feat: process ontology bridge terms

asset-schemas/all_ontology_schema.json

@@ -31,6 +31,16 @@
           "type": "integer"
         }
       },
+      "bridge_terms": {
+        "type": "object",
+        "description": "Map of bridge terms that connect this ontology term to other ontologies.",
+        "patternProperties": {
+          "^[A-Za-z0-9]+$": {
+            "$ref": "ontology_term_id_schema.json#/definitions/supported_term_id"
+          }
+        },
+        "additionalProperties": false
+      },
       "comments": {
         "type": "array",
         "items": {

asset-schemas/ontology_info_schema.json

@@ -17,15 +17,6 @@
           "patternProperties": {
             "^[A-Za-z0-9]+$": {
               "$ref": "#/definitions/ontologyEntry"
-            },
-            "FBbt": {
-              "$ref": "#/definitions/ontologyEntry"
-            },
-            "FBdv": {
-              "$ref": "#/definitions/ontologyEntry"
-            },
-            "ZFA": {
-              "$ref": "#/definitions/ontologyEntry"
             }
           },
           "additionalProperties": false
@@ -60,15 +51,20 @@
             "type": "string"
           },
           "description": "List of additional term id prefixes to extracted from the source ontology file."
+        },
+        "bridges": {
+          "type": "object",
+          "description": "ontology with mapping files from their terms to this ontology entry's terms.",
+          "patternProperties": {
+            "^[A-Za-z0-9]+$": {
+              "type": "string",
+              "format": "uri",
+              "description": "URI to file mapping between the ontology entry and this ontology"
+            }
+          },
+          "additionalProperties": false
         }
-      },
-      "required": [
-        "version",
-        "source",
-        "filename"
-      ],
-      "additionalProperties": false
+      }
     }
   }
 }
-

ontology-assets/ontology_info.json

@@ -49,7 +49,11 @@
       "FBbt": {
         "version": "v2024-10-17",
         "source": "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/releases/download",
-        "filename": "fbbt.owl"
+        "filename": "fbbt.owl",
+        "bridges": {
+          "CL": "https://github.com/obophenotype/uberon/raw/refs/heads/master/src/ontology/bridge/cl-bridge-to-fbbt.owl",
+          "UBERON": "https://github.com/obophenotype/uberon/raw/refs/heads/master/src/ontology/bridge/uberon-bridge-to-fbbt.owl"
+        }
       },
       "FBdv": {
         "version": "v2024-10-17",
@@ -62,7 +66,11 @@
         "filename": "zfa.owl",
         "additional_ontologies": [
           "ZFS"
-        ]
+        ],
+        "bridges": {
+          "CL": "https://github.com/obophenotype/uberon/raw/refs/heads/master/src/ontology/bridge/cl-bridge-to-zfa.owl",
+          "UBERON": "https://github.com/obophenotype/uberon/raw/refs/heads/master/src/ontology/bridge/cl-bridge-to-zfa.owl"
+        }
       }
     }
   },

tools/ontology-builder/src/all_ontology_generator.py

@@ -70,19 +70,29 @@ def _build_url(_ontology: str) -> str:
         onto_ref_data = ontology_info[_ontology]
         return f"{onto_ref_data['source']}/{onto_ref_data['version']}/{onto_ref_data['filename']}"
 
-    threads = []
-    for ontology, _ in ontology_info.items():
-        url = _build_url(ontology)
+    def _check_url(_ontology: str, _url: str) -> None:
         try:
-            urllib.request.urlopen(url)
+            urllib.request.urlopen(_url)
         except HTTPError as e:
-            raise Exception(f"{ontology} with pinned URL {url} returns status code {e.code}") from e
+            raise Exception(f"{_ontology} with pinned URL {_url} returns status code {e.code}") from e
         except URLError as e:
-            raise Exception(f"{ontology} with pinned URL {url} fails due to {e.reason}") from e
+            raise Exception(f"{_ontology} with pinned URL {_url} fails due to {e.reason}") from e
+
+    threads = []
+    for ontology, info in ontology_info.items():
+        url = _build_url(ontology)
+        _check_url(ontology, url)
 
         t = Thread(target=download, args=(ontology, url))
         t.start()
         threads.append(t)
+        if bridges := info.get("bridges"):
+            for bridge_ontology, bridge_url in bridges.items():
+                bridge_ontology = f"{ontology}_to_{bridge_ontology}"
+                _check_url(bridge_ontology, bridge_url)
+                t = Thread(target=download, args=(bridge_ontology, bridge_url))
+                t.start()
+                threads.append(t)
 
     for t in threads:
         t.join()
@@ -162,12 +172,28 @@ def _get_ancestors(onto_class: owlready2.entity.ThingClass, allowed_ontologies:
     }
 
 
-def _extract_ontology_term_metadata(onto: owlready2.entity.ThingClass, allowed_ontologies: list[str]) -> Dict[str, Any]:
+def _extract_bridge_terms(onto_term: owlready2.entity.ThingClass, bridge_ontologies: Dict[str, str]) -> Dict[str, str]:
+    """
+    Extract mapping of ontology term ID to equivalent term IDs in another ontology.
+
+    :param: onto_term: Ontology Term ID to find equivalent terms for
+    :param: bridge_ontologies: Map of ontologies to bridge file URIs to extract equivalent terms from
+    :return: Dict[str, str] map of bridged ontology term prefix to the equivalent term ID in that ontology for
+    onto_term, i.e. ZFA:0000001 -> {"UBERON": "UBERON:0000001", "CL": "CL:0000001",...}
+    """
+    # TODO: implement
+    return {}
+
+
+def _extract_ontology_term_metadata(
+    onto: owlready2.entity.ThingClass, allowed_ontologies: list[str], bridge_ontologies: Dict[str, str]
+) -> Dict[str, Any]:
     """
     Extract relevant metadata from ontology object and save into a dictionary following our JSON Schema
 
     :param: onto: Ontology Object to Process
     :param: allowed_ontologies: List of term prefixes to filter out terms that are not direct children from this ontology
+    :param: bridge_ontologies: Bridge files to map terms to equivalent terms in another ontology
     :return: Dict[str, Any] map of ontology term IDs to pertinent metadata from ontology files
     """
     term_dict: Dict[str, Any] = dict()
@@ -191,6 +217,8 @@ def _extract_ontology_term_metadata(onto: owlready2.entity.ThingClass, allowed_o
         # no current use-case for NCBITaxon
         term_dict[term_id]["ancestors"] = {} if onto.name == "NCBITaxon" else ancestors
 
+        term_dict[term_id]["bridge_terms"] = _extract_bridge_terms(onto_term, bridge_ontologies)
+
         term_dict[term_id]["label"] = onto_term.label[0] if onto_term.label else ""
 
         # optional description, if available
@@ -269,7 +297,8 @@ def _parse_ontologies(
         output_file = os.path.join(output_path, get_ontology_file_name(onto.name, version))
         logging.info(f"Processing {output_file}")
         allowed_ontologies = [onto.name] + ontology_info[onto.name].get("additional_ontologies", [])
-        onto_dict = _extract_ontology_term_metadata(onto, allowed_ontologies)
+        bridge_ontologies = ontology_info[onto.name].get("bridges", [])
+        onto_dict = _extract_ontology_term_metadata(onto, allowed_ontologies, bridge_ontologies)
 
         with gzip.GzipFile(output_file, mode="wb", mtime=0) as fp:
             fp.write(json.dumps(onto_dict, indent=2).encode("utf-8"))