Merge branch 'master' into remove-has_skeleton-injections

.github/CODEOWNERS

@@ -1,10 +1,9 @@
 # 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
+*uberon.Makefile @gouttegd @matentzn
 
 
 #docs/*  action@github.com 

.github/workflows/diff.yml

@@ -10,7 +10,7 @@ env:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   branch_status:
-    if: ${{ github.event.issue.pull_request }}
+    if: ${{ github.event.issue.pull_request && github.event.issue.state == 'open' }}
     runs-on: ubuntu-latest
     permissions:
       contents: read

.github/workflows/reviewers.yml

@@ -0,0 +1,47 @@
+name: Assign Reviewers for Uberon
+
+on:
+  pull_request:
+    types: [opened, synchronize]
+    paths:
+      - src/ontology/uberon-edit.obo
+
+jobs:
+  assign-reviewer:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0  # Fetch the entire history for all branches
+
+      - name: Fetch base branch
+        run: |
+          git fetch origin ${{ github.base_ref }}  # Fetch base branch explicitly
+      
+      - name: Check if equivalent class axiom was edited
+        id: check_intersection_of
+        run: |
+          git diff origin/${{ github.base_ref }}...HEAD -- src/ontology/uberon-edit.obo > diff.txt
+          if grep -E '^(-|\+)intersection_of:' diff.txt; then
+            echo "intersection_of_found=true" >> $GITHUB_ENV
+          else
+            echo "intersection_of_found=false" >> $GITHUB_ENV
+          fi
+
+      - name: Assign reviewer
+        if: env.intersection_of_found == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh api repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/requested_reviewers \
+            --method POST \
+            --field reviewers[]=cmungall
+
+      - name: Block PR by requesting changes
+        if: env.intersection_of_found == 'true'
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh pr review ${{ github.event.pull_request.number }} --request-changes --body "Changes detected in \`src/ontology/uberon-edit.obo\` involving \`intersection_of\`. Review by specific Uberon Core Team member is required."

.gitignore

@@ -113,6 +113,7 @@ src/ontology/ed_definitions_merged.owl
 src/ontology/imports/*.obo
 imports/*.obo
 uberon-lastbuild.owl
+uberon-lastbuild.obo
 src/mappings/uberon-local.sssom.tsv
 src/mappings/uberon.sssom.tsv
 src/ontology/imports/*_terms_combined.txt

docs/uberon-editor-sop.md

@@ -119,7 +119,7 @@ Guidelines on the type of synonyms:
 
 Example: the terms “aorta wall”, “aortic wall” and “wall of aorta” all refer to the exact same concept and would be considered exact synonyms. Terms that may refer to other concepts, especially within the biomedical domain, should not be annotated as exact synonyms, including abbreviations. 
 
-2. A synonym that is an abbreviation should be annotated as a _related_ synonym and with property type “abbreviation” (technically: the synonym annotation assertion axiom should itself be annotated with a `http://www.geneontology.org/formats/oboInOwl#hasSynonymType` property with value `http://purl.obolibrary.org/obo/uberon/core#ABBREVIATION`). 
+2. A synonym that is an abbreviation should be annotated as a _related_ synonym and with property type “abbreviation” (technically: the synonym annotation assertion axiom should itself be annotated with a `http://www.geneontology.org/formats/oboInOwl#hasSynonymType` property with value `http://purl.obolibrary.org/obo/OMO_0003000`). 
 
 Example: “BA” is a related synonym for both 'basilar artery' and 'bed nucleus of the accessory olfactory tract' at the time of this writing. Additionally, within the biomedical domain, it can also represent 'brachial artery' or 'Bone Age', two other distinct concepts with separate OBO ontology terms.
 

src/mappings/biomappings.sssom.tsv

@@ -1,24 +1,26 @@
 #curie_map:
-#  BTO: http://purl.obolibrary.org/obo/BTO_
-#  IDOMAL: http://purl.obolibrary.org/obo/IDOMAL_
-#  UBERON: http://purl.obolibrary.org/obo/UBERON_
-#  VO: http://purl.obolibrary.org/obo/VO_
-#  mesh: http://id.nlm.nih.gov/mesh/
-#  orcid: https://orcid.org/
-#mapping_set_id: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv
-#mapping_set_version: 0.3.8.dev0
-#mapping_set_title: Biomappings
-#mapping_set_description: Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings.
+#  BTO: "http://purl.obolibrary.org/obo/BTO_"
+#  IDOMAL: "http://purl.obolibrary.org/obo/IDOMAL_"
+#  UBERON: "http://purl.obolibrary.org/obo/UBERON_"
+#  VO: "http://purl.obolibrary.org/obo/VO_"
+#  mesh: "http://id.nlm.nih.gov/mesh/"
+#  obo: "http://purl.obolibrary.org/obo/"
+#  orcid: "https://orcid.org/"
+#mapping_set_id: "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv"
+#mapping_set_version: "0.3.8.dev0"
+#mapping_set_title: "Biomappings"
+#mapping_set_description: "Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings."
 #creator_id:
-#  - orcid:0000-0001-9439-5346
-#  - orcid:0000-0002-1216-4761
-#  - orcid:0000-0002-2046-6145
-#  - orcid:0000-0002-2627-0696
-#  - orcid:0000-0002-6601-2165
-#  - orcid:0000-0003-1307-2508
-#  - orcid:0000-0003-4423-4370
-#license: https://creativecommons.org/publicdomain/zero/1.0/
-#mapping_provider: https://github.com/biopragmatics/biomappings
+#  - "orcid:0000-0001-9439-5346"
+#  - "orcid:0000-0002-1216-4761"
+#  - "orcid:0000-0002-2046-6145"
+#  - "orcid:0000-0002-2627-0696"
+#  - "orcid:0000-0002-6601-2165"
+#  - "orcid:0000-0003-1307-2508"
+#  - "orcid:0000-0003-4423-4370"
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#subject_source: "obo:uberon/core.owl"
+#mapping_provider: "https://github.com/biopragmatics/biomappings"
 subject_id	subject_label	predicate_id	predicate_modifier	object_id	object_label	mapping_justification	author_id	mapping_tool	confidence
 UBERON:0000016	endocrine pancreas	skos:exactMatch		mesh:D007515	Islets of Langerhans	semapv:LexicalMatching		generate_uberon_mesh_mappings.py	0.9
 UBERON:0000017	exocrine pancreas	skos:exactMatch		mesh:D046790	Pancreas, Exocrine	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
@@ -286,8 +288,6 @@ UBERON:2001553	manubrium	skos:exactMatch		mesh:D008371	Manubrium	semapv:ManualMa
 UBERON:2001977	pad	skos:exactMatch	Not	mesh:D058729	Peripheral Arterial Disease	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 UBERON:3010463	animal cap	skos:exactMatch		BTO:0004724	animal cap	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	generate_uberon_bto_mappings.py	0.9
 UBERON:3010586	vasa efferentia	skos:exactMatch		BTO:0002254	vas efferens	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py	0.556
-UBERON:3011045	gasserian ganglion	skos:exactMatch		mesh:D012668	Trigeminal Ganglion	semapv:LexicalMatching		generate_uberon_mesh_mappings.py	0.9
-UBERON:3011048	genital system	skos:exactMatch		mesh:D005835	Genitalia	semapv:LexicalMatching		generate_uberon_mesh_mappings.py	0.9
 UBERON:4000104	ganoine	skos:exactMatch		mesh:C067951	ganoine	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 UBERON:4000163	anal fin	skos:exactMatch		BTO:0004652	anal fin	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	generate_uberon_bto_mappings.py	0.9
 UBERON:4000164	caudal fin	skos:exactMatch		BTO:0001827	tail fin	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py	0.556