Merge branch 'master' into issue2707

Fix the conflicts in uberon.Makefile caused by the overhaul of that Makefile (which occured while this PR was under way).
obophenotype · Sep 6, 2023 · 9d70842 · 9d70842
2 parents 09caf74 + 34cd601
commit 9d70842
Show file tree

Hide file tree

Showing 175 changed files with 36,278 additions and 32,753 deletions.
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -0,0 +1,11 @@
+# Uberon code owners (Guardians of the main branch)
+# GitHub documentation about CODEOWNERS file - https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+*       @anitacaron
+*.yaml @matentzn
+*Makefile @gouttegd
+*uberon.Makefile @gouttegd @matentzn @anitacaron
+
+
+#docs/*  [email protected] 
+#docs/*  actions-user
diff --git a/.github/ISSUE_TEMPLATE/b_adding_synonym.md b/.github/ISSUE_TEMPLATE/b_adding_synonym.md
@@ -1,7 +1,7 @@
 ---
 name: Add synonym
 about: New synonym suggestion for an existing Uberon term
-assignees: nicolevasilevsky
+assignees: 
 labels: synonym
 ---
 

diff --git a/.github/ISSUE_TEMPLATE/c_revise_textual_def.md b/.github/ISSUE_TEMPLATE/c_revise_textual_def.md
@@ -1,7 +1,7 @@
 ---
 name: Revise textual definition
 about: Change the textual definition of an Uberon term
-assignees: nicolevasilevsky
+assignees:
 labels: 'textual definition'
 ---
 

diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.4
+    container: obolibrary/odkfull:v1.4.1
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

diff --git a/bridge/external-disjoints.owl b/bridge/external-disjoints.owl
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
@@ -43,3 +43,4 @@ These are the components in UBERON
 | in-subset.owl | None |
 | hra_subset.owl | None |
 | vasculature_class.owl | None |
+| hra_depiction_3d_images.owl | None |
diff --git a/docs/team.md b/docs/team.md
@@ -29,7 +29,6 @@ The Uberon team is responsible for managing the Uberon project. It usually compr
 | Tiago Lubiana Alves (@lubianat) |  | 0 | [Editors](https://github.com/orgs/obophenotype/teams/uberon-cl-curators) | Ontology Editor | New Term Requests. |
 | Wasila Dahdul (@wdahdul) | | 0 | [Editors](https://github.com/orgs/obophenotype/teams/uberon-cl-curators) | Ontology Editor | External advisor. |
 | Yvonne Bradford (@ybradford) | [ZFIN](https://zfin.org/) | 0 | [Editors](https://github.com/orgs/obophenotype/teams/uberon-cl-curators) | Ontology Editor | ZFA-Uberon mappings. |
-| Bradley Varner (@bvarner-ebi) | [Cell Annotation Platform]() | 1 | [Editors](https://github.com/orgs/obophenotype/teams/uberon-cl-curators) | Ontology Editor | New cell types & edits for CAP |
 
 
 ## Past team members and major contributors

diff --git a/docs/uberon-editor-sop.md b/docs/uberon-editor-sop.md
@@ -85,24 +85,29 @@ Citations are made by cross-references, that is by adding `http://www.geneontolo
 
 If the main source for an assertion is a term in another ontology, the short identifier for that term may be used as a cross-reference. For example, `WBbt:0006799` to cross-reference a term in the _C. elegans_ Gross Anatomy Ontology.
 
+If using a MeSH (Medical Subject Heading) term as a cross-reference, add the database_cross_reference annotation using the MeSH Unique ID, NOT MeSH Tree Number. For example, a database_cross_reference can be MESH:D054326, NOT MESH:A07.015.908.194.500.
+
 ORCID identifiers may also be used when the only available source for an assertion is an individual researcher. This should be done sparingly.
 
 **Technical details of adding a cross-reference using Protégé**:
 
-For CURIEs and ORCIDs: In the "Create Annotation" window, select the annotation property **database_cross_reference**.
+For CURIEs, ORCIDs: In the "Create Annotation" window, select the annotation property [**database_cross_reference**](http://www.geneontology.org/formats/oboInOwl#hasDbXref).
+For adding URLs to text definitions or synonyms:  In the "Create Annotation" window, select the annotation property [**database_cross_reference**](http://www.geneontology.org/formats/oboInOwl#hasDbXref).
+For adding URLs to axioms that are NOT text definitions or synonyms:  In the "Create Annotation" window, select the annotation property [**source**](http://www.geneontology.org/formats/oboInOwl#source).
+
 
 For CURIEs: Enter the CURIE, using the [bioregistry OBO context](https://bioregistry.io/context/obo) prefix ([link to prefixmap](https://github.com/biopragmatics/bioregistry/blob/main/exports/contexts/obo.context.jsonld)), as a Value on the "Literal" tab. Leave Datatype empty.
 
 In cases where more than one CURIE is available for a resource, either is acceptable, but using the more semantically specific identifier is recommended. For example, when both a PMID and a doi are available for a resource, using the PMID is recommended since it indicates the cross-reference points to a paper, as opposed to a doi which could point to any digital object.
 
 For ORCIDs: Enter the ORCID as an IRI in the IRI field on the "IRI Editor" tab, for example `https://orcid.org/0000-0002-7356-1779`.
 
-For URLs: In the "Create Annotation" window, select the annotation property **seeAlso** (`rdfs:seeAlso`). Enter the URL as a literal string with Datatype `xsd:anyURI` selected.
-DO NOT use database_cross_reference with a value that is a URL. 
+For URLs: Enter the URL as a literal string. Note: In OWL-based files (like cl-edit.owl), Datatype `xsd:anyURI` is also selected; however, in OBO-based files (like uberon-edit.obo) these always become strings, so no selection needs to be made for Datatype in Uberon. Datatype selection is planned to be implemented in a future OBO revision, and updates can be checked at https://github.com/owlcollab/oboformat/issues/128.
+NOTE: URLs should be avoided when a cross-reference with a CURIE is otherwise available.
 
-To restate, in all cases above except ORCIDs, the values are entered as literal strings. An ORCID MUST BE entered as an IRI.
 
-The above instructions apply whether the cross-reference is added to another annotation (e.g., annotating a text defintion or comment) or adding to the overall class (i.e., not an annotation of another annotation). 
+
+To restate, in all cases above except ORCIDs, the values are entered as literal strings. An ORCID MUST BE entered as an IRI.
 
 ## Synonyms
 

diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for uberon
 # Generated using ontology-development-kit
-# ODK Version: v1.4
+# ODK Version: v1.4.1
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead
 
@@ -42,16 +42,16 @@ REPORT_FAIL_ON =            ERROR
 REPORT_LABEL =              
 REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
-SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy 
+SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format 
 SPARQL_EXPORTS =            basic-report 
-ODK_VERSION_MAKEFILE =      v1.4
+ODK_VERSION_MAKEFILE =      v1.4.1
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl 
+OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/mappings.owl $(COMPONENTSDIR)/in-subset.owl $(COMPONENTSDIR)/hra_subset.owl $(COMPONENTSDIR)/vasculature_class.owl $(COMPONENTSDIR)/hra_depiction_3d_images.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 PATTERNDIR=                 ../patterns
@@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic ext basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
 
 # ----------------------------------------
 # Top-level targets
@@ -395,6 +395,7 @@ $(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 
 
 
+
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------
@@ -667,12 +668,6 @@ $(ONT)-basic.json: $(ONT)-basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
-ext.obo: ext.owl
-	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
-ext.json: ext.owl
-	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		convert --check false -f json -o $@.tmp.json &&\
-		mv $@.tmp.json $@
 basic.obo: basic.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 basic.json: basic.owl
@@ -780,9 +775,6 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 
-ext.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
-
 basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 

diff --git a/src/ontology/bridge/cl-bridge-to-aao.obo b/src/ontology/bridge/cl-bridge-to-aao.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-aao
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 property_value: dc-title "CL bridge to aao" xsd:string
 property_value: dc-description "Equivalence axioms between AAO and CL. Note that AAO is in the process of being merged into the core CL, so this mapping will become deprecated" xsd:string

diff --git a/src/ontology/bridge/cl-bridge-to-aao.owl b/src/ontology/bridge/cl-bridge-to-aao.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-aao.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-aao/2023-06-27/uberon/bridge/cl-bridge-to-aao.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-aao/2023-09-05/uberon/bridge/cl-bridge-to-aao.owl"/>
         <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Erik Segerdell</dc:contributor>
         <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Paula Mabee</dc:contributor>
         <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL editors</dc:creator>

diff --git a/src/ontology/bridge/cl-bridge-to-aeo.obo b/src/ontology/bridge/cl-bridge-to-aeo.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-aeo
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Term]

diff --git a/src/ontology/bridge/cl-bridge-to-aeo.owl b/src/ontology/bridge/cl-bridge-to-aeo.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-aeo.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-aeo/2023-06-27/uberon/bridge/cl-bridge-to-aeo.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-aeo/2023-09-05/uberon/bridge/cl-bridge-to-aeo.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-bila.obo b/src/ontology/bridge/cl-bridge-to-bila.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-bila
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Typedef]

diff --git a/src/ontology/bridge/cl-bridge-to-bila.owl b/src/ontology/bridge/cl-bridge-to-bila.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-bila.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-bila/2023-06-27/uberon/bridge/cl-bridge-to-bila.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-bila/2023-09-05/uberon/bridge/cl-bridge-to-bila.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-bspo.obo b/src/ontology/bridge/cl-bridge-to-bspo.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-bspo
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Typedef]

diff --git a/src/ontology/bridge/cl-bridge-to-bspo.owl b/src/ontology/bridge/cl-bridge-to-bspo.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-bspo.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-bspo/2023-06-27/uberon/bridge/cl-bridge-to-bspo.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-bspo/2023-09-05/uberon/bridge/cl-bridge-to-bspo.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-caro.obo b/src/ontology/bridge/cl-bridge-to-caro.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-caro
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Term]

diff --git a/src/ontology/bridge/cl-bridge-to-caro.owl b/src/ontology/bridge/cl-bridge-to-caro.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-caro.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-caro/2023-06-27/uberon/bridge/cl-bridge-to-caro.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-caro/2023-09-05/uberon/bridge/cl-bridge-to-caro.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-dhba.obo b/src/ontology/bridge/cl-bridge-to-dhba.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-dhba
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Term]

diff --git a/src/ontology/bridge/cl-bridge-to-dhba.owl b/src/ontology/bridge/cl-bridge-to-dhba.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-dhba.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-dhba/2023-06-27/uberon/bridge/cl-bridge-to-dhba.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-dhba/2023-09-05/uberon/bridge/cl-bridge-to-dhba.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-efo.obo b/src/ontology/bridge/cl-bridge-to-efo.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-efo
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Term]

diff --git a/src/ontology/bridge/cl-bridge-to-efo.owl b/src/ontology/bridge/cl-bridge-to-efo.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-efo.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-efo/2023-06-27/uberon/bridge/cl-bridge-to-efo.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-efo/2023-09-05/uberon/bridge/cl-bridge-to-efo.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-ehdaa.obo b/src/ontology/bridge/cl-bridge-to-ehdaa.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-ehdaa
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 
 [Typedef]

diff --git a/src/ontology/bridge/cl-bridge-to-ehdaa.owl b/src/ontology/bridge/cl-bridge-to-ehdaa.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa/2023-06-27/uberon/bridge/cl-bridge-to-ehdaa.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa/2023-09-05/uberon/bridge/cl-bridge-to-ehdaa.owl"/>
         <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.obolibrary.org/obo/uberon/references/reference_0000026</rdfs:seeAlso>
     </owl:Ontology>
 

diff --git a/src/ontology/bridge/cl-bridge-to-ehdaa2.obo b/src/ontology/bridge/cl-bridge-to-ehdaa2.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-ehdaa2
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 property_value: dc-title "CL bridge to ehdaa2" xsd:string
 property_value: dc-description "Equivalence axioms between EHDAA2 and CL. EHDAA2 replaces EHDAA" xsd:string

diff --git a/src/ontology/bridge/cl-bridge-to-ehdaa2.owl b/src/ontology/bridge/cl-bridge-to-ehdaa2.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa2.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa2/2023-06-27/uberon/bridge/cl-bridge-to-ehdaa2.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa2/2023-09-05/uberon/bridge/cl-bridge-to-ehdaa2.owl"/>
         <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Jonathan Bard</dc:contributor>
         <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL editors</dc:creator>
         <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Equivalence axioms between EHDAA2 and CL. EHDAA2 replaces EHDAA</dc:description>

diff --git a/src/ontology/bridge/cl-bridge-to-emapa.obo b/src/ontology/bridge/cl-bridge-to-emapa.obo
@@ -1,5 +1,5 @@
 ontology: uberon/bridge/cl-bridge-to-emapa
-data-version: 2023-06-27
+data-version: 2023-09-05
 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/references/reference_0000026" xsd:anyURI
 property_value: dc-title "CL bridge to emapa" xsd:string
 property_value: dc-description "Taxonomic equivalence axioms between EMAPA (abstract developmental mouse) and CL" xsd:string

diff --git a/src/ontology/bridge/cl-bridge-to-emapa.owl b/src/ontology/bridge/cl-bridge-to-emapa.owl
@@ -13,7 +13,7 @@
      xmlns:terms="http://purl.org/dc/terms/"
      xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
     <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl">
-        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa/2023-06-27/uberon/bridge/cl-bridge-to-emapa.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa/2023-09-05/uberon/bridge/cl-bridge-to-emapa.owl"/>
         <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anne Niknejad</dc:creator>
         <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Aurelie Comte</dc:creator>
         <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#string">CL editors</dc:creator>