feat: pinned ontologies for schema 5.3.0 (#275)

## Reason for Change
- #229 

## Changes
- modify pinned ontology versions

## Testing steps
- NONE


## Notes for Reviewer

---------

Co-authored-by: Evan Molinelli <[email protected]>
Co-authored-by: Evan Molinelli <[email protected]>
Co-authored-by: github-actions <[email protected]>

Author: 4 people

.github/workflows/generate_all_ontology.yml

@@ -10,6 +10,7 @@ on:
       - "**/asset-schemas/ontology_info_schema.json"
       - "**/asset-schemas/all_ontology_schema.json"
       - "**/tools/ontology-builder/src/all_ontology_generator.py"
+      - "**/ontology-assets/ontology_info.json"
     branches-ignore:
       - main
 

.github/workflows/generate_diff_ontology.yml

@@ -13,6 +13,7 @@ on:
 
 jobs:
   ontology-processing:
+    if: false # DISABLE. Should run instead of generate_all_ontology.yml
     runs-on: ubuntu-latest
     steps:
       - name: Checkout

api/python/ontology-assets-version.txt

@@ -1 +1 @@
-1b41e396a7ce1aaca9dfcc6959880a310a62cd5d
+ab022d6d60ffed979f804eeef451ae1412c1f57a

api/python/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cellxgene_ontology_guide"
-version = "1.5.0-alpha"
+version = "1.5.0"
 description = "Access ontology metadata used by CZ cellxgene"
 authors = [
     { name = "Chan Zuckerberg Initiative Foundation", email = "[email protected]" }
@@ -31,7 +31,13 @@ Issues = "https://github.com/chanzuckerberg/cellxgene-ontology-guide/issues"
 Changelog = "https://github.com/chanzuckerberg/cellxgene-ontology-guide/blob/main/api/python/CHANGELOG.md"
 
 [project.optional-dependencies]
-test = ["pytest", "coverage", "nbconvert", "jupyter"]
+test = [
+    "pytest",
+    "coverage",
+    "nbconvert",
+    "jupyter",
+    "nbformat>=5.10.4",
+]
 docs = ["pdoc"]
 
 [tool.setuptools.packages.find]

ontology-assets/CL-ontology-v2025-02-13.json.gz

@@ -1,13 +1,13 @@
 {
   "ontologies": {
     "CL": {
-      "version": "v2024-08-16",
+      "version": "v2025-02-13",
       "source": "https://github.com/obophenotype/cell-ontology/releases/download",
       "filename": "cl.owl",
       "cross_ontology_mapping": "cl.sssom.tsv"
     },
     "EFO": {
-      "version": "v3.74.0",
+      "version": "v3.75.0",
       "source": "https://github.com/EBISPOT/efo/releases/download",
       "filename": "efo.owl"
     },
@@ -17,38 +17,38 @@
       "filename": "hancestro.owl"
     },
     "HsapDv": {
-      "version": "v2024-05-28",
+      "version": "v2025-01-23",
       "source": "https://github.com/obophenotype/developmental-stage-ontologies/releases/download",
       "filename": "hsapdv.owl"
     },
     "MONDO": {
-      "version": "v2024-08-06",
+      "version": "v2025-02-04",
       "source": "https://github.com/monarch-initiative/mondo/releases/download",
       "filename": "mondo.owl"
     },
     "MmusDv": {
-      "version": "v2024-05-28",
+      "version": "v2025-01-23",
       "source": "https://github.com/obophenotype/developmental-stage-ontologies/releases/download",
       "filename": "mmusdv.owl"
     },
     "NCBITaxon": {
-      "version": "v2023-06-20",
+      "version": "v2024-11-25",
       "source": "https://github.com/obophenotype/ncbitaxon/releases/download",
       "filename": "ncbitaxon.owl.gz"
     },
     "UBERON": {
-      "version": "v2024-08-07",
+      "version": "v2025-01-15",
       "source": "https://github.com/obophenotype/uberon/releases/download",
       "filename": "uberon.owl",
       "cross_ontology_mapping": "uberon.sssom.tsv"
     },
     "PATO": {
-      "version": "v2023-05-18",
+      "version": "v2025-02-01",
       "source": "https://github.com/pato-ontology/pato/raw",
       "filename": "pato.owl"
     },
     "FBbt": {
-      "version": "v2024-12-05",
+      "version": "v2025-02-13",
       "source": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/releases/download",
       "filename": "fbbt.owl",
       "map_to": [
@@ -57,12 +57,12 @@
       ]
     },
     "FBdv": {
-      "version": "v2024-12-04",
+      "version": "v2025-02-12",
       "source": "https://github.com/FlyBase/drosophila-developmental-ontology/releases/download",
       "filename": "fbdv.owl"
     },
     "ZFA": {
-      "version": "v2022-12-09",
+      "version": "v2025-01-28",
       "source": "https://github.com/ZFIN/zebrafish-anatomical-ontology/raw",
       "filename": "zfa.owl",
       "additional_ontologies": [
@@ -74,12 +74,12 @@
       ]
     },
     "WBls": {
-      "version": "vWS295",
+      "version": "vWS296",
       "source": "https://github.com/obophenotype/c-elegans-development-ontology/raw/",
       "filename": "wbls.owl"
     },
     "WBbt": {
-      "version": "v2024-09-24",
+      "version": "v2025-01-02",
       "source": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/raw",
       "filename": "wbbt.owl",
       "map_to": [

ontology-assets/EFO-ontology-v3.75.0.json.gz

@@ -2,13 +2,13 @@
   "5.3.0": {
     "ontologies": {
       "CL": {
-        "version": "v2024-08-16",
+        "version": "v2025-02-13",
         "source": "https://github.com/obophenotype/cell-ontology/releases/download",
         "filename": "cl.owl",
         "cross_ontology_mapping": "cl.sssom.tsv"
       },
       "EFO": {
-        "version": "v3.74.0",
+        "version": "v3.75.0",
         "source": "https://github.com/EBISPOT/efo/releases/download",
         "filename": "efo.owl"
       },
@@ -18,38 +18,38 @@
         "filename": "hancestro.owl"
       },
       "HsapDv": {
-        "version": "v2024-05-28",
+        "version": "v2025-01-23",
         "source": "https://github.com/obophenotype/developmental-stage-ontologies/releases/download",
         "filename": "hsapdv.owl"
       },
       "MONDO": {
-        "version": "v2024-08-06",
+        "version": "v2025-02-04",
         "source": "https://github.com/monarch-initiative/mondo/releases/download",
         "filename": "mondo.owl"
       },
       "MmusDv": {
-        "version": "v2024-05-28",
+        "version": "v2025-01-23",
         "source": "https://github.com/obophenotype/developmental-stage-ontologies/releases/download",
         "filename": "mmusdv.owl"
       },
       "NCBITaxon": {
-        "version": "v2023-06-20",
+        "version": "v2024-11-25",
         "source": "https://github.com/obophenotype/ncbitaxon/releases/download",
         "filename": "ncbitaxon.owl.gz"
       },
       "UBERON": {
-        "version": "v2024-08-07",
+        "version": "v2025-01-15",
         "source": "https://github.com/obophenotype/uberon/releases/download",
         "filename": "uberon.owl",
         "cross_ontology_mapping": "uberon.sssom.tsv"
       },
       "PATO": {
-        "version": "v2023-05-18",
+        "version": "v2025-02-01",
         "source": "https://github.com/pato-ontology/pato/raw",
         "filename": "pato.owl"
       },
       "FBbt": {
-        "version": "v2024-12-05",
+        "version": "v2025-02-13",
         "source": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/releases/download",
         "filename": "fbbt.owl",
         "map_to": [
@@ -58,12 +58,12 @@
         ]
       },
       "FBdv": {
-        "version": "v2024-12-04",
+        "version": "v2025-02-12",
         "source": "https://github.com/FlyBase/drosophila-developmental-ontology/releases/download",
         "filename": "fbdv.owl"
       },
       "ZFA": {
-        "version": "v2022-12-09",
+        "version": "v2025-01-28",
         "source": "https://github.com/ZFIN/zebrafish-anatomical-ontology/raw",
         "filename": "zfa.owl",
         "additional_ontologies": [
@@ -75,12 +75,12 @@
         ]
       },
       "WBls": {
-        "version": "vWS295",
+        "version": "vWS296",
         "source": "https://github.com/obophenotype/c-elegans-development-ontology/raw/",
         "filename": "wbls.owl"
       },
       "WBbt": {
-        "version": "v2024-09-24",
+        "version": "v2025-01-02",
         "source": "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/raw",
         "filename": "wbbt.owl",
         "map_to": [

ontology-assets/FBbt-ontology-v2025-02-13.json.gz

@@ -338,7 +338,11 @@ def _parse_ontologies(
     for onto_file in os.listdir(working_dir):
         if not onto_file.endswith(".owl"):
             continue
+        elif onto_file.rstrip(".owl") not in ontology_info:
+            logging.info(f"Skipping {onto_file} as it is not in the ontology_info.json")
+            continue
         onto = _load_ontology_object(os.path.join(working_dir, onto_file))
+
         version = ontology_info[onto.name]["version"]
         output_file = os.path.join(output_path, get_ontology_file_name(onto.name, version))
         logging.info(f"Processing {output_file}")