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ont_metadata.tsv
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ID Title Description License
bfo The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. See the BFO 2 release notes for further information about BFO 2. Please note that the current release of bfo.owl uses temporal relations when the subject or object is a continuant, a major change from BFO 1. This is an early version of BFO version 2 and has not yet been extensively reviewed by the project team members. Please see the project site http://code.google.com/p/bfo/ , the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/ and with the code that generates the OWL version in http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif
chebi ChEBI subsumes and replaces the Chemical Ontology first Author: ChEBI curation team developed by Michael Ashburner & Pankaj Jaiswal. ChEBI Release version 158 For any queries contact [email protected]
doid The Disease Ontology content is available via the Creative Commons Public Domain Dedication CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0/).
go Includes Ontology(OntologyID(Anonymous-35)) [Axioms: 217 Logical Axioms: 217] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/go/never_in_taxon.owl>))) [Axioms: 18 Logical Axioms: 0] cvs version: $Revision: 38972 $
obi Ontology for Biomedical Investigation The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
pato
po
pr The PRotein Ontology is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/pr for details. Use reasoner in OBO Edit to see the correct hierarchy.
xao Version: 5.0 Citation for XAO v1 by Xenbase: Segerdell E, Bowes JB, Pollet N, Vize PD; BMC Dev Biol 2008 8:92; PMID:18817563. Supported by NIH R01 HD045776 and NICHD P41 HD064556. Citation for XAO v3 by Xenbase: Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM; J Biomed Semantics 2013 4(1):31; PMID:24139024.
zfa SVN version: $Revision: 1.100$
aeo this version corrects the namespace and includes some flybase alt_IDs
agro agro
apo Filtered by Subset contains "SGD"
bcgo This file is based on checkout of our SVN repository revision $Revision: 204$ The ontology is built based on OBI release 2015-04-13
bco
bspo based on FBql
bto*
caro Based on CARO 1.0, with modifications and additions by David Osumi-Sutherland, Chris Mungall, Ramona Walls and Melissa Haendal.
cdao Comparative Data Analysis Ontology The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.
ceph
cheminf chemical information ontology (cheminf) - information entities about chemical entities The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals. To develop the ontology, you must change the default auto-create settings in Protege 4. Go to file>preferences>New Entities. Change the following: specified URI = http://semanticscience.org/resource/ Followed by '/', End with : AutoID AutoID - digit count = 6, prefix = CHEMINF_
chmo
cio
cl See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, [email protected], University at Buffalo.
clo CLO: Cell Line Ontology The Cell Line Ontology.
cmf*
cmo
cro*
cteno CTENO is an ontology describing the anatomy and developmet of ctenophores.
cvdo CVDO is an ontology of cardiovascular diseases structured on OBO foundry’s principle and based on BFO. CVDO reorganizes and completes DOID cardiovascular diseases following OGMS tripartite model of disease, and builds its taxonomy of diseases largely by automatic reasoning.
ddanat
ddpheno
dideo http://creativecommons.org/licenses/by/4.0/ The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). The Drug-drug Interaction and Drug-drug Interaction Evidence Ontology (DIDEO) by the DIDEO development group is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
dinto This ontology has been created and is maintained by the Department of Computer Science at University Carlos III of Madrid. This new realeased version of DINTO (1.2) is version DINTO 1 extended to include information about adverse drug reactions (ADRs). We have imported a reduced version of the Ontology for Advese Events (OAE 1.1.247) including only the top class 'adverse event' and its subclasses. This reduced subset of OAE can be downladed from https://drive.google.com/folderview?id=0B-7Po9tR1KLUUDZPRkFGOFFmVjA&usp=sharing In addition to this, we have imported drug-ADR relationships for the database SIDER, that can be used with the SWRL rules to infer DDIs occurring by the addition of a common ADR.
dpo*
dron https://creativecommons.org/licenses/by/3.0/ An ontology of drugs. When citing DrOn, use the permanent URL of the ontology: http://purl.obolibrary.org/obo/dron.owl. When referencing a specific component of the DrOn, such as a class, object property, annotation property, or individual, use the Uniform Resource Identifier (URI) of that component. DrOn contains content developed by the National Library of Medicine in RxNorm. In creating DrOn, we have used RxNorm content only with SAB = RXNORM.
duo
eco ECO (https://github.com/evidenceontology/evidenceontology) is released into the public domain under CC0 1.0 Universal (CC0 1.0). Anyone is free to copy, modify, or distribute the work, even for commercial purposes, without asking permission. Please see the Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) for an easy-to-read description of CC0 1.0 or the full legal code (https://creativecommons.org/publicdomain/zero/1.0/legalcode) for more detailed information. To get a sense of why ECO is CC0 as opposed to licensed under CC-BY, please read this thoughtful discussion (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/285) on the OBO Foundry GitHub site.
ecocore*
ehdaa2 Jonathon Bard Human Ontology this version corrects the namespace and includes some flybase alt_IDs
emapa Version 012
envo ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities. It interoperates with other ontologies in the OBO Foundry and Library. New terms or revisions can be requested at https://github.com/EnvironmentOntology/envo/issues/ Please see www.environmentontology.org for more information and citations. Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/bfo_import.owl>))) [Axioms: 92 Logical Axioms: 35] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/chebi_import.owl>))) [Axioms: 2434 Logical Axioms: 1036] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/clo_import.owl>))) [Axioms: 34 Logical Axioms: 8] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/fao_import.owl>))) [Axioms: 4 Logical Axioms: 0] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/flopo_import.owl>))) [Axioms: 1536 Logical Axioms: 352] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/foodon_import.owl>))) [Axioms: 63 Logical Axioms: 7] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/go_import.owl>))) [Axioms: 270 Logical Axioms: 76] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/ncbitaxon_import.owl>))) [Axioms: 542 Logical Axioms: 123] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/obi_import.owl>))) [Axioms: 50 Logical Axioms: 12] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/omp_import.owl>))) [Axioms: 47 Logical Axioms: 11] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/pato_import.owl>))) [Axioms: 1362 Logical Axioms: 337] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/pco_import.owl>))) [Axioms: 21 Logical Axioms: 3] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/po_import.owl>))) [Axioms: 151 Logical Axioms: 18] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/ro_import.owl>))) [Axioms: 1192 Logical Axioms: 302] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/imports/uberon_import.owl>))) [Axioms: 24081 Logical Axioms: 4670] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>))) [Axioms: 79 Logical Axioms: 12] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>))) [Axioms: 131 Logical Axioms: 22] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>))) [Axioms: 45 Logical Axioms: 6] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>))) [Axioms: 21 Logical Axioms: 2]
eo*
epo*
ero
exo
fao version: $Revision: 1.7 $
fbbi This CV covers sample preparation, visualization and imaging methods. corrections and additions to [email protected] editor:Chris Woodcock (The Cell: An Image Library) Biological Imaging Methods CV
fbbt Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbbt.owl>) VersionIRI(<null>))) [Axioms: 28 Logical Axioms: 0] Contains terms imported from http://purl.obolibrary.org/obo/go/releases/2017-09-05/go-simple.obo and from PATO - datestamp = 13:06:2011 11:15. Use of the -non-classified.owl version of this ontology requires a reasoner. Recommended reasoners are FaCT++, JFACT and ELK. Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/FBbt_RO.owl>) VersionIRI(<null>))) [Axioms: 47 Logical Axioms: 12]
fbcv Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dpo.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbcv/2017-07-05/dpo.owl>))) [Axioms: 4806 Logical Axioms: 930] Imports terms from CHEBI - datestamp = 02:12:2011 01:47. And terms imported from http://purl.obolibrary.org/obo/go/releases/2017-06-29/go-simple.obo
fbdv Drosophila temporal ontology. Contains terms imported from http://purl.obolibrary.org/obo/go/releases/2016-10-13/go-simple.obo
fix autogenerated-by: DAG-Edit version 1.419 rev 3 date: Mon Apr 04 14:05:41 BST 2005 saved-by: kirill version: $Revision: 1.2 $
flopo
fma this is an ALPHA version of the FMA2.0 in obo. Conversion based on http://www.bioontology.org/wiki/index.php/FMAInOwl
foodon
fypo svn version: $Revision: 303 $
gaz
genepio
geno GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. Documentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013
geo Geographical Entity Ontology https://creativecommons.org/licenses/by/3.0/ When citing the Geographical Entities Ontology (GEO), use the permanent URL of the ontology: http://purl.obolibrary.org/obo/geo.owl. When referencing a specific component of GEO such as a class, object property, or individual, use that component's Uniform Resource Identifier (URI).
hao
hom
hp see http://www.human-phenotype-ontology.org Please see license of HPO at http://www.human-phenotype-ontology.org
hsapdv
iao http://creativecommons.org/licenses/by/4.0/ IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 The Information Artifact Ontology (IAO) is licensed under the Creative Commons Attribution License (CC-BY) version 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. For more information see http://www.obofoundry.org/docs/Citation.html IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO This version of the ontology is the merge of all its imports and has added axioms inferred by an OWL reasoner
ico The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field. Terms were identified from a sample of informed consent templates, and definitions were selected based on concordance between the defintion and the use of the term in the source informed consent template document. We preferentially selected defintioins from the NCI thesuarus.
ido The core Infectious Disease Ontology is an ontology of entities generally relevant to both the biomedical and clinical aspects of infectious diseases, including terms such as 'pathogen', 'host', 'vector', and 'vaccine'. The structure of IDO adheres to the Basic Formal Ontology. Terms in IDO that are within the scope of other OBO Foundry ontologies, such as the Gene Ontology, are derived from those ontologies. Other terms are defined as cross-products of terms from Foundry ontologies to the extent possible. For more information, see http://www.infectiousdiseaseontology.org/Home.html.
idomal*
kisao Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes)
ma
mamo
mf Mental Functioning Ontology https://creativecommons.org/licenses/by/3.0/ The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning, founded on the Basic Formal Ontology (BFO) and related to the Ontology for General Medical Science (OGMS). The Mental Functioning Ontology (MF) was first described in the publication available at http://www.jbiomedsem.com/content/1/1/10 entitled 'Foundations for a realist ontology of mental disease' (Barry Smith and Werner Ceusters). This OWL version of the MF ontology was originally created by Janna Hastings and is maintained by all committers to the MF ontology project. The OWL representaions of MF and MD were split on 22 May 2012.
mfmo
mfoem Emotion Ontology https://creativecommons.org/licenses/by/3.0/ Sources for terms and synonyms / translations : -- GRID project vocabulary resources (Cristina Soriano) Sources for definitions: OCEAS => Oxford Companion to Emotion and the Affective Sciences, ed. David Sander and Klaus Scherer, Oxford University Press, 2009.
mfomd Mental Disease Ontology The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF). The Mental Disease Ontology was first described in the publication 'Foundations for a realist ontology of mental disease' (Barry Smith and Werner Ceusters) which is available at http://www.jbiomedsem.com/content/1/1/10 .
mi CVversion: 2.5.5 Each of the top level terms in this file is the root term of an independent controlled vocabulary Notes: The PSI MI schema defines short labels for controlled vocabulary terms The correct use of these vocabularies in the PSI Molecular Interaction XML schema is The last accession number used in this file is stored in a separate file, The maintenance of this file is ensured by Sandra Orchard [email protected] and Luisa Montecchi Palazzi [email protected] coverage: This file collect controlled vocabularies describing different aspects of molecular interactions. formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml. mapping an element of the PSI Molecular Interaction XML schema. psi-mi.lastac. It MUST be updated when this file is updated. publisher: This file is published by the PSI MI working group see http://psidev.info/MI short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.
miapa Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies. This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at [email protected]. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA.
micro Many thanks to Chris Mungall (LBNL), Elvis Hsin-Hui Wu (University of Arizona), Gail Gasparich (Towson University), and Gordon Burleigh (University of Florida) for comments and/or assistance with ontology construction and compilation of taxonomic descriptions and term definitions. Thanks to Oliver He (University of Michigan) for technical assistance with OntoBee and OntoFox, and Gareth Owen (ChEBI project leader, head curator) and other curators at ChEBI for assistance in the incorporation of microbial-specific chemical terms and synonyms into ChEBI. Thanks also to the instructors (Melissa Haendel, Matt Yoder, Jim Baihoff) and students of the 2013 NESCent Ontologies for Evolutionary Biology workshop, and to Karen Cranston (NESCent director) and the support staff at NESCent. This work was supported by a grant from the National Science Foundation Assembling the Tree of Life Program (DBI-1208534), and by a travel grant to attend the 2013 NESCent Ontologies for Evolutionary Biology workshop. Note regarding term synonyms: Some synonyms listed in this ontology are synonyms for terms and classes as they were used in published microbiological taxonomic descriptions. Thus, the synonyms are not necessarily applicable to the wider world. If the term synonyms could not be classified as broad, exact, or narrow synonyms, they were labeled as related synonyms. The synonym lists were developed to facilitate the automated extraction of phenotypic data and character states from prokaryotic taxonomic descriptions using a natural language processing algorithm (MicroPIE).
mirnao*
miro*
mmo
mmusdv
mod Annotation note 1 - "[PSI-MOD:ref]" has been replaced by PubMed:18688235. Annotation note 2 - When an entry in the RESID Database is annotated with different sources because the same modification can arise from different encoded amino acids, then the PSI-MOD definition for each different source instance carries the RESID cross-reference followed by a hash symbol "#" and a 3 or 4 character label. When an entry in the RESID Database is annotated as a general modification with the same enzymatic activity producing different chemical structures depending on natural variation in the nonproteinaceous substrate, on secondary modifications that do not change the nature of the primary modification, or on a combination of a primary and one or more secondary modifications on the same residue, then the PSI-MOD definition for each different instance carries the RESID cross-reference followed by the special tag "#var". Annotation note 3 - When an entry in the UniMod database is annotated as a general modification, and one or more instance sites are listed, then the PSI-MOD definition for each different site instance carries the UniMod cross-reference followed by a hash symbol and an amino acid code, "N-term" or "C-term". Annotation note 4 - The elemental formulas are in strict alphabetical order, not in CAS ("C" and "H" first) order. Isotope numbers are in parentheses before the element symbol, and an element should not occur in a formula both with and without an isotope number. In difference formulas, counts can be zero or negative. Annotation note 5 - In entries with an isotope indicator in the formula, average masses are meaningless and are assigned the value equal to the monoisotopic mass, but rounded to a lower precision; monoisotopic masses are calculated by using the masses for the indicated isotopes and the most common isotopes for other elements without isotope indicators in the formulas. Annotation note 6 - For cross-link modifications, the number following "Cross-link" in the comment record indicates the number of amino acid residues that appear in the origin record, used to check the difference formula and masses. This usage differs from RESID, where the cross-link number indicates the maximum number of peptide chains that can be cross-linked. Annotation note 7 - The synonym cross-reference "MOD:old name" has been replaced by "MOD:alternate name". Annotation note 8 - The DeltaMass listings for free amino acids have been removed. Most UniMod entries that have not been "approved" have by general agreement not been incorporated unless there has been a request for a specific term by a PRIDE submitter. Annotation note 9 - The Open Mass Spectrometry Search Algorithm, OMSSA, enumerated list of modifications are being incorporated. The string values are synonyms with the synonymtypedef "OMSSA-label", and their integer values (which are supposed to be stable) are definition cross-references. ISO-8601 date: 2014-01-28 14:22Z PSI-MOD version: 1.013.0 RESID release: 75.00
mondo Includes Ontology(OntologyID(OntologyIRI(
mop
mp The Mammalian Phenotype Ontology The Mammalian Phenotype Ontology is being developed by Cynthia L. Smith, Susan M. Bello, Carroll W. Goldsmith and Janan T. Eppig, as part of the Mouse Genome Database (MGD) Project, Mouse Genome Informatics (MGI), The Jackson Laboratory, Bar Harbor, ME. This file contains pre-coordinated phenotype terms, definitions and synonyms that can be used to describe mammalian phenotypes. The ontology is represented as a directed acyclic graph (DAG). It organizes phenotype terms into major biological system headers such as nervous system and respiratory system. This ontology is currently under development. Weekly updates are available at the Mouse Genome Informatics (MGI) ftp site (ftp://ftp.informatics.jax.org/pub/reports/index.html#pheno) as well as the OBO Foundry site (http://obofoundry.org/). Questions, comments and suggestions are welcome, and should be directed to [email protected], [email protected] or to GitHub tracker (https://github.com/obophenotype/mammalian-phenotype-ontology/issues) MGD is funded by NIH/NHGRI grant HG000330. Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/mp/mp-equivalent-axioms-subq.owl>))) [Axioms: 7389 Logical Axioms: 7251] The Mammalian Phenotype Ontology Copyright © 2007, 2008, 2011, 2012, 2015 by The Jackson Laboratory.
mpath The Pathbase mouse pathology ontology provides a description of mutant and transgenic mouse pathology phenotypes and incorporates 643 known mouse pathologies hierarchically organised as "instances of" pathological processes. Questions, comments and suggestions for amendment should be sent to the Co-ordinator, Dr. Paul Schofield, Dept. of Anatomy, University of Cambridge ([email protected]).The ontology was developed by the Pathbase consortium (http://www.pathbase.net) funded under the European Commission's Fifth Framework programme, Contract number QLRI-CT-1999-00320.
mpio
mro
ms namespace: MS When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page creator: Gerhard Mayer <mayerg97 <-at-> rub.de> coverage: Mass spectrometer output files and spectra interpretation creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org> creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch> creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se> URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de> To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu> For any queries contact [email protected] creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de> This work is licensed under the Creative Commons Attribution 3.0 Unported License.
nbo Includes Ontology(OntologyID(OntologyIRI(<http://ethotools.sourceforge.net/owlwatcher/test/abocore.owl>))) [Axioms: 911 Logical Axioms: 292]
ncbitaxon Autogenerated by OWLTools-NCBIConverter.
ncit NCI Thesaurus OBO Edition The NCIt OBO Edition project aims to increase integration of the NCIt with OBO Library ontologies. NCIt is a reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities. NCIt OBO Edition releases should be considered experimental. NCI Thesaurus, a controlled vocabulary in support of NCI administrative and scientific activities. Produced by the Enterprise Vocabulary System (EVS), a project by the NCI Center for Biomedical Informatics and Information Technology. National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U.S.A.
ncro This is the release of December 12, 2015. It will always be available at http://purl.obolibrary.org/ncro/2015-12-10/ncro.owl. While current, this ontology is also available at http://purl.obolibrary.org/obo/ncro.owl This file is a merge of NCRO and any imported ontologies or terms. You can access the ontology that existed before the merge, with imports intact, at http://purl.obolibrary.org/obo/ncro/YYYY-MM-DD/ncro.owl or, for the current version, http://purl.obolibrary.org/obo/ncro/prebuild/ncro.owl This ontology is currently undergoing changes. ID deprecation policies will start in the next couple of months. In the mean time, identifiers may be deleted and not marked obsolete. d
oae OAE: Ontology of Adverse Events The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
oarcs
oba Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/oba/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 1000 Logical Axioms: 167] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/oba/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 47537 Logical Axioms: 14594] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/oba/modules/attribute_location.owl>) VersionIRI(<null>))) [Axioms: 126 Logical Axioms: 23]
obcs OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012.
obib Ontology for BIoBanking (OBIB) The ontology for biobanking is an ontology built for annotation and modeling of biobank repository and biobanking administration. It is developed based on subset of Ontology for Biomedical Investigation (OBI) using Basic Formal Ontology (BFO) and following OBO Foundry principles. The first version of the ontology is merged of two existing biobank related ontologies, OMIABIS and biobank ontology.
ogg OGG: Ontology of Genes and Genomes OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets.
ogi*
ogms The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is always available at http://purl.obolibrary.org/obo/ogms.owl This is version 2011-09-20 aka '0.9' http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl The OGMS developer site is http://code.google.com/p/ogms/ The discussion group is http://groups.google.com/group/ogms-discuss If you are interested in participating in the development of OGMS, please send email to [email protected]. Be sure to include a google-account username with your request (this will be the username associated with a gmail address). This ontology is in early development. Expect it to change.
ogsf*
ohd Status of this document: This is a work in progress and we do not yet make any promises about the stability of URIs. A known issue is that the upper level of this ontology is an exploratory version of BFO developed in the interim between when BFO 1 was current and before BFO 2 development started. The representation of the CDT codes is tentative - we are discussing this with the ADA. The integration between OBI and OGMS is not complete - we add some axioms here in order to use both in a consistent way. The version of the subject of the FMA used here is an automatic translation of a portion of the entities and relations present in the original FMA. Work is ongoing on improving this subset and using an up-to-date version of the FMA as its basis. The Oral Health and Disease Ontology is an ontology built to be compatible with the OBO Foundry ontologies, and is a collaboration between researchers at the University at Buffalo School of Dental Medicine, the University of Pittsburg School of Dental Medicine, and the Oregon Health and Science University. This ontology is licensed under the CC-BY License. Please see http://creativecommons.org/licenses/by/4.0/ Attribution is satisfied by using the URIs defined in this file when using terms from this ontology. This version of the ontology has the imports merged and inferred-axioms added. The development version is at http://purl.obolibrary.org/obo/ohd/dev/ohd.owl This ontology is in early development. Expect it to change. This document was an early experimental prototype of bfo2, not blessed by the working group. It is archived because it was used by some projects. There was very little change other than ids relative to earlier versions of BFO, and ids used here will be used in the ultimate release
ohmi OHMI: Ontology of Host-Microbiome Interactions OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions.
olatdv adapted from MFO by Thorsten Henrich
omiabis Ontologized MIABIS
omit Filtered by Name equals "Entity" OR Ancestor Name equals "Entity" OR Is Property
omp select is_a closure
omrse This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt
ontoneo PERSON: Fernanda Farinelli OntONeo development prioritizes the reuse of classes and entities from FMA ontology to deal with human anatomy approaches. Every class reference of others ontology for the anatomy domain, for example, UBERON and CARO, in which has the cross-reference annotation to some FMA class are replaced by the FMA class referred. PERSON: Fernanda Farinelli Ontoneo is a ontology that the development is in progress, then take in mind for while the stability of URIs and labels. We are sure that the upper level ontology used is BFO version 2 and that we are priorize the reuse of terms find on OBO Foundry ontologies. IDs allocated to individuals: ONTONEO_90000000 - ONTONEO_99999999 OntoNeo, is developed by Fernanda Farinelli and her contributor group is licensed under CC BY 4.0. PERSON: Fernanda Farinelli The default language of this ontology is English mainly because the reusable ontologies are conceived in English. However, this ontology intends to be bilingual in order to attend the necessities of Brazilian issues. Then, every relevant term we defined in Portuguese (Brazilian portuguese) using the tag xml:lang="pt" the follow annotations: label, definition, alternative term.
oostt Ontology of Organizational Structures of Trauma centers and Trauma Systems http://creativecommons.org/licenses/by/4.0/ Development of this ontology is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health.
opl The Parasite Life Cycle ontology was developed as part of the NIH-funded "Semantics and Services enabled Problem Solving Environment for Tcruzi" project (Grant#1R01HL087795-01A1). The Kno.e.sis center, Computer Science and Engineering Department, Wright State University, Center for Bioinformatics, Department of Genetics, University of Pennsylvania School of Medicine, USA and the Tarleton Lab, Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, USA collaborated to create this ontology. Resource page: http://knoesis.wright.edu/trykipedia This file is based on checkout of our SVN repository revision $Revision: 27 $
ovae OVAE: Ontology of Vaccine Adverse Events OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).
pco http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators.
pdro An ontology of drug prescriptions
pdumdv Modified from PD_ST by Thorsten Henrich
peco
plana
poro Porifera (sponge) ontology An ontology describing the anatomical structures and characteristics of Porifera (sponges)
ppo
pw
rex saved-by: kirill autogenerated-by: DAG-Edit version 1.419 rev 3 version: $Revision: 1.13 $ date: Thu Jan 04 14:25:43 GMT 2007
rnao*
ro OBO Relations Ontology The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies. Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 26 Logical Axioms: 0] Includes Ontology(OntologyID(Anonymous-21)) [Axioms: 32 Logical Axioms: 0]
rs
rxno
sbo Systems Biology Ontology, OWL export generated by SBO Browser (http://www.ebi.ac.uk/sbo/)
sep*
sepio*
sibo
so
spd
stato
swo Bioinformatics operations, data types, formats, identifiers and topics SWO and EDAM include some terms released under CC-BY license from the OBO Foundry. We acknowledge those with the use of the OBO PURLs were appropriate. Some of the definitions have been modified from the original; for the latest original definition please visit the URI. The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains SWO-specific classes and axioms as well as imported information from a variety of sources including OBI, IAO, BFO and EDAM. Please note that EDAM is imported as a whole and as such, some comments in the ontology header directly relate to EDAM only. Date of release: 1 February 2017
symp
tads*
taxrank To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Taxonomic Rank Vocabulary (TAXRANK). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: http://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary
tgma*
to
trans
tto To the extent possible under law, Peter E. Midford has waived all copyright and related or neighboring rights to the Teleost Taxonomy Ontology (TTO). This work is published from the United States. It is requested that users of this vocabulary cite it at the following URI: https://www.phenoscape.org/wiki/Teleost_Taxonomy_Ontology
uberon Uber-anatomy ontology Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/TEMP>) VersionIRI(<null>))) [Axioms: 437 Logical Axioms: 0] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon-bridge-to-bfo.owl>) VersionIRI(<null>))) [Axioms: 20 Logical Axioms: 9] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/ext.owl>) VersionIRI(<null>))) [Axioms: 25837 Logical Axioms: 4725] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/insect-anatomy.owl>) VersionIRI(<null>))) [Axioms: 2098 Logical Axioms: 650] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/reflexivity_axioms.owl>) VersionIRI(<null>))) [Axioms: 2 Logical Axioms: 2]
uo Filtered by Ancestor ID equals "UO:0000000"
upheno
vario A Variation Ontology
vo Vaccine Ontology The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is initiated and primarily developed by Dr. Yongqun "Oliver" He at the University of Michigan Medical School. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities.
vt
vto
wbbt $
wbls Version: 1.04 Editors: Wen J. Chen & Daniela Raciti, WormBase, Caltech. Jane Lomax, Wellcome Trust Sanger Institute.
wbphenotype
xco
xl*
zeco
zfs