Update genesis/api_clients/bioportal_api.py

genesis/api_clients/bioportal_api.py

@@ -3,71 +3,71 @@ import os
 import requests
 from typing import List, Dict, Optional
 
-# BioPortal API
+BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")  # From your Hugging Face secrets or .env
 BIOPORTAL_BASE = "https://data.bioontology.org"
-BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")  # You must add this to Hugging Face secrets or .env
-
-if not BIOPORTAL_API_KEY:
-    raise EnvironmentError("BIOPORTAL_API_KEY is missing. Add it to your environment variables or Hugging Face secrets.")
 
 HEADERS = {
     "Authorization": f"apikey token={BIOPORTAL_API_KEY}"
 }
 
-def search_terms(query: str, ontologies: Optional[List[str]] = None, max_results: int = 20) -> List[Dict]:
+def search_ontology(term: str, ontology: Optional[str] = None, max_results: int = 10) -> List[Dict]:
     """
-    Search BioPortal for ontology terms.
-    Optionally limit search to specific ontologies like 'GO', 'CHEBI', 'DOID', etc.
+    Search BioPortal for a given term, optionally within a specific ontology.
     """
     params = {
-        "q": query,
+        "q": term,
         "pagesize": max_results
     }
-    if ontologies:
-        params["ontologies"] = ",".join(ontologies)
+    if ontology:
+        params["ontology"] = ontology
     
-    r = requests.get(f"{BIOPORTAL_BASE}/search", headers=HEADERS, params=params)
+    r = requests.get(f"{BIOPORTAL_BASE}/search", params=params, headers=HEADERS)
     r.raise_for_status()
     data = r.json()
     
     results = []
     for item in data.get("collection", []):
         results.append({
-            "prefLabel": item.get("prefLabel"),
-            "definition": item.get("definition", []),
+            "label": item.get("prefLabel"),
+            "definition": item.get("definition"),
             "synonyms": item.get("synonym", []),
             "ontology": item.get("links", {}).get("ontology"),
-            "uri": item.get("@id"),
-            "cui": item.get("cui", []),
-            "semanticType": item.get("semanticType", []),
+            "iri": item.get("@id"),
+            "cui": item.get("cui", None),
+            "semantic_types": item.get("semanticType", [])
         })
     return results
 
-
-def get_term_details(term_uri: str) -> Dict:
+def get_term_details(ontology_acronym: str, term_id: str) -> Dict:
     """
-    Fetch full details for a given ontology term URI.
+    Get detailed information about a specific term in an ontology.
     """
-    encoded_uri = requests.utils.quote(term_uri, safe="")
-    r = requests.get(f"{BIOPORTAL_BASE}/ontologies/{encoded_uri}", headers=HEADERS)
+    encoded_term_id = term_id.replace(":", "%3A").replace("/", "%2F")
+    r = requests.get(
+        f"{BIOPORTAL_BASE}/ontologies/{ontology_acronym}/classes/{encoded_term_id}",
+        headers=HEADERS
+    )
     r.raise_for_status()
     return r.json()
 
-
-def find_related_terms(term_uri: str) -> List[Dict]:
+def map_to_ontologies(term: str) -> List[Dict]:
     """
-    Find related terms for a given ontology concept.
+    Search multiple ontologies for mappings of a term.
     """
-    encoded_uri = requests.utils.quote(term_uri, safe="")
-    r = requests.get(f"{BIOPORTAL_BASE}/ontologies/{encoded_uri}/related", headers=HEADERS)
+    params = {
+        "q": term,
+        "include": "mappings"
+    }
+    r = requests.get(f"{BIOPORTAL_BASE}/search", params=params, headers=HEADERS)
     r.raise_for_status()
-    return r.json()
-
-
-def map_to_ontology(entity_name: str, preferred_ontologies: Optional[List[str]] = None) -> Optional[Dict]:
-    """
-    Try to map a free-text biomedical entity name to an ontology concept.
-    Useful for linking PubMed entities, ChEMBL molecules, clinical trials to ontology terms.
-    """
-    matches = search_terms(entity_name, ontologies=preferred_ontologies, max_results=1)
-    return matches[0] if matches else None
+    data = r.json()
+    
+    mappings = []
+    for item in data.get("collection", []):
+        for mapping in item.get("mappings", []):
+            mappings.append({
+                "source": mapping.get("source"),
+                "target": mapping.get("target"),
+                "relation": mapping.get("relation")
+            })
+    return mappings