Update genesis/api_clients/bioportal_api.py

genesis/api_clients/bioportal_api.py

@@ -38,6 +38,26 @@ def search_ontology(term: str, max_results: int = 5) -> List[Dict]:
 
     return terms
 
+# -------------------------
+# Expand Query with Related Ontology Terms
+# -------------------------
+def expand_with_bioportal(term: str, max_results: int = 5) -> List[str]:
+    """
+    Expand a biomedical term into related ontology labels.
+    This is the function called by pipeline.py
+    """
+    try:
+        results = search_ontology(term, max_results)
+        expanded = []
+        for res in results:
+            if res["prefLabel"] and res["prefLabel"].lower() != term.lower():
+                expanded.append(res["prefLabel"])
+            expanded.extend(res.get("synonyms", []))
+        return list(set(expanded))  # unique terms only
+    except Exception as e:
+        print(f"[BioPortal] Expansion failed for '{term}': {e}")
+        return []
+
 # -------------------------
 # Get Term Details
 # -------------------------
@@ -84,5 +104,5 @@ def ontology_context(term: str) -> Dict:
     return {
         "ontology_terms": ontology_terms,
         "umls_cuis": list(set(cuis)),
-        "literature": pubmed_api.search_pubmed(term)
+        "literature": pubmed_api.search_pubmed_literature(term)  # fixed call name
     }