + An anatomical structure that develops (entirely or partially) from the ectoderm. + + + + + + ectodermal deriviative + FBbt:00025990 + + + + + + + + + + + + + + + The first recognizable structure derived from the heart field + TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO + (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] + EHDAA2:0000215 + EMAPA:16106 + VHOG:0000975 + myocardial plate + uberon + cardiac crescent + cardiogenic crescent + heart rudiment + UBERON:0004139 + + cardiogenic plate + + + + + The first recognizable structure derived from the heart field + GO:0003142 + + + + + (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] + 2012-09-17 + VHOG:0000975 + VHOG + + PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) + + + + + myocardial plate + EHDAA2:0000215 + + + + + cardiac crescent + EMAPA:16106 + + + + + cardiogenic crescent + GO:0003142 + + + + + + + + + + + + + + + + + + + + + + + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. + this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] + XAO:0004185 + first heart field + primary heart field + uberon + FHF + PHF + heart field + UBERON:0004140 + primary heart field + + + + + + + + + + + GO:0003128 + + + + + + + + + + + BGEE:ann + + + + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. + GO:0003138 + GOC:mtg_heart + GOC:rl + + + + + this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] + GO + + + + + first heart field + XAO:0004185 + + + + + primary heart field + + XAO:0004185 + + + + + FHF + XAO:0004185 + + + + + + PHF + XAO:0004185 + + + + + + heart field + XAO:0004185 + + + + + + + + + + + + + + + + + + + + + + + An epithelial tube that will give rise to the mature heart. + the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. + AAO:0010411 + EFO:0003526 + EMAPA:32685 + NCIT:C34161 + TAO:0000360 + XAO:0000337 + ZFA:0000360 + embryonic heart tube + endocardial heart tube + endocardial tube + uberon + UBERON:0004141 + + + + heart tube + + + + + + + + + + + ZFA-modified + + + + + An epithelial tube that will give rise to the mature heart. + GO:0003143 + GOC:mtg_heart + + + + + the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. + MP:0012700 + + + + + embryonic heart tube + GO:0003143 + + + + + endocardial heart tube + MP:0012700 + + + + + endocardial tube + XAO:0000337 + + + + + + + + + + + + + + + + + + + + + + + + + + The outflow tract septum is a partition in the outflow tract + uberon + UBERON:0004142 + outflow tract septum + + + + + The outflow tract septum is a partition in the outflow tract + GO:0003148 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The outflow tract is the portion of the heart through which blood flows into the arteries + Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] + EHDAA2:0001351 + EHDAA:464 + EHDAA:798 + EMAPA:16346 + MA:0000100 + VHOG:0000670 + XAO:0004139 + cardiac outflow tract + heart outflow tract + uberon + arterial (outflow) pole + UBERON:0004145 + + outflow tract + + + + + The outflow tract is the portion of the heart through which blood flows into the arteries + GO:0003151 + + + + + cardiac outflow tract + + + + + + arterial (outflow) pole + + + + + + + + + + + + + + + + + A cardiac chamber surrounds an enclosed cavity within the heart + + FMA:7095 + OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw + chamber of heart + heart chamber + uberon + UBERON:0004151 + generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus + cardiac chamber + + + + + A cardiac chamber surrounds an enclosed cavity within the heart + GO:0003205 + + + + + + + + + + + + + + + + + + + + + + + + + + + Organ that is part of the hematopoietic system. + consider splitting out lymph organ, compare with lymph node + the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. + the FMA class 'lymphoid organ' is a general anatomical term + + BTO:0004605 + EMAPA:37665 + FMA:7143 + MA:0000747 + haematological system organ + haemopoietic system organ + hematopoeitic organ + hematopoietic system organ + organ of haematological system + organ of haemopoietic system + organ of hematopoietic system + organ of organa haemopoietica + organa haemopoietica organ + hematopoeitic or lymphoid organ + lymph organ + lymphoid organ + uberon + UBERON:0004177 + + + hemopoietic organ + + + + + Organ that is part of the hematopoietic system. + GOC:Obol + + + + + the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. + + + + + + the FMA class 'lymphoid organ' is a general anatomical term + FMA + + + + + EMAPA:37665 + MA:th + + + + + haematological system organ + OBOL:automatic + + + + + haemopoietic system organ + OBOL:automatic + + + + + hematopoietic system organ + OBOL:automatic + + + + + organ of haematological system + OBOL:automatic + + + + + organ of haemopoietic system + OBOL:automatic + + + + + organ of hematopoietic system + OBOL:automatic + + + + + organ of organa haemopoietica + OBOL:automatic + + + + + organa haemopoietica organ + OBOL:automatic + + + + + lymph organ + MA:0000747 + + + + + lymphoid organ + BTO:0004605 + FMA:7143 + + + + + + + + + + + + + + + + + + + + + + + + + A portions of the gut that is derived from endoderm. + EMAPA:32930 + endodermal gut + gut endoderm + uberon + UBERON:0004185 + endodermal part of digestive tract + + + + + A portions of the gut that is derived from endoderm. + GO:0061031 + + + + + gut endoderm + EMAPA:32930 + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. + BTO:0001660 + EMAPA:35734 + MA:0001830 + respiratory smooth muscle + smooth muscle of respiratory system + uberon + airway smooth muscle + airway smooth muscle cell + UBERON:0004225 + respiratory system smooth muscle + + + + + A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + respiratory smooth muscle + BTO:0001660 + + + + + smooth muscle of respiratory system + OBOL:automatic + + + + + airway smooth muscle + BTO:0001660 + + + + + airway smooth muscle cell + BTO:0001660 + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. + EMAPA:35520 + MA:0002410 + involuntary muscle of lower respiratory tract + lower respiratory tract involuntary muscle + lower respiratory tract non-striated muscle + lower respiratory tract smooth muscle tissue + non-striated muscle of lower respiratory tract + smooth muscle of lower respiratory tract + smooth muscle tissue of lower respiratory tract + uberon + UBERON:0004233 + lower respiratory tract smooth muscle + + + + + A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. + OBOL:automatic + + + + + involuntary muscle of lower respiratory tract + OBOL:automatic + + + + + lower respiratory tract involuntary muscle + OBOL:automatic + + + + + lower respiratory tract non-striated muscle + OBOL:automatic + + + + + lower respiratory tract smooth muscle tissue + OBOL:automatic + + + + + non-striated muscle of lower respiratory tract + OBOL:automatic + + + + + smooth muscle of lower respiratory tract + OBOL:automatic + + + + + smooth muscle tissue of lower respiratory tract + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. + EMAPA:36287 + FMA:312251 + MA:0000706 + uberon + UBERON:0004236 + arteriole smooth muscle + + + + + A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + smooth muscle found within, and composing the majority of the wall of blood vessels. + Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. + UBERON:0010508 + + + BTO:0001431 + CALOHA:TS-1107 + EMAPA:35177 + MA:0000710 + MESH:D009131 + NCIT:C33853 + TAO:0005321 + UMLS:C1519956 + ZFA:0005321 + blood vessel involuntary muscle + blood vessel non-striated muscle + blood vessel smooth muscle tissue + involuntary muscle of blood vessel + non-striated muscle of blood vessel + smooth muscle of blood vessel + smooth muscle tissue of blood vessel + vascular smooth muscle + vascular smooth muscle tissue + uberon + UBERON:0004237 + + blood vessel smooth muscle + + + + + smooth muscle found within, and composing the majority of the wall of blood vessels. + + + + + + UMLS:C1519956 + ncithesaurus:Vascular_Smooth_Muscle_Tissue + + + + + blood vessel involuntary muscle + OBOL:automatic + + + + + blood vessel non-striated muscle + OBOL:automatic + + + + + blood vessel smooth muscle tissue + OBOL:automatic + + + + + involuntary muscle of blood vessel + OBOL:automatic + + + + + non-striated muscle of blood vessel + OBOL:automatic + + + + + smooth muscle of blood vessel + OBOL:automatic + + + + + smooth muscle tissue of blood vessel + OBOL:automatic + + + + + vascular smooth muscle + ZFA:0005321 + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. + EMAPA:37708 + MA:0000492 + involuntary muscle of outflow tract + non-striated muscle of outflow tract + outflow tract involuntary muscle + outflow tract non-striated muscle + outflow tract smooth muscle tissue + smooth muscle of outflow tract + smooth muscle tissue of outflow tract + uberon + UBERON:0004246 + outflow tract smooth muscle + + + + + A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37708 + MA:th + + + + + involuntary muscle of outflow tract + OBOL:automatic + + + + + non-striated muscle of outflow tract + OBOL:automatic + + + + + outflow tract involuntary muscle + OBOL:automatic + + + + + outflow tract non-striated muscle + OBOL:automatic + + + + + outflow tract smooth muscle tissue + OBOL:automatic + + + + + smooth muscle of outflow tract + OBOL:automatic + + + + + smooth muscle tissue of outflow tract + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any muscle organ that is part of a skin of body [Automatically generated definition]. + review as part of general integumentary system review - part of skin, or more generally, integumental system + in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only + UBERON:0015797 + EMAPA:18187 + EMAPA:35776 + MA:0002710 + MA:0003139 + integumental system muscle + muscle of integumental system + muscle organ of skin + skin muscle organ + uberon + UBERON:0004253 + skin muscle + + + + + Any muscle organ that is part of a skin of body [Automatically generated definition]. + OBOL:automatic + + + + + in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only + MA + + + + + integumental system muscle + MA:0003139 + + + + + muscle of integumental system + EMAPA:18187 + + + + + muscle organ of skin + OBOL:automatic + + + + + skin muscle organ + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel that is part of a back [Automatically generated definition]. + EMAPA:37243 + MA:0000493 + blood vessel of back + uberon + UBERON:0004258 + back blood vessel + + + + + A blood vessel that is part of a back [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37243 + MA:th + + + + + blood vessel of back + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of connective tissue that is part of a back [Automatically generated definition]. + EMAPA:37256 + MA:0000495 + uberon + mesenchyne of back + UBERON:0004267 + back connective tissue + + + + + A portion of connective tissue that is part of a back [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37256 + MA:th + + + + + mesenchyne of back + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. + Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] + skeletal + + + AEO:0000168 + EHDAA2:0001843 + EHDAA:5047 + EMAPA:17213 + FMA:23875 + GAID:177 + MA:0003006 + MAT:0000032 + MESH:D012863 + MIAA:0000032 + OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA + VSAO:0000026 + XAO:0004053 + galen:Skeleton + set of all bones + set of bones of body + uberon + UBERON:0004288 + + + + skeleton + https://github.com/obophenotype/uberon/wiki/The-skeletal-system + + + + + Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. + VSAO:0000026 + + + + + Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] + 2012-08-14 + VSAO:0000026 + VSAO + GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 + + + + + + + + + + + + + + + + The bilaminar epithelium formed from the myotome and dermatome. + Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. + Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] + Portion of somites that gives rise to dermis and muscles.[AAO] + all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. + Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] + + AAO:0010572 + AEO:0000214 + EHDAA2:0003259 + EMAPA:31109 + FMA:295654 + NCIT:C34140 + TAO:0001513 + UMLS:C1511786 + VHOG:0000676 + ZFA:0001513 + uberon + dermamyotome + dermomyotomes + UBERON:0004290 + dermomyotome + + + + + + AEO + + + + + + AEO + + + + + + + + + + + EHDAA2 + ZFA + + + + + The bilaminar epithelium formed from the myotome and dermatome. + AEO:0000214 + + + + + Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. + + + + + + Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] + 2012-08-14 + TAO:0001513 + TAO + ZFIN:curator + + + + + Portion of somites that gives rise to dermis and muscles.[AAO] + 2012-06-20 + AAO:0010572 + AAO + AAO:EJS + + + + + all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. + + + + + + Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] + 2012-09-17 + VHOG:0000676 + VHOG + + DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) + + + + + UMLS:C1511786 + ncithesaurus:Dermomyotome + + + + + dermamyotome + VHOG:0000676 + + + + + dermomyotomes + VHOG:0000676 + + + + + + + + + + + + + + + + A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. + The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] + TAO:0000115 + ZFA:0000115 + heart cone + rudimentary heart + uberon + UBERON:0004291 + heart rudiment + + + + + A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. + GO:0003313 + + + + + The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] + 2012-08-14 + TAO:0000115 + TAO + ZFIN:curator + + + + + heart cone + GO:0003313 + + + + + rudimentary heart + ZFA:0000115 + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. + EMAPA:37573 + MA:0001806 + smooth muscle tissue of blood vessel of respiratory system + uberon + UBERON:0004297 + respiratory system blood vessel smooth muscle + + + + + A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37573 + MA:th + + + + + smooth muscle tissue of blood vessel of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] + add specific artery derivatives + Do not confuse with arch of aorta. + Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] + When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] + Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods + The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches + UBERON:0004342 + + + AAO:0010414 + EFO:0003695 + EHDAA2:0000186 + EHDAA:398 + EHDAA:7327 + EMAPA:16684 + NCIT:C32123 + TAO:0005004 + UMLS:C0003489 + VHOG:0000122 + XAO:0000341 + ZFA:0005004 + PAA + aortic arch + aortic arches + branchial aortic arches + branchial arch artery + embryonic aortic arch artery + pharyngeal arch artery + uberon + a. arcuum pharyngeorum + aortic arch artery + arteriae arcuum pharyngeorum + branchial aortic arches + pharyngeal arch arteries + pharyngeal arch artery + UBERON:0004363 + + + + + pharyngeal arch artery + + + + + + + + + + + + ZFA + + + + + One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] + MP:0002672 + + + + + Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] + 2012-09-17 + VHOG:0000122 + VHOG + + + + + + + When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] + 2012-09-17 + VHOG:0000122 + VHOG + + ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 + + + + + UMLS:C0003489 + ncithesaurus:Aortic_Arch + + + + + PAA + MP:0002672 + + + + + + aortic arch + ZFA:0005004 + + + + + aortic arches + ZFA:0005004 + + + + + + branchial aortic arches + ZFIN:ZDB-PUB-080512-6 + + + + + + branchial arch artery + EMAPA:16684 + + + + + embryonic aortic arch artery + EMAPA:16684 + MP:0002672 + + + + + pharyngeal arch artery + MP:0002672 + + + + + a. arcuum pharyngeorum + + + + + + + aortic arch artery + EMAPA:16684 + + + + + arteriae arcuum pharyngeorum + + + + + + + branchial aortic arches + ZFA:0005004,ZFIN:ZDB-PUB-080512-6 + + + + + + pharyngeal arch arteries + + + + + + pharyngeal arch artery + VHOG:0000122 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An embryo at the neurula stage. + UBERON:0007013 + + BILA:0000061 + BTO:0001766 + NCIT:C34229 + UMLS:C1518306 + neurula + uberon + UBERON:0004455 + neurula embryo + + + + + An embryo at the neurula stage. + + + + + + UMLS:C1518306 + ncithesaurus:Neurula + + + + + neurula + BTO:0001766 + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a thorax [Automatically generated definition]. + BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm + BTO:0000508 + EMAPA:37260 + FMA:71293 + muscle group of thorax + muscles of thorax + musculi thoracis + set of muscles of thorax + thoracic musculature + uberon + UBERON:0004464 + + musculature of thorax + + + + + Any collection of muscles that is part of a thorax [Automatically generated definition]. + OBOL:automatic + + + + + BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm + BTO + + + + + EMAPA:37260 + MA:th + + + + + muscle group of thorax + FMA:71293 + + + + + muscles of thorax + FMA:71293 + + + + + musculi thoracis + FMA:71293 + FMA:TA + + + + + + set of muscles of thorax + FMA:71293 + + + + + thoracic musculature + FMA:71293 + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a neck [Automatically generated definition]. + AAO:0000091 + EMAPA:36050 + FMA:71290 + MESH:D009334 + cervical muscles + muscle group of neck + muscles of neck + musculi cervicis + musculi colli + neck musculature + set of muscles of neck + uberon + UBERON:0004465 + + musculature of neck + + + + + Any collection of muscles that is part of a neck [Automatically generated definition]. + OBOL:automatic + + + + + cervical muscles + AAO:0000091 + + + + + muscle group of neck + FMA:71290 + + + + + muscles of neck + FMA:71290 + + + + + musculi cervicis + FMA:71290 + FMA:TA + + + + + + musculi colli + FMA:71290 + FMA:TA + + + + + + neck musculature + FMA:71290 + + + + + set of muscles of neck + FMA:71290 + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a back [Automatically generated definition]. + FMA:71291 + muscle group of back + muscles of back + musculi dorsi + set of muscles of back + uberon + UBERON:0004469 + musculature of back + + + + + Any collection of muscles that is part of a back [Automatically generated definition]. + OBOL:automatic + + + + + muscle group of back + FMA:71291 + + + + + muscles of back + FMA:71291 + + + + + musculi dorsi + FMA:71291 + FMA:TA + + + + + + set of muscles of back + FMA:71291 + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a face. + originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose + FMA:71288 + entire facial musculature + facial muscles + muscle group of face + musculi faciei + uberon + set of facial muscles + set of muscles of face + UBERON:0004473 + + musculature of face + + + + + Any collection of muscles that is part of a face. + OBOL:automatic + + + + + entire facial musculature + + + + + + facial muscles + FMA:71288 + + + + + muscle group of face + FMA:71288 + + + + + musculi faciei + FMA:71288 + FMA:TA + + + + + + set of facial muscles + FMA:71288 + + + + + set of muscles of face + FMA:71288 + + + + + + + + + + + + + + + + + + + + + + + + + + Any collection of muscles that is part of a trunk [Automatically generated definition]. + currently defined by location rather than attachment + AAO:0011572 + EFO:0003531 + FMA:50187 + muscle group of trunk + set of muscles of trunk + uberon + muscular system of trunk + UBERON:0004479 + + + musculature of trunk + + + + + Any collection of muscles that is part of a trunk [Automatically generated definition]. + OBOL:automatic + + + + + muscle group of trunk + FMA:50187 + + + + + set of muscles of trunk + FMA:50187 + + + + + muscular system of trunk + FMA:50187 + + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a muscle organ [Automatically generated definition]. + FMA:87123 + muscular organ vasculature + uberon + UBERON:0004521 + vasculature of muscle organ + + + + + A vasculature that is part of a muscle organ [Automatically generated definition]. + OBOL:automatic + + + + + muscular organ vasculature + FMA:87123 + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a musculoskeletal system [Automatically generated definition]. + FMA:239607 + uberon + UBERON:0004522 + vasculature of musculoskeletal system + + + + + A vasculature that is part of a musculoskeletal system [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that has as its parts the heart and blood vessels. + we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. + The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] + + + AAO:0011001 + BILA:0000016 + BTO:0000088 + CALOHA:TS-1297 + EFO:0000791 + EHDAA2:0000216 + EHDAA:394 + EMAPA:16104 + EMAPA:16370 + EV:0100017 + FMA:7161 + GAID:467 + MA:0000010 + MAT:0000016 + MESH:D002319 + MIAA:0000016 + NCIT:C12686 + OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA + TAO:0000010 + UMLS:C0007226 + VHOG:0000302 + WikipediaCategory:Cardiovascular_system + XAO:0000100 + XAO:0001010 + ZFA:0000010 + uberon + CV system + Herz und Gefaesssystem + UBERON:0004535 + + + + + cardiovascular system + + + + + Anatomical system that has as its parts the heart and blood vessels. + BTO:0000088 + + + + + The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] + 2012-09-17 + VHOG:0000302 + VHOG + + ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 + + + + + UMLS:C0007226 + ncithesaurus:Cardiovascular_System + + + + + CV system + BTO:0000088 + + + + + Herz und Gefaesssystem + BTO:0000088 + + + + + + + + + + + + + + + + + + + + + + + + + + A vascular network consisting of blood vessels. + TAO:0001079 + ZFA:0001079 + blood vascular network + set of blood vessels + uberon + blood system + blood vessel system + blood vessels + UBERON:0004537 + blood vasculature + + + + + A vascular network consisting of blood vessels. + + + + + + blood vessels + TAO:0001079 + + + + + + + + + + + + + + + The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. + + FMA:45623 + systemic arterial circulatory system + uberon + UBERON:0004571 + + systemic arterial system + + + + + + MA-inferred + + + + + The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. + + + + + + + systemic arterial circulatory system + FMA:45623 + + + + + + + + + + + + + + + The part of the cardiovascular system consisting of all arteries. + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + + BTO:0004690 + EHDAA2:0000143 + EHDAA:396 + EMAPA:16201 + EMAPA:16371 + MA:0002719 + VHOG:0000273 + uberon + UBERON:0004572 + + arterial system + + + + + + MA + + + + + The part of the cardiovascular system consisting of all arteries. + + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0000273 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) + + + + + + + + + + + + + + + + + + + + + + + + + + An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. + + EMAPA:37126 + FMA:66464 + systemic arterial subtree + uberon + UBERON:0004573 + + systemic artery + + + + + An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. + + + + + + + EMAPA:37126 + MA:th + + + + + systemic arterial subtree + FMA:66464 + + + + + + + + + + + + + + + The part of the venous system that drains the general body tissues[Kardong] + In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] + Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + + FMA:45626 + systemic venous circulatory system + uberon + UBERON:0004581 + systemic venous system + + + + + The part of the venous system that drains the general body tissues[Kardong] + + ISBN10:0073040584 + + + + + In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] + + + + + + Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] + FMA + FMA:45626 + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0000277 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) + + + + + systemic venous circulatory system + FMA:45626 + + + + + + + + + + + + + + + The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + + + BTO:0004692 + EHDAA2:0002171 + EHDAA:486 + EMAPA:16240 + MA:0002720 + NCIT:C33858 + UMLS:C1267406 + VHOG:0000277 + vein system + uberon + UBERON:0004582 + venous system + + + + + + MA + + + + + The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. + + + + + + The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] + 2012-09-17 + VHOG:0000277 + VHOG + + DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) + + + + + UMLS:C1267406 + ncithesaurus:Venous_System + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart + + BTO:0000766 + CALOHA:TS-2155 + EMAPA:35176 + MA:0000709 + NCIT:C53395 + TAO:0005257 + UMLS:C1706972 + ZFA:0005257 + uberon + UBERON:0004638 + + + blood vessel endothelium + + + + + An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart + + + + + + UMLS:C1706972 + ncithesaurus:Blood_Vessel_Endothelium + + + + + + + + + The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. + + + EMAPA:37496 + FMA:10636 + MA:0001939 + costocervical trunk + trunk of costocervical artery + uberon + truncus costocervicalis + UBERON:0004688 + costo-cervical trunk + + + + + + The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. + + + + + + EMAPA:37496 + MA:th + + + + + costocervical trunk + FMA:10636 + + + + + trunk of costocervical artery + FMA:10636 + + + + + truncus costocervicalis + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. + EMAPA:36503 + MA:0000704 + uberon + UBERON:0004695 + arterial system smooth muscle + + + + + A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. + EMAPA:36613 + MA:0000715 + uberon + UBERON:0004696 + venous system smooth muscle + + + + + A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a outflow tract [Automatically generated definition]. + It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] + MA:0000490 + VHOG:0001524 + uberon + UBERON:0004699 + outflow tract endothelium + + + + + An endothelium that is part of a outflow tract [Automatically generated definition]. + OBOL:automatic + + + + + It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] + 2012-09-17 + VHOG:0001524 + VHOG + + DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001) + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of an arterial system [Automatically generated definition]. + + EMAPA:35145 + MA:0000703 + NCIT:C49329 + UMLS:C1706849 + uberon + UBERON:0004700 + arterial system endothelium + + + + + An endothelium that is part of an arterial system [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1706849 + ncithesaurus:Arterial_System_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a venous system [Automatically generated definition]. + + EMAPA:35907 + MA:0000714 + NCIT:C49320 + UMLS:C1710626 + uberon + UBERON:0004701 + venous system endothelium + + + + + An endothelium that is part of a venous system [Automatically generated definition]. + OBOL:automatic + + + + + UMLS:C1710626 + ncithesaurus:Venous_System_Endothelium + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. + EMAPA:35732 + MA:0001805 + uberon + UBERON:0004702 + respiratory system blood vessel endothelium + + + + + A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. + + + + BTO:0001744 + CALOHA:TS-0497 + EMAPA:18638 + GAID:536 + MA:0002154 + MESH:D007601 + NCIT:C12738 + UMLS:C0022427 + uberon + jugular + vena jugularis + UBERON:0004711 + jugular vein + + + + + + The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. + + + + + + UMLS:C0022427 + ncithesaurus:Jugular_Vein + + + + + vena jugularis + BTO:0001744 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. + EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus + + + AEO:0000194 + BTO:0003834 + EHDAA2:0000001 + EHDAA2:0003235 + EMAPA:36040 + NCIT:C34131 + UMLS:C1516779 + embryo plus adnexa + uberon + UBERON:0004716 + conceptus + + + + + The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. + + BTO:0003834 + + + + + UMLS:C1516779 + ncithesaurus:Conceptus + + + + + + + + + + + + + + + + + + + + + + + + + + + A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). + We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted + A metameric segment of the central nervous system.[ZFA] + Melissa Haendel + 2009-06-18T09:00:04Z + + + TAO:0001328 + ZFA:0001328 + neural tube metameric segment + neural tube segment + neuromere + neuromeres + uberon + neural metamere + neural segment + UBERON:0004731 + + neuromere + + + + + A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). + + + + + + + A metameric segment of the central nervous system.[ZFA] + 2012-08-14 + TAO:0001328 + TAO + ZFIN:curator + + + + + neural tube metameric segment + + + + + + neuromeres + TAO:0001328 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. + revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) + FBbt:00005140 + uberon + neuromere + UBERON:0004732 + + segmental subdivision of nervous system + + + + + Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. + + FBbt:00005140 + + + + + neuromere + FBbt:00005140 + + + + + + + + + + + + + + + + + + + + + + + + + + + + An organ subunit that is part of a hindbrain [Automatically generated definition]. + FMA:61998 + hindbrain segment + segment of hindbrain + uberon + UBERON:0004733 + + segmental subdivision of hindbrain + + + + + An organ subunit that is part of a hindbrain [Automatically generated definition]. + OBOL:automatic + + + + + hindbrain segment + FMA:61998 + + + + + segment of hindbrain + FMA:61998 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Organism at the gastrula stage. + We explicitly merge the NCITA terms here + UBERON:0007012 + + + + + BILA:0000060 + BTO:0001403 + FBbt:00005317 + FMA:293108 + GAID:1302 + MESH:A16.254.412 + MIAA:0000179 + NCIT:C34057 + NCIT:C34058 + UMLS:C0017199 + UMLS:C1284022 + gastrula embryo + uberon + blastocystis trilaminaris + tri-laminar disc + tri-laminar disk + trilaminar blastocyst + trilaminar blastoderm + trilaminar disc + trilaminar disk + trilaminar germ + UBERON:0004734 + + gastrula + + + + + Organism at the gastrula stage. + + + + + + + We explicitly merge the NCITA terms here + NCIT + + + + + UMLS:C0017199 + ncithesaurus:Gastrula + + + + + UMLS:C1284022 + ncithesaurus:Trilaminar_Embryonic_Disc + + + + + gastrula embryo + BILA:0000060 + + + + + blastocystis trilaminaris + + + + + + tri-laminar disc + + + + + + tri-laminar disk + + + + + + trilaminar blastocyst + + + + + + trilaminar blastoderm + + + + + + trilaminar disc + + + + + + trilaminar disk + + + + + + trilaminar germ + + + + + + + + + + + + + + + + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. + Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] + Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] + AAO:0011129 + TAO:0001890 + VSAO:0000128 + XAO:0004012 + ZFA:0005494 + galen:SkeletalStructure + uberon + UBERON:0004765 + + + skeletal element + + + + + + + + + + + VSAO + + + + + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. + + + + + + Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] + 2012-08-14 + VSAO:0000128 + VSAO + PSPUB:0000170 + + + + + Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] + 2012-08-14 + TAO:0001890 + TAO + TAO:VSAO_workshop + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of all the joints of the body. + + EMAPA:35150 + FMA:23878 + MA:0003007 + VSAO:0000181 + joint system + set of all joints of body + uberon + set of all joints + set of joints of body + UBERON:0004770 + articular system + + + + + + + + + + + FMA + + + + + Anatomical system that consists of all the joints of the body. + VSAO:0000181 + + + + + joint system + FMA:23878 + + + + + set of all joints of body + FMA:23878 + + + + + set of joints of body + FMA:23878 + + + + + + + + + + + + + + + + + + + + + + + + + + A submucosa that is part of a respiratory system [Automatically generated definition]. + EMAPA:37578 + MA:0001822 + apparatus respiratorius submucosa + submucosa of apparatus respiratorius + submucosa of respiratory system + uberon + UBERON:0004777 + respiratory system submucosa + + + + + A submucosa that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37578 + MA:th + + + + + apparatus respiratorius submucosa + OBOL:automatic + + + + + submucosa of apparatus respiratorius + OBOL:automatic + + + + + submucosa of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + the mucous membrane lining the respiratory tract + TODO - split respiratory tract mucosa from respiratory system mucosa + BTO:0000973 + EMAPA:18334 + EMAPA:37577 + FMA:302092 + GAID:304 + MA:0001827 + MESH:D020545 + apparatus respiratorius mucosa + apparatus respiratorius mucosa of organ + apparatus respiratorius mucous membrane + mucosa of apparatus respiratorius + mucosa of organ of apparatus respiratorius + mucosa of organ of respiratory system + mucosa of respiratory system + mucous membrane of apparatus respiratorius + mucous membrane of respiratory system + respiratory system mucosa of organ + respiratory system mucous membrane + uberon + laryngeal mucous membrane + respiratory mucosa + respiratory tract mucosa + UBERON:0004785 + + respiratory system mucosa + + + + + the mucous membrane lining the respiratory tract + MESH:A04.760 + MGI:cwg + MP:0002277 + + + + + EMAPA:37577 + MA:th + + + + + apparatus respiratorius mucosa + OBOL:automatic + + + + + apparatus respiratorius mucosa of organ + OBOL:automatic + + + + + apparatus respiratorius mucous membrane + OBOL:automatic + + + + + mucosa of apparatus respiratorius + OBOL:automatic + + + + + mucosa of organ of apparatus respiratorius + OBOL:automatic + + + + + mucosa of organ of respiratory system + OBOL:automatic + + + + + mucosa of respiratory system + OBOL:automatic + + + + + mucous membrane of apparatus respiratorius + OBOL:automatic + + + + + mucous membrane of respiratory system + OBOL:automatic + + + + + respiratory system mucosa of organ + OBOL:automatic + + + + + respiratory system mucous membrane + OBOL:automatic + + + + + laryngeal mucous membrane + EMAPA:18334 + + + + + respiratory mucosa + BTO:0000973 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. + EMAPA:36296 + MA:0002854 + uberon + UBERON:0004797 + blood vessel layer + + + + + + Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi + + BTO:0000419 + CALOHA:TS-0023 + EMAPA:32827 + MA:0001480 + VHOG:0000981 + epithelial tissue of respiratory tract + epithelium of respiratory tract + respiratory tract epithelial tissue + uberon + airway epithelium + respiratory epithelium + UBERON:0004802 + + respiratory tract epithelium + + + + + the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi + ISBN:0-683-40008-8 + MGI:anna + MP:0010942 + + + + + epithelial tissue of respiratory tract + OBOL:automatic + + + + + epithelium of respiratory tract + OBOL:automatic + + + + + respiratory tract epithelial tissue + OBOL:automatic + + + + + airway epithelium + BTO:0000419 + + + + + respiratory epithelium + BTO:0000419 + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a respiratory system [Automatically generated definition]. + CALOHA:TS-0023 + EMAPA:32826 + MA:0001823 + VHOG:0000981 + apparatus respiratorius epithelial tissue + apparatus respiratorius epithelium + epithelial tissue of apparatus respiratorius + epithelial tissue of respiratory system + epithelium of apparatus respiratorius + epithelium of respiratory system + respiratory system epithelial tissue + uberon + UBERON:0004807 + + respiratory system epithelium + + + + + An epithelium that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + apparatus respiratorius epithelial tissue + OBOL:automatic + + + + + apparatus respiratorius epithelium + OBOL:automatic + + + + + epithelial tissue of apparatus respiratorius + OBOL:automatic + + + + + epithelial tissue of respiratory system + OBOL:automatic + + + + + epithelium of apparatus respiratorius + OBOL:automatic + + + + + epithelium of respiratory system + OBOL:automatic + + + + + respiratory system epithelial tissue + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a lower respiratory tract [Automatically generated definition]. + EMAPA:37549 + MA:0001481 + epithelial tissue of lower respiratory tract + epithelium of lower respiratory tract + lower respiratory tract epithelial tissue + uberon + UBERON:0004815 + lower respiratory tract epithelium + + + + + An epithelium that is part of a lower respiratory tract [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37549 + MA:th + + + + + epithelial tissue of lower respiratory tract + OBOL:automatic + + + + + epithelium of lower respiratory tract + OBOL:automatic + + + + + lower respiratory tract epithelial tissue + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium of artery that is part of a respiratory system [Automatically generated definition]. + EMAPA:37566 + MA:0001801 + apparatus respiratorius arterial endothelium + apparatus respiratorius artery endothelium + apparatus respiratorius endothelium of artery + arterial endothelium of apparatus respiratorius + arterial endothelium of respiratory system + artery endothelium of apparatus respiratorius + artery endothelium of respiratory system + endothelium of artery of apparatus respiratorius + endothelium of artery of respiratory system + respiratory system artery endothelium + respiratory system endothelium of artery + uberon + UBERON:0004848 + respiratory system arterial endothelium + + + + + + + + + + + true + + + + + + An endothelium of artery that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37566 + MA:th + + + + + apparatus respiratorius arterial endothelium + OBOL:automatic + + + + + apparatus respiratorius artery endothelium + OBOL:automatic + + + + + apparatus respiratorius endothelium of artery + OBOL:automatic + + + + + arterial endothelium of apparatus respiratorius + OBOL:automatic + + + + + arterial endothelium of respiratory system + OBOL:automatic + + + + + artery endothelium of apparatus respiratorius + OBOL:automatic + + + + + artery endothelium of respiratory system + OBOL:automatic + + + + + endothelium of artery of apparatus respiratorius + OBOL:automatic + + + + + endothelium of artery of respiratory system + OBOL:automatic + + + + + respiratory system artery endothelium + OBOL:automatic + + + + + respiratory system endothelium of artery + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium of vein that is part of a respiratory system [Automatically generated definition]. + EMAPA:37585 + MA:0001811 + apparatus respiratorius endothelium of vein + apparatus respiratorius vein endothelium + apparatus respiratorius venous endothelium + endothelium of vein of apparatus respiratorius + endothelium of vein of respiratory system + respiratory system endothelium of vein + respiratory system vein endothelium + vein endothelium of apparatus respiratorius + vein endothelium of respiratory system + venous endothelium of apparatus respiratorius + venous endothelium of respiratory system + uberon + UBERON:0004849 + respiratory system venous endothelium + + + + + An endothelium of vein that is part of a respiratory system [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37585 + MA:th + + + + + apparatus respiratorius endothelium of vein + OBOL:automatic + + + + + apparatus respiratorius vein endothelium + OBOL:automatic + + + + + apparatus respiratorius venous endothelium + OBOL:automatic + + + + + endothelium of vein of apparatus respiratorius + OBOL:automatic + + + + + endothelium of vein of respiratory system + OBOL:automatic + + + + + respiratory system endothelium of vein + OBOL:automatic + + + + + respiratory system vein endothelium + OBOL:automatic + + + + + vein endothelium of apparatus respiratorius + OBOL:automatic + + + + + vein endothelium of respiratory system + OBOL:automatic + + + + + venous endothelium of apparatus respiratorius + OBOL:automatic + + + + + venous endothelium of respiratory system + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of the cardiovascular system. + consider merging with 'endothelium' + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + + BTO:0001853 + EMAPA:35201 + GAID:519 + MA:0000717 + MESH:D004730 + NCIT:C13053 + TAO:0002171 + UMLS:C0014261 + VHOG:0001217 + XAO:0000356 + ZFA:0001639 + uberon + endothelia + vascular endothelia + UBERON:0004852 + + cardiovascular system endothelium + + + + + An endothelium that is part of the cardiovascular system. + + + + + + Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] + 2012-09-17 + VHOG:0001217 + VHOG + + ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 + + + + + UMLS:C0014261 + ncithesaurus:Vascular_Endothelium + + + + + endothelia + ZFA:0001639 + + + + + + vascular endothelia + XAO:0000356 + + + + + + + + + + + + + + + + Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. + We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors + visceral mesoderm + + AAO:0011102 + BILA:0000044 + FMA:295568 + XAO:0000276 + inner layer of lateral plate mesoderm + uberon + splanchnic mesoderm + UBERON:0004872 + + splanchnic layer of lateral plate mesoderm + + + + + Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. + + + + + + We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors + BILA + + + + + visceral mesoderm + + + BILA:0000044 + + + + + splanchnic mesoderm + ISBN:9780878932504 + + + + + + + + + + + + + + + + + + + + + + + + + + A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. + TODO - check relationship to LPM + + + EHDAA2:0001903 + EHDAA:383 + EMAPA:16181 + FMA:295564 + NCIT:C34303 + UMLS:C1519472 + VHOG:0000558 + uberon + ventral splanchnic mesoderm + UBERON:0004873 + splanchnopleure + + + + + + + + + + + + EHDAA2 + + + + + A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. + + + + + + UMLS:C1519472 + ncithesaurus:Splanchnopleure + + + + + ventral splanchnic mesoderm + + + + + + + + + + + + + + + + The central region of trunk mesoderm. This tissue forms the notochord + Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. + WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. + AAO:0000478 + EFO:0003426 + TAO:0000091 + ZFA:0000091 + axial chorda mesoderm + chorda mesoderm + dorsal mesoderm + presumptive notochord + uberon + UBERON:0004880 + + + chordamesoderm + + + + + The central region of trunk mesoderm. This tissue forms the notochord + + + + + + Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. + ZFIN:ZDB-PUB-961014-576 + + + + + axial chorda mesoderm + ZFA:0000091 + + + + + dorsal mesoderm + + + + + + presumptive notochord + ZFA:0000091 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The mass of tissue made up of mesenchymal cells in the lung. + EMAPA:32866 + lung-associated mesenchyme + mesenchyme of lung + pulmonary mesenchyme + uberon + UBERON:0004883 + + lung mesenchyme + + + + + The mass of tissue made up of mesenchymal cells in the lung. + GO:0060484 + + + + + lung-associated mesenchyme + GO:0060484 + + + + + mesenchyme of lung + OBOL:automatic + + + + + pulmonary mesenchyme + GO:0060484 + + + + + + + + + + + + + + + Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. + FBbt:00005811 + joint + uberon + UBERON:0004905 + + articulation + + + + + Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of the gut that is derived from ectoderm. + ectodermal gut + gut ectoderm + uberon + UBERON:0004906 + ectodermal part of digestive tract + + + + + A portion of the gut that is derived from ectoderm. + GO:0007439 + + + + + gut ectoderm + EMAPA:32930 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A proximal-distal subdivision of the digestive tract. + intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. + FBbt:00100315 + FMA:71131 + uberon + alimentary system subdivision + intestinal tract + segment of intestinal tract + subdivision of alimentary system + UBERON:0004921 + + subdivision of digestive tract + + + + + A proximal-distal subdivision of the digestive tract. + + + + + + alimentary system subdivision + FMA:71131 + + + + + subdivision of alimentary system + FMA:71131 + + + + + + + + + + + + + + + A part of a wall of an organ that forms a layer. + FMA:82485 + uberon + UBERON:0004923 + + organ component layer + + + + + A part of a wall of an organ that forms a layer. + + + + + + + + + + + + + + + + + + + + + + + + + + + + The tissue underlying the tunica mucosa of the pharynx. + + BTO:0002113 + FMA:75144 + pharyngeal submucosa + pharynx submucosa + tela submucosa pharyngea + tela submucosa pharyngis + uberon + pharyngobasilar fascia + submucous coat of pharynx + submucous layer of pharynx + UBERON:0004924 + submucosa of pharynx + + + + + The tissue underlying the tunica mucosa of the pharynx. + BTO:0002113 + + + + + pharyngeal submucosa + FMA:75144 + + + + + pharynx submucosa + OBOL:automatic + + + + + tela submucosa pharyngea + FMA:75144 + FMA:TA + + + + + + tela submucosa pharyngis + BTO:0002113 + + + + + + submucous coat of pharynx + BTO:0002113 + + + + + submucous layer of pharynx + BTO:0002113 + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a hemolymphoid system [Automatically generated definition]. + hemopoietic or lymphoid organ + EMAPA:18766 + MA:0002962 + hemopoietic or lymphoid gland + uberon + haemolymphoid system gland + UBERON:0005058 + + hemolymphoid system gland + + + + + A gland that is part of a hemolymphoid system [Automatically generated definition]. + OBOL:automatic + + + + + hemopoietic or lymphoid organ + GO:0048534 + + + + + hemopoietic or lymphoid gland + + + + + + haemolymphoid system gland + EMAPA:18766 + + + + + + + + + + + + + + + The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. + The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. + + + + + AAO:0011071 + EMAPA:35594 + FMA:295624 + NCIT:C34224 + UMLS:C0814992 + XAO:0000248 + uberon + UBERON:0005061 + neural groove + + + + + The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. + + + GO:0001842 + + + + + The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. + + + + + + UMLS:C0814992 + ncithesaurus:Neural_Groove + + + + + + + + + + + + + + + + + + + + + + + + + One of the two elevated edges of the neural groove[GO,MP]. + In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. + + + + + EHDAA2:0001249 + FMA:295618 + NCIT:C34223 + UMLS:C0814993 + XAO:0004087 + medullary fold + uberon + UBERON:0005062 + + neural fold + + + + + One of the two elevated edges of the neural groove[GO,MP]. + + GO:0001842 + MP:0011256 + + + + + In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. + + + + + + UMLS:C0814993 + ncithesaurus:Neural_Fold + + + + + medullary fold + MP:0011256 + + + + + + + + + + + + + + + A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. + An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] + EFO:0003498 + TAO:0000133 + ZFA:0000133 + uberon + neural tube rod + UBERON:0005068 + + neural rod + + + + + A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. + GO:0014024 + ZFA:0000133 + + + + + An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000133 + TAO + ZFIN:curator + + + + + neural tube rod + GO:0014027 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. + hindbrain-spinal cord boundary region + uberon + UBERON:0005076 + hindbrain-spinal cord boundary + + + + + An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A hole in a tube[GO]. + AEO:0000078 + EHDAA2:0004618 + RETIRED_EHDAA2:0003078 + uberon + UBERON:0005082 + tube lumen + + + + + A hole in a tube[GO]. + GO:0060609 + + + + + + + + + Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. + in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila + EMAPA:32715 + FBbt:00005073 + FMA:30316 + musculus + uberon + muscle + muscle element + UBERON:0005090 + muscle structure + + + + + Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. + GO:0061061 + + + + + musculus + FMA:30316 + + + + + + + + + A bud is a protrusion that forms from an epithelial sheet by localized folding. + BTO:0001639 + uberon + UBERON:0005153 + epithelial bud + + + + + A bud is a protrusion that forms from an epithelial sheet by localized folding. + GO:0060572 + + + + + + + + + An epithelial sheet bent on a linear axis. + uberon + UBERON:0005157 + epithelial fold + + + + + An epithelial sheet bent on a linear axis. + GO:0060571 + + + + + + + + + A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. + we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' + AAO:0011000 + CARO:0001000 + FBbt:00007060 + FMA:83115 + multi-cell-component structure + multi-cell-part structure + uberon + cell part cluster + UBERON:0005162 + + multi cell part structure + + + + + + FMA + + + + + A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. + CARO:0001000 + + + + + we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' + CARO + FMA + + + + + multi-cell-component structure + CARO:0001000 + + + + + multi-cell-part structure + CARO:0001000 + + + + + cell part cluster + FMA:83115 + + + + + + + + + + + + + + + + + + + + + + + + + + An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. + EMAPA:37274 + MA:0001901 + back organ + dorsal region organ + uberon + UBERON:0005174 + + dorsal region element + + + + + An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. + + + + + + EMAPA:37274 + MA:th + + + + + back organ + MA:0001901 + + + + + + + + + + + + + + + + + + + + + + + + + + An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. + EMAPA:37270 + MA:0000516 + trunk organ + uberon + UBERON:0005177 + + + trunk region element + + + + + An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. + + + + + + EMAPA:37270 + MA:th + + + + + trunk organ + MA:0000516 + + + + + + + + + + + + + + + + + + + + + + + + + + An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + EMAPA:37273 + MA:0000557 + thoracic cavity organ + uberon + UBERON:0005178 + + + thoracic cavity element + + + + + An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. + + + + + + EMAPA:37273 + MA:th + + + + + thoracic cavity organ + MA:0000557 + + + + + + + + + + + + + + + + + + + + + + + + + + An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. + EMAPA:37271 + MA:0000563 + uberon + upper body organ + UBERON:0005181 + + thoracic segment organ + + + + + An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. + + + + + + EMAPA:37271 + MA:th + + + + + upper body organ + MA:0000563 + + + + + + + + + + + + + + + + + + + + + A vein that is part of a thorax [Automatically generated definition]. + + + EMAPA:37197 + MA:0002235 + NCIT:C53142 + UMLS:C0226629 + uberon + UBERON:0005194 + thoracic vein + + + + + A vein that is part of a thorax [Automatically generated definition]. + OBOL:automatic + + + + + EMAPA:37197 + MA:th + + + + + UMLS:C0226629 + ncithesaurus:Thoracic_Vein + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a stomodeum. + check this + VHOG:0000658 + stomatodaeum gland + uberon + UBERON:0005250 + + stomatodeum gland + + + + + A gland that is part of a stomodeum. + OBOL:automatic + + + + + stomatodaeum gland + VHOG:0000658 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. + Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] + EFO:0003492 + EHDAA2:0000732 + EHDAA:179 + EMAPA:16098 + EMAPA_RETIRED:16269 + FMA:76622 + TAO:0000113 + VHOG:0000332 + ZFA:0000113 + cephalic mesenchyme + uberon + cranial mesenchyme + desmocranium + UBERON:0005253 + + + + head mesenchyme + + + + + + + + + + + EHDAA2 + + + + + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. + ISBN:0683400088 + MP:0011260 + + + + + Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] + 2012-08-14 + TAO:0000113 + TAO + ZFIN:curator + + + + + cephalic mesenchyme + MP:0011260 + + + + + cranial mesenchyme + MGI:anna + + + + + desmocranium + FMA:76622 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing trunk. + EFO:0003485 + EHDAA2:0002092 + EHDAA:377 + EMAPA:16177 + TAO:0000081 + VHOG:0000281 + ZFA:0000081 + uberon + trunk and cervical mesenchyme + UBERON:0005256 + + + trunk mesenchyme + + + + + + + + + + + EHDAA2 + + + + + Mesenchyme that is part of a developing trunk. + OBOL:automatic + + + + + trunk and cervical mesenchyme + EHDAA2:0002092 + + + + + + + + + + + + + + + + + + + + + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. + + The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] + The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] + the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes + + BTO:0000758 + CALOHA:TS-0607 + CALOHA:TS-2365 + DHBA:10662 + EHDAA2:0001207 + EHDAA:5526 + EMAPA:17082 + HBA:9512 + MA:0000205 + VHOG:0000456 + uberon + myelencephalon (medulla oblongata) + UBERON:0005290 + + myelencephalon + + + + + + + + + + + + definitional + + + + + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. + + BTO:0000758 + + + + + The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] + 2012-09-17 + VHOG:0000456 + VHOG + + + + + + + The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] + 2012-09-17 + VHOG:0000456 + VHOG + + ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 + + + + + myelencephalon (medulla oblongata) + DHBA:10662 + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of tissue that is part of an embryo. + CALOHA:TS-2100 + portion of embryonic tissue + uberon + developing tissue + UBERON:0005291 + + + embryonic tissue + + + + + A portion of tissue that is part of an embryo. + OBOL:automatic + + + + + portion of embryonic tissue + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. + BTO:0003360 + CALOHA:TS-2119 + EFO:0001406 + MAT:0000061 + MIAA:0000061 + extra-embryonic tissue + uberon + UBERON:0005292 + + extraembryonic tissue + + + + + Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. + + + + + + + + + + + + + + + + + + + + + + + + + + + The endothelial lining of the endocardium. + FMA:83596 + endocardium endothelium + endothelium of endocardium + uberon + UBERON:0005316 + endocardial endothelium + + + + + The endothelial lining of the endocardium. + UBERON:cjm + + + + + endocardium endothelium + FMA:83596 + + + + + endothelium of endocardium + FMA:83596 + + + + + + + + + + + + + + + + + + + + + + + + + + + An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. + BTO:0000137 + pulmonary artery endothelial tube + uberon + UBERON:0005317 + pulmonary artery endothelium + + + + + An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. + GO:0061155 + + + + + pulmonary artery endothelial tube + GO:0061155 + + + + + + + + + merge with RVOT? + EHDAA2:0001359 + EHDAA:4401 + EMAPA:17330 + MA:0000102 + VHOG:0001395 + uberon + UBERON:0005339 + outflow tract pulmonary component + + + + + + + + + AEO:0000125 + CALOHA:TS-2122 + EHDAA2:0003125 + FBbt:00007006 + FMA:292313 + MIAA:0000019 + uberon + developing structure + developmental structure + developmental tissue + UBERON:0005423 + developing anatomical structure + + + + + developmental tissue + MIAA:0000019 + + + + + + + + + + + + + + + + + + + + + + + + The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates + the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. + + EHDAA2:0004145 + EHDAA:9826 + EMAPA:36461 + FMA:71008 + RETIRED_EHDAA2:0000133 + saccus aorticus + uberon + UBERON:0005432 + + aortic sac + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates + MP:0012510 + + + + + the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. + + + + + + saccus aorticus + + + + + + + + + + + + + + + + Portion of tissue on the side of the lumen of the neural tube. + EHDAA2:0001257 + EHDAA:2873 + EHDAA:912 + EMAPA:16166 + TAO:0001435 + VHOG:0000513 + ZFA:0001435 + lateral wall neural tube + uberon + UBERON:0005496 + + neural tube lateral wall + + + + + Portion of tissue on the side of the lumen of the neural tube. + ZFA:0001435 + + + + + lateral wall neural tube + ZFA:0001435 + + + + + + + + + + + + + + + + + + + + + + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. + + + EHDAA2:0001512 + EHDAA:424 + EHDAA:436 + EMAPA:16215 + FMA:321916 + TAO:0000149 + ZFA:0000149 + primitive heart tube + early primitive heart tube + uberon + UBERON:0005498 + + primitive heart tube + + + + + + + + + + + ZFA + + + + + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. + ZFA:0000149 + + + + + primitive heart tube + EMAPA:16215 + + + + + early primitive heart tube + EMAPA:16208 + + + + + + + + + + + + + + + + + + + + + + + + + + A neural tube lateral wall that is part of a rhombomere. + EMAPA:32819 + EMAPA:35364 + uberon + future hindbrain lateral wall + UBERON:0005501 + rhombomere lateral wall + + + + + A neural tube lateral wall that is part of a rhombomere. + OBOL:automatic + + + + + future hindbrain lateral wall + EMAPA:35364 + + + + + + + + + + + + + + + + + + + + + + + + + + + A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. + UBERON:3010717 + AAO:0011059 + EFO:0002578 + EMAPA:36007 + XAO:0001002 + uberon + lateral diverticula + lung diverticulum + lung endoderm + UBERON:0005597 + + lung primordium + + + + + + XAO + + + + + + + + + + + XAO + + + + + A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. + XAO:0001002 + + + + + lateral diverticula + XAO:0001002 + + + + + lung diverticulum + AAO:3010717 + + + + + lung endoderm + EFO:0002578 + + + + + + + + + + + + + + + + + + + + + + + + + + A somite that is part of a trunk. + AAO:0010385 + EHDAA2:0003438 + EMAPA:16184 + XAO:0000314 + uberon + UBERON:0005598 + trunk somite + + + + + A somite that is part of a trunk. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a right lung. + EHDAA2:0001755 + uberon + UBERON:0005672 + right lung endothelium + + + + + An endothelium that is part of a right lung. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a left lung. + EHDAA2:0000961 + uberon + UBERON:0005673 + left lung endothelium + + + + + An endothelium that is part of a left lung. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + A venous system that is part of a hindbrain. + EHDAA2:0000776 + EMAPA:18632 + VHOG:0001322 + uberon + rhombencephalon venous system + UBERON:0005720 + hindbrain venous system + + + + + A venous system that is part of a hindbrain. + OBOL:automatic + + + + + rhombencephalon venous system + VHOG:0001322 + + + + + + + + + + + + + + + + The outermost layer of a blood vessel, composed mainly of fibrous tissue. + TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings + The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29]. + + + + BTO:0002010 + EMAPA:36299 + NCIT:C33818 + UMLS:C0225342 + adventitia externa + tunica adventitia + tunica adventitia of vessel + uberon + external coat + tunica adventitia vasorum + tunica externa vasorum + UBERON:0005734 + tunica adventitia of blood vessel + + + + + + + cjm + + + + + The outermost layer of a blood vessel, composed mainly of fibrous tissue. + + ISBN10:0073040584 + + + + + The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_%28vessels%29]. + + + + + + UMLS:C0225342 + ncithesaurus:Tunica_Adventitia + + + + + adventitia externa + + + + + + tunica adventitia + + + + + + tunica adventitia of vessel + + + + + + external coat + + + + + + tunica adventitia vasorum + + + + + + + tunica externa vasorum + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tunica intima that is part of a artery. + + EMAPA:36293 + EV:0100028 + FMA:14272 + galen:IntimaOfArtery + arterial intima + tunica interna (intima)(arteriae) + uberon + UBERON:0005740 + tunica intima of artery + + + + + A tunica intima that is part of a artery. + OBOL:automatic + + + + + arterial intima + EV:0100028 + + + + + tunica interna (intima)(arteriae) + FMA:14272 + + + + + + + + + + + + + + + An outermost connective tissue covering of an organ, vessel, or other structure[WP]. + + + BTO:0002010 + FMA:45635 + tunica advetitia + tunica externa + uberon + UBERON:0005742 + + adventitia + + + + + + An outermost connective tissue covering of an organ, vessel, or other structure[WP]. + + + + + + tunica advetitia + + + + + + tunica externa + FMA:45635 + + + + + + + + + + + + + + + + + + + + + + + + + + A acellular anatomical structure that is the bounding layer of a anatomical structure. + FMA:63871 + uberon + UBERON:0005764 + acellular membrane + + + + + A acellular anatomical structure that is the bounding layer of a anatomical structure. + OBOL:automatic + + + + + + + + + + + + + + + An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. + this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. + + + + + AAO:0010596 + FMA:63872 + GAID:915 + NCIT:C13191 + UMLS:C0004799 + basement membrane of connective tissue + membrana basalis + uberon + basement membrane + UBERON:0005769 + basement membrane of epithelium + + + + + + FMA + + + + + An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. + + + + + + + + + + + + + UMLS:C0004799 + ncithesaurus:Basement_Membrane + + + + + basement membrane of connective tissue + FMA:63872 + + + + + membrana basalis + + + + + + + basement membrane + FMA:63872 + + + + + + + + + + A delimited region of dense mesenchyme within looser mesenchyme. + AEO:0000148 + EHDAA2_RETIRED:0003148 + EHDAA:8979 + mesenchyme condensation + uberon + UBERON:0005856 + developing mesenchymal condensation + + + + + + AEO + + + + + + cjm + + + + + A delimited region of dense mesenchyme within looser mesenchyme. + AEO:0000148 + + + + + mesenchyme condensation + EMAPA:25351 + + + + + + + + + + + + + + + + + + + + + Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] + + + EMAPA:16060 + FMA:9689 + MA:0000005 + uberon + UBERON:0005906 + See notes for serous membrane + serous sac + + + + + Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] + + FMA:9689 + + + + + + + + + + + + + + + + + + + + + Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] + FMA:69065 + endoderm-derived epithelium + endoepithelium + uberon + UBERON:0005911 + endo-epithelium + + + + + Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] + FMA:69065 + + + + + + + + + + + + + + + + + + + + + + + + + + + Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. + Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] + + + + + AAO:0000963 + EMAPA:17214 + EMAPA:18043 + MA:0000308 + NCIT:C32172 + UMLS:C0222645 + VSAO:0000056 + XAO:0004011 + uberon + skeleton axiale + UBERON:0005944 + + + axial skeleton plus cranial skeleton + http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + + + + + + Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. + + + + FMA:71221 + VSAO:0000056 + + + + + Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] + 2012-08-14 + VSAO:0000056 + VSAO + PSPUB:0000170 + + + + + UMLS:C0222645 + ncithesaurus:Axial_Skeleton + + + + + skeleton axiale + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The laminar structure of the heart + uberon + UBERON:0005983 + + + heart layer + + + + + The laminar structure of the heart + MP:0010545 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation + TODO - change relation from part_of + + MESH:D003331 + uberon + UBERON:0005985 + + coronary vessel + + + + + Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation + MP:0010551 + + + + + + + + + + + + + + + Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. + add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. + the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] + + EMAPA:37883 + body hair or bristle + uberon + adnexae cutis + skin adnexa + skin adnexal structure + skin appendage + UBERON:0006003 + + integumentary adnexa + + + + + Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. + + + + + + + the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] + MP:0010678 + + + + + EMAPA:37883 + MA:th + + + + + body hair or bristle + GO:GO + + + + + adnexae cutis + + + + + + + skin adnexa + + + + + + skin appendage + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. + + + EHDAA2:0000189 + EHDAA:536 + EMAPA:16259 + FMA:313607 + VHOG:0000380 + uberon + oral membrane + oral plate + oropharyngeal membrane + pharyngeal membrane + UBERON:0006211 + + + buccopharyngeal membrane + + + + + + + + + + + + EHDAA2 + + + + + The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. + MP:0012521 + + + + + oral membrane + MP:0012521 + + + + + oral plate + MP:0012521 + + + + + oropharyngeal membrane + + + + + + pharyngeal membrane + MP:0012521 + + + + + + + + + + + + + + + + + + + + + + The embryonic precursor of the brain. + The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) + BAMS:Enc + BTO:0004726 + EFO:0003431 + EHDAA:300 + EHDAA:830 + EMAPA:16089 + FMA:312967 + RETIRED_EHDAA2:0000591 + TAO:0000146 + ZFA:0000146 + brain rudiment + presumptive brain + encephalon + uberon + embryonic brain + UBERON:0006238 + + + + + future brain + + + + + The embryonic precursor of the brain. + NIFSTD:nlx_94995 + + + + + The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) + + + + + + brain rudiment + TAO:0000146 + + + + + presumptive brain + ZFA:0000146 + + + + + encephalon + NIFSTD:nlx_94995 + + + + + embryonic brain + BTO:0004726 + + + + + + + + + + + + + + + + + + + + + + + + + + + EFO:0003438 + EHDAA2:0000674 + EHDAA:898 + EMAPA:16092 + EMAPA:16755 + TAO:0000417 + ZFA:0000417 + presumptive spinal cord + presumptive spinal cord neural keel + presumptive spinal cord neural plate + presumptive spinal cord neural rod + uberon + UBERON:0006241 + + + future spinal cord + + + + + + + + + + + EHDAA2 + + + + + presumptive spinal cord + ZFA:0000417 + + + + + presumptive spinal cord neural keel + TAO:0000417 + + + + + presumptive spinal cord neural plate + TAO:0000417 + + + + + presumptive spinal cord neural rod + TAO:0000417 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical junctions that overlaps the mouth and foregut. + EHDAA:534 + EMAPA:16258 + RETIRED_EHDAA2:0001205 + VHOG:0000592 + uberon + UBERON:0006264 + + mouth-foregut junction + + + + + An anatomical junctions that overlaps the mouth and foregut. + OBOL:automatic + + + + + + + + + + + + + + + + + + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. + TODO - check ordering; awaiting confirmation from JB + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] + + EHDAA2:0001278 + EHDAA:264 + EMAPA:16101 + NCIT:C34231 + UMLS:C1518429 + VHOG:0001212 + uberon + UBERON:0006267 + + notochordal plate + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. + VHOG:0001212 + + + + + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] + 2012-09-17 + VHOG:0001212 + VHOG + + + + + + UMLS:C1518429 + ncithesaurus:Notochordal_Plate + + + + + + + + + + + + + + + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot + + EHDAA2:0001279 + EHDAA:224 + EMAPA:16102 + FMA:293135 + NCIT:C34232 + UMLS:C1518430 + VHOG:0001213 + uberon + chordamesoderm + presumptive notochord + UBERON:0006268 + + The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. + notochordal process + + + + + + + + + + + EHDAA2 + + + + + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot + + + + + + UMLS:C1518430 + ncithesaurus:Notochordal_Process + + + + + + + + + Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + fluid + + + EMAPA:37441 + FMA:280556 + GAID:266 + MESH:D001826 + galen:BodyFluid + body fluid + uberon + UBERON:0006314 + + bodily fluid + + + + + Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. + + MESH:A12.207 + + + + + EMAPA:37441 + MA:th + + + + + body fluid + GAID:266 + + + + + + + + + + + + + + + + 2 + + + + + 2 + + + + + + + + + + + + + + + An artery that connects two larger arteries. + + EMAPA:18598 + MA:0001938 + NCIT:C52851 + UMLS:C1707451 + uberon + UBERON:0006347 + Grouping for anterior and posterior + communicating artery + + + + + An artery that connects two larger arteries. + ncithesaurus:Communicating_Artery + + + + + UMLS:C1707451 + ncithesaurus:Communicating_Artery + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of organism substance that secreted_by a zone of skin. + MA:0002537 + skin fluid/secretion + uberon + skin fluid + skin substance + UBERON:0006535 + skin secretion + + + + + A portion of organism substance that secreted_by a zone of skin. + OBOL:automatic + + + + + skin fluid/secretion + MA:0002537 + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of organism substance that secreted_by a respiratory system. + + EMAPA:36550 + MA:0002533 + NCIT:C13722 + UMLS:C1514899 + uberon + respiratory system fluid + respiratory system secretion + UBERON:0006538 + respiratory system fluid/secretion + + + + + A portion of organism substance that secreted_by a respiratory system. + OBOL:automatic + + + + + UMLS:C1514899 + ncithesaurus:Respiratory_System_Fluid_or_Secretion + + + + + + + + + The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. + currently this is an extremely generic class, encompassing both protostomes and deuterostomes. + branchial + pharyngeal + FBbt:00005380 + MAT:0000049 + MIAA:0000049 + uberon + anterior part of foregut + pharyngeal tube + UBERON:0006562 + + + pharynx + + + + + The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. + GO:0060465 + + + + + + + + + + + + + + + + + + + + + + + + + + Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] + FMA:85030 + uberon + UBERON:0006563 + tunica media of pulmonary trunk + + + + + Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] + FMA:85030 + FMA:FMA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into endoderm. + AAO:0000471 + EFO:0003437 + TAO:0000416 + ZFA:0000416 + uberon + UBERON:0006595 + + presumptive endoderm + + + + + Presumptive structure of the blastula that will develop into endoderm. + + + + + + + + + + + + + + + + + + + + + + + + + + + AAO:0000468 + EFO:0003439 + TAO:0000568 + ZFA:0000568 + future blood + uberon + UBERON:0006596 + + presumptive blood + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Portion of embryonic tissue determined by fate mapping to become a structure. + Consider merging with anlage + AAO:0000479 + TAO:0001116 + ZFA:0001116 + future structure + presumptive structures + uberon + UBERON:0006598 + presumptive structure + + + + + Portion of embryonic tissue determined by fate mapping to become a structure. + GOC:CVS + GOC:YMB + ZFA:0001116 + + + + + presumptive structures + ZFA:0001116 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into ectoderm. + AAO:0000470 + EFO:0003466 + TAO:0001376 + XAO:0004132 + ZFA:0001376 + uberon + presumptive epidermis + UBERON:0006601 + + presumptive ectoderm + + + + + Presumptive structure of the blastula that will develop into ectoderm. + + + + + + presumptive epidermis + ZFA:0001376 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Presumptive structure of the blastula that will develop into mesoderm. + AAO:0000476 + EFO:0003467 + TAO:0001377 + ZFA:0001377 + uberon + UBERON:0006603 + + presumptive mesoderm + + + + + Presumptive structure of the blastula that will develop into mesoderm. + + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a organ. + FMA:74612 + organ vasculature + set of blood vessels of organ + uberon + UBERON:0006876 + + vasculature of organ + + + + + A vasculature that is part of a organ. + OBOL:automatic + + + + + organ vasculature + FMA:74612 + + + + + set of blood vessels of organ + FMA:74612 + + + + + + + + + + + + + + + + + + + + + + + + + + + A head mesenchyme that develops_from a mesoderm. + merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme + AAO:0011051 + EFO:0003337 + EFO:0003603 + EHDAA2:0001118 + EHDAA:655 + EMAPA:16099 + EMAPA_RETIRED:16270 + FMA:293859 + TAO:0000998 + VHOG:0000185 + XAO:0000053 + ZFA:0000998 + head mesenchyme derived from mesoderm + head mesenchyme from head mesoderm + head mesenchyme from mesoderm + mesenchyme derived from head mesoderm + mesenchyme from head mesoderm + uberon + cranial mesoderm + head mesoderm + UBERON:0006904 + + + head mesenchyme from mesoderm + + + + + + ZFA + + + + + + + + + + + EHDAA2 + XAO + + + + + A head mesenchyme that develops_from a mesoderm. + OBOL:automatic + + + + + head mesenchyme from head mesoderm + EHDAA2:0001118 + + + + + mesenchyme derived from head mesoderm + EHDAA:1057 + + + + + cranial mesoderm + UBERON:0005280 + + + + + head mesoderm + AAO:0011051 + UBERON:0005280 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical space that surrounded_by a digestive tract. + BTO:0000349 + EMAPA:32908 + FMA:45677 + digestive tract lumen + gut cavity + gut lumen + lumen of alimentary tract + lumen of digestive tract + lumen of gut + uberon + UBERON:0006909 + lumen of digestive tract + + + + + An anatomical space that surrounded_by a digestive tract. + OBOL:automatic + + + + + digestive tract lumen + + + + + + gut cavity + BTO:0000349 + + + + + gut lumen + FMA:45677 + + + + + lumen of alimentary tract + + + + + + lumen of digestive tract + + + + + + lumen of gut + FMA:45677 + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a lip. + The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] + BTO:0004468 + TAO:0005334 + ZFA:0005334 + uberon + UBERON:0006913 + lip epithelium + + + + + An epithelium that is part of a lip. + OBOL:automatic + + + + + The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] + 2012-08-14 + TAO:0005334 + TAO + ZFIN:ZDB-PUB-060921-12 + + + + + + + + + An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. + FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium + + + + BTO:0002072 + NCIT:C12848 + UMLS:C0221909 + uberon + UBERON:0006914 + squamous epithelium + + + + + An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. + + + + + + FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium + FBbt + + + + + UMLS:C0221909 + ncithesaurus:Squamous_Epithelium + + + + + + + + + + + + + + + The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. + EFO:0003709 + TAO:0005077 + ZFA:0005077 + uberon + UBERON:0006965 + + vascular cord + + + + + The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. + GO:0072360 + ZFA:0005077 + + + + + + + + + + + + + + + + + + + + + A capillary that is part of the coronary system. + ZFA:0005813 + heart capillary + uberon + UBERON:0006966 + coronary capillary + + + + + A capillary that is part of the coronary system. + + + + + + heart capillary + GO:0003248 + + + + + + + + + A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n + + BILA:0000010 + CARO:0001002 + EHDAA2_RETIRED:0003192 + FMA:24137 + NCIT:C34022 + UMLS:C1515977 + uberon + UBERON:0006984 + + Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. + anatomical surface + + + + + + via morphological boundary in CARO + + + + + A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n + CARO:0001002 + + + + + UMLS:C1515977 + ncithesaurus:Anatomic_Surface + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. + consider FBbt:00005541 ! cardiogenic mesoderm + review EHDAA2 placement + + AAO:0011021 + BILA:0000051 + EFO:0000315 + EHDAA2:0000214 + EHDAA:385 + FMA:293143 + VHOG:0001641 + XAO:0000235 + cardiogenic splanchnopleure + uberon + cardiac mesoderm + cardiogenic mesoderm + cardiogenic region + heart primordia + UBERON:0007005 + + + cardiogenic splanchnic mesoderm + + + + + The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. + + + XAO:0000235 + + + + + cardiogenic splanchnopleure + EHDAA2:0000214 + + + + + cardiac mesoderm + XAO:0000235 + + + + + cardiogenic mesoderm + + + + + + cardiogenic region + + + + + + heart primordia + XAO:0000235 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Organism at the cleavage stage. + BILA:0000058 + uberon + UBERON:0007010 + cleaving embryo + + + + + Organism at the cleavage stage. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis + + + BILA:0000084 + NCIT:C34268 + UMLS:C1514442 + future digestive tract + future digestive tube + future gut + primitive gut + uberon + embryonic digestive tube + primordial digestive tube + primordial gut + UBERON:0007026 + presumptive gut + + + + + The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis + NCBIBook:NBK10107 + + + + + UMLS:C1514442 + ncithesaurus:Primordial_Gut + + + + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. + note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis + + FBbt:00003154 + SPD:0000130 + TADS:0000147 + dorsal tube + heart + uberon + adult heart + UBERON:0007100 + + Gene notes: Bmp, Nkx, Gata + primary circulatory organ + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. + GO:0007507 + + + + + dorsal tube + + + + + + heart + GO:0007507 + + + + + adult heart + FBbt:00003154 + + + + + + + + + + + + + + + An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. + An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] + EFO:0003497 + TAO:0000131 + ZFA:0000131 + uberon + presumptive central nervous system + UBERON:0007135 + + neural keel + + + + + An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. + ZFIN:ZDB-PUB-961014-576 + + + + + An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000131 + TAO + ZFIN:curator + + + + + presumptive central nervous system + ZFA:0000131 + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a cranial neural crest. + EFO:0003572 + EHDAA2:0000735 + EMAPA:16169 + EMAPA:16271 + EMAPA_RETIRED:16271 + TAO:0000787 + ZFA:0000787 + head mesenchyme from cranial neural crest + head mesenchyme from neural crest + head neural crest derived mesenchyme + uberon + UBERON:0007213 + + + mesenchyme derived from head neural crest + + + + + + ZFA + + + + + Mesenchyme that develops_from a cranial neural crest. + OBOL:automatic + + + + + head mesenchyme from neural crest + EHDAA2:0000735 + + + + + + + + + + + + + + + + + + + + + + + + + + A tunica media that is part of a artery. + + + EMAPA:36294 + EV:0100029 + FMA:14273 + NCIT:C49321 + UMLS:C1710627 + arterial media + tunica media (arteriae) + uberon + UBERON:0007239 + tunica media of artery + + + + + A tunica media that is part of a artery. + OBOL:automatic + + + + + UMLS:C1710627 + ncithesaurus:Venous_System_Smooth_Muscle_Tissue + + + + + arterial media + EV:0100029 + + + + + tunica media (arteriae) + FMA:14273 + + + + + + + + + + + + + + + + + + + + + + + + + + A tunica adventitia that is part of a artery. + + EMAPA:36295 + EV:0100030 + FMA:14274 + arterial adventitia + tunica externa (adventitia)(arteriae) + uberon + UBERON:0007240 + tunica adventitia of artery + + + + + A tunica adventitia that is part of a artery. + OBOL:automatic + + + + + arterial adventitia + EV:0100030 + + + + + tunica externa (adventitia)(arteriae) + FMA:14274 + + + + + + + + + + + + + + + + + + + + + + + + + + A tunica adventitia that is part of a vein. + + EMAPA:36310 + EV:0100034 + FMA:14355 + tunica externa (adventitia)(venae) + venous adventitia + uberon + UBERON:0007241 + tunica adventitia of vein + + + + + A tunica adventitia that is part of a vein. + OBOL:automatic + + + + + tunica externa (adventitia)(venae) + FMA:14355 + + + + + venous adventitia + EV:0100034 + + + + + + + + + + + + + + + + + + + + + + + + + + + A tunica intima that is part of a vein. + + EMAPA:36308 + EV:0100032 + FMA:14353 + tunica interna (intima)(venae) + venous intima + uberon + UBERON:0007242 + tunica intima of vein + + + + + A tunica intima that is part of a vein. + OBOL:automatic + + + + + tunica interna (intima)(venae) + FMA:14353 + + + + + venous intima + EV:0100032 + + + + + + + + + + + + + + + + + + + + + + + + + + A tunica media that is part of a vein. + + EMAPA:36309 + EV:0100033 + FMA:14354 + tunica media (venae) + venous media + uberon + UBERON:0007243 + tunica media of vein + + + + + A tunica media that is part of a vein. + OBOL:automatic + + + + + tunica media (venae) + FMA:14354 + + + + + venous media + EV:0100033 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. + TODO - unify naming conventions + The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. + + BAMS:HB + CALOHA:TS-2118 + EFO:0003440 + EHDAA2:0001630 + FMA:295640 + TAO:0000569 + ZFA:0000569 + presumptive rhombencephalon + uberon + embryonic rhombencephalon + future hindbrain + rhombencephalon + UBERON:0007277 + + presumptive hindbrain + + + + + + + + + + + XAO-abduced + + + + + + + + + + + cjm + + + + + The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. + + + + + + The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. + NPX:PDR + + + + + presumptive rhombencephalon + ZFA:0000569 + + + + + embryonic rhombencephalon + CALOHA:TS-2118 + + + + + future hindbrain + + + + + + rhombencephalon + EHDAA2:0001630 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A presumptive structure that has the potential to develop into a endocardium. + Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] + TAO:0002233 + ZFA:0001724 + uberon + UBERON:0007280 + presumptive endocardium + + + + + A presumptive structure that has the potential to develop into a endocardium. + OBOL:automatic + + + + + Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] + 2012-08-14 + TAO:0002233 + TAO + ZFIN:curator + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Embryonic structure that gives rise to the midbrain hindbrain boundary. + EFO:0003446 + TAO:0001187 + XAO:0004086 + ZFA:0001187 + presumptive MHB + presumptive midbrain-hindbrain boundary + uberon + UBERON:0007281 + + presumptive midbrain hindbrain boundary + + + + + + + + + + + ZFA + + + + + Embryonic structure that gives rise to the midbrain hindbrain boundary. + ZFA:0001187 + + + + + presumptive MHB + + + + + + presumptive midbrain-hindbrain boundary + ZFA:0001187 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A presumptive structure that has the potential to develop into a presomitic mesoderm. + EFO:0003421 + TAO:0000053 + ZFA:0000053 + uberon + presumptive segmental plates + UBERON:0007282 + + presumptive segmental plate + + + + + + + + + + + https://github.com/obophenotype/uberon/wiki/The-neural-crest + EDHAA2 + + + + + A presumptive structure that has the potential to develop into a presomitic mesoderm. + OBOL:automatic + + + + + presumptive segmental plates + ZFA:0000053 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A presumptive structure that has the potential to develop into a neural plate. + consider merging + Region of the gastrula which gives rise to the neural plate.[TAO] + EFO:0003424 + TAO:0000063 + ZFA:0000063 + prospective neuroectoderm + prospective vegetal ectoderm + uberon + UBERON:0007284 + + presumptive neural plate + + + + + A presumptive structure that has the potential to develop into a neural plate. + OBOL:automatic + + + + + Region of the gastrula which gives rise to the neural plate.[TAO] + 2012-08-14 + TAO:0000063 + TAO + ZFIN:curator + + + + + prospective neuroectoderm + ZFA:0000063 + + + + + prospective vegetal ectoderm + ZFA:0000063 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The part of the blastula that has the potential to develop into a paraxial mesoderm. + EFO:0003443 + TAO:0000591 + XAO:0004134 + ZFA:0000591 + future paraxial mesenchyme + future paraxial mesoderm + uberon + UBERON:0007285 + + presumptive paraxial mesoderm + + + + + + + + + + + + + + + + + + + + + + + + + The part of the blastula that has the potential to develop into a paraxial mesoderm. + + UBERON:cjm + + + + + future paraxial mesenchyme + UBERON:cjm + + + + + + + + + + + + + + + + + + + + + + + + + + A vasculature that is part of a chordate pharynx. + TAO:0005003 + ZFA:0005003 + branchial vasculature + uberon + UBERON:0007303 + pharyngeal vasculature + + + + + A vasculature that is part of a chordate pharynx. + OBOL:automatic + + + + + branchial vasculature + ZFA:0005003 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. + this grouping class exists primarily to align with GO - see GO:0008544. + + BSA:0000073 + BTO:0000313 + FBbt:00004993 + HAO:0000298 + TADS:0000109 + WBbt:0005733 + epidermis + epidermis (sensu Metazoa) + outer epidermal layer + outer epithelial layer + uberon + hypoderm + hypodermis + UBERON:0007376 + + outer epithelium + + + + + The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. + GO:0008544 + + + + + epidermis + GO:0008544 + + + + + hypoderm + BTO:0000313 + + + + + + hypodermis + GO:0008544 + WBbt:0005733 + + + + + + + + + + + + + + + + + + + + + + + + Outermost layer of cells surrounding the embryo. + Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] + relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] + Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. + EFO:0003425 + TAO:0000086 + ZFA:0000086 + EVL + enveloping layer + uberon + UBERON:0007383 + + enveloping layer of ectoderm + + + + + Outermost layer of cells surrounding the embryo. + + + + + + Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] + 2012-08-14 + TAO:0000086 + TAO + ZFIN:curator + + + + + relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] + 2012-08-14 + TAO:0000086 + TAO + + + + + EVL + ZFA:0000086 + + + + + enveloping layer + ZFIN:ZDB-PUB-961014-576 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The space within an epithelial sphere. + EHDAA2:0003079 + AEO:0000079 + cavity of vesicle + uberon + UBERON:0007473 + lumen of epithelial sac + + + + + The space within an epithelial sphere. + AEO:JB + + + + + cavity of vesicle + AEO:0000079 + + + + + + + + + + An epithelial tube that is open at one end only. + AEO:0000115 + EHDAA2:0003115 + uberon + UBERON:0007499 + epithelial sac + + + + + + AEO + + + + + An epithelial tube that is open at one end only. + AEO:JB + UBERONREF:0000001 + + + + + + + + + An epithelial tube open at both ends that allows fluid flow. + AEO_RETIRED:0000116 + RETIRED_EHDAA2:0003116 + uberon + UBERON:0007500 + epithelial tube open at both ends + + + + + + AEO + + + + + An epithelial tube open at both ends that allows fluid flow. + AEO:JB + UBERONREF:0000001 + + + + + + + + + A closed epithelium with a lumen. + EHDAA2:0003119 + AEO:0000119 + EHDAA2:0003119 + uberon + UBERON:0007503 + epithelial vesicle + + + + + + AEO + + + + + A closed epithelium with a lumen. + AEO:JB + + + + + + + + + Mesenchyme with little extracellular matrix. + EHDAA2:0003146 + AEO:0000146 + EHDAA2:0003146 + uberon + UBERON:0007524 + dense mesenchyme tissue + + + + + + AEO + + + + + Mesenchyme with little extracellular matrix. + AEO:JB + + + + + + + + + Mesenchymal cells that are migrating. + this class will be an important part of the NC reorganization + EHDAA2:0003152 + AEO:0000152 + EHDAA2:0003152 + uberon + UBERON:0007530 + migrating mesenchyme population + + + + + Mesenchymal cells that are migrating. + AEO:JB + + + + + + + + + + Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] + In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system + Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] + FMA:64798 + uberon + UBERON:0007592 + ciliated columnar epithelium + + + + + + FMA + + + + + Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] + FMA:64798 + + + + + + + + + Epithelium bearing vibratile cilia on the free surface. + uberon + UBERON:0007601 + ciliated epithelium + + + + + Epithelium bearing vibratile cilia on the free surface. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. + BTO:0001338 + CALOHA:TS-0998 + FMA:66762 + synovium + stratum synoviale + synovial layer + synovial membrane + uberon + synovial tissue + UBERON:0007616 + layer of synovial tissue + + + + + + + + + + + BTO + + + + + A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. + + BTO:0001338 + + + + + synovium + CALOHA:TS-0998 + + + + + stratum synoviale + FMA:TA + + + + + synovial layer + FMA:66762 + + + + + synovial membrane + FMA:66762 + + + + + synovial tissue + BTO:0001338 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical cavity that surrounded_by a synovial joint. + FMA:11356 + articular cavity (synovial joint) + cavitas articularis (junctura synovialis) + cavity of synovial joint + uberon + joint cavity + synovial cavity + UBERON:0007617 + synovial cavity of joint + + + + + An anatomical cavity that surrounded_by a synovial joint. + OBOL:automatic + + + + + articular cavity (synovial joint) + FMA:11356 + + + + + cavitas articularis (junctura synovialis) + FMA:11356 + + + + + cavity of synovial joint + FMA:11356 + + + + + joint cavity + FMA:11356 + + + + + synovial cavity + FMA:11356 + + + + + + + + + + + + 2 + + + + An anatomical structure that connects two structures + junction + + FMA:5898 + anatomical junction + uberon + UBERON:0007651 + + anatomical junction + + + + + + FMA + + + + + An anatomical structure that connects two structures + + + + + + + + + + + Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. + field + + AEO:0000170 + EFO:0001649 + EHDAA2:0003170 + FBbt:00005426 + developmental field + uberon + future organ + organ field + UBERON:0007688 + + anlage + + + + + + FBbt + + + + + + AEO + FBbt + + + + + Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. + + FBbt:00005426 + JB:DEF + + + + + + + + + + + + + + + + . + EFO:0003626 + EHDAA2:0001457 + EHDAA:962 + EMAPA:32754 + FMA:293087 + TAO:0001104 + ZFA:0001104 + early pharyngeal arch endoderm + uberon + pharyngeal arch endoderm + pharyngeal endoderm + pharyngeal region endoderm + UBERON:0007690 + + relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' + early pharyngeal endoderm + + + + + + + + + + + cjm + + + + + . + + + + + + early pharyngeal arch endoderm + EHDAA2:0001457 + + + + + pharyngeal endoderm + ZFA:0001104 + + + + + pharyngeal region endoderm + EHDAA2:0001456 + + + + + + + + + + + + + + + + + + + + + + + + + + A gland that is part of a epidermis. + FMA:59153 + epidermal gland + gland of epidermis + uberon + UBERON:0007771 + + epidermis gland + + + + + A gland that is part of a epidermis. + OBOL:automatic + + + + + gland of epidermis + FMA:59153 + + + + + + + + + + + + + + + + + + + + + + + + + + + Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces + transudative + characteristically low in protein and cellular content (unless there has been secondary concentration) + FMA:12276 + GAID:1195 + MESH:D005122 + ncithesaurus:Transudate + uberon + plasma ultrafiltrate + UBERON:0007779 + transudate + + + + + Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any fluid produced by a serous gland. + serous fluid + + serosal fluid + serous gland fluid + uberon + UBERON:0007794 + secretion of serous gland + + + + + Any fluid produced by a serous gland. + UBERON:cjm + + + + + serosal fluid + + + + + + + + + + + + + + + + Anatomical system that consists of all blood and lymph vessels. + consider merging with vasculature + The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. + in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system + + BTO:0001085 + CALOHA:TS-2053 + EHDAA2:0004520 + EMAPA:35905 + MA:0002718 + NCIT:C33854 + UMLS:C0489903 + uberon + Gefaesssystem@de + UBERON:0007798 + + vascular system + + + + + + + + + + + MA + + + + + Anatomical system that consists of all blood and lymph vessels. + + + + + + The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. + ncithesaurus:Vascular_System + + + + + in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system + MA + + + + + UMLS:C0489903 + ncithesaurus:Vascular_System + + + + + Gefaesssystem@de + BTO:0001085 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. + + + CALOHA:TS-2356 + EV:0100009 + FMA:280881 + MA:0000006 + NCIT:C12418 + UMLS:C0460004 + WikipediaCategory:Head_and_neck + galen:HeadAndNeck + uberon + cephalic area + cephalic part of animal + cephalic region + head and neck + head or neck + UBERON:0007811 + + craniocervical region + + + + + + MA + + + + + The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. + + + + + + UMLS:C0460004 + ncithesaurus:Head_and_Neck + + + + + cephalic area + + + + + + cephalic part of animal + + + + + + cephalic region + + + + + + head and neck + FMA:280881 + + + + + + + + + + + + + + + + + + + + + + + + + + Musculature system of the pharyngeal and head regions. + in MA this is restricted to skeletal muscles + EMAPA:37259 + MA:0000571 + TAO:0000328 + ZFA:0000328 + head or neck muscle + uberon + head muscles + head or neck muscle + UBERON:0008229 + craniocervical region musculature + + + + + + MA + + + + + + + + + + + MA + + + + + Musculature system of the pharyngeal and head regions. + ZFA:0000328 + ZFA:curator + + + + + in MA this is restricted to skeletal muscles + MA + + + + + EMAPA:37259 + MA:th + + + + + head or neck muscle + MA:0000571 + + + + + head muscles + ZFA:0000328 + + + + + head or neck muscle + MA:0000571 + + + + + + + + + + + + + + + + + + + + + + + + + + An endothelium that is part of a heart [Automatically generated definition]. + this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class. + BTO:0004293 + uberon + cardiac endothelium + UBERON:0008307 + heart endothelium + + + + + An endothelium that is part of a heart [Automatically generated definition]. + OBOL:automatic + + + + + cardiac endothelium + BTO:0004293 + + + + + + + + + + + + + + + + + + + + + A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. + Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing + + EHDAA2:0000187 + FMA:293041 + NCIT:C34248 + UMLS:C1519038 + embryonic pharyngeal complex + pharyngeal apparatus + pharyngeal system + uberon + pharyngeal arch complex + pharyngeal arch region + pharyngeal arches and clefts + pharyngeal complex + UBERON:0008814 + pharyngeal arch system + + + + + A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. + GO:0060037 + GOC:dph + + + + + UMLS:C1519038 + ncithesaurus:Pharyngeal_Apparatus + + + + + pharyngeal system + GO:0060037 + + + + + pharyngeal arch region + EHDAA2:0000187 + + + + + + + + + + + + + + + + + + + + + + + + + + A head that is part of a embryo. + CALOHA:TS-0246 + FBbt:00000155 + FMA:293011 + uberon + UBERON:0008816 + + embryonic head + + + + + A head that is part of a embryo. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A brain that develops_from a neural tube. + a reasoner should automatically classify all the vertebrate ontology brain classes here + vertebrate brain + uberon + UBERON:0008823 + neural tube derived brain + + + + + + + ZFA + + + + + + + + + + + FMA + + + + + A brain that develops_from a neural tube. + + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. + Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] + + FMA:45621 + pulmonary circulatory system + pulmonary system + uberon + UBERON:0008886 + pulmonary vascular system + + + + + + Obol + + + + + The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. + + ISBN10:0073040584 + + + + + Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] + FMA + FMA:45621 + + + + + pulmonary circulatory system + FMA:45621 + + + + + pulmonary system + ISBN10:0073040584 + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0004069 + NCIT:C34283 + UMLS:C1514898 + uberon + UBERON:0008947 + respiratory primordium + + + + + + Obol + + + + + UMLS:C1514898 + ncithesaurus:Respiratory_Primordium + + + + + + + + + + + + + + + System pertaining to blood vessels in the brain. + UBERON:0005284 + + BTO:0003840 + EFO:0003491 + EMAPA:35186 + FMA:242007 + FMA:61935 + TAO:0000099 + ZFA:0000099 + brain vasculature + cerebrovascular system + intracerebral vasculature + uberon + UBERON:0008998 + + vasculature of brain + + + + + System pertaining to blood vessels in the brain. + BTO:0003840 + + + + + cerebrovascular system + BTO:0003840 + + + + + intracerebral vasculature + FMA:61935 + + + + + + + + + + + + + + + + + + + + + + + + + + Vein that drains left lung and returns blood to the heart. + A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. + + + EMAPA:37165 + MA:0002207 + NCIT:C48946 + UMLS:C0226670 + uberon + UBERON:0009030 + left pulmonary vein + + + + + Vein that drains left lung and returns blood to the heart. + + + + + + A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. + ncithesaurus:Left_Pulmonary_Vein + + + + + EMAPA:37165 + MA:th + + + + + UMLS:C0226670 + ncithesaurus:Left_Pulmonary_Vein + + + + + + + + + + + + + + + + + + + + + + + + + + Vein that drains right lung and returns blood to the heart. + A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. + + + EMAPA:37379 + MA:0002208 + NCIT:C48947 + UMLS:C0226669 + uberon + UBERON:0009032 + right pulmonary vein + + + + + Vein that drains right lung and returns blood to the heart. + + + + + + A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. + ncithesaurus:Right_Pulmonary_Vein + + + + + EMAPA:37379 + MA:th + + + + + UMLS:C0226669 + ncithesaurus:Right_Pulmonary_Vein + + + + + + + + + + + + + + + + + + + + + + + + + + A vein that is part of a craniocervical region. + + EHDAA2:0004542 + craniocervical vein + head and neck veins + vein of head and neck + uberon + UBERON:0009141 + craniocervical region vein + + + + + A vein that is part of a craniocervical region. + OBOL:automatic + + + + + head and neck veins + EHDAA2:0004542 + + + + + + + + + + + + + + + + + + + + + + + + + + + Sum total of mesenchyme in the embryo. + consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) + UBERON:0003313 + EHDAA2:0001113 + EHDAA:177 + EMAPA:16097 + uberon + UBERON:0009142 + entire embryonic mesenchyme + + + + + + + + + + + EHDAA2 + + + + + Sum total of mesenchyme in the embryo. + + + + + + + + + + + + + + + + EMAPA:16549 + RETIRED_EHDAA2:0001454 + pharyngeal region + uberon + UBERON:0009145 + pharyngeal region of foregut + + + + + + + + + + + EHDAA2 + + + + + pharyngeal region + EMAPA:16549 + + + + + + + + + + + + + + + + + + + + + + + + + + An ectoderm that is part of a buccopharyngeal membrane. + EHDAA2:0000190 + EMAPA:16260 + uberon + UBERON:0009479 + + ectoderm of buccopharyngeal membrane + + + + + An ectoderm that is part of a buccopharyngeal membrane. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + An endoderm that is part of a buccopharyngeal membrane. + EHDAA2:0000191 + EMAPA:16261 + uberon + UBERON:0009480 + + endoderm of buccopharyngeal membrane + + + + + An endoderm that is part of a buccopharyngeal membrane. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of mesenchymal tissue associated with an individual pharyngeal arch. + this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. + EMAPA:32755 + FMA:295694 + branchial arch mesenchyme + pharyngeal arch mesenchyme + uberon + UBERON:0009494 + + pharyngeal arch mesenchymal region + + + + + + EHDAA2 + + + + + + + + + + + cjm + + + + + A portion of mesenchymal tissue associated with an individual pharyngeal arch. + + + + + + this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. + MP:0011262 + + + + + branchial arch mesenchyme + MP:0011262 + + + + + pharyngeal arch mesenchyme + + + + + + + + + + + + + + + + + FMA:25054 + region of trunk + trunk subdivision + uberon + UBERON:0009569 + + subdivision of trunk + + + + + region of trunk + FMA:25054 + + + + + trunk subdivision + FMA:25054 + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0001172 + EMAPA:16977 + VHOG:0000910 + mantle layer lateral wall midbrain + midbrain lateral wall mantle layer + uberon + mantle layer lateral wall mesencephalon + UBERON:0009581 + midbrain mantle layer + + + + + mantle layer lateral wall midbrain + VHOG:0000910 + + + + + mantle layer lateral wall mesencephalon + VHOG:0000910 + + + + + + + + + + + + + + + + + + + + + + + + + + EMAPA:17580 + VHOG:0000911 + mantle layer lateral wall spinal cord + spinal cord lateral wall mantle layer + uberon + UBERON:0009583 + spinal cord mantle layer + + + + + mantle layer lateral wall spinal cord + VHOG:0000911 + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing left lung. + EHDAA2:0000944 + EMAPA:16730 + EMAPA:17654 + left lung mesenchyme + uberon + UBERON:0009602 + left lung associated mesenchyme + + + + + Mesenchyme that is part of a developing left lung. + OBOL:automatic + + + + + left lung mesenchyme + EMAPA:17654 + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing right lung. + EHDAA2:0001739 + EMAPA:17662 + right lung mesenchyme + uberon + UBERON:0009603 + right lung associated mesenchyme + + + + + Mesenchyme that is part of a developing right lung. + OBOL:automatic + + + + + right lung mesenchyme + EMAPA:17662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A neural plate that develops_from a presumptive midbrain. + TAO:0007019 + ZFA:0007019 + uberon + UBERON:0009611 + midbrain neural plate + + + + + + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + A neural plate that develops_from a presumptive midbrain. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A neural plate that develops_from a presumptive hindbrain. + TAO:0007022 + ZFA:0007022 + uberon + UBERON:0009614 + hindbrain neural plate + + + + + + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + A neural plate that develops_from a presumptive hindbrain. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + TODO - developmental relationships for lines + TAO:0007044 + ZFA:0007044 + MHB neural plate + midbrain-hindbrain boundary neural plate + uberon + UBERON:0009615 + midbrain hindbrain boundary neural plate + + + + + + + + + + + ZFA + + + + + + + + + + + https://github.com/obophenotype/uberon/issues/438 + Bgee:AN + + + + + MHB neural plate + + + + + + midbrain-hindbrain boundary neural plate + ZFA:0007044 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A presumptive structure that has the potential to develop into a midbrain. + TODO - unify naming conventions + + BAMS:MES + EFO:0003432 + EHDAA2:0000615 + EMAPA:16140 + TAO:0000148 + ZFA:0000148 + presumptive mesencephalon + uberon + early midbrain + future midbrain + mesencephalon + UBERON:0009616 + + presumptive midbrain + + + + + + + + + + + ZFA + + + + + + + + + + + ZFA + + + + + A presumptive structure that has the potential to develop into a midbrain. + OBOL:automatic + + + + + presumptive mesencephalon + ZFA:0000148 + + + + + early midbrain + + + + + + future midbrain + + + + + + mesencephalon + EHDAA2:0000615 + + + + + + + + + + + + + + + EHDAA2:0002094 + trunk and cervical paraxial mesenchyme + uberon + trunk paraxial mesenchyme + UBERON:0009618 + trunk paraxial mesoderm + + + + + trunk and cervical paraxial mesenchyme + EHDAA2:0002094 + + + + + trunk paraxial mesenchyme + + + + + + + + + + + + + + + + + + + + + + + + + + + + EMAPA:37092 + MA:0001987 + NCIT:C52947 + UMLS:C1708633 + labial artery + uberon + UBERON:0009657 + artery of lip + + + + + EMAPA:37092 + MA:th + + + + + UMLS:C1708633 + ncithesaurus:Labial_Artery + + + + + labial artery + MA:0001987 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical cavity that surrounded_by a stomodeum. + lumen of stomatodaeum + lumen of stomodeum + stomatodeal cavity + uberon + UBERON:0009715 + stomodeal lumen + + + + + An anatomical cavity that surrounded_by a stomodeum. + OBOL:automatic + + + + + + + + + + + + + + + + + EHDAA2:0004621 + EMAPA:32754 + FMA:293087 + uberon + pharyngeal arch endoderm + UBERON:0009722 + entire pharyngeal arch endoderm + + + + + pharyngeal arch endoderm + EHDAA2:0004621 + + + + + + + + + + + + + + + + + + + + + + + + + + + The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures + decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts + EHDAA2:0004162 + EMAPA:36438 + heart mesenchyme + uberon + UBERON:0009751 + + cardiac mesenchyme + + + + + The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures + MP:0011264 + + + + + heart mesenchyme + EMAPA:36438 + + + + + + + + + + + + + + + The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. + acinar + acinus + + FMA:55588 + uberon + acini + UBERON:0009842 + glandular acinus + + + + + + The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. + + + + + + acinus + FMA:55588 + + + + + acini + + + + + + + + + + + + + + + + + + + + + + + Branch or outpocketing of the digestive tract. + FBbt:00100316 + uberon + diverticulum of gut + intestinal pouch + UBERON:0009854 + digestive tract diverticulum + + + + + Branch or outpocketing of the digestive tract. + + + + + + diverticulum of gut + FBbt:00100316 + + + + + + + + + galen:Diverticulum + pouch + uberon + diverticulum + UBERON:0009856 + sac + + + + + + + + + + + + + + + + EFO:0003704 + TAO:0005041 + ZFA:0005041 + ALPM + uberon + UBERON:0009881 + + anterior lateral plate mesoderm + + + + + + + + + + + ZFA + + + + + ALPM + ZFA:0005041 + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a developing face. + EMAPA:35337 + FMA:302884 + face mesenchyme + mesenchyme of face + uberon + UBERON:0009891 + facial mesenchyme + + + + + Mesenchyme that is part of a developing face. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A multicellular organism that existence_starts_with a post-embryonic stage. + MA:0002405 + postnatal organism + TS28 mouse + post-hatching organism + post-natal organism + postnatal mouse + uberon + UBERON:0009953 + post-embryonic organism + + + + + + A multicellular organism that existence_starts_with a post-embryonic stage. + OBOL:automatic + + + + + TS28 mouse + MA:0002405 + + + + + post-hatching organism + + + + + + post-natal organism + + + + + + postnatal mouse + MA:0002405 + + + + + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + FBbt:00100313 + multicellular structure + uberon + UBERON:0010000 + + multicellular anatomical structure + + + + + An anatomical structure that has more than one cell as a part. + CARO:0010000 + + + + + multicellular structure + FBbt:00100313 + + + + + + CARO + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that is part of a pharyngeal arch 6. + EHDAA2:0004076 + EMAPA:32765 + FMA:318209 + 6th pharyngeal arch mesenchyme + uberon + 6th branchial arch mesenchyme + pharyngeal arch 6 mesenchyme + UBERON:0010031 + 6th arch mesenchyme + + + + + Mesenchyme that is part of a pharyngeal arch 6. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. + EHDAA2:0001459 + EMAPA:16550 + XAO:0004524 + associated mesenchyme of pharyngeal region + entire branchial arch associated mesenchyme + pharyngeal arch associated mesenchyme + uberon + UBERON:0010046 + entire pharyngeal arch associated mesenchyme + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + cjm + + + + + The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. + + XAO:0004524 + + + + + associated mesenchyme of pharyngeal region + EMAPA:16550 + + + + + entire branchial arch associated mesenchyme + + + + + + pharyngeal arch associated mesenchyme + EHDAA2:0001459 + + + + + + + + + + + + + + + + + + + + + + + + + + + Gland of the epithelium lining the oral cavity. The most common are the salivary glands. + Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa + UBERON:0003293 + EHDAA2:0001327 + EHDAA:2181 + EMAPA:16572 + EMAPA:16723 + VHOG:0000652 + buccal gland + uberon + gland of oral opening + gland of oral region + mouth gland + oral cavity gland + oral region gland + UBERON:0010047 + oral gland + + + + + Gland of the epithelium lining the oral cavity. The most common are the salivary glands. + ISBN10:0073040584 + + + + + Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa + EHDAA2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that has the potential to develop into a dermis. + check development + EHDAA2:0000598 + uberon + UBERON:0010083 + future dermis + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + XAO + + + + + Mesenchyme that has the potential to develop into a dermis. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A developing anatomical structure that has the potential to develop into a myelencephalon. + EHDAA2:0000640 + uberon + UBERON:0010096 + future myelencephalon + + + + + A developing anatomical structure that has the potential to develop into a myelencephalon. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical cavity that surrounded_by a blood vessel. + + FMA:312610 + blood vessel lumen + uberon + UBERON:0010161 + lumen of blood vessel + + + + + An anatomical cavity that surrounded_by a blood vessel. + OBOL:automatic + + + + + + + + + A roughly circular bulge in a surface. + requires review + AEO:0000205 + EHDAA2:0003250 + FMA:82506 + uberon + UBERON:0010188 + protuberance + + + + + + EHDAA2 + + + + + A roughly circular bulge in a surface. + EHDAA2:0003250 + + + + + + + + + An anatomical boundary that corresponds to some physical discontinuity. + CARO:0001004 + uberon + UBERON:0010199 + + One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) + bona-fide anatomical boundary + + + + + + CARO + + + + + An anatomical boundary that corresponds to some physical discontinuity. + CARO:0001004 + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. + EHDAA2:0004077 + neural crest derived arch 6 mesenchyme + pharyngeal arch 6 mesenchyme from neural crest + uberon + branchial arch 6 mesenchyme from neural crest + UBERON:0010257 + 6th arch mesenchyme from neural crest + + + + + Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a rhombencephalon neural crest. + EHDAA2:0004423 + uberon + UBERON:0010258 + mesenchyme from rhombencephalic neural crest + + + + + Mesenchyme that develops_from a rhombencephalon neural crest. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. + DHBA:12322 + EFO:0003567 + EHDAA2:0004375 + TAO:0000761 + ZFA:0000761 + basal plate midbrain + basal plate midbrain region + uberon + UBERON:0010285 + + midbrain basal plate + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + ZFA + + + + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. + ZFA:0000761 + + + + + basal plate midbrain + TAO:0000761 + + + + + basal plate midbrain region + ZFA:0000761 + + + + + + + + + + + + + + + + Portion of neural tube that gives rise to the midbrain. + we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed + TAO:0007039 + ZFA:0007039 + uberon + UBERON:0010286 + midbrain neural tube + + + + + + + + + + + ZFA + + + + + Portion of neural tube that gives rise to the midbrain. + ZFA:0007039 + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that is part of a extraembryonic structure. + extra-embryonic epithelium + uberon + UBERON:0010303 + extraembryonic epithelium + + + + + An epithelium that is part of a extraembryonic structure. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that develops from the neural crest. + Grouping term for query purposes + uberon + UBERON:0010313 + + neural crest-derived structure + + + + + An anatomical structure that develops from the neural crest. + + + + + + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that has some part that develops from the neural crest. + Grouping term for query purposes + uberon + UBERON:0010314 + + structure with developmental contribution from neural crest + + + + + An anatomical structure that has some part that develops from the neural crest. + + + + + + + + + + + + + + + + + uberon + UBERON:0010316 + germ layer / neural crest + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. + EHDAA2:0004078 + head mesenchyme derived arch 6 mesenchyme + pharyngeal arch 6 mesenchyme from head mesenchyme + uberon + branchial arch 6 mesenchyme from head mesenchyme + UBERON:0010347 + 6th arch mesenchyme from head mesenchyme + + + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. + arch mesenchyme from neural crest + branchial arch mesenchyme from neural crest + neural crest derived arch mesenchyme + uberon + UBERON:0010359 + Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme + pharyngeal arch mesenchyme from neural crest + + + + + Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. + arch mesenchyme from head mesenchyme + branchial arch mesenchyme from head mesenchyme + head mesenchyme derived arch mesenchyme + uberon + UBERON:0010360 + Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme + pharyngeal arch mesenchyme from head mesenchyme + + + + + Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + Epithelium composed of cells that develops from the ectoderm[FMA,modified]. + FMA:69064 + ectoderm-derived epithelium + uberon + UBERON:0010371 + ecto-epithelium + + + + + Epithelium composed of cells that develops from the ectoderm[FMA,modified]. + FMA:69064 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from a splanchnopleure. + EHDAA2:0001122 + uberon + UBERON:0010378 + mesenchyme from splanchnopleure + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + Mesenchyme that develops_from a splanchnopleure. + OBOL:automatic + + + + + + + + + A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. + Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. + glandular in NCIT; we consider the two NCIT terms synonymous + + + + FMA:45572 + NCIT:C33419 + NCIT:C49316 + UMLS:C0836138 + UMLS:C1514590 + uberon + UBERON:0010498 + pseudostratified columnar epithelium + + + + + + FMA + + + + + A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. + + + + + + + glandular in NCIT; we consider the two NCIT terms synonymous + NCIT + + + + + UMLS:C0836138 + ncithesaurus:Pseudostratified_Columnar_Epithelium + + + + + UMLS:C1514590 + ncithesaurus:Pseudostratified_Epithelium + + + + + + + + + + Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. + + FMA:13146 + NCIT:C13181 + UMLS:C0506992 + epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) + uberon + UBERON:0010499 + pseudostratified ciliated columnar epithelium + + + + + Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. + NCIT:NCIT + + + + + UMLS:C0506992 + ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium + + + + + epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) + FMA:13146 + + + + + + + + + + + + + + + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. + MESH:A07.231.432 + TAO:0005251 + ZFA:0005251 + uberon + microcirculatory vessels + UBERON:0010523 + microcirculatory vessel + + + + + + + + + + + ZFA + + + + + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. + + MESH:A07.231.432 + ZFA:0005251 + + + + + microcirculatory vessels + TAO:0005251 + + + + + + + + + + + + + + + + + + + + + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. + Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] + + FMA:23879 + VSAO:0000042 + skeletal subdivision + uberon + subdivision of skeleton (in vivo) + UBERON:0010912 + + subdivision of skeleton + + + + + + cjm + + + + + + + + + + + UBERONREF:0000003 + + + + + + + + + + + VSAO + + + + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. + + UBERONREF:0000003 + + + + + Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] + 2012-08-14 + VSAO:0000042 + incorrect + VSAO + VSAO:curator + + + + + skeletal subdivision + VSAO:0000042 + + + + + subdivision of skeleton (in vivo) + FMA:23879 + + + + + + + + + Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. + FMA:7491 + solid joint + uberon + UBERON:0011134 + nonsynovial joint + + + + + + FMA + + + + + Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. + FMA:7491 + + + + + solid joint + FMA:7491 + + + + + + + + + + + + + + + + + + + + + Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. + FMA:7483 + uberon + UBERON:0011137 + axial skeletal system + http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + + + + + + FMA + + + + + Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. + + + + + + + + + + + + + + + + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. + + axial skeletal system + FMA:302077 + post-cranial axial skeletal system + uberon + UBERON:0011138 + postcranial axial skeletal system + http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton + + + + + + FMA + + + + + + + + + + + cjm + + + + + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. + + + + + + + axial skeletal system + + + + + + + + + + + + + + + + + + + + + + + + + + + A multi cell part structure that is part of a central nervous system. + FMA:83143 + cell part cluster of neuraxis + neuraxis layer + uberon + UBERON:0011215 + + central nervous system cell part cluster + + + + + A multi cell part structure that is part of a central nervous system. + OBOL:automatic + + + + + cell part cluster of neuraxis + FMA:83143 + + + + + neuraxis layer + FMA:83143 + + + + + + + + + + + + + + + A subdivision of an anatomical system. + + FBbt:00007330 + FMA:67509 + uberon + UBERON:0011216 + + organ system subdivision + + + + + + FBbt + + + + + A subdivision of an anatomical system. + + + + + + + + + + + + + + + + The part of the trunk that is in the dorsum[cjm]. + In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] + + EMAPA:35162 + FMA:25056 + MA:0000020 + back of trunk + dorsal part of trunk + dorsum of trunk + trunk back + uberon + UBERON:0011270 + dorsal trunk + + + + + + FMA + + + + + + + + + + + FMA + + + + + The part of the trunk that is in the dorsum[cjm]. + + UBERONREF:0000006 + + + + + back of trunk + FMA:25056 + + + + + dorsum of trunk + FMA:25056 + + + + + trunk back + FMA:25056 + + + + + + + + + + + + + + + + + + + + + + compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' + EHDAA2:0001845 + uberon + basal cell layer of skin + outer epithelium of body + UBERON:0011272 + embryonic skin basal layer + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + outer epithelium of body + Wikipathways:WP2062 + + + + + + + + + + + + + + + + + + + + + A blood vasculature that is part of a head. + Blood vessel part of cranial vasculature.[TAO] + TAO:0005297 + ZFA:0005297 + cranial blood vessel + set of blood vessels of head + uberon + cranial blood vessels + UBERON:0011362 + cranial blood vasculature + + + + + A blood vasculature that is part of a head. + OBOL:automatic + + + + + Blood vessel part of cranial vasculature.[TAO] + 2012-08-14 + TAO:0005297 + TAO + ZFIN:curator + + + + + cranial blood vessel + ZFA:0005297 + + + + + cranial blood vessels + TAO:0005297 + + + + + + + + + + Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). + consider obsoleting, coordinate with VSAO + VSAO:0000006 + XAO:0004021 + uberon + UBERON:0011585 + cell condensation + + + + + + VSAO + + + + + Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). + + GO_REF:0000034 + PSPUB:0000170 + VSAO:0000006 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An epithelium that develops_from a ectoderm and is part of a oral epithelium. + EHDAA2:0004137 + uberon + UBERON:0011642 + oral epithelium from ectoderm + + + + + + EHDAA2 + + + + + + + + + + + EHDAA2 + + + + + An epithelium that develops_from a ectoderm and is part of a oral epithelium. + OBOL:automatic + + + + + + + + + + + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem + axial subdivision of organism + uberon + body segment + main body segment + UBERON:0011676 + + subdivision of organism along main body axis + + + + + A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. + + + + + + + + + + + + + + + + + + + + + + + + + + + A cardiovascular system that is part of a conceptus. + EHDAA2:0000216 + FMA:305965 + NCIT:C34148 + conceptus cardiovascular system + uberon + embryonic circulatory system + fetal circulatory system + UBERON:0011695 + embryonic cardiovascular system + + + + + A cardiovascular system that is part of a conceptus. + OBOL:automatic + + + + + + + + + Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. + FMA:20107 + uberon + UBERON:0011821 + irregular connective tissue + + + + + + FMA + + + + + Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. + FMA:20107 + + + + + + + + + + Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. + Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] + + + FMA:20109 + NCIT:C32882 + UMLS:C0738366 + irregular dense connective tissue + typus irregularis (textus connectivus collagenosus compactus) + uberon + UBERON:0011822 + dense irregular connective tissue + + + + + + FMA + + + + + Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. + + FMA:20109 + + + + + Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] + 2012-08-29 + ncithesaurus:Irregular_Dense_Connective_Tissue + NCIT + + + + + UMLS:C0738366 + ncithesaurus:Irregular_Dense_Connective_Tissue + + + + + typus irregularis (textus connectivus collagenosus compactus) + FMA:20109 + + + + + + + + + + + + + + + + + + + + + + + + + + + Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets + our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. + Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] + + + AAO:0000121 + NCIT:C32450 + UMLS:C1511770 + uberon + UBERON:0011823 + dense connective tissue + + + + + Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets + + + + + + Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] + 2012-08-29 + ncithesaurus:Dense_Connective_Tissue + NCIT + + + + + UMLS:C1511770 + ncithesaurus:Dense_Connective_Tissue + + + + + + + + + + FMA:75634 + uberon + UBERON:0011824 + fibrous connective tissue + + + + + + FMA + + + + + + + + + Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. + + + FMA:19783 + NCIT:C33007 + UMLS:C1253917 + textus connectivus collagenosus laxus + textus connectivus laxus + uberon + UBERON:0011825 + loose connective tissue + + + + + + FMA + + + + + Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. + FMA:19783 + + + + + UMLS:C1253917 + ncithesaurus:Loose_Connective_Tissue + + + + + textus connectivus collagenosus laxus + FMA:19783 + FMA:TA + + + + + + textus connectivus laxus + FMA:19783 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + An acinus that is part of a exocrine gland. + exocrine gland acinus + uberon + UBERON:0011858 + acinus of exocrine gland + + + + + An acinus that is part of a exocrine gland. + OBOL:automatic + + + + + + + + + the FMA class specifically refers to ureter + FMA:63212 + MESH:D024022 + NCIT:C32339 + NIF_Subcellular:sao7547390221 + uberon + UBERON:0011860 + collection of collagen fibrils + + + + + + + ZFA + + + + + the FMA class specifically refers to ureter + FMA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity + uberon + UBERON:0011862 + + pulmonary collagen fibril + + + + + The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity + MP:0011641 + + + + + + + + + The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. + EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. + coelomic + + EHDAA2:0004731 + enterocoelom + haemocoelom + schizocoelom + uberon + coelem + coelomic cavity + UBERON:0011997 + coelom + + + + + + EHDAA2 + + + + + The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. + + + UBERON:cjm + + + + + enterocoelom + NCBITaxon:33511 + + + + + coelomic cavity + EHDAA2:0004731 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical system that consists of the integumental system plus all mucosae and submucosae. + + + uberon + dermatological system + UBERON:0012125 + dermatological-muscosal system + + + + + Anatomical system that consists of the integumental system plus all mucosae and submucosae. + + + + + + dermatological system + OBI:MC + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of a craniocervical region. + + EMAPA:37276 + MA:0000574 + NCIT:C12294 + UMLS:C1522650 + uberon + UBERON:0012180 + head or neck skin + + + + + A zone of skin that is part of a craniocervical region. + OBOL:automatic + + + + + EMAPA:37276 + MA:th + + + + + UMLS:C1522650 + ncithesaurus:Skin_of_the_Scalp_and_Neck + + + + + + + + + An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] + + uberon + UBERON:0012274 + columnar epithelium + + + + + An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] + + + + + + + + + + + + + + + + + + + + + + Epithelium that derives from the mesoderm. [Automatically generated definition]. + FMA:86452 + mesoderm-derived epithelium + mesoepithelium + uberon + UBERON:0012275 + meso-epithelium + + + + + Epithelium that derives from the mesoderm. [Automatically generated definition]. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + An artery of the neck + + EMAPA:37075 + NCIT:C52850 + UMLS:C1707349 + uberon + UBERON:0012320 + cervical artery + + + + + An artery of the neck + + + + + + EMAPA:37075 + MA:th + + + + + UMLS:C1707349 + ncithesaurus:Cervical_Artery + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The deep cervical artery (Profunda cervicalis) is an artery of the neck. + + + FMA:10659 + uberon + profunda cervicalis + UBERON:0012321 + deep cervical artery + + + + + + + + + + + FMA + + + + + The deep cervical artery (Profunda cervicalis) is an artery of the neck. + + + + + + profunda cervicalis + + + + + + + + + + + + + + + + + + + + + + + + + + + + EMAPA:37567 + MA:0001802 + uberon + UBERON:0012416 + respiratory system arterial smooth muscle + + + + + EMAPA:37567 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + A smooth muscle tissue that is part of a respiratory system venous blood vessel. + EMAPA:37586 + MA:0001812 + uberon + UBERON:0012418 + respiratory system venous smooth muscle + + + + + A smooth muscle tissue that is part of a respiratory system venous blood vessel. + OBOL:automatic + + + + + EMAPA:37586 + MA:th + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0000472 + EMAPA:16054 + VHOG:0000767 + uberon + extraembryonic cavities + UBERON:0012466 + extraembryonic cavity + + + + + extraembryonic cavities + EHDAA2:0000472 + + + + + + + + + + An anatomical space with no opening to another space or to the exterior. + AEO:0000222 + closed anatomical space + uberon + UBERON:0012467 + enclosed anatomical space + + + + + An anatomical space with no opening to another space or to the exterior. + AEO:0000222 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A vein that drains a lip. + + labial vein of face + lip vein + vena labialis + uberon + labial vein + UBERON:0013136 + vein of lip + + + + + + + + + + + FMA + + + + + A vein that drains a lip. + OBOL:automatic + + + + + lip vein + OBOL:automatic + + + + + vena labialis + + + + + + + + + + + + + + + + + + + + + + + + + + + Any vein within the general circulation that transports blood back to the right atrium of the heart. + + + FMA:66644 + NCIT:C33719 + UMLS:C0447117 + systemic venous tree organ part + uberon + UBERON:0013140 + systemic vein + + + + + Any vein within the general circulation that transports blood back to the right atrium of the heart. + ncithesaurus:Systemic_Vein + + + + + UMLS:C0447117 + ncithesaurus:Systemic_Vein + + + + + systemic venous tree organ part + FMA:66644 + + + + + + + + + + + + + + + + + + + + + + + + + + The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. + FMA:86279 + acinus of serous gland + uberon + UBERON:0013232 + serous acinus + + + + + The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel endothelium that is part of a lung [Automatically generated definition]. + BTO:0004128 + CALOHA:TS-0573 + uberon + respiratory endothelium + UBERON:0013479 + lung endothelium + + + + + A blood vessel endothelium that is part of a lung [Automatically generated definition]. + OBOL:automatic + + + + + respiratory endothelium + BTO:0004128 + + + + + + + + + + + + + + + + + + + + + + + + + + The space that surrounds an organism. + external to organism + outside of body + uberon + UBERON:0013514 + space surrounding organism + + + + + The space that surrounds an organism. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + uberon + UBERON:0013522 + subdivision of tube + + + + + + + + + + + + + + 2 + + + + + 2 + + + + + + + + + + + + + + + + + + An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. + FMA:9338 + foramen space + uberon + UBERON:0013686 + anatomical conduit space + + + + + + FMA + + + + + An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. + + FMA:9338 + + + + + + + + + + + + + + + + + + + + + + + + + + + Vascular endothelium found in blood vessels of the blood-brain-barrier. + BTO:0001852 + BTO:0003248 + CALOHA:TS-0092 + uberon + cerebromicrovascular endothelium + UBERON:0013694 + brain endothelium + + + + + Vascular endothelium found in blood vessels of the blood-brain-barrier. + CALOHA:TS-0092 + + + + + cerebromicrovascular endothelium + CALOHA:TS-0092 + + + + + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + uberon + UBERON:0013701 + + main body axis + + + + + A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. + + + + + + + + + + + + + + + + The region of the organism associated with the visceral organs. + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + AEO:0000103 + BTO:0001489 + EMAPA:36031 + FMA:231424 + uberon + body + whole body + UBERON:0013702 + + body proper + + + + + + AEO + + + + + The region of the organism associated with the visceral organs. + AEO:0000103 + + + + + Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. + FMA:231424 + + + + + body + AEO:0000103 + + + + + whole body + BTO:0001489 + + + + + + + + + + + + + + + + + + + + + + + + + + + A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. + + FMA:293127 + NCIT:C34230 + UMLS:C1518428 + uberon + chordal canal + UBERON:0013704 + notochordal canal + + + + + A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. + + + + + + UMLS:C1518428 + ncithesaurus:Notochordal_Canal + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Fluid contained within the notochordal canal + notochord fluid + portion of notochordal fluid + uberon + UBERON:0013727 + Distinct feature of coelocanths + notochordal fluid + + + + + Fluid contained within the notochordal canal + + + + + + + + + + + + + + + + + + + + + + + + + + + + A organ component layer that is part of a integumental system. + + layer of skin + skin layer + uberon + UBERON:0013754 + + integumentary system layer + + + + + A organ component layer that is part of a integumental system. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + + + + + + A blood that is part of a artery. + FMA:83066 + arterial blood + blood in artery + portion of arterial blood + uberon + UBERON:0013755 + + arterial blood + + + + + A blood that is part of a artery. + OBOL:automatic + + + + + arterial blood + FMA:83066 + + + + + blood in artery + FMA:83066 + + + + + portion of arterial blood + FMA:83066 + + + + + + + + + + + + + + + + + + + + + + + + + + A blood that is part of a vein. + FMA:83067 + blood in vein + portion of venous blood + venous blood + uberon + UBERON:0013756 + venous blood + + + + + A blood that is part of a vein. + OBOL:automatic + + + + + blood in vein + FMA:83067 + + + + + portion of venous blood + FMA:83067 + + + + + venous blood + FMA:83067 + + + + + + + + + + + + + + + + + + + + + + + + + + A blood that is part of a capillary. + FMA:263901 + NCIT:C32212 + blood in capillary + portion of blood in capillary + portion of capillary blood + uberon + UBERON:0013757 + capillary blood + + + + + A blood that is part of a capillary. + OBOL:automatic + + + + + portion of blood in capillary + FMA:263901 + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. + + EMAPA:37843 + digestive organ + digestive system organ + uberon + UBERON:0013765 + + + digestive system element + + + + + Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. + + + + + + EMAPA:37843 + MA:th + + + + + + + + + Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. + great vessel + + + EMAPA:36460 + great vessel of thorax + uberon + UBERON:0013768 + + Groupings may vary - typically pulmonary vessels and aorta and vena cavae + great vessel of heart + + + + + Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. + + + + + + + + + + + + + + + + + + + + + + Mesenchyme that develops_from the neural crest[Automatically generated definition]. + EMAPA:32735 + FMA:293883 + mesenchyme from neural crest + neural crest derived mesenchyme + neural crest mesenchyme + uberon + UBERON:0014387 + mesenchyme derived from neural crest + + + + + Mesenchyme that develops_from the neural crest[Automatically generated definition]. + + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. + + EHDAA2:0002013 + FMA:77169 + skeleton of thorax + thoracic part of axial skeleton + thoracic skeleton + uberon + UBERON:0014477 + + thoracic skeleton + + + + + Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. + + + + + + + thoracic skeleton + EHDAA2:0002013 + + + + + + + + + + + + + + + + + + + + + + + + + + A neuromere that is part of the presumptive midbrain + mesomere + midbrain segment + segment of midbrain + EHDAA2:0004352 + FMA:61997 + mesomere of nervous system + neuromere of mesomere group + uberon + future mesencephalon + mesomere group + UBERON:0014776 + midbrain neuromere + + + + + A neuromere that is part of the presumptive midbrain + + + + + + mesomere group + EHDAA2:0004352 + + + + + + + + + + + + + + + + + + + + + + + + + + A neuromere that is part of the presumptive spinal cord + TAO:0001332 + ZFA:0001332 + spinal cord metameric segment + spinal neuromeres + uberon + spinal cord segment + UBERON:0014777 + spinal neuromere + + + + + A neuromere that is part of the presumptive spinal cord + + + + + + spinal neuromeres + TAO:0001332 + + + + + + spinal cord segment + TAO:0001332 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A portion of tissue that will develop into vasculature. + EFO:0003708 + TAO:0005076 + ZFA:0005076 + uberon + UBERON:0014903 + primordial vasculature + + + + + A portion of tissue that will develop into vasculature. + ZFA:0005076 + ZFA:curator + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A region of somite adjacent to presomitic mesoderm. + TAO:0001462 + XAO:0004074 + ZFA:0001462 + uberon + inter-somited border + intersomitic boundary + intersomitic fissure + intersomitic junction + segmental border + somite boundary + UBERON:0015178 + + somite border + + + + + A region of somite adjacent to presomitic mesoderm. + + + + + + intersomitic junction + XAO:0004074 + + + + + somite boundary + ZFA:0001462 + + + + + + + + + + + + + + + + + + + + + + + + + + Epithelium located in the intersomitic region. + XAO:0004077 + intersomitic epithelium + intersomitic membrane + uberon + UBERON:0015179 + somite boundary epithelium + + + + + Epithelium located in the intersomitic region. + XAO:0004077 + XAO:EJS + + + + + intersomitic epithelium + XAO:0004077 + + + + + intersomitic membrane + XAO:0004077 + + + + + + + + + + + + + + + + + + + + + + + + + + Any structure that is placed on one side of the left-right axis of a bilaterian. + This class is primarily to implement taxon constraints. It may be removed in the future. + uberon + UBERON:0015212 + + + lateral structure + + + + + Any structure that is placed on one side of the left-right axis of a bilaterian. + + + + + + + + + + + + + + + + A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. + heart + SPD:0000130 + cardiac pump + heart or heart like organ + circulatory vessel + uberon + cardiac structure + UBERON:0015228 + + circulatory organ + + + + + A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. + + + + + + + + + + + + + + + + + + + + + + + + + + + A basement membrane of epithelium that is part of a respiratory system. + EMAPA:37570 + MA:0001815 + uberon + UBERON:0015329 + respiratory system basement membrane + + + + + + + + + + + MA + + + + + A basement membrane of epithelium that is part of a respiratory system. + OBOL:automatic + + + + + EMAPA:37570 + MA:th + + + + + + + + + + + + + + + EMAPA:37597 + MA:0002449 + heart/pericardium + uberon + UBERON:0015410 + heart plus pericardium + + + + + + MA + + + + + EMAPA:37597 + MA:th + + + + + heart/pericardium + MA:0002449 + + + + + + + + + + + + + + + + + + + + + + + + + + A smooth muscle tissue that is part of a hypodermis. + FMA:77862 + muscle layer in fatty layer of subcutaneous tissue + stratum musculosum panniculi adiposi telae subcutaneae + uberon + UBERON:0015783 + smooth muscle layer in fatty layer of subcutaneous tissue + + + + + A smooth muscle tissue that is part of a hypodermis. + OBOL:automatic + + + + + muscle layer in fatty layer of subcutaneous tissue + FMA:77862 + + + + + stratum musculosum panniculi adiposi telae subcutaneae + FMA:77862 + FMA:TA + + + + + + + + + + + + + + + + + + + + + + + + + + + A epithelium that is part of a foregut. + EMAPA:32922 + MA:0003204 + uberon + UBERON:0015833 + foregut epithelium + + + + + A epithelium that is part of a foregut. + OBOL:automatic + + + + + + + + + + + + + + + + + + + + + A capillary that is part of a lung. + FMA:14121 + capillary of lung + uberon + UBERON:0016405 + + pulmonary capillary + + + + + A capillary that is part of a lung. + OBOL:automatic + + + + + capillary of lung + FMA:14121 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. + UBERON:2001379 + TAO:0001379 + ZFA:0001379 + uberon + UBERON:0016545 + pharyngeal ectoderm + + + + + The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Primordium that develops into the central nervous system + UBERON:3000469 + future CNS + presumptive central nervous system + uberon + UBERON:0016879 + future central nervous system + + + + + Primordium that develops into the central nervous system + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Primordium that develops into the nervous system + UBERON:3000477 + AAO:0000477 + presumptive nervous system + uberon + UBERON:0016880 + future nervous system + + + + + Primordium that develops into the nervous system + + + + + + presumptive nervous system + AAO:0000477 + + + + + + + + + + + + + + + + + + + + + + + + + + + The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. + AEO:0000195 + EHDAA2:0000003 + EMAPA:16042 + extra-embryonic component + extraembryonic component + uberon + UBERON:0016887 + entire extraembryonic component + + + + + + AEO + + + + + + + + + + + AEO + + + + + The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. + AEO:0000195 + AEO:JB + + + + + extraembryonic component + AEO:0000195 + + + + + + + + + An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. + AEO:0000132 + uberon + UBERON:0016888 + transitional anatomical structure + + + + + + AEO + + + + + An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. + AEO:0000132 + AEO:JB + + + + + + + + + + + + + + + + + + + + + + + + + + A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. + AEO:0001016 + uberon + UBERON:0017650 + developing mesenchymal structure + + + + + A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. + AEO:0001016 + AEO:JB + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A boundary delimiting a rhombomere. + rhombomere junction + uberon + UBERON:0018239 + rhombomere boundary + + + + + A boundary delimiting a rhombomere. + GO:0021654 + + + + + + + + + + + + + + + + + + + + + + + + + + Any portion of submucosa that lines the digestive tract. + uberon + UBERON:0018257 + submucosa of digestive tract + + + + + Any portion of submucosa that lines the digestive tract. + + + + + + + + + + + + + + + + + + + + + + + + + + + Any organ component layer that consists of muscle tissue. + NCITA class may refer to smooth muscle only + + FMA:45634 + NCIT:C75444 + uberon + UBERON:0018260 + layer of muscle tissue + + + + + Any organ component layer that consists of muscle tissue. + + + + + + NCITA class may refer to smooth muscle only + NCIT + + + + + + + + + + + + + + + + + + + + + + + + + + + An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. + FMA:73747 + ZFA:0005811 + cardiac vasculature + uberon + UBERON:0018674 + heart vasculature + + + + + An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. + ZFA:0005811 + ZFA:CVS + + + + + cardiac vasculature + FMA:73747 + + + + + + + + + + + + + + + + + + + + + + + + + + Any region of epithelium that is part of a skin region. + BTO:0004382 + uberon + UBERON:0019204 + skin epithelium + + + + + Any region of epithelium that is part of a skin region. + + + + + + + + + + + + + + + + + + + + + + + + + + + DHBA:10654 + FMA:268630 + gray matter of the hindbrain + uberon + UBERON:0019263 + gray matter of hindbrain + + + + + gray matter of the hindbrain + DHBA:HGM + + + + + + + + + + + + + + + + + + + + + + + + + + DHBA:10649 + FMA:83913 + uberon + UBERON:0019267 + gray matter of midbrain + + + + + + + + + + + + + + + + + + + + + An exocrine gland that is part of a integumental system. + integumental exocrine gland + integumental system exocrine gland + uberon + UBERON:0019319 + exocrine gland of integumental system + + + + + An exocrine gland that is part of a integumental system. + + GOC:dos + + + + + integumental exocrine gland + + + + + + integumental system exocrine gland + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Serous membrane layer that is adjacent to and lines an organ. + FMA:15860 + visceral wall of serous membrane + uberon + UBERON:0022350 + visceral serous membrane + + + + + Serous membrane layer that is adjacent to and lines an organ. + + + + + + visceral wall of serous membrane + FMA:15860 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Serous membrane layer that lines to a body cavity. + cavity lining + FMA:15859 + MA:0002448 + parietal wall of serous membrane + uberon + UBERON:0022351 + parietal serous membrane + + + + + Serous membrane layer that lines to a body cavity. + + + + + + cavity lining + MA:0002448 + + + + + parietal wall of serous membrane + FMA:15859 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specific region of the foregut into the area in which the lung will develop. + + lung field + uberon + UBERON:0022361 + lung field + + + + + A specific region of the foregut into the area in which the lung will develop. + GOC:dph + GOC:mtg_lung + + + + + + + + + + + + + + + An embryonic or larval epithelium that is committed to form part of the nervous system. + neurepithelium + AEO:0001008 + BTO:0000314 + EHDAA2_RETIRED:0004654 + FMA:64807 + embryonic neuroepithelium + neuroepithelium + uberon + UBERON:0034705 + developing neuroepithelium + + + + + An embryonic or larval epithelium that is committed to form part of the nervous system. + AEO:0001008 + AEO:JB + + + + + neurepithelium + BTO:0000314 + + + + + embryonic neuroepithelium + + + + + + neuroepithelium + AEO:0001008 + + + + + + + + + An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. + AEO:0001009 + uberon + UBERON:0034706 + proliferating neuroepithelium + + + + + + AEO + + + + + An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. + AEO:0001009 + + + + + + + + + A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. + AEO:0001010 + uberon + UBERON:0034707 + differentiating neuroepithelium + + + + + + AEO + + + + + A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. + AEO:0001010 + + + + + + + + + + + + + + + + + + + + + + + + + + + DHBA:12694 + EMAPA:32916 + marginal zone of hindbrain + uberon + MZH + UBERON:0034709 + hindbrain marginal layer + + + + + marginal zone of hindbrain + DHBA:12694 + + + + + MZH + DHBA:12694 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0001267 + EMAPA:17585 + spinal cord lateral wall ventricular layer + uberon + UBERON:0034710 + spinal cord ventricular layer + + + + + + + + + + + EHDAA2 + + + + + spinal cord lateral wall ventricular layer + EHDAA2:0001267 + + + + + + + + + Any substance in the body or expelled from the body that is in a gaseous state. + FMA:84580 + gas in anatomical space + portion of gas in anatomical space + uberon + UBERON:0034873 + bodily gas + + + + + Any substance in the body or expelled from the body that is in a gaseous state. + + + + + + portion of gas in anatomical space + FMA:84580 + + + + + + + + + Any portion of gas located in a part of the respiratory system that is composed primarily of air. + FMA:84581 + respiratory air + respiratory system air + uberon + UBERON:0034874 + air in respiratory system + + + + + Any portion of gas located in a part of the respiratory system that is composed primarily of air. + + + + + + respiratory air + FMA:84581 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + the area of axial mesoderm that develops into the prechordal plate + prechordal mesenchyme + uberon + UBERON:0034878 + prechordal mesoderm + + + + + the area of axial mesoderm that develops into the prechordal plate + MGI:anna + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + lumen of gland + uberon + UBERON:0034905 + gland lumen + + + + + + + + + + + + + + + An multicellular anatomical structure that has subparts of multiple organs as a part. + CARO:0020001 + uberon + anatomical cluster + UBERON:0034921 + multi organ part structure + + + + + + CARO + + + + + An multicellular anatomical structure that has subparts of multiple organs as a part. + CARO:0020001 + + + + + anatomical cluster + CARO:0020001 + + + + + + + + + + + + + + + A cluster of cells, largely surrounded by a morphological boundary. + CARO:0020002 + FMA:62807 + uberon + UBERON:0034922 + cell cluster + + + + + + CARO + + + + + A cluster of cells, largely surrounded by a morphological boundary. + CARO:0020002 + + + + + + + + + + + + + + + A collection of anatomical structures that are alike in terms of their morphology or developmental origin. + resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected + uberon + UBERON:0034925 + anatomical collection + + + + + A collection of anatomical structures that are alike in terms of their morphology or developmental origin. + + + + + + + + + + + + + + + + + + + + + + + + + + + Any organ component layer that consists of smooth muscle tissue. + uberon + UBERON:0034933 + layer of smooth muscle tissue + + + + + Any organ component layer that consists of smooth muscle tissue. + + + + + + + + + + FMA:55268 + organ sector + organ zonal region + organ zone + uberon + organ region with floating fiat boundary + UBERON:0034944 + zone of organ + + + + + organ sector + FMA:55268 + + + + + organ zone + FMA:55268 + + + + + organ region with floating fiat boundary + FMA:55268 + + + + + + + + + + + + + + + + + + + + + + + + + + Any portion of gas located in a part of the respiratory system. + respiratory gas + respiratory system gas + uberon + UBERON:0034947 + gas in respiratory system + + + + + Any portion of gas located in a part of the respiratory system. + + + + + + + + + + + + + + + + + + + + + + + + + + + + NCIT:C25787 + uberon + duct epithelium + ductal epithelium + UBERON:0034969 + epithelial layer of duct + + + + + + + + + + + + + + + + + + + + + + + + + + Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. + Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat + digestive tract contents + uberon + ingested material entity + UBERON:0035118 + material entity in digestive tract + + + + + Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. + + + + + + digestive tract contents + + + + + + + + + + + + + + + + + + + + + + + + + + + Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. + + + FMA:61695 + NCIT:C29667 + surface of body + uberon + UBERON:0035159 + entire surface of organism + + + + + Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. + FMA:61695 + + + + + surface of body + FMA:61695 + + + + + + + + + + + + + + + + + + + + + + + + + + The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. + FMA:225275 + superficial part of circulatory system + superficial vasculature + dermis vasculature + hypodermis vasculature + uberon + skin vasculature + subcutaneous vasculature + vasculature of skin + UBERON:0035549 + vasculature of integument + + + + + The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. + + + + + + vasculature of skin + FMA:225275 + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. + + + + FMA:76719 + NCIT:C33666 + uberon + superfical vein + superficial veins + superficial vessels + UBERON:0035550 + superficial vein + + + + + Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. + ncithesaurus:Superficial_Vein + + + + + superfical vein + + + + + + superficial veins + + + + + + superficial vessels + + + + + + + + + + + + + + + + + + + + + + + + + + + The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. + deep part of circulatory system + uberon + UBERON:0035551 + deep vasculature + + + + + The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. + + + + + + + + + + + + + + + + + + + + + + + + + + + A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. + + + + FMA:76718 + NCIT:C32444 + uberon + deep veins + deep vessels + UBERON:0035552 + deep vein + + + + + A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. + ncithesaurus:Deep_Vein + + + + + deep veins + + + + + + deep vessels + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any chamber of the left side of the heart + + FMA:7166 + uberon + UBERON:0035553 + left cardiac chamber + + + + + Any chamber of the left side of the heart + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any chamber of the right side of the heart + + FMA:7165 + uberon + UBERON:0035554 + right cardiac chamber + + + + + Any chamber of the right side of the heart + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0004181 + FMA:9464 + cardiac chamber cavity + heart cavity + heart lumen + uberon + UBERON:0035763 + cavity of cardiac chamber + + + + + + + + + + + FMA + + + + + cardiac chamber cavity + FMA:9464 + + + + + heart cavity + FMA:9464 + + + + + heart lumen + EHDAA2:0004181 + + + + + + + + + + + + + + + + + + + + + + + + + + + The primordial mouth region of the developing head. + FMA:293105 + primitive mouth + primordial mouth + uberon + UBERON:0035804 + future mouth + + + + + The primordial mouth region of the developing head. + MP:0003119 + + + + + primitive mouth + FMA:293105 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + FMA:12241 + uberon + UBERON:0035809 + serous cavity + + + + + + + + + + + + + + + + + + + + + + + + + + The sum of epicardial and paracardial fat deposits. + + ZFA:0005765 + uberon + UBERON:0035814 + pericardial fat + + + + + The sum of epicardial and paracardial fat deposits. + + + + + + + + + + + + + + + + + + + + + + + + + + + Any fat deposit surrounding a visceral organ. + uberon + UBERON:0035818 + visceral fat + + + + + Any fat deposit surrounding a visceral organ. + UBERON:cjm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + BTO:0004378 + EMAPA:37987 + FMA:67473 + blood vessel wall + uberon + vascular wall + UBERON:0035965 + wall of blood vessel + + + + + EMAPA:37987 + MA:th + + + + + blood vessel wall + FMA:67473 + + + + + vascular wall + BTO:0004378 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0004070 + uberon + UBERON:0036072 + respiratory primordium epithelium + + + + + + + + + + + EHDAA2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EHDAA2:0004071 + respiratory primordium associated mesenchyme + uberon + UBERON:0036073 + respiratory primordium mesenchyme + + + + + + + + + + + EHDAA2 + + + + + respiratory primordium associated mesenchyme + EHDAA2:0004071 + + + + + + + + + + + + An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. + uberon + UBERON:0036146 + cardiopharyngeal field + + + + + An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. + + BGEE:ann + + + + + + + + + + + + + + + + + + + + + + + + + + A bodily fluid that is located in the coelom. + he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste[https://en.wikipedia.org/wiki/Coelom#Coelomic_fluid] + BTO:0001708 + uberon + UBERON:0036217 + coelomic fluid + + + + + A bodily fluid that is located in the coelom. + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any gland that is part os the respiratory system. + uberon + UBERON:0036225 + respiratory system gland + + + + + Any gland that is part os the respiratory system. + UBERON:cjm + + + + + + + + + + + + + + + + + + + + + + + + + + A notochord that has persisted beyond the embryonic stage. + + + + + + uberon + UBERON:0036242 + post-embryonic notochord + + + + + A notochord that has persisted beyond the embryonic stage. + UBERON:cjm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transudate found in the serous sac. + serous fluid + FMA:20932 + serous sac fluid + uberon + UBERON:0036244 + secretion of serous membrane + + + + + A transudate found in the serous sac. + FMA:20932 + + + + + serous fluid + FMA:20932 + + + + + + + + + + + + + + + + + + + + + + + + + + A zone of skin that is part of the face. + + + eriks + 2012-02-05T05:23:01Z + + + EMAPA:36657 + FMA:24758 + NCIT:C33561 + UMLS:C0222084 + face skin + uberon + facial skin + UBERON:1000021 + + + skin of face + + + + + A zone of skin that is part of the face. + + UBERON:EJS + + + + + UMLS:C0222084 + ncithesaurus:Skin_of_the_Face + + + + + face skin + EMAPA:36657 + FMA:24758 + + + + + + + + + + + + + + + + + + + + + + + + + + Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. + This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon + amphibian_anatomy_curators + uberon/phenoscape-anatomy + Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 + external integument structure + + + + + Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. + AAO:EJS + + + + + + + + + + + + + + + + + + + + + + + + + + Dermal, epidermal, glandular and pigment structures of the external head integument. + This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon + amphibian_anatomy_curators + uberon/phenoscape-anatomy + head external integument structure + + + + + Dermal, epidermal, glandular and pigment structures of the external head integument. + AAO:EJS + + + + + + + + + + + + + + + + + + + + + + + + + + Dermal, epidermal, glandular and pigment structures of the body integument. + This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon + amphibian_anatomy_curators + uberon/phenoscape-anatomy + body external integument structure + + + + + Dermal, epidermal, glandular and pigment structures of the body integument. + AAO:EJS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Blood vessels in respiratory skin. + Modified from the original AAO source + amphibian_anatomy_curators + uberon/phenoscape-anatomy + vasculature of respiratory integument + + + + + Blood vessels in respiratory skin. + AAO:EJS + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/uberon_terms.txt b/src/ontology/imports/uberon_terms.txt new file mode 100644 index 00000000..44e91278 --- /dev/null +++ b/src/ontology/imports/uberon_terms.txt @@ -0,0 +1,35 @@ +http://purl.obolibrary.org/obo/XXX_0000001 ## Optional Label +http://purl.obolibrary.org/obo/PATO_0000001 ## quality +http://purl.obolibrary.org/obo/BFO_0000050 ## part of +http://purl.obolibrary.org/obo/CHEBI_24431 ## chemical entity +http://purl.obolibrary.org/obo/UBERON_0002048 ## lung +http://purl.obolibrary.org/obo/CL_0000540 ## neuron +http://purl.obolibrary.org/obo/GO_0008150 ## biological_process +http://purl.obolibrary.org/obo/MI_0000 +http://purl.obolibrary.org/obo/PW_0000001 +http://purl.obolibrary.org/obo/REX_0000000 +http://purl.obolibrary.org/obo/RO_0002573 +http://purl.obolibrary.org/obo/RS_0000457 +http://purl.obolibrary.org/obo/VTO_9031916 +http://purl.obolibrary.org/obo/VT_0000001 +http://purl.obolibrary.org/obo/VariO_0001 +http://purl.obolibrary.org/obo/WBbt_0000100 +http://purl.obolibrary.org/obo/WBls_0000075 +http://purl.obolibrary.org/obo/DDANAT_0010001 +http://purl.obolibrary.org/obo/DDPHENO_0010000 +http://purl.obolibrary.org/obo/EHDAA2_0000000 +http://purl.obolibrary.org/obo/EHDAA_1 +http://purl.obolibrary.org/obo/EHDA_1 +http://purl.obolibrary.org/obo/EMAPA_0 +http://purl.obolibrary.org/obo/EMAP_0 +http://purl.obolibrary.org/obo/FBbi_root_00000000 +http://purl.obolibrary.org/obo/FBbt_10000000 +http://purl.obolibrary.org/obo/FBcv_0000000 +http://purl.obolibrary.org/obo/FBdv_00007008 +http://purl.obolibrary.org/obo/FBsp_00000000 +http://purl.obolibrary.org/obo/FIX_0000000 +http://purl.obolibrary.org/obo/FMA_50592 +http://purl.obolibrary.org/obo/FMA_85802 +http://purl.obolibrary.org/obo/FYPO_0000001 +http://purl.obolibrary.org/obo/GENEPIO_0002034 +http://purl.obolibrary.org/obo/BFO_0000001 diff --git a/src/ontology/patterns.sh b/src/ontology/patterns.sh new file mode 100755 index 00000000..e2fb401b --- /dev/null +++ b/src/ontology/patterns.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make patterns diff --git a/src/ontology/prepare_release.sh b/src/ontology/prepare_release.sh new file mode 100755 index 00000000..6aefd945 --- /dev/null +++ b/src/ontology/prepare_release.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make prepare_release diff --git a/src/ontology/reports/README.md b/src/ontology/reports/README.md new file mode 100644 index 00000000..933492c7 --- /dev/null +++ b/src/ontology/reports/README.md @@ -0,0 +1,3 @@ +# Reports folder + +Files are added to this during the release process diff --git a/src/ontology/run.bat b/src/ontology/run.bat new file mode 100644 index 00000000..717ca499 --- /dev/null +++ b/src/ontology/run.bat @@ -0,0 +1 @@ +docker run -v %cd%\..\..\:/work -w /work/src/ontology --rm -ti obolibrary/odkfull %* diff --git a/src/ontology/run.sh b/src/ontology/run.sh new file mode 100755 index 00000000..cd235221 --- /dev/null +++ b/src/ontology/run.sh @@ -0,0 +1,12 @@ +#!/bin/sh +# Wrapper script for docker. +# +# This is used primarily for wrapping the GNU Make workflow. +# Instead of typing "make TARGET", type "./run.sh make TARGET". +# This will run the make workflow within a docker container. +# +# The assumption is that you are working in the src/ontology folder; +# we therefore map the whole repo (../..) to a docker volume. +# +# See README-editors.md for more details. +docker run -v $PWD/../../:/work -w /work/src/ontology --rm -ti obolibrary/odkfull "$@" diff --git a/src/ontology/test.sh b/src/ontology/test.sh new file mode 100755 index 00000000..dfd54a7e --- /dev/null +++ b/src/ontology/test.sh @@ -0,0 +1,2 @@ +#!/bin/sh +./run.sh make test diff --git a/src/ontology/upheno-edit.owl b/src/ontology/upheno-edit.owl new file mode 100644 index 00000000..72d8eef4 --- /dev/null +++ b/src/ontology/upheno-edit.owl @@ -0,0 +1,32 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Import() +Annotation(rdfs:comment "upheno") + +Declaration(Class()) + + +############################ +# Classes +############################ + +# Class: (upheno) + +AnnotationAssertion(rdfs:label "upheno"@en) + + +) \ No newline at end of file diff --git a/src/ontology/upheno-idranges.owl b/src/ontology/upheno-idranges.owl new file mode 100644 index 00000000..200ec227 --- /dev/null +++ b/src/ontology/upheno-idranges.owl @@ -0,0 +1,67 @@ +Prefix: rdf: +Prefix: idsfor: +Prefix: dc: +Prefix: xsd: +Prefix: allocatedto: +Prefix: xml: +Prefix: idprefix: +Prefix: iddigits: +Prefix: rdfs: +Prefix: idrange: +Prefix: owl: + + + +Ontology: + + +Annotations: + idsfor: "UPHENO", + idprefix: "http://purl.obolibrary.org/obo/UPHENO_", + iddigits: 7 + +AnnotationProperty: idprefix: + + +AnnotationProperty: iddigits: + + +AnnotationProperty: idsfor: + + +AnnotationProperty: allocatedto: + +Datatype: idrange:1 + + Annotations: + allocatedto: "ONTOLOGY-CREATOR" + + EquivalentTo: + xsd:integer[>= 0 , <= 999999] + + +Datatype: idrange:2 + + Annotations: + allocatedto: "ADDITIONAL EDITOR" + + EquivalentTo: + xsd:integer[>= 1000000 , <= 1999999] + + +Datatype: xsd:integer + + + +Datatype: idrange:3 + + Annotations: + allocatedto: "TermGenie" + + EquivalentTo: + xsd:integer[> 2000000 , <= 2999999] + + +Datatype: rdf:PlainLiteral + + diff --git a/src/patterns/data/auto/abnormal.tsv b/src/patterns/data/auto/abnormal.tsv new file mode 100644 index 00000000..fd7b468a --- /dev/null +++ b/src/patterns/data/auto/abnormal.tsv @@ -0,0 +1,461 @@ +entity defined_class +http://purl.obolibrary.org/obo/GO_0051716 http://purl.obolibrary.org/obo/UPHENO_0000060 +http://purl.obolibrary.org/obo/BSPO_0000679 http://purl.obolibrary.org/obo/UPHENO_0000061 +http://purl.obolibrary.org/obo/BSPO_0000677 http://purl.obolibrary.org/obo/UPHENO_0000062 +http://purl.obolibrary.org/obo/BSPO_0000678 http://purl.obolibrary.org/obo/UPHENO_0000063 +http://purl.obolibrary.org/obo/GO_0046483 http://purl.obolibrary.org/obo/UPHENO_0000064 +http://purl.obolibrary.org/obo/GO_0048666 http://purl.obolibrary.org/obo/UPHENO_0000065 +http://purl.obolibrary.org/obo/GO_0002790 http://purl.obolibrary.org/obo/UPHENO_0000066 +http://purl.obolibrary.org/obo/GO_0006911 http://purl.obolibrary.org/obo/UPHENO_0000067 +http://purl.obolibrary.org/obo/BSPO_0000684 http://purl.obolibrary.org/obo/UPHENO_0000068 +http://purl.obolibrary.org/obo/GO_0006915 http://purl.obolibrary.org/obo/UPHENO_0000069 +http://purl.obolibrary.org/obo/BSPO_0000201 http://purl.obolibrary.org/obo/UPHENO_0000070 +http://purl.obolibrary.org/obo/BSPO_0000685 http://purl.obolibrary.org/obo/UPHENO_0000071 +http://purl.obolibrary.org/obo/BSPO_0000682 http://purl.obolibrary.org/obo/UPHENO_0000072 +http://purl.obolibrary.org/obo/GO_0006913 http://purl.obolibrary.org/obo/UPHENO_0000073 +http://purl.obolibrary.org/obo/BSPO_0000683 http://purl.obolibrary.org/obo/UPHENO_0000074 +http://purl.obolibrary.org/obo/BSPO_0000680 http://purl.obolibrary.org/obo/UPHENO_0000075 +http://purl.obolibrary.org/obo/GO_0033058 http://purl.obolibrary.org/obo/UPHENO_0000076 +http://purl.obolibrary.org/obo/GO_0098813 http://purl.obolibrary.org/obo/UPHENO_0000077 +http://purl.obolibrary.org/obo/GO_0050877 http://purl.obolibrary.org/obo/UPHENO_0000078 +http://purl.obolibrary.org/obo/BSPO_0000688 http://purl.obolibrary.org/obo/UPHENO_0000079 +http://purl.obolibrary.org/obo/GO_0051726 http://purl.obolibrary.org/obo/UPHENO_0000080 +http://purl.obolibrary.org/obo/BSPO_0000689 http://purl.obolibrary.org/obo/UPHENO_0000081 +http://purl.obolibrary.org/obo/BSPO_0000202 http://purl.obolibrary.org/obo/UPHENO_0000082 +http://purl.obolibrary.org/obo/BSPO_0000686 http://purl.obolibrary.org/obo/UPHENO_0000083 +http://purl.obolibrary.org/obo/BSPO_0000687 http://purl.obolibrary.org/obo/UPHENO_0000084 +http://purl.obolibrary.org/obo/GO_0071684 http://purl.obolibrary.org/obo/UPHENO_0000085 +http://purl.obolibrary.org/obo/GO_0006807 http://purl.obolibrary.org/obo/UPHENO_0000086 +http://purl.obolibrary.org/obo/GO_0006928 http://purl.obolibrary.org/obo/UPHENO_0000087 +http://purl.obolibrary.org/obo/GO_0048569 http://purl.obolibrary.org/obo/UPHENO_0000088 +http://purl.obolibrary.org/obo/GO_1901990 http://purl.obolibrary.org/obo/UPHENO_0000089 +http://purl.obolibrary.org/obo/GO_0045055 http://purl.obolibrary.org/obo/UPHENO_0000090 +http://purl.obolibrary.org/obo/GO_1901991 http://purl.obolibrary.org/obo/UPHENO_0000091 +http://purl.obolibrary.org/obo/GO_0048565 http://purl.obolibrary.org/obo/UPHENO_0000092 +http://purl.obolibrary.org/obo/GO_0006810 http://purl.obolibrary.org/obo/UPHENO_0000093 +http://purl.obolibrary.org/obo/GO_0006935 http://purl.obolibrary.org/obo/UPHENO_0000094 +http://purl.obolibrary.org/obo/GO_0036464 http://purl.obolibrary.org/obo/UPHENO_0000095 +http://purl.obolibrary.org/obo/GO_0051705 http://purl.obolibrary.org/obo/UPHENO_0000096 +http://purl.obolibrary.org/obo/GO_0051703 http://purl.obolibrary.org/obo/UPHENO_0000097 +http://purl.obolibrary.org/obo/GO_0051704 http://purl.obolibrary.org/obo/UPHENO_0000098 +http://purl.obolibrary.org/obo/GO_0060537 http://purl.obolibrary.org/obo/UPHENO_0000099 +http://purl.obolibrary.org/obo/GO_0005730 http://purl.obolibrary.org/obo/UPHENO_0000100 +http://purl.obolibrary.org/obo/GO_0098840 http://purl.obolibrary.org/obo/UPHENO_0000101 +http://purl.obolibrary.org/obo/BSPO_0000112 http://purl.obolibrary.org/obo/UPHENO_0000102 +http://purl.obolibrary.org/obo/GO_0005859 http://purl.obolibrary.org/obo/UPHENO_0000103 +http://purl.obolibrary.org/obo/GO_0032094 http://purl.obolibrary.org/obo/UPHENO_0000104 +http://purl.obolibrary.org/obo/GO_0036211 http://purl.obolibrary.org/obo/UPHENO_0000105 +http://purl.obolibrary.org/obo/GO_0050789 http://purl.obolibrary.org/obo/UPHENO_0000106 +http://purl.obolibrary.org/obo/GO_0048102 http://purl.obolibrary.org/obo/UPHENO_0000107 +http://purl.obolibrary.org/obo/GO_0048468 http://purl.obolibrary.org/obo/UPHENO_0000108 +http://purl.obolibrary.org/obo/GO_0048589 http://purl.obolibrary.org/obo/UPHENO_0000109 +http://purl.obolibrary.org/obo/GO_1901576 http://purl.obolibrary.org/obo/UPHENO_0000110 +http://purl.obolibrary.org/obo/GO_0006950 http://purl.obolibrary.org/obo/UPHENO_0000111 +http://purl.obolibrary.org/obo/GO_0005863 http://purl.obolibrary.org/obo/UPHENO_0000112 +http://purl.obolibrary.org/obo/GO_0051642 http://purl.obolibrary.org/obo/UPHENO_0000113 +http://purl.obolibrary.org/obo/GO_0051640 http://purl.obolibrary.org/obo/UPHENO_0000114 +http://purl.obolibrary.org/obo/GO_0051641 http://purl.obolibrary.org/obo/UPHENO_0000115 +http://purl.obolibrary.org/obo/GO_0050794 http://purl.obolibrary.org/obo/UPHENO_0000116 +http://purl.obolibrary.org/obo/GO_0050793 http://purl.obolibrary.org/obo/UPHENO_0000117 +http://purl.obolibrary.org/obo/GO_0051648 http://purl.obolibrary.org/obo/UPHENO_0000118 +http://purl.obolibrary.org/obo/GO_0051649 http://purl.obolibrary.org/obo/UPHENO_0000119 +http://purl.obolibrary.org/obo/BSPO_0000400 http://purl.obolibrary.org/obo/UPHENO_0000120 +http://purl.obolibrary.org/obo/GO_0001764 http://purl.obolibrary.org/obo/UPHENO_0000121 +http://purl.obolibrary.org/obo/GO_0045184 http://purl.obolibrary.org/obo/UPHENO_0000122 +http://purl.obolibrary.org/obo/GO_0023052 http://purl.obolibrary.org/obo/UPHENO_0000123 +http://purl.obolibrary.org/obo/GO_0051656 http://purl.obolibrary.org/obo/UPHENO_0000124 +http://purl.obolibrary.org/obo/GO_0006725 http://purl.obolibrary.org/obo/UPHENO_0000125 +http://purl.obolibrary.org/obo/GO_0051650 http://purl.obolibrary.org/obo/UPHENO_0000126 +http://purl.obolibrary.org/obo/BSPO_0000417 http://purl.obolibrary.org/obo/UPHENO_0000127 +http://purl.obolibrary.org/obo/GO_0018958 http://purl.obolibrary.org/obo/UPHENO_0000128 +http://purl.obolibrary.org/obo/GO_0048489 http://purl.obolibrary.org/obo/UPHENO_0000129 +http://purl.obolibrary.org/obo/GO_0023061 http://purl.obolibrary.org/obo/UPHENO_0000130 +http://purl.obolibrary.org/obo/GO_0006974 http://purl.obolibrary.org/obo/UPHENO_0000131 +http://purl.obolibrary.org/obo/GO_0035177 http://purl.obolibrary.org/obo/UPHENO_0000132 +http://purl.obolibrary.org/obo/GO_0035176 http://purl.obolibrary.org/obo/UPHENO_0000133 +http://purl.obolibrary.org/obo/GO_0035295 http://purl.obolibrary.org/obo/UPHENO_0000134 +http://purl.obolibrary.org/obo/GO_0050896 http://purl.obolibrary.org/obo/UPHENO_0000135 +http://purl.obolibrary.org/obo/GO_0050890 http://purl.obolibrary.org/obo/UPHENO_0000136 +http://purl.obolibrary.org/obo/GO_0001505 http://purl.obolibrary.org/obo/UPHENO_0000137 +http://purl.obolibrary.org/obo/GO_0098916 http://purl.obolibrary.org/obo/UPHENO_0000138 +http://purl.obolibrary.org/obo/GO_0050657 http://purl.obolibrary.org/obo/UPHENO_0000139 +http://purl.obolibrary.org/obo/GO_0050658 http://purl.obolibrary.org/obo/UPHENO_0000140 +http://purl.obolibrary.org/obo/GO_0048232 http://purl.obolibrary.org/obo/UPHENO_0000141 +http://purl.obolibrary.org/obo/GO_0030705 http://purl.obolibrary.org/obo/UPHENO_0000142 +http://purl.obolibrary.org/obo/GO_0048599 http://purl.obolibrary.org/obo/UPHENO_0000143 +http://purl.obolibrary.org/obo/GO_1901564 http://purl.obolibrary.org/obo/UPHENO_0000144 +http://purl.obolibrary.org/obo/GO_0048598 http://purl.obolibrary.org/obo/UPHENO_0000145 +http://purl.obolibrary.org/obo/GO_1901566 http://purl.obolibrary.org/obo/UPHENO_0000146 +http://purl.obolibrary.org/obo/BSPO_0000673 http://purl.obolibrary.org/obo/UPHENO_0000147 +http://purl.obolibrary.org/obo/GO_0006629 http://purl.obolibrary.org/obo/UPHENO_0000148 +http://purl.obolibrary.org/obo/BSPO_0000674 http://purl.obolibrary.org/obo/UPHENO_0000149 +http://purl.obolibrary.org/obo/GO_0036379 http://purl.obolibrary.org/obo/UPHENO_0000150 +http://purl.obolibrary.org/obo/BSPO_0000671 http://purl.obolibrary.org/obo/UPHENO_0000151 +http://purl.obolibrary.org/obo/BSPO_0000672 http://purl.obolibrary.org/obo/UPHENO_0000152 +http://purl.obolibrary.org/obo/GO_0071103 http://purl.obolibrary.org/obo/UPHENO_0000153 +http://purl.obolibrary.org/obo/GO_0016310 http://purl.obolibrary.org/obo/UPHENO_0000154 +http://purl.obolibrary.org/obo/BSPO_0000039 http://purl.obolibrary.org/obo/UPHENO_0000155 +http://purl.obolibrary.org/obo/BSPO_0000037 http://purl.obolibrary.org/obo/UPHENO_0000156 +http://purl.obolibrary.org/obo/BSPO_0000038 http://purl.obolibrary.org/obo/UPHENO_0000157 +http://purl.obolibrary.org/obo/GO_0006996 http://purl.obolibrary.org/obo/UPHENO_0000158 +http://purl.obolibrary.org/obo/GO_0003006 http://purl.obolibrary.org/obo/UPHENO_0000159 +http://purl.obolibrary.org/obo/GO_0006518 http://purl.obolibrary.org/obo/UPHENO_0000160 +http://purl.obolibrary.org/obo/BSPO_0000046 http://purl.obolibrary.org/obo/UPHENO_0000161 +http://purl.obolibrary.org/obo/GO_0003008 http://purl.obolibrary.org/obo/UPHENO_0000162 +http://purl.obolibrary.org/obo/BSPO_0000047 http://purl.obolibrary.org/obo/UPHENO_0000163 +http://purl.obolibrary.org/obo/BSPO_0000044 http://purl.obolibrary.org/obo/UPHENO_0000164 +http://purl.obolibrary.org/obo/BSPO_0000045 http://purl.obolibrary.org/obo/UPHENO_0000165 +http://purl.obolibrary.org/obo/BSPO_0000042 http://purl.obolibrary.org/obo/UPHENO_0000166 +http://purl.obolibrary.org/obo/BSPO_0000043 http://purl.obolibrary.org/obo/UPHENO_0000167 +http://purl.obolibrary.org/obo/BSPO_0000041 http://purl.obolibrary.org/obo/UPHENO_0000168 +http://purl.obolibrary.org/obo/GO_0016203 http://purl.obolibrary.org/obo/UPHENO_0000169 +http://purl.obolibrary.org/obo/BSPO_0000048 http://purl.obolibrary.org/obo/UPHENO_0000170 +http://purl.obolibrary.org/obo/BSPO_0000049 http://purl.obolibrary.org/obo/UPHENO_0000171 +http://purl.obolibrary.org/obo/GO_0030728 http://purl.obolibrary.org/obo/UPHENO_0000172 +http://purl.obolibrary.org/obo/GO_0048137 http://purl.obolibrary.org/obo/UPHENO_0000173 +http://purl.obolibrary.org/obo/GO_0007610 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+ + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/BSPO_0000084. + abnormality of http://purl.obolibrary.org/obo/BSPO_0000084 + abnormal http://purl.obolibrary.org/obo/BSPO_0000084 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of regulation of metabolic process. + abnormality of regulation of metabolic process + abnormal regulation of metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/BSPO_0000085. + abnormality of http://purl.obolibrary.org/obo/BSPO_0000085 + abnormal http://purl.obolibrary.org/obo/BSPO_0000085 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of molting cycle process. + abnormality of molting cycle process + abnormal molting cycle process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of mitotic DNA integrity checkpoint. + abnormality of mitotic DNA integrity checkpoint + abnormal mitotic DNA integrity checkpoint + + + + + + + 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+ + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/BSPO_0000093. + abnormality of http://purl.obolibrary.org/obo/BSPO_0000093 + abnormal http://purl.obolibrary.org/obo/BSPO_0000093 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of microtubule-based process. + abnormality of microtubule-based process + abnormal microtubule-based process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/BSPO_0000094. + abnormality of http://purl.obolibrary.org/obo/BSPO_0000094 + abnormal http://purl.obolibrary.org/obo/BSPO_0000094 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of protein localization. + abnormality of protein localization + abnormal protein localization + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/BSPO_0000092. + abnormality of http://purl.obolibrary.org/obo/BSPO_0000092 + abnormal http://purl.obolibrary.org/obo/BSPO_0000092 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of microtubule-based movement. + abnormality of microtubule-based movement + abnormal microtubule-based movement + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of nucleic acid metabolic process. + abnormality of nucleic acid metabolic process + abnormal nucleic acid metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cytoplasmic part. + abnormality of cytoplasmic part + abnormal cytoplasmic part + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of intracellular organelle part. + abnormality of intracellular organelle part + abnormal intracellular organelle part + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of contractile fiber part. + abnormality of contractile fiber part + abnormal contractile fiber part + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular process involved in reproduction in multicellular organism. + abnormality of cellular process involved in reproduction in multicellular organism + abnormal cellular process involved in reproduction in multicellular organism + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of reproductive process. + abnormality of reproductive process + abnormal reproductive process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of pigmentation. + abnormality of pigmentation + abnormal pigmentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of intracellular non-membrane-bounded organelle. + abnormality of intracellular non-membrane-bounded organelle + abnormal intracellular non-membrane-bounded organelle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular macromolecule biosynthetic process. + abnormality of cellular macromolecule biosynthetic process + abnormal cellular macromolecule biosynthetic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular response to stress. + abnormality of cellular response to stress + abnormal cellular response to stress + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell-cell signaling. + abnormality of cell-cell signaling + abnormal cell-cell signaling + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of chemical synaptic transmission. + abnormality of chemical synaptic transmission + abnormal chemical synaptic transmission + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular nitrogen compound metabolic process. + abnormality of cellular nitrogen compound metabolic process + abnormal cellular nitrogen compound metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of organelle. + abnormality of organelle + abnormal organelle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of ribonucleoprotein complex. + abnormality of ribonucleoprotein complex + abnormal ribonucleoprotein complex + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of non-membrane-bounded organelle. + abnormality of non-membrane-bounded organelle + abnormal non-membrane-bounded organelle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of intracellular organelle. + abnormality of intracellular organelle + abnormal intracellular organelle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cytoskeletal part. + abnormality of cytoskeletal part + abnormal cytoskeletal part + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of gamete generation. + abnormality of gamete generation + abnormal gamete generation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of alcohol metabolic process. + abnormality of alcohol metabolic process + abnormal alcohol metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of response to drug. + abnormality of response to drug + abnormal response to drug + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of neuromuscular synaptic transmission. + abnormality of neuromuscular synaptic transmission + abnormal neuromuscular synaptic transmission + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of neurotransmitter metabolic process. + abnormality of neurotransmitter metabolic process + abnormal neurotransmitter metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of multicellular organism development. + abnormality of multicellular organism development + abnormal multicellular organism development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell communication. + abnormality of cell communication + abnormal cell communication + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of nervous system development. + abnormality of nervous system development + abnormal nervous system development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of regulation of cell cycle process. + abnormality of regulation of cell cycle process + abnormal regulation of cell cycle process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of membrane invagination. + abnormality of membrane invagination + abnormal membrane invagination + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of programmed cell death. + abnormality of programmed cell death + abnormal programmed cell death + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell projection organization. + abnormality of cell projection organization + abnormal cell projection organization + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell differentiation. + abnormality of cell differentiation + abnormal cell differentiation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular amine metabolic process. + abnormality of cellular amine metabolic process + abnormal cellular amine metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of spermatogenesis. + abnormality of spermatogenesis + abnormal spermatogenesis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of germ cell development. + abnormality of germ cell development + abnormal germ cell development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell part. + abnormality of cell part + abnormal cell part + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell cycle. + abnormality of cell cycle + abnormal cell cycle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of muscle cell development. + abnormality of muscle cell development + abnormal muscle cell development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative regulation of cell cycle. + abnormality of negative regulation of cell cycle + abnormal negative regulation of cell cycle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of neuron projection morphogenesis. + abnormality of neuron projection morphogenesis + abnormal neuron projection morphogenesis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of DNA damage checkpoint. + abnormality of DNA damage checkpoint + abnormal DNA damage checkpoint + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of positive chemotaxis. + abnormality of positive chemotaxis + abnormal positive chemotaxis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell cycle checkpoint. + abnormality of cell cycle checkpoint + abnormal cell cycle checkpoint + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative chemotaxis. + abnormality of negative chemotaxis + abnormal negative chemotaxis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of striated muscle tissue development. + abnormality of striated muscle tissue development + abnormal striated muscle tissue development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of mitotic sister chromatid segregation. + abnormality of mitotic sister chromatid segregation + abnormal mitotic sister chromatid segregation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of chromosome segregation. + abnormality of chromosome segregation + abnormal chromosome segregation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of regulation of gene expression. + abnormality of regulation of gene expression + abnormal regulation of gene expression + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of acetate ester metabolic process. + abnormality of acetate ester metabolic process + abnormal acetate ester metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular component organization or biogenesis. + abnormality of cellular component organization or biogenesis + abnormal cellular component organization or biogenesis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of regulation of G1/S transition of mitotic cell cycle. + abnormality of regulation of G1/S transition of mitotic cell cycle + abnormal regulation of G1/S transition of mitotic cell cycle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of organic substance transport. + abnormality of organic substance transport + abnormal organic substance transport + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular biosynthetic process. + abnormality of cellular biosynthetic process + abnormal cellular biosynthetic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of nitrogen compound transport. + abnormality of nitrogen compound transport + abnormal nitrogen compound transport + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of multicellular organismal reproductive process. + abnormality of multicellular organismal reproductive process + abnormal multicellular organismal reproductive process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of reproductive structure development. + abnormality of reproductive structure development + abnormal reproductive structure development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of organic substance metabolic process. + abnormality of organic substance metabolic process + abnormal organic substance metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of metabolic process. + abnormality of metabolic process + abnormal metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of biological_process. + abnormality of biological_process + abnormal biological_process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative regulation of G1/S transition of mitotic cell cycle. + abnormality of negative regulation of G1/S transition of mitotic cell cycle + abnormal negative regulation of G1/S transition of mitotic cell cycle + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of ribonucleoprotein granule. + abnormality of ribonucleoprotein granule + abnormal ribonucleoprotein granule + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of neuron projection development. + abnormality of neuron projection development + abnormal neuron projection development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of primary metabolic process. + abnormality of primary metabolic process + abnormal primary metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular metabolic process. + abnormality of cellular metabolic process + abnormal cellular metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell proliferation. + abnormality of cell proliferation + abnormal cell proliferation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of methylation. + abnormality of methylation + abnormal methylation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of nucleobase-containing compound transport. + abnormality of nucleobase-containing compound transport + abnormal nucleobase-containing compound transport + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular developmental process. + abnormality of cellular developmental process + abnormal cellular developmental process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of acetylcholine metabolic process. + abnormality of acetylcholine metabolic process + abnormal acetylcholine metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular macromolecule metabolic process. + abnormality of cellular macromolecule metabolic process + abnormal cellular macromolecule metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of pharyngeal pumping. + abnormality of pharyngeal pumping + abnormal pharyngeal pumping + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of microtubule organizing center localization. + abnormality of microtubule organizing center localization + abnormal microtubule organizing center localization + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of thermotaxis. + abnormality of thermotaxis + abnormal thermotaxis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular protein metabolic process. + abnormality of cellular protein metabolic process + abnormal cellular protein metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of response to temperature stimulus. + abnormality of response to temperature stimulus + abnormal response to temperature stimulus + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of backward locomotion. + abnormality of backward locomotion + abnormal backward locomotion + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/CARO_0000000. + abnormality of http://purl.obolibrary.org/obo/CARO_0000000 + abnormal http://purl.obolibrary.org/obo/CARO_0000000 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of nuclear division. + abnormality of nuclear division + abnormal nuclear division + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of plasma membrane invagination. + abnormality of plasma membrane invagination + abnormal plasma membrane invagination + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of organic hydroxy compound metabolic process. + abnormality of organic hydroxy compound metabolic process + abnormal organic hydroxy compound metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of macromolecule metabolic process. + abnormality of macromolecule metabolic process + abnormal macromolecule metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of immaterial anatomical entity. + abnormality of immaterial anatomical entity + abnormal immaterial anatomical entity + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/CARO_0000008. + abnormality of http://purl.obolibrary.org/obo/CARO_0000008 + abnormal http://purl.obolibrary.org/obo/CARO_0000008 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of material anatomical entity. + abnormality of material anatomical entity + abnormal material anatomical entity + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of anatomical structure. + abnormality of anatomical structure + abnormal anatomical structure + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell projection morphogenesis. + abnormality of cell projection morphogenesis + abnormal cell projection morphogenesis + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of anatomical structure development. + abnormality of anatomical structure development + abnormal anatomical structure development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of mitotic cell cycle checkpoint. + abnormality of mitotic cell cycle checkpoint + abnormal mitotic cell cycle checkpoint + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of intraciliary transport. + abnormality of intraciliary transport + abnormal intraciliary transport + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of peptide biosynthetic process. + abnormality of peptide biosynthetic process + abnormal peptide biosynthetic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of system development. + abnormality of system development + abnormal system development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of foraging behavior. + abnormality of foraging behavior + abnormal foraging behavior + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of regulation of cell cycle phase transition. + abnormality of regulation of cell cycle phase transition + abnormal regulation of cell cycle phase transition + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative regulation of cell cycle phase transition. + abnormality of negative regulation of cell cycle phase transition + abnormal negative regulation of cell cycle phase transition + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of peptide transport. + abnormality of peptide transport + abnormal peptide transport + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of meiotic chromosome segregation. + abnormality of meiotic chromosome segregation + abnormal meiotic chromosome segregation + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of synapse organization. + abnormality of synapse organization + abnormal synapse organization + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative regulation of cellular process. + abnormality of negative regulation of cellular process + abnormal negative regulation of cellular process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of small molecule metabolic process. + abnormality of small molecule metabolic process + abnormal small molecule metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of regulation of cell cycle G1/S phase transition. + abnormality of regulation of cell cycle G1/S phase transition + abnormal regulation of cell cycle G1/S phase transition + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative regulation of cell cycle G1/S phase transition. + abnormality of negative regulation of cell cycle G1/S phase transition + abnormal negative regulation of cell cycle G1/S phase transition + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of macromolecule localization. + abnormality of macromolecule localization + abnormal macromolecule localization + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of negative regulation of biological process. + abnormality of negative regulation of biological process + abnormal negative regulation of biological process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cellular nitrogen compound biosynthetic process. + abnormality of cellular nitrogen compound biosynthetic process + abnormal cellular nitrogen compound biosynthetic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of cell motility. + abnormality of cell motility + abnormal cell motility + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of animal organ development. + abnormality of animal organ development + abnormal animal organ development + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of macromolecule biosynthetic process. + abnormality of macromolecule biosynthetic process + abnormal macromolecule biosynthetic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of biosynthetic process. + abnormality of biosynthetic process + abnormal biosynthetic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of P granule. + abnormality of P granule + abnormal P granule + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of octopamine metabolic process. + abnormality of octopamine metabolic process + abnormal octopamine metabolic process + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of http://purl.obolibrary.org/obo/CARO_0000010. + abnormality of http://purl.obolibrary.org/obo/CARO_0000010 + abnormal http://purl.obolibrary.org/obo/CARO_0000010 + + + + + + + + + + + + + + + + + + + + + + + + + + + + Abnormality of reproductive behavior. + abnormality of reproductive behavior + abnormal reproductive behavior + + + + + + + diff --git a/src/patterns/increasedImmunoglobulinComplexAgainstEntity.yaml b/src/patterns/dosdp-patterns-dev/increasedImmunoglobulinComplexAgainstEntity.yaml similarity index 100% rename from src/patterns/increasedImmunoglobulinComplexAgainstEntity.yaml rename to src/patterns/dosdp-patterns-dev/increasedImmunoglobulinComplexAgainstEntity.yaml diff --git a/src/patterns/dosdp-patterns-dev/protrudingMorphologyInLocation.yaml b/src/patterns/dosdp-patterns-dev/protrudingMorphologyInLocation.yaml new file mode 100644 index 00000000..8c192739 --- /dev/null +++ b/src/patterns/dosdp-patterns-dev/protrudingMorphologyInLocation.yaml @@ -0,0 +1,49 @@ +pattern_name: protrudingMorphologyInLocation +pattern_iri: http://purl.oboibrary.org/obo/upheno/patterns/abnormalMorphologyInLocation + +classes: + position: PATO:0000140 + abnormal: PATO:0000460 + entity: BFO:0000001 + morphology: PATO:0000051 + protruding out of: PATO:0001646 + +relations: + inheres_in: RO:0000052 + qualifier: RO:0002573 + has_part: BFO:0000051 + part_of: BFO:0000050 + Towards: RO:0002503 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + entity: "'entity'" + location: "'entity'" + +name: + text: "abnormal protrusion of % through %” + vars: + - entity + - location + +annotations: + - annotationProperty: exact_synonym + text: "" + vars: + - entity + - location + +def: + text: "hernial protrusion of the % through an opening or defect in the %." + vars: + - entity + - location + +equivalentTo: + text: 'has part' some ('protruding out of' and ('inheres in' some (%s) and ('towards' some %s) and ('has modifier' some abnormal)) + + vars: + - entity + - location diff --git a/src/patterns/abnormal.yaml b/src/patterns/dosdp-patterns/abnormal.yaml similarity index 100% rename from src/patterns/abnormal.yaml rename to src/patterns/dosdp-patterns/abnormal.yaml diff --git a/src/patterns/abnormalBehavior.yaml b/src/patterns/dosdp-patterns/abnormalBehavior.yaml similarity index 100% rename from src/patterns/abnormalBehavior.yaml rename to src/patterns/dosdp-patterns/abnormalBehavior.yaml diff --git a/src/patterns/abnormalCellProliferation.yaml b/src/patterns/dosdp-patterns/abnormalCellProliferation.yaml similarity index 100% rename from src/patterns/abnormalCellProliferation.yaml rename to src/patterns/dosdp-patterns/abnormalCellProliferation.yaml diff --git a/src/patterns/abnormalFunctionality.yaml b/src/patterns/dosdp-patterns/abnormalFunctionality.yaml similarity index 100% rename from src/patterns/abnormalFunctionality.yaml rename to src/patterns/dosdp-patterns/abnormalFunctionality.yaml diff --git a/src/patterns/abnormalLevelOfCellularComponent.yaml b/src/patterns/dosdp-patterns/abnormalLevelOfCellularComponent.yaml similarity index 100% rename from src/patterns/abnormalLevelOfCellularComponent.yaml rename to src/patterns/dosdp-patterns/abnormalLevelOfCellularComponent.yaml diff --git a/src/patterns/abnormalLevelOfChemical.yaml b/src/patterns/dosdp-patterns/abnormalLevelOfChemical.yaml similarity index 100% rename from src/patterns/abnormalLevelOfChemical.yaml rename to src/patterns/dosdp-patterns/abnormalLevelOfChemical.yaml diff --git a/src/patterns/abnormalLevelOfChemicalInEntity.yaml b/src/patterns/dosdp-patterns/abnormalLevelOfChemicalInEntity.yaml similarity index 100% rename from src/patterns/abnormalLevelOfChemicalInEntity.yaml rename to src/patterns/dosdp-patterns/abnormalLevelOfChemicalInEntity.yaml diff --git a/src/patterns/abnormalLevelOfMolecularEntity.yaml b/src/patterns/dosdp-patterns/abnormalLevelOfMolecularEntity.yaml similarity index 100% rename from src/patterns/abnormalLevelOfMolecularEntity.yaml rename to src/patterns/dosdp-patterns/abnormalLevelOfMolecularEntity.yaml diff --git a/src/patterns/abnormalLevelOfMolecularEntityInLocation.yaml b/src/patterns/dosdp-patterns/abnormalLevelOfMolecularEntityInLocation.yaml similarity index 100% rename from src/patterns/abnormalLevelOfMolecularEntityInLocation.yaml rename to src/patterns/dosdp-patterns/abnormalLevelOfMolecularEntityInLocation.yaml diff --git a/src/patterns/abnormalMolecularFunction.yaml b/src/patterns/dosdp-patterns/abnormalMolecularFunction.yaml similarity index 100% rename from src/patterns/abnormalMolecularFunction.yaml rename to src/patterns/dosdp-patterns/abnormalMolecularFunction.yaml diff --git a/src/patterns/abnormalMorphology.yaml b/src/patterns/dosdp-patterns/abnormalMorphology.yaml similarity index 100% rename from src/patterns/abnormalMorphology.yaml rename to src/patterns/dosdp-patterns/abnormalMorphology.yaml diff --git a/src/patterns/abnormalMorphologyInLocation.yaml b/src/patterns/dosdp-patterns/abnormalMorphologyInLocation.yaml similarity index 100% rename from src/patterns/abnormalMorphologyInLocation.yaml rename to src/patterns/dosdp-patterns/abnormalMorphologyInLocation.yaml diff --git a/src/patterns/abnormalPathology.yaml b/src/patterns/dosdp-patterns/abnormalPathology.yaml similarity index 100% rename from src/patterns/abnormalPathology.yaml rename to src/patterns/dosdp-patterns/abnormalPathology.yaml diff --git a/src/patterns/abnormalProcess.yaml b/src/patterns/dosdp-patterns/abnormalProcess.yaml similarity index 100% rename from src/patterns/abnormalProcess.yaml rename to src/patterns/dosdp-patterns/abnormalProcess.yaml diff --git a/src/patterns/abnormalProcessInALocation.yaml b/src/patterns/dosdp-patterns/abnormalProcessInALocation.yaml similarity index 100% rename from src/patterns/abnormalProcessInALocation.yaml rename to src/patterns/dosdp-patterns/abnormalProcessInALocation.yaml diff --git a/src/patterns/abnormalSize.yaml b/src/patterns/dosdp-patterns/abnormalSize.yaml similarity index 100% rename from src/patterns/abnormalSize.yaml rename to src/patterns/dosdp-patterns/abnormalSize.yaml diff --git a/src/patterns/abnormalTopology.yaml b/src/patterns/dosdp-patterns/abnormalTopology.yaml similarity index 100% rename from src/patterns/abnormalTopology.yaml rename to src/patterns/dosdp-patterns/abnormalTopology.yaml diff --git a/src/patterns/abnormalTopologyInLocation.yaml b/src/patterns/dosdp-patterns/abnormalTopologyInLocation.yaml similarity index 100% rename from src/patterns/abnormalTopologyInLocation.yaml rename to src/patterns/dosdp-patterns/abnormalTopologyInLocation.yaml diff --git a/src/patterns/abnormalWeight.yaml b/src/patterns/dosdp-patterns/abnormalWeight.yaml similarity index 100% rename from src/patterns/abnormalWeight.yaml rename to src/patterns/dosdp-patterns/abnormalWeight.yaml diff --git a/src/patterns/abscess.yaml b/src/patterns/dosdp-patterns/abscess.yaml similarity index 100% rename from src/patterns/abscess.yaml rename to src/patterns/dosdp-patterns/abscess.yaml diff --git a/src/patterns/absent.yaml b/src/patterns/dosdp-patterns/absent.yaml similarity index 100% rename from src/patterns/absent.yaml rename to src/patterns/dosdp-patterns/absent.yaml diff --git a/src/patterns/absentMolecularEntity.yaml b/src/patterns/dosdp-patterns/absentMolecularEntity.yaml similarity index 100% rename from src/patterns/absentMolecularEntity.yaml rename to src/patterns/dosdp-patterns/absentMolecularEntity.yaml diff --git a/src/patterns/absentMolecularEntityInLocation.yaml b/src/patterns/dosdp-patterns/absentMolecularEntityInLocation.yaml similarity index 100% rename from src/patterns/absentMolecularEntityInLocation.yaml rename to src/patterns/dosdp-patterns/absentMolecularEntityInLocation.yaml diff --git a/src/patterns/aneurysm.yaml b/src/patterns/dosdp-patterns/aneurysm.yaml similarity index 100% rename from src/patterns/aneurysm.yaml rename to src/patterns/dosdp-patterns/aneurysm.yaml diff --git a/src/patterns/atresia.yaml b/src/patterns/dosdp-patterns/atresia.yaml similarity index 100% rename from src/patterns/atresia.yaml rename to src/patterns/dosdp-patterns/atresia.yaml diff --git a/src/patterns/atrophy.yaml b/src/patterns/dosdp-patterns/atrophy.yaml similarity index 100% rename from src/patterns/atrophy.yaml rename to src/patterns/dosdp-patterns/atrophy.yaml diff --git a/src/patterns/calcified.yaml b/src/patterns/dosdp-patterns/calcified.yaml similarity index 100% rename from src/patterns/calcified.yaml rename to src/patterns/dosdp-patterns/calcified.yaml diff --git a/src/patterns/decreasedFunctionalityInLocation.yaml b/src/patterns/dosdp-patterns/decreasedFunctionalityInLocation.yaml similarity index 100% rename from src/patterns/decreasedFunctionalityInLocation.yaml rename to src/patterns/dosdp-patterns/decreasedFunctionalityInLocation.yaml diff --git a/src/patterns/decreasedLevel.yaml b/src/patterns/dosdp-patterns/decreasedLevel.yaml similarity index 100% rename from src/patterns/decreasedLevel.yaml rename to src/patterns/dosdp-patterns/decreasedLevel.yaml diff --git a/src/patterns/decreasedLevelOfMolecularEntity.yaml b/src/patterns/dosdp-patterns/decreasedLevelOfMolecularEntity.yaml similarity index 100% rename from src/patterns/decreasedLevelOfMolecularEntity.yaml rename to src/patterns/dosdp-patterns/decreasedLevelOfMolecularEntity.yaml diff --git a/src/patterns/decreasedLevelOfMolecularEntityInLocation.yaml b/src/patterns/dosdp-patterns/decreasedLevelOfMolecularEntityInLocation.yaml similarity index 100% rename from src/patterns/decreasedLevelOfMolecularEntityInLocation.yaml rename to src/patterns/dosdp-patterns/decreasedLevelOfMolecularEntityInLocation.yaml diff --git a/src/patterns/decreasedMolecularFunction.yaml b/src/patterns/dosdp-patterns/decreasedMolecularFunction.yaml similarity index 100% rename from src/patterns/decreasedMolecularFunction.yaml rename to src/patterns/dosdp-patterns/decreasedMolecularFunction.yaml diff --git a/src/patterns/decreasedSize.yaml b/src/patterns/dosdp-patterns/decreasedSize.yaml similarity index 100% rename from src/patterns/decreasedSize.yaml rename to src/patterns/dosdp-patterns/decreasedSize.yaml diff --git a/src/patterns/decreasedWeight.yaml b/src/patterns/dosdp-patterns/decreasedWeight.yaml similarity index 100% rename from src/patterns/decreasedWeight.yaml rename to src/patterns/dosdp-patterns/decreasedWeight.yaml diff --git a/src/patterns/degeneration.yaml b/src/patterns/dosdp-patterns/degeneration.yaml similarity index 100% rename from src/patterns/degeneration.yaml rename to src/patterns/dosdp-patterns/degeneration.yaml diff --git a/src/patterns/delayedProcess.yaml b/src/patterns/dosdp-patterns/delayedProcess.yaml similarity index 100% rename from src/patterns/delayedProcess.yaml rename to src/patterns/dosdp-patterns/delayedProcess.yaml diff --git a/src/patterns/dysgenesis.yaml b/src/patterns/dosdp-patterns/dysgenesis.yaml similarity index 100% rename from src/patterns/dysgenesis.yaml rename to src/patterns/dosdp-patterns/dysgenesis.yaml diff --git a/src/patterns/enhancedBehavior.yaml b/src/patterns/dosdp-patterns/enhancedBehavior.yaml similarity index 100% rename from src/patterns/enhancedBehavior.yaml rename to src/patterns/dosdp-patterns/enhancedBehavior.yaml diff --git a/src/patterns/dosdp-patterns/external.txt b/src/patterns/dosdp-patterns/external.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/patterns/fibrosis.yaml b/src/patterns/dosdp-patterns/fibrosis.yaml similarity index 100% rename from src/patterns/fibrosis.yaml rename to src/patterns/dosdp-patterns/fibrosis.yaml diff --git a/src/patterns/impairedBehavior.yaml b/src/patterns/dosdp-patterns/impairedBehavior.yaml similarity index 100% rename from src/patterns/impairedBehavior.yaml rename to src/patterns/dosdp-patterns/impairedBehavior.yaml diff --git a/src/patterns/increasedFunctionalityInLocation.yaml b/src/patterns/dosdp-patterns/increasedFunctionalityInLocation.yaml similarity index 100% rename from src/patterns/increasedFunctionalityInLocation.yaml rename to src/patterns/dosdp-patterns/increasedFunctionalityInLocation.yaml diff --git a/src/patterns/increasedLevel.yaml b/src/patterns/dosdp-patterns/increasedLevel.yaml similarity index 100% rename from src/patterns/increasedLevel.yaml rename to src/patterns/dosdp-patterns/increasedLevel.yaml diff --git a/src/patterns/increasedLevelOfMolecularEntity.yaml b/src/patterns/dosdp-patterns/increasedLevelOfMolecularEntity.yaml similarity index 100% rename from src/patterns/increasedLevelOfMolecularEntity.yaml rename to src/patterns/dosdp-patterns/increasedLevelOfMolecularEntity.yaml diff --git a/src/patterns/increasedLevelOfMolecularEntityInLocation.yaml b/src/patterns/dosdp-patterns/increasedLevelOfMolecularEntityInLocation.yaml similarity index 100% rename from src/patterns/increasedLevelOfMolecularEntityInLocation.yaml rename to src/patterns/dosdp-patterns/increasedLevelOfMolecularEntityInLocation.yaml diff --git a/src/patterns/increasedMolecularFunction.yaml b/src/patterns/dosdp-patterns/increasedMolecularFunction.yaml similarity index 100% rename from src/patterns/increasedMolecularFunction.yaml rename to src/patterns/dosdp-patterns/increasedMolecularFunction.yaml diff --git a/src/patterns/increasedSize.yaml b/src/patterns/dosdp-patterns/increasedSize.yaml similarity index 100% rename from src/patterns/increasedSize.yaml rename to src/patterns/dosdp-patterns/increasedSize.yaml diff --git a/src/patterns/increasedWeight.yaml b/src/patterns/dosdp-patterns/increasedWeight.yaml similarity index 100% rename from src/patterns/increasedWeight.yaml rename to src/patterns/dosdp-patterns/increasedWeight.yaml diff --git a/src/patterns/missingProcess.yaml b/src/patterns/dosdp-patterns/missingProcess.yaml similarity index 100% rename from src/patterns/missingProcess.yaml rename to src/patterns/dosdp-patterns/missingProcess.yaml diff --git a/src/patterns/vascularEctasia.yaml b/src/patterns/dosdp-patterns/vascularEctasia.yaml similarity index 100% rename from src/patterns/vascularEctasia.yaml rename to src/patterns/dosdp-patterns/vascularEctasia.yaml diff --git a/src/patterns/imports/seed.txt b/src/patterns/imports/seed.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/patterns/pattern.owl b/src/patterns/pattern.owl new file mode 100644 index 00000000..49718562 --- /dev/null +++ b/src/patterns/pattern.owl @@ -0,0 +1,484 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + + + +############################ +# Classes +############################ + +# Class: (abnormal 'entity') + +AnnotationAssertion( "Abnormality of 'entity'."^^xsd:string) +AnnotationAssertion( "abnormal"^^xsd:string) +AnnotationAssertion( "abnormality of 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal 'behavior process') + +AnnotationAssertion( "An anomaly in 'behavior process'."^^xsd:string) +AnnotationAssertion( "abnormalBehavior"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'behavior process'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal 'anatomical entity' cell proliferation) + +AnnotationAssertion( "An abnormality in proliferation of cells in the 'anatomical entity'."^^xsd:string) +AnnotationAssertion( "abnormalCellProliferation"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'anatomical entity' cell proliferation"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (abnormality of 'entity' physiology) + +AnnotationAssertion( "Any functional anomaly of the 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalFunctionality"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormality of 'entity' physiology"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal cellularcomponent level) + +AnnotationAssertion( "An abnormal level of cellularcomponent."^^xsd:string) +AnnotationAssertion( "abnormalLevelOfCellularComponent"^^xsd:string) +AnnotationAssertion( "Elevated cellularcomponent"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal cellularcomponent level"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal chemical level) + +AnnotationAssertion( "An abnormal level of chemical."^^xsd:string) +AnnotationAssertion( "abnormalLevelOfChemical"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal chemical level"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal 'entity' 'chemical entity' level) + +AnnotationAssertion( "An abnormal level of 'chemical entity' in the 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalLevelOfChemicalInEntity"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'entity' 'chemical entity' level"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (abnormal level of 'molecular entity') + +AnnotationAssertion( "An anomaly in the level of 'molecular entity'."^^xsd:string) +AnnotationAssertion( "abnormalLevelOfMolecularEntity"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal level of 'molecular entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal level of 'molecular entity' in 'entity') + +AnnotationAssertion( "An anomaly in the level of 'molecular entity' in 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalLevelOfMolecularEntityInLocation"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal level of 'molecular entity' in 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (abnormal 'molecular function') + +AnnotationAssertion( "Abnormal 'molecular function'."^^xsd:string) +AnnotationAssertion( "abnormalMolecularFunction"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'molecular function'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (morphological abnormality of the 'entity' in the 'entity') + +AnnotationAssertion( "A morphological abnormality of the 'entity' in the 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalMorphologyInLocation"^^xsd:string) +AnnotationAssertion( "Abnormal 'entity' in the 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "morphological abnormality of the 'entity' in the 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: ('anatomical structure' 'pathological entity') + +AnnotationAssertion( "An 'pathological entity' in the 'anatomical structure'."^^xsd:string) +AnnotationAssertion( "abnormalPathology"^^xsd:string) +AnnotationAssertion(rdfs:label "'anatomical structure' 'pathological entity'"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ))) + +# Class: (abnormal 'biological_process') + +AnnotationAssertion( "An abnormality in 'biological_process'."^^xsd:string) +AnnotationAssertion( "abnormalProcess"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'biological_process'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal 'biological process' in 'entity') + +AnnotationAssertion( "An abnormality of the 'biological process' in 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalProcessInALocation"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'biological process' in 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (abnormal size of 'entity') + +AnnotationAssertion( "A deviation from the normal size of the 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalSize"^^xsd:string) +AnnotationAssertion( "abnormal size of the 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal size of 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal location of 'entity') + +AnnotationAssertion( "An abnormal location of 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalTopology"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal location of 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (abnormal 'entity' topology in 'anatomical entity') + +AnnotationAssertion( "An abnormal position of the 'entity' in the 'anatomical entity'."^^xsd:string) +AnnotationAssertion( "abnormalTopologyInLocation"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal 'entity' topology in 'anatomical entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (abnormality of 'entity' weight) + +AnnotationAssertion( "An abnormal increase or decrease of weight or an abnormal distribution of mass in the 'entity'."^^xsd:string) +AnnotationAssertion( "abnormalWeight"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormality of 'entity' weight"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('anatomical entity' abscess) + +AnnotationAssertion( "The presence of an abscess of the 'anatomical entity'."^^xsd:string) +AnnotationAssertion( "abscess"^^xsd:string) +AnnotationAssertion(rdfs:label "'anatomical entity' abscess"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))) + +# Class: (absent 'entity') + +AnnotationAssertion( "Absence of 'entity'."^^xsd:string) +AnnotationAssertion( "absent"^^xsd:string) +AnnotationAssertion( "missing 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "absent 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (absent 'molecular entity') + +AnnotationAssertion( "Absent or undetectable level of 'molecular entity'."^^xsd:string) +AnnotationAssertion( "absentMolecularEntity"^^xsd:string) +AnnotationAssertion(rdfs:label "absent 'molecular entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (absent 'molecular entity' in 'entity') + +AnnotationAssertion( "Absent or undetectable level of 'molecular entity' in 'entity'."^^xsd:string) +AnnotationAssertion( "absentMolecularEntityInLocation"^^xsd:string) +AnnotationAssertion(rdfs:label "absent 'molecular entity' in 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: ('anatomical structure' aneurysm) + +AnnotationAssertion( "An aneurysm in the 'anatomical structure'."^^xsd:string) +AnnotationAssertion( "aneurysm"^^xsd:string) +AnnotationAssertion(rdfs:label "'anatomical structure' aneurysm"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: ('entity' atresia) + +AnnotationAssertion( "A developmental defect resulting in complete obliteration of the lumen of the 'entity'."^^xsd:string) +AnnotationAssertion( "atresia"^^xsd:string) +AnnotationAssertion( "atresia of the 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "'entity' atresia"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('entity' atrophy) + +AnnotationAssertion( "Partial or complete wasting (loss) of 'entity' tissue that was once present."^^xsd:string) +AnnotationAssertion( "atrophy"^^xsd:string) +AnnotationAssertion( "atrophy of the 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "'entity' atrophy"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('entity' calcification) + +AnnotationAssertion( "Calcification of the 'entity'."^^xsd:string) +AnnotationAssertion( "calcified"^^xsd:string) +AnnotationAssertion( "calcified 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "'entity' calcification"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('anatomical entity' dysfunction) + +AnnotationAssertion( "A functional abnormality of the 'anatomical entity'."^^xsd:string) +AnnotationAssertion( "decreasedFunctionalityInLocation"^^xsd:string) +AnnotationAssertion(rdfs:label "'anatomical entity' dysfunction"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ))) + +# Class: (abnormal morphology of 'entity' ) + +AnnotationAssertion( "Any structural anomaly of the 'entity'."^^xsd:string) +AnnotationAssertion( "morphology"^^xsd:string) +AnnotationAssertion( "abnormal shape of 'entity'"^^xsd:string) +AnnotationAssertion( "abnormally shaped 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "abnormal morphology of 'entity' "^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (decreased 'entity' level) + +AnnotationAssertion( "An abnormally decreased level of 'entity'."^^xsd:string) +AnnotationAssertion( "decreasedLevel"^^xsd:string) +AnnotationAssertion( "reduced 'entity' level"^^xsd:string) +AnnotationAssertion(rdfs:label "decreased 'entity' level"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (decreased level of 'molecular entity') + +AnnotationAssertion( "A decreased amount in the level of 'molecular entity'."^^xsd:string) +AnnotationAssertion( "decreasedLevelOfMolecularEntity"^^xsd:string) +AnnotationAssertion(rdfs:label "decreased level of 'molecular entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (decreased level of 'molecular entity' in 'entity') + +AnnotationAssertion( "A decrease in the level of 'molecular entity' in 'entity'."^^xsd:string) +AnnotationAssertion( "decreasedLevelOfMolecularEntityInLocation"^^xsd:string) +AnnotationAssertion(rdfs:label "decreased level of 'molecular entity' in 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (decreased 'molecular function') + +AnnotationAssertion( "Decreased 'molecular function'."^^xsd:string) +AnnotationAssertion( "decreasedMolecularFunction"^^xsd:string) +AnnotationAssertion(rdfs:label "decreased 'molecular function'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (decreased size of the 'entity') + +AnnotationAssertion( "A reduction in the size of the 'entity'."^^xsd:string) +AnnotationAssertion( "decreasedSize"^^xsd:string) +AnnotationAssertion( "small 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "decreased size of the 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (decreased 'entity' weight) + +AnnotationAssertion( "An abnormal decrease in weight or a decreased distribution of mass in the 'entity'."^^xsd:string) +AnnotationAssertion( "decreasedWeight"^^xsd:string) +AnnotationAssertion(rdfs:label "decreased 'entity' weight"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('entity' degeneration) + +AnnotationAssertion( "Partial or complete wasting (loss) of 'entity' tissue that was once present."^^xsd:string) +AnnotationAssertion( "degeneration"^^xsd:string) +AnnotationAssertion( "degeneration of the 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "'entity' degeneration"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (delayed 'entity') + +AnnotationAssertion( "Delayed 'entity'."^^xsd:string) +AnnotationAssertion( "delayedProcess"^^xsd:string) +AnnotationAssertion(rdfs:label "delayed 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (dysgenesis of the 'entity') + +AnnotationAssertion( "Defective development of the 'entity'."^^xsd:string) +AnnotationAssertion( "dysgenesis"^^xsd:string) +AnnotationAssertion( "'entity' dysgenesis"^^xsd:string) +AnnotationAssertion(rdfs:label "dysgenesis of the 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (Enhanced 'behavior process') + +AnnotationAssertion( "Enhanced or improved 'behavior process'."^^xsd:string) +AnnotationAssertion( "enhancedBehavior"^^xsd:string) +AnnotationAssertion(rdfs:label "Enhanced 'behavior process'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (Fibrosis of the 'anatomical entity') + +AnnotationAssertion( "The presence of excessive fibrous connective tissue in the 'anatomical entity'."^^xsd:string) +AnnotationAssertion( "fibrosis"^^xsd:string) +AnnotationAssertion( "'anatomical entity' fibrosis"^^xsd:string) +AnnotationAssertion(rdfs:label "Fibrosis of the 'anatomical entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (impaired 'behavior process') + +AnnotationAssertion( "Impaired or decreased 'behavior process'."^^xsd:string) +AnnotationAssertion( "impairedBehavior"^^xsd:string) +AnnotationAssertion(rdfs:label "impaired 'behavior process'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('anatomical entity' dysfunction) + +AnnotationAssertion( "A functional abnormality of the 'anatomical entity'."^^xsd:string) +AnnotationAssertion( "increasedFunctionalityInLocation"^^xsd:string) +AnnotationAssertion(rdfs:label "'anatomical entity' dysfunction"^^xsd:string) +EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ))) + +# Class: (increased 'entity' level) + +AnnotationAssertion( "An abnormally increased level of 'entity'."^^xsd:string) +AnnotationAssertion( "increasedLevel"^^xsd:string) +AnnotationAssertion( "elevated 'entity' level"^^xsd:string) +AnnotationAssertion( "increased level of 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "increased 'entity' level"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (increased level of 'molecular entity') + +AnnotationAssertion( "An increased amount in the level of 'molecular entity'."^^xsd:string) +AnnotationAssertion( "increasedLevelOfMolecularEntity"^^xsd:string) +AnnotationAssertion( "increased 'molecular entity' level"^^xsd:string) +AnnotationAssertion(rdfs:label "increased level of 'molecular entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (increased level of 'molecular entity' in 'entity') + +AnnotationAssertion( "An increase in the level of 'molecular entity' in 'entity'."^^xsd:string) +AnnotationAssertion( "increasedLevelOfMolecularEntityInLocation"^^xsd:string) +AnnotationAssertion( "reduced level of 'molecular entity' in 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "increased level of 'molecular entity' in 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + +# Class: (increased 'molecular function') + +AnnotationAssertion( "Increased 'molecular function'."^^xsd:string) +AnnotationAssertion( "increasedMolecularFunction"^^xsd:string) +AnnotationAssertion(rdfs:label "increased 'molecular function'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (increased size of the 'entity') + +AnnotationAssertion( "An increase in the size of the 'entity'."^^xsd:string) +AnnotationAssertion( "increasedSize"^^xsd:string) +AnnotationAssertion( "enlarged 'entity'"^^xsd:string) +AnnotationAssertion(rdfs:label "increased size of the 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (increased 'entity' weight) + +AnnotationAssertion( "An abnormal increase in weight or an increased distribution of mass in the 'entity'."^^xsd:string) +AnnotationAssertion( "increasedWeight"^^xsd:string) +AnnotationAssertion(rdfs:label "increased 'entity' weight"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: (absent 'entity') + +AnnotationAssertion( "Lack of 'entity'."^^xsd:string) +AnnotationAssertion( "missingProcess"^^xsd:string) +AnnotationAssertion(rdfs:label "absent 'entity'"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )))) + +# Class: ('entity' lymphangiectasia) + +AnnotationAssertion( "A dilatation in the vessel of the 'entity'."^^xsd:string) +AnnotationAssertion( "vascularEctasia"^^xsd:string) +AnnotationAssertion(rdfs:label "'entity' lymphangiectasia"^^xsd:string) +EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( )))) + + +) \ No newline at end of file diff --git a/src/patterns_out/patterns_merged.owl b/src/patterns_out/patterns_merged.owl deleted file mode 100644 index d3397a18..00000000 --- a/src/patterns_out/patterns_merged.owl +++ /dev/null @@ -1,1783 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Partial or complete wasting (loss) of http://www.w3.org/2002/07/owl#Thing tissue that was once present. - http://www.w3.org/2002/07/owl#Thing atrophy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A decrease in the level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing. - decreased level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any structural anomaly of the http://www.w3.org/2002/07/owl#Thing. - abnormal morphology of http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Impaired or decreased http://purl.obolibrary.org/obo/NBO_0000313. - impaired http://purl.obolibrary.org/obo/NBO_0000313 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Absence of http://www.w3.org/2002/07/owl#Thing. - absent http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal position of the http://www.w3.org/2002/07/owl#Thing in the http://purl.obolibrary.org/obo/UBERON_0001062. - abnormal http://www.w3.org/2002/07/owl#Thing topology in http://purl.obolibrary.org/obo/UBERON_0001062 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormality in proliferation of cells in the http://purl.obolibrary.org/obo/UBERON_0001062. - abnormal http://purl.obolibrary.org/obo/UBERON_0001062 cell proliferation - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal level of http://purl.obolibrary.org/obo/CHEBI_24431 in the http://www.w3.org/2002/07/owl#Thing. - abnormal http://www.w3.org/2002/07/owl#Thing http://purl.obolibrary.org/obo/CHEBI_24431 level - - - - - - - - - - - - - - - - - - - - - - - - - - - - Delayed http://www.w3.org/2002/07/owl#Thing. - delayed http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Abnormal http://purl.obolibrary.org/obo/GO_0003674. - abnormal http://purl.obolibrary.org/obo/GO_0003674 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormality of the http://purl.obolibrary.org/obo/GO_0008150 in http://www.w3.org/2002/07/owl#Thing. - abnormal http://purl.obolibrary.org/obo/GO_0008150 in http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal increase in weight or an increased distribution of mass in the http://www.w3.org/2002/07/owl#Thing. - increased http://www.w3.org/2002/07/owl#Thing weight - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormally increased level of http://www.w3.org/2002/07/owl#Thing. - increased http://www.w3.org/2002/07/owl#Thing level - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal level of http://purl.obolibrary.org/obo/CHEBI_24431. - abnormal http://purl.obolibrary.org/obo/CHEBI_24431 level - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal location of http://www.w3.org/2002/07/owl#Thing. - abnormal location of http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An http://purl.obolibrary.org/obo/MPATH_0 in the http://purl.obolibrary.org/obo/UBERON_0000061. - http://purl.obolibrary.org/obo/UBERON_0000061 http://purl.obolibrary.org/obo/MPATH_0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - A reduction in the size of the http://www.w3.org/2002/07/owl#Thing. - decreased size of the http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anomaly in http://purl.obolibrary.org/obo/NBO_0000313. - abnormal http://purl.obolibrary.org/obo/NBO_0000313 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Defective development of the http://www.w3.org/2002/07/owl#Thing. - dysgenesis of the http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A functional abnormality of the http://purl.obolibrary.org/obo/UBERON_0001062. - http://purl.obolibrary.org/obo/UBERON_0001062 dysfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormality in http://purl.obolibrary.org/obo/GO_0008150. - abnormal http://purl.obolibrary.org/obo/GO_0008150 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anomaly in the level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing. - abnormal level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Enhanced or improved http://purl.obolibrary.org/obo/NBO_0000313. - Enhanced http://purl.obolibrary.org/obo/NBO_0000313 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calcification of the http://www.w3.org/2002/07/owl#Thing. - http://www.w3.org/2002/07/owl#Thing calcification - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An increase in the level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing. - increased level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Lack of http://www.w3.org/2002/07/owl#Thing. - absent http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Absent or undetectable level of http://purl.obolibrary.org/obo/CHEBI_23367. - absent http://purl.obolibrary.org/obo/CHEBI_23367 - - - - - - - - - - - - - - - - - - - - - - - - - - - - A developmental defect resulting in complete obliteration of the lumen of the http://www.w3.org/2002/07/owl#Thing. - http://www.w3.org/2002/07/owl#Thing atresia - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A morphological abnormality of the http://www.w3.org/2002/07/owl#Thing in the http://www.w3.org/2002/07/owl#Thing. - morphological abnormality of the http://www.w3.org/2002/07/owl#Thing in the http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormally decreased level of http://www.w3.org/2002/07/owl#Thing. - decreased http://www.w3.org/2002/07/owl#Thing level - - - - - - - - - - - - - - - - - - - - - - - - - - - - An increase in the size of the http://www.w3.org/2002/07/owl#Thing. - increased size of the http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - A decreased amount in the level of http://purl.obolibrary.org/obo/CHEBI_23367. - decreased level of http://purl.obolibrary.org/obo/CHEBI_23367 - - - - - - - - - - - - - - - - - - - - - - - - - - - - An anomaly in the level of http://purl.obolibrary.org/obo/CHEBI_23367. - abnormal level of http://purl.obolibrary.org/obo/CHEBI_23367 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The presence of excessive fibrous connective tissue in the http://purl.obolibrary.org/obo/UBERON_0001062. - Fibrosis of the http://purl.obolibrary.org/obo/UBERON_0001062 - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal increase or decrease of weight or an abnormal distribution of mass in the http://www.w3.org/2002/07/owl#Thing. - abnormality of http://www.w3.org/2002/07/owl#Thing weight - - - - - - - - - - - - - - - - - - - - - - - - - - - - Any functional anomaly of the http://www.w3.org/2002/07/owl#Thing. - abnormality of http://www.w3.org/2002/07/owl#Thing physiology - - - - - - - - - - - - - - - - - - - - - - - - - - - - Abnormality of http://www.w3.org/2002/07/owl#Thing. - abnormal http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - Decreased http://purl.obolibrary.org/obo/GO_0003674. - decreased http://purl.obolibrary.org/obo/GO_0003674 - - - - - - - - - - - - - - - - - - - - - - - - - - - - A deviation from the normal size of the http://www.w3.org/2002/07/owl#Thing. - abnormal size of http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Absent or undetectable level of http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing. - absent http://purl.obolibrary.org/obo/CHEBI_23367 in http://www.w3.org/2002/07/owl#Thing - - - - - - - - - - - - - - - - - - - - - - - - - - - - An abnormal decrease in weight or a decreased distribution of mass in the http://www.w3.org/2002/07/owl#Thing. - decreased http://www.w3.org/2002/07/owl#Thing weight - - - - - - - - - - - - - - - - - - - - - - - - - - - - An increased amount in the level of http://purl.obolibrary.org/obo/CHEBI_23367. - increased level of http://purl.obolibrary.org/obo/CHEBI_23367 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An http://purl.obolibrary.org/obo/MPATH_90 in the http://purl.obolibrary.org/obo/UBERON_0000061. - http://purl.obolibrary.org/obo/UBERON_0000061 http://purl.obolibrary.org/obo/MPATH_90 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Increased http://purl.obolibrary.org/obo/GO_0003674. - increased http://purl.obolibrary.org/obo/GO_0003674 - - - - - - - - - - - - - - - - - - - - - - - - - - - - Partial or complete wasting (loss) of http://www.w3.org/2002/07/owl#Thing tissue that was once present. - http://www.w3.org/2002/07/owl#Thing degeneration - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A functional abnormality of the http://purl.obolibrary.org/obo/UBERON_0001062. - http://purl.obolibrary.org/obo/UBERON_0001062 dysfunction - - - - - - - diff --git a/src/sparql/README.md b/src/sparql/README.md new file mode 100644 index 00000000..081b46d3 --- /dev/null +++ b/src/sparql/README.md @@ -0,0 +1,32 @@ +# Sparql checks + +[SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard +query language for RDF. This directory contains useful SPARQL queries +for perfoming over the ontology. + +SPARQL can be executed on a triplestore or directly on any OWL +file. The queries here are all executed on either upheno-edit.obo or +downstream products in the [ontology](../ontology/) folder. We use +`robot` as this allows easy execution over any Obo-format or OWL file. + +We break the queries into 3 categories: + +## Constraint Violation checks + +These are all named `*violation.sparql`. A subset of these are +configured to be executed via travis. If these return any results, +then the build will fail. + +Consult the individual sparql files to see the intent of the check + +## Construct queries + +These are named `construct*.sparql`, and always have the form `CONSTRUCT ...`. + +These are used to generate new OWL axioms that can be inserted back +into the ontology. + +## Reports + +The remaining SPARQL queries are for informative purposes. A subset +may be executed with each release. diff --git a/src/sparql/basic-report.sparql b/src/sparql/basic-report.sparql new file mode 100644 index 00000000..cff97737 --- /dev/null +++ b/src/sparql/basic-report.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql new file mode 100644 index 00000000..0c4d2844 --- /dev/null +++ b/src/sparql/class-count-by-prefix.sparql @@ -0,0 +1,10 @@ +prefix owl: +prefix obo: + +SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE +{ + ?cls a owl:Class . + FILTER (!isBlank(?cls)) + BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) +} +GROUP BY ?prefix diff --git a/src/sparql/def-lacks-xref-violation.sparql b/src/sparql/def-lacks-xref-violation.sparql new file mode 100644 index 00000000..cff97737 --- /dev/null +++ b/src/sparql/def-lacks-xref-violation.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql new file mode 100644 index 00000000..5fec04ea --- /dev/null +++ b/src/sparql/edges.sparql @@ -0,0 +1,19 @@ +prefix obo: +prefix owl: +prefix rdfs: +prefix rdf: + +SELECT ?x ?p ?y +WHERE { + {?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty ?p ; + owl:someValuesFrom ?y ] + } + UNION { + ?x rdfs:subClassOf ?y . + BIND(rdfs:subClassOf AS ?p) + } + ?x a owl:Class . + ?y a owl:Class . +} diff --git a/src/sparql/equivalent-classes-violation.sparql b/src/sparql/equivalent-classes-violation.sparql new file mode 100644 index 00000000..ed5ccdd0 --- /dev/null +++ b/src/sparql/equivalent-classes-violation.sparql @@ -0,0 +1,14 @@ +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?baseClass ?baseLabel ?equivalentClass ?equivalentLabel WHERE +{ + ?baseClass owl:equivalentClass ?equivalentClass . + ?baseClass rdfs:label ?baseLabel . + ?equivalentClass rdfs:label ?equivalentLabel . + + FILTER (!isBlank(?baseClass)) . + FILTER (!isBlank(?equivalentClass)) + +} diff --git a/src/sparql/nolabels-violation.sparql b/src/sparql/nolabels-violation.sparql new file mode 100644 index 00000000..d506a41e --- /dev/null +++ b/src/sparql/nolabels-violation.sparql @@ -0,0 +1,13 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: + +SELECT ?cls WHERE { + ?cls a owl:Class + FILTER NOT EXISTS {?cls rdfs:label ?lab} + FILTER NOT EXISTS {?cls replaced_by: ?replCls} + FILTER (!isBlank(?cls)) + FILTER ( regex(str(?cls), "^http://purl.obolibrary.org/obo/GO_")) +} +ORDER BY ?cls diff --git a/src/sparql/obsolete-violation.sparql b/src/sparql/obsolete-violation.sparql new file mode 100644 index 00000000..c81bf718 --- /dev/null +++ b/src/sparql/obsolete-violation.sparql @@ -0,0 +1,24 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?clsLabel ?rule WHERE { + ?cls a owl:Class ; + rdfs:label ?clsLabel ; + owl:deprecated "true"^^xsd:boolean + { + { + FILTER ( ! regex(str(?clsLabel), "^obsolete ") ) + BIND ("obsolete label must start with obsolete" AS ?rule) + } + UNION + { + ?cls rdfs:subClassOf ?parent + BIND("no logical axioms for obsolete" AS ?rule) + } + } +} +ORDER BY ?cls diff --git a/src/sparql/obsoletes.sparql b/src/sparql/obsoletes.sparql new file mode 100644 index 00000000..7aff433b --- /dev/null +++ b/src/sparql/obsoletes.sparql @@ -0,0 +1,14 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?replCls ?consCls WHERE { + ?cls a owl:Class ; + owl:deprecated "true"^^xsd:boolean . + OPTIONAL {?cls replaced_by: ?replCls} + OPTIONAL {?cls consider: ?consCls} +} +ORDER BY ?cls diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql new file mode 100644 index 00000000..63857fea --- /dev/null +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -0,0 +1,11 @@ +prefix rdf: +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?c +WHERE { + { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?c ] ] } + UNION + { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?c ] ] ] } +} diff --git a/src/sparql/owldef-violation.sparql b/src/sparql/owldef-violation.sparql new file mode 100644 index 00000000..3b59f882 --- /dev/null +++ b/src/sparql/owldef-violation.sparql @@ -0,0 +1,9 @@ +prefix oio: +prefix owl: +prefix rdfs: + +WELECT * +WHERE { + ?c rdfs:subClassOf ?d ; + owl:equivalentClass [ + owl:intersectionOf TODO diff --git a/src/sparql/redundant-subClassOf-violation.sparql b/src/sparql/redundant-subClassOf-violation.sparql new file mode 100644 index 00000000..bed15cd9 --- /dev/null +++ b/src/sparql/redundant-subClassOf-violation.sparql @@ -0,0 +1,15 @@ +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?x ?xl ?y ?yl ?z ?zl WHERE +{ + ?x rdfs:subClassOf ?y ; + rdfs:label ?xl . + ?y rdfs:subClassOf+ ?z ; + rdfs:label ?yl . + ?x rdfs:subClassOf ?z . + ?z rdfs:label ?zl . + + +} diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql new file mode 100644 index 00000000..9f8aca68 --- /dev/null +++ b/src/sparql/subsets-labeled.sparql @@ -0,0 +1,14 @@ +prefix oio: +prefix def: +prefix owl: +prefix inSubset: +prefix rdfs: + +SELECT ?subset ?clsLabel +WHERE +{ + ?cls a owl:Class . + inSubset: ?subset ; + rdfs:label ?clsLabel +} +ORDER BY ?subset ?cls diff --git a/src/sparql/synonyms.sparql b/src/sparql/synonyms.sparql new file mode 100644 index 00000000..ba6b03a7 --- /dev/null +++ b/src/sparql/synonyms.sparql @@ -0,0 +1,26 @@ +prefix owl: +prefix oboInOwl: +prefix rdfs: + +SELECT ?cls ?pred ?val ?synType +WHERE + { ?cls ?pred ?val ; + a owl:Class . + FILTER ( + ?pred = rdfs:label || + ?pred = oboInOwl:hasRelatedSynonym || + ?pred = oboInOwl:hasNarrowSynonym || + ?pred = oboInOwl:hasBroadSynonym || + ?pred = oboInOwl:hasExactSynonym + ) + + OPTIONAL { + [ + a owl:Axiom ; + owl:annotatedSource ?cls ; + owl:annotatedProperty ?pred ; + owl:annotatedTarget ?val ; + oboInOwl:hasSynonymType ?synType + ] + } + } diff --git a/src/sparql/terms.sparql b/src/sparql/terms.sparql new file mode 100644 index 00000000..e65a105a --- /dev/null +++ b/src/sparql/terms.sparql @@ -0,0 +1,7 @@ +SELECT DISTINCT ?term +WHERE { + { ?s1 ?p1 ?term . } + UNION + { ?term ?p2 ?o2 . } + FILTER(isIRI(?term)) +} \ No newline at end of file diff --git a/src/sparql/trailing-whitespace-violation.sparql b/src/sparql/trailing-whitespace-violation.sparql new file mode 100644 index 00000000..1d69472d --- /dev/null +++ b/src/sparql/trailing-whitespace-violation.sparql @@ -0,0 +1,11 @@ +# home: hp/sparql/trailing-whitespace-violation.sparql +prefix owl: +prefix rdfs: + +SELECT ?c ?p ?x WHERE +{ + ?c ?p ?x . + + FILTER( regex(STR(?x), "^ ") || regex(STR(?x), " $") ) + FILTER( ?p != owl:annotatedTarget ) +} diff --git a/src/sparql/xref-syntax-violation.sparql b/src/sparql/xref-syntax-violation.sparql new file mode 100644 index 00000000..98a61720 --- /dev/null +++ b/src/sparql/xref-syntax-violation.sparql @@ -0,0 +1,13 @@ +# home: hp +prefix hasDbXref: +prefix oio: +prefix owl: +prefix rdfs: + +SELECT ?c ?x WHERE +{ + ?c hasDbXref: ?x . + + FILTER( regex(STR(?x), " ") || regex(STR(?x), ";") || STR(?x) = "" ) + +} diff --git a/src/sparql/xrefs.sparql b/src/sparql/xrefs.sparql new file mode 100644 index 00000000..bde8fc98 --- /dev/null +++ b/src/sparql/xrefs.sparql @@ -0,0 +1,8 @@ +prefix oio: +prefix owl: + +SELECT ?cls ?xref WHERE +{ + ?cls a owl:Class ; + oio:hasDbXref ?xref +}