EFO 3.0 Release

EBISPOT · Oct 15, 2018 · 443b211 · 443b211
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Showing 5 changed files with 20 additions and 19 deletions.
diff --git a/ExFactor Ontology release notes.txt b/ExFactor Ontology release notes.txt
@@ -22,7 +22,7 @@ EFO 3.0 release contains major restructuring to the disease branch in order to i
 All mapped terms (EFO terms and their MONDO mapped term) can be found in the mondo_efo_mappings.tsv file situated in the imports folder. This file contains on each line: the URI of the MONDO term, the URI of the EFO term, the MONDO label and the EFO label for each mapped pair. All terms that are mapped must be added to this file in order for the MONDO term to be extracted and merged into EFO. Additionally, all MONDO terms to be extracted that are listed in the mappings file are contained in the mondo_terms.txt file.
 
 ----------------------------------
-1.    Changes to URIs
+1.	Changes to URIs
 2.	Changes to EFO
 3.	Obsolete Classes in EFO
 4.	Scope of the Ontology

diff --git a/README.md b/README.md
@@ -27,7 +27,8 @@ Changes in annotation properties are:
      - This will allow us to use the spectrum of synonym annotation including [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) and [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) more effectively to provide further information per each term.
 - [Bioportal_provenance](http://www.ebi.ac.uk/efo/bioportal_provenance) has been removed from EFO3 entirely. 
      - This has cleaned up annotations, removing the imported fingerprints from bioportal provenance from previous importing.
-
+- All definition citations have been replaced by [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref).
+- Deprecated terms are no longer children of obsolete class (http://www.geneontology.org/formats/oboInOwl#ObsoleteClass), instead, they are given the annotation property owl:Deprecated (http://www.w3.org/2002/07/owl#deprecated). 
 
 ### Stable release versions
 
@@ -40,7 +41,7 @@ This is the asserted ontology and requires an OWL-DL reasoner to view the inferr
 
 ### Editors' version
 
-Editors of this ontology should use the edit version, [master:src/ontology/efo-edit.owl](https://github.com/EBISPOT/efo/blob/master/src/ontology/efo-edit.owl)
+Editors of this ontology should use the edit version, [master src/ontology/efo-edit.owl](https://github.com/EBISPOT/efo/blob/master/src/ontology/efo-edit.owl)
 
 ## Term requests and contact
 

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -28,7 +28,7 @@ EFOFIXER = ../../bin/efo-fixer.jar
 # Top-level targets
 # ----------------------------------------
 
-all: $(BUILDDIR)/$(ONT).owl #$(BUILDDIR)/$(ONT).obo
+all: $(BUILDDIR)/$(ONT).owl $(BUILDDIR)/$(ONT).obo
 test: all sparql_test
 prepare_release: all
 	cp $(BUILDDIR)/$(ONT).owl $(BUILDDIR)/$(ONT).obo $(RELEASEDIR) &&\

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -1,19 +1,19 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="http://purl.obolibrary.org/obo/hancestro.owl" uri="imports/hancestro_import.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="http://www.ebi.ac.uk/efo" uri="efo-edit.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo_inferred.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo_inferred_all.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo-obo.tmp.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="http://www.ebi.ac.uk/efo/imports/mondo_efo_import.owl" uri="imports/mondo_efo_import.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="http://www.ebi.ac.uk/efo/imports/mondo_import.owl" uri="imports/mondo_import.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="http://www.ebi.ac.uk/efo/untitled-ontology-144/" uri="validation_flags.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="shadowed:http://purl.obolibrary.org/obo/hancestro.owl" uri="mirror/hancestro.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="shadowed:http://www.ebi.ac.uk/efo" uri="results/efo-hancestro.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="shadowed:http://www.ebi.ac.uk/efo" uri="build/efo-edit-fixed-raw.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="shadowed:http://www.ebi.ac.uk/efo" uri="build/efo-edit-fixed.owl"/>
-        <uri id="Automatically generated entry, Timestamp=1539599839880" name="shadowed:http://www.ebi.ac.uk/efo/efo.owl" uri="build/efo.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="http://purl.obolibrary.org/obo/hancestro.owl" uri="imports/hancestro_import.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="http://www.ebi.ac.uk/efo" uri="efo-edit.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo_inferred.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo_inferred_all.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="duplicate:http://www.ebi.ac.uk/efo/efo.owl" uri="efo-obo.tmp.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="http://www.ebi.ac.uk/efo/imports/mondo_efo_import.owl" uri="imports/mondo_efo_import.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="http://www.ebi.ac.uk/efo/imports/mondo_import.owl" uri="imports/mondo_import.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="http://www.ebi.ac.uk/efo/untitled-ontology-144/" uri="validation_flags.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="shadowed:http://purl.obolibrary.org/obo/hancestro.owl" uri="mirror/hancestro.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="shadowed:http://www.ebi.ac.uk/efo" uri="results/efo-hancestro.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="shadowed:http://www.ebi.ac.uk/efo" uri="build/efo-edit-fixed-raw.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="shadowed:http://www.ebi.ac.uk/efo" uri="build/efo-edit-fixed.owl"/>
+        <uri id="Automatically generated entry, Timestamp=1539612020698" name="shadowed:http://www.ebi.ac.uk/efo/efo.owl" uri="build/efo.owl"/>
     </group>
 </catalog>
diff --git a/src/ontology/version.txt b/src/ontology/version.txt
@@ -1 +1 @@
-3.0-beta
+3.0