chore: update ontology decendant mappings (#162)

chanzuckerberg · Apr 2, 2024 · 12def74 · 12def74
1 parent 2e9d483
commit 12def74
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Showing 6 changed files with 64 additions and 32 deletions.
diff --git a/.../workflows/generate_decendant_mapping.yml → ...workflows/generate_descendant_mapping.yml b/.../workflows/generate_decendant_mapping.yml → ...workflows/generate_descendant_mapping.yml
@@ -1,7 +1,7 @@
 #This is a github actions that run every monday at 12am. It will run generate_decendant_mapping.py off the main
 #  github branch and open a pull request to commit the new ontology_decendant files to cellxgene-ontology-guide
 
-name: Generate Ontology Decendant Mappings
+name: Generate Ontology Descendant Mappings
 on:
   schedule:
     - cron: "0 0 * * 1"
@@ -20,7 +20,7 @@ permissions:
   pull-requests: write
 
 jobs:
-  generate-ontology-decendant-mappings:
+  generate-ontology-descendant-mappings:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout main
@@ -45,13 +45,9 @@ jobs:
           git config user.email [email protected]
       - name: install requirements
         run: |
-          cd ./tools/ontology-builder/ 
+          cd ./tools/ontology-builder/
           pip install -r requirements.txt
-      - name: install local cellxgene-ontology-guide api version #TODO: this or the pypi version?
-        run: |
-          cd ./api/python
-          make install
-      - name: generate ontology decendant mappings
+      - name: generate ontology descendant mappings
         run: |
           python3 tools/ontology-builder/src/descendent_mapping_generator.py
       - name: Create Pull Request
@@ -60,9 +56,9 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
           add-paths: |
             ./ontology-assets/*.json
-          commit-message: "chore: update ontology decendant mappings"
-          title: "chore: update ontology decendant mappings"
-          branch: update-ontology-decendant-mappings
+          commit-message: "chore: update ontology descendant mappings"
+          title: "chore: update ontology descendant mappings"
+          branch: update-ontology-descendant-mappings
           base: main
           signoff: true
           draft: false
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -90,17 +90,3 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           packages-dir: api/python/dist
-
-  tag-latest-release:
-    runs-on: [ubuntu-latest]
-    needs: publish-pypi-package
-    steps:
-      - name: Checkout main branch
-        uses: actions/checkout@v4
-        with:
-          ref: main
-          fetch-depth: 0
-      - name: Reassign 'latest' tag
-        run: |
-          git tag -f latest
-          git push origin latest
diff --git a/.github/workflows/tag-latest-ontology-assets.yml b/.github/workflows/tag-latest-ontology-assets.yml
@@ -0,0 +1,25 @@
+name: Tag 'Latest' Ontology Assets
+
+on:
+  push:
+    paths:
+      - "**/ontology-assets/**descendants.json"
+      - "**/ontology-assets/**list.json"
+      - "**/ontology-assets/ontology_info.json"
+    branches:
+      - main
+
+jobs:
+  tag-latest-release:
+    runs-on: [ubuntu-latest]
+    needs: publish-pypi-package
+    steps:
+      - name: Checkout main branch
+        uses: actions/checkout@v4
+        with:
+          ref: main
+          fetch-depth: 0
+      - name: Reassign 'latest' tag
+        run: |
+          git tag -f latest
+          git push origin latest
diff --git a/ontology-assets/cell_type_descendants.json b/ontology-assets/cell_type_descendants.json
@@ -13,9 +13,12 @@
     "CL:1000147",
     "CL:1000309",
     "CL:1000311",
+    "CL:1000409",
     "CL:1000477",
     "CL:2000018",
-    "CL:2000046"
+    "CL:2000046",
+    "CL:4030032",
+    "CL:4030033"
   ],
   "CL:0002320": [
     "CL:0000057",
@@ -162,6 +165,7 @@
     "CL:0000216",
     "CL:0000242",
     "CL:0000244",
+    "CL:0000307",
     "CL:0000312",
     "CL:0000322",
     "CL:0000362",
@@ -380,6 +384,7 @@
     "CL:4030011",
     "CL:4030018",
     "CL:4030023",
+    "CL:4030033",
     "CL:4030066",
     "CL:4033044",
     "CL:4033048"
@@ -670,6 +675,7 @@
     "CL:0000749",
     "CL:0000750",
     "CL:0000751",
+    "CL:0000752",
     "CL:0000753",
     "CL:0000754",
     "CL:0000756",
@@ -784,6 +790,7 @@
     "CL:4030063",
     "CL:4030065",
     "CL:4030067",
+    "CL:4033015",
     "CL:4033019",
     "CL:4033027",
     "CL:4033028",
@@ -934,6 +941,7 @@
     "CL:0000749",
     "CL:0000750",
     "CL:0000751",
+    "CL:0000752",
     "CL:0000753",
     "CL:0000754",
     "CL:0000756",
@@ -1028,6 +1036,7 @@
     "CL:4030006",
     "CL:4030027",
     "CL:4030028",
+    "CL:4030032",
     "CL:4030059",
     "CL:4030061",
     "CL:4030062",
@@ -1108,6 +1117,7 @@
     "CL:1000275",
     "CL:1000278",
     "CL:1000279",
+    "CL:1000409",
     "CL:1000443",
     "CL:1000477",
     "CL:1000487",
@@ -2110,6 +2120,7 @@
     "CL:0000749",
     "CL:0000750",
     "CL:0000751",
+    "CL:0000752",
     "CL:0000753",
     "CL:0000754",
     "CL:0000756",
@@ -2189,6 +2200,7 @@
     "CL:0000749",
     "CL:0000750",
     "CL:0000751",
+    "CL:0000752",
     "CL:0000753",
     "CL:0000754",
     "CL:0000756",
@@ -2254,7 +2266,8 @@
     "CL:0002627",
     "CL:0002629",
     "CL:0011028",
-    "CL:0013000"
+    "CL:0013000",
+    "CL:4033015"
   ],
   "CL:0000101": [
     "CL:0000006",
@@ -2297,6 +2310,7 @@
     "CL:0000006",
     "CL:0000099",
     "CL:0000100",
+    "CL:0000101",
     "CL:0000103",
     "CL:0000108",
     "CL:0000118",
@@ -2331,6 +2345,7 @@
     "CL:0000749",
     "CL:0000750",
     "CL:0000751",
+    "CL:0000752",
     "CL:0000753",
     "CL:0000754",
     "CL:0000756",
@@ -2553,13 +2568,15 @@
     "CL:2000016",
     "CL:2000018",
     "CL:2000041",
-    "CL:2000059"
+    "CL:2000059",
+    "CL:4030033"
   ],
   "CL:0002076": [
     "CL:0000155",
     "CL:0000158",
     "CL:0000162",
     "CL:0000209",
+    "CL:0000307",
     "CL:0000508",
     "CL:0000510",
     "CL:0000577",
@@ -2699,7 +2716,8 @@
     "CL:2000041",
     "CL:2000059",
     "CL:4030009",
-    "CL:4030011"
+    "CL:4030011",
+    "CL:4030033"
   ],
   "CL:0011026": [
     "CL:0000037",
@@ -2954,7 +2972,8 @@
     "CL:0002629",
     "CL:0011028",
     "CL:0013000",
-    "CL:4023059"
+    "CL:4023059",
+    "CL:4033015"
   ],
   "CL:0000098": [
     "CL:0000209",
@@ -3083,6 +3102,7 @@
     "CL:1000275",
     "CL:1000278",
     "CL:1000279",
+    "CL:1000409",
     "CL:1000443",
     "CL:1000477",
     "CL:1000487",
@@ -3290,6 +3310,7 @@
     "CL:1000698",
     "CL:1001318",
     "CL:4028004",
-    "CL:4028006"
+    "CL:4028006",
+    "CL:4030032"
   ]
 }
diff --git a/ontology-assets/tissue_descendants.json b/ontology-assets/tissue_descendants.json
@@ -253,6 +253,7 @@
   "UBERON:0000922": [
     "UBERON:0000088 (organoid)",
     "UBERON:0000926",
+    "UBERON:0001049",
     "UBERON:0004023",
     "UBERON:0004024",
     "UBERON:0004025",
@@ -465,6 +466,7 @@
     "UBERON:0016530",
     "UBERON:0016538",
     "UBERON:0016540",
+    "UBERON:0018105",
     "UBERON:0022232",
     "UBERON:0022352",
     "UBERON:0023787",
@@ -572,6 +574,7 @@
     "UBERON:0010032",
     "UBERON:0010033",
     "UBERON:0013682",
+    "UBERON:0018105",
     "UBERON:0019207"
   ],
   "UBERON:0001434": [
@@ -793,6 +796,7 @@
     "UBERON:0006761",
     "UBERON:0007625",
     "UBERON:0013682",
+    "UBERON:0018105",
     "UBERON:0019207"
   ],
   "UBERON:0000948": [

diff --git a/tools/ontology-builder/requirements.txt b/tools/ontology-builder/requirements.txt
@@ -1,5 +1,5 @@
+cellxgene-ontology-guide
 owlready2==0.45
 jsonschema>=4.21.1, <5
 semantic-version>=2.10.0, <3
 referencing>=0.33
-../../api/python