feat: update ontology_info.json for 5.1

api/python/ontology-assets-version.txt

@@ -1 +1 @@
-22dd42053d936b87d05c9786328723226e36c84e
+6c11b719f1b469696aac64b16ccde2428c0dfaa6

api/python/src/cellxgene_ontology_guide/ontology_parser.py

@@ -500,7 +500,7 @@ def get_term_label(self, term_id: str) -> str:
         >>> from cellxgene_ontology_guide.ontology_parser import OntologyParser
         >>> ontology_parser = OntologyParser()
         >>> ontology_parser.get_term_label("CL:0000005")
-        'fibroblast neural crest derived'
+        'neural crest derived fibroblast'
 
         :param term_id: str ontology term to fetch label for
         :return: str human-readable label for the term
@@ -520,7 +520,7 @@ def map_term_labels(self, term_ids: Iterable[str]) -> Dict[str, str]:
         >>> from cellxgene_ontology_guide.ontology_parser import OntologyParser
         >>> ontology_parser = OntologyParser()
         >>> ontology_parser.map_term_labels(["CL:0000005", "CL:0000003"])
-        {'CL:0000005': 'fibroblast neural crest derived', 'CL:0000003': 'obsolete native cell'}
+        {'CL:0000005': 'neural crest derived fibroblast', 'CL:0000003': 'obsolete native cell'}
 
         :param term_ids: list of str ontology terms to fetch label for
         :return: Dict[str, str] mapping term IDs to their respective human-readable labels
@@ -536,7 +536,7 @@ def get_term_description(self, term_id: str) -> Optional[str]:
         >>> from cellxgene_ontology_guide.ontology_parser import OntologyParser
         >>> ontology_parser = OntologyParser()
         >>> ontology_parser.get_term_description("CL:0000005")
-        'Any fibroblast that is deriived from the neural crest.'
+        'Any fibroblast that is derived from the neural crest.'
 
         :param term_id: str ontology term to fetch description for
         :return: str description for the term
@@ -556,7 +556,7 @@ def map_term_descriptions(self, term_ids: List[str]) -> Dict[str, Optional[str]]
         >>> from cellxgene_ontology_guide.ontology_parser import OntologyParser
         >>> ontology_parser = OntologyParser()
         >>> ontology_parser.map_term_descriptions(["CL:0000005", "CL:0000006"])
-        {'CL:0000005': 'Any fibroblast that is deriived from the neural crest.', 'CL:0000006': None}
+        {'CL:0000005': 'Any fibroblast that is derived from the neural crest.', 'CL:0000006': None}
 
         :param term_ids: list of str ontology terms to fetch descriptions for
         :return: Dict[str, str] mapping term IDs to their respective descriptions
@@ -592,7 +592,7 @@ def map_term_synonyms(self, term_ids: List[str]) -> Dict[str, List[str]]:
         >>> from cellxgene_ontology_guide.ontology_parser import OntologyParser
         >>> ontology_parser = OntologyParser()
         >>> ontology_parser.map_term_synonyms(["CL:0000005", "CL:0000019"])
-        {'CL:0000005': [], 'CL:0000019': ['sperm cell', 'spermatozoid', 'spermatozoon']}
+        {'CL:0000005': ['fibroblast neural crest derived'], 'CL:0000019': ['sperm cell', 'spermatozoid', 'spermatozoon']}
 
         :param term_ids: list of str ontology terms to fetch synonyms for
         :return: Dict[str, List[str]] mapping term IDs to their respective synonym lists

ontology-assets/ontology_info.json

@@ -1,4 +1,53 @@
 {
+  "5.1.0": {
+    "ontologies": {
+      "CL": {
+        "version": "v2024-04-05",
+        "source": "https://github.com/obophenotype/cell-ontology/releases/download",
+        "filename": "cl.owl"
+      },
+      "EFO": {
+        "version": "v3.65.0",
+        "source": "https://github.com/EBISPOT/efo/releases/download",
+        "filename": "efo.owl"
+      },
+      "HANCESTRO": {
+        "version": "3.0",
+        "source": "https://github.com/EBISPOT/hancestro/raw",
+        "filename": "hancestro.owl"
+      },
+      "HsapDv": {
+        "version": "11",
+        "source": "http://aber-owl.net/media/ontologies/HSAPDV",
+        "filename": "hsapdv.owl"
+      },
+      "MONDO": {
+        "version": "v2024-05-08",
+        "source": "https://github.com/monarch-initiative/mondo/releases/download",
+        "filename": "mondo.owl"
+      },
+      "MmusDv": {
+        "version": "9",
+        "source": "http://aber-owl.net/media/ontologies/MMUSDV",
+        "filename": "mmusdv.owl"
+      },
+      "NCBITaxon": {
+        "version": "v2023-06-20",
+        "source": "https://github.com/obophenotype/ncbitaxon/releases/download",
+        "filename": "ncbitaxon.owl.gz"
+      },
+      "UBERON": {
+        "version": "v2024-03-22",
+        "source": "https://github.com/obophenotype/uberon/releases/download",
+        "filename": "uberon.owl"
+      },
+      "PATO": {
+        "version": "v2023-05-18",
+        "source": "https://github.com/pato-ontology/pato/raw",
+        "filename": "pato.owl"
+      }
+    }
+  },
   "5.0.0": {
     "ontologies": {
       "CL": {
@@ -46,6 +95,7 @@
         "source": "https://github.com/pato-ontology/pato/raw",
         "filename": "pato.owl"
       }
-    }
+    },
+    "deprecated_on": "2024-05-10"
   }
 }

tools/ontology-builder/src/all_ontology_generator.py

@@ -195,9 +195,8 @@ def _extract_ontology_term_metadata(onto: owlready2.entity.ThingClass) -> Dict[s
         if getattr(onto_term, "IAO_0000115", None):
             term_dict[term_id]["description"] = onto_term.IAO_0000115[0]
         # optional synonym list, if available
-        if getattr(onto_term, "hasExactSynonym", None):
-            term_dict[term_id]["synonyms"] = onto_term.hasExactSynonym
-
+        if hasExactSynonym := getattr(onto_term, "hasExactSynonym", None):
+            term_dict[term_id]["synonyms"] = [str(x) for x in hasExactSynonym]
         # Add the "deprecated" status and associated metadata if True
         term_dict[term_id]["deprecated"] = False
         if onto_term.deprecated and onto_term.deprecated.first():