Update genesis/ontology.py

genesis/ontology.py

@@ -1,8 +1,7 @@
 # genesis/ontology.py
 """
 Ontology Expansion & Merging for GENESIS-AI
-Uses UMLS & BioPortal to find related terms, synonyms, and hierarchies,
-and provides merging utilities for deduplication.
+Uses UMLS & BioPortal to find related terms, synonyms, and hierarchies.
 """
 
 import os
@@ -48,61 +47,42 @@ def expand_with_umls(term: str) -> Union[List[str], Dict]:
         return {"error": str(e)}
 
 
-# -------------------------
-# Combined Expansion
-# -------------------------
-def expand_terms_with_ontology(term: str) -> List[str]:
-    """Combine BioPortal and UMLS expansions."""
-    logging.info(f"[Ontology] Expanding term: {term}")
-    bioportal_terms = expand_with_bioportal(term)
-    umls_terms = expand_with_umls(term)
-    results = set()
-    if isinstance(bioportal_terms, list):
-        results.update(bioportal_terms)
-    if isinstance(umls_terms, list):
-        results.update(umls_terms)
-    final_terms = list(results) if results else [term]
-    logging.info(f"[Ontology] Found {len(final_terms)} expanded terms.")
-    return final_terms
-
-
 # -------------------------
 # Merge Ontology Terms
 # -------------------------
-def merge_ontology_terms(ontology_lists: List[List[Dict]]) -> List[Dict]:
+def merge_ontology_terms(query_term: str,
+                         umls_terms: Union[List[str], Dict, None] = None,
+                         bioportal_terms: Union[List[str], Dict, None] = None) -> List[str]:
     """
-    Merge ontology term lists from multiple sources and remove duplicates.
+    Merge the original query term with expanded terms from UMLS and BioPortal.
 
     Args:
-        ontology_lists: A list where each element is a list of ontology term dicts.
-            Example term: {"id": "GO:0008150", "label": "biological_process"}
+        query_term: Original search term.
+        umls_terms: List or error dict from expand_with_umls().
+        bioportal_terms: List or error dict from expand_with_bioportal().
 
     Returns:
-        Merged list of unique ontology terms.
+        List of unique merged terms (strings).
     """
-    logging.info("[Ontology] Merging ontology term lists...")
-    merged_terms = {}
-
-    for source_list in ontology_lists:
-        for term in source_list:
-            if not isinstance(term, dict):
-                continue
-            term_id = term.get("id") or term.get("iri") or term.get("label")
-            if term_id and term_id not in merged_terms:
-                merged_terms[term_id] = {
-                    "id": term_id,
-                    "label": term.get("label", ""),
-                    "source": term.get("source", "unknown")
-                }
-
-    merged_list = list(merged_terms.values())
-    logging.info(f"[Ontology] Merged total {len(merged_list)} unique terms.")
+    logging.info(f"[Ontology] Merging terms for query: {query_term}")
+    results = set()
+
+    if query_term:
+        results.add(query_term.strip())
+
+    if isinstance(umls_terms, list):
+        results.update(t.strip() for t in umls_terms if t and isinstance(t, str))
+
+    if isinstance(bioportal_terms, list):
+        results.update(t.strip() for t in bioportal_terms if t and isinstance(t, str))
+
+    merged_list = list(results)
+    logging.info(f"[Ontology] Merged {len(merged_list)} unique terms.")
     return merged_list
 
 
 __all__ = [
     "expand_with_bioportal",
     "expand_with_umls",
-    "expand_terms_with_ontology",
     "merge_ontology_terms"
 ]