Merge branch 'master' into 3414_NTR_antimesosalpinx

.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."

src/ontology/uberon-edit.obo

@@ -72993,8 +72993,8 @@ id: UBERON:0003532
 name: hindlimb skin
 def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic]
 synonym: "hind limb skin" EXACT [OBOL:automatic]
-synonym: "lower limb skin" EXACT [FMA:23102]
 synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473]
+synonym: "lower limb skin" EXACT [FMA:23102]
 synonym: "skin of hind limb" EXACT [OBOL:automatic]
 synonym: "skin of hindlimb" EXACT [OBOL:automatic]
 synonym: "skin of lower extremity" EXACT [OBOL:automatic]
@@ -224699,6 +224699,14 @@ relationship: dc-contributor https://orcid.org/0000-0001-7655-4833 ! Ellen Quard
 relationship: part_of UBERON:0012331 ! mesosalpinx
 property_value: dcterms-date "2024-11-14T09:59:53Z" xsd:dateTime
 
+[Term]
+id: UBERON:8700000
+name: aorta-gonad-mesonephros
+def: "A transient organ in the developing embryo composed of the dorsal aorta, developing gonads, and embryonic kidney. This structure is located in the embryonic mesoderm and serves as the primary site for the generation of definitive hematopoietic stem cells." [PMID:25686881, PMID:25749005, PMID:31813624]
+is_a: UBERON:0002050 ! embryonic structure
+relationship: dc-contributor https://orcid.org/0009-0005-7919-4905
+property_value: dcterms-date "2024-10-25T08:42:34Z" xsd:dateTime
+
 [Term]
 id: UBERON:8700001
 name: follicle associated epithelium
@@ -224708,6 +224716,15 @@ is_a: UBERON:0004693 ! Peyer's patch epithelium
 relationship: dc-contributor https://orcid.org/0009-0005-7919-4905
 property_value: dcterms-date "2024-11-07T11:44:27Z" xsd:dateTime
 
+[Term]
+id: UBERON:8700002
+name: stratum spinosum of esophageal epithelium
+def: "The second deepest layer of the stratified squamous epithelium lining the esophagus, positioned directly above the stratum basale. It consists of multiple layers of keratinocytes connected by strong intercellular junctions called desmosomes, giving the cells a characteristic \"spiny\" appearance. This layer provides structural support, contributes to the epithelial barrier function, and serves as a transitional zone for keratinocytes migrating towards the luminal surface, playing a crucial role in maintaining the integrity and protective properties of the esophageal lining." [PMID:21126700, PMID:26019440]
+is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium
+relationship: dc-contributor https://orcid.org/0009-0005-7919-4905
+relationship: part_of UBERON:0001043 ! esophagus
+property_value: dcterms-date "2024-11-14T15:00:21Z" xsd:dateTime
+
 [Term]
 id: UBERON:8850000
 name: lumen of pulmonary alveolus

src/ontology/uberon-idranges.owl

@@ -261,4 +261,10 @@ Datatype: idrange:35
     Annotations:
         allocatedto: "Tiago Lubiana"
     EquivalentTo:
-        xsd:integer[>= 8900000, <= 8909999]
+        xsd:integer[>= 8900000, <= 8909999]
+
+Datatype: idrange:40
+    Annotations:
+        allocatedto: "NDI Cloud"
+    EquivalentTo:
+        xsd:integer[>= 8910000, <= 8919999]