Create agent/clinical_nlp.py

agent/clinical_nlp.py

@@ -0,0 +1,46 @@
+import requests
+import os
+
+def get_umls_api_key():
+    return os.getenv("UMLS_API_KEY")
+
+def get_bioportal_api_key():
+    return os.getenv("BIOPORTAL_API_KEY")
+
+def umls_concept_lookup(term):
+    key = get_umls_api_key()
+    if not key:
+        return [{"error": "UMLS API key not set."}]
+    url = f"https://uts-ws.nlm.nih.gov/rest/search/current?string={term}&apiKey={key}"
+    try:
+        response = requests.get(url, timeout=10)
+        results = response.json().get("result", {}).get("results", [])
+        return [
+            {
+                "name": r.get("name"),
+                "ui": r.get("ui"),
+                "rootSource": r.get("rootSource")
+            }
+            for r in results[:8]
+        ]
+    except Exception as e:
+        return [{"error": f"UMLS error: {e}"}]
+
+def bioportal_concept_lookup(term):
+    key = get_bioportal_api_key()
+    if not key:
+        return [{"error": "BioPortal API key not set."}]
+    url = f"https://data.bioontology.org/search?q={term}&apikey={key}"
+    try:
+        response = requests.get(url, timeout=10)
+        matches = response.json().get("collection", [])
+        return [
+            {
+                "prefLabel": m.get("prefLabel"),
+                "ontology": m.get("links", {}).get("ontology"),
+                "id": m.get("@id")
+            }
+            for m in matches[:8]
+        ]
+    except Exception as e:
+        return [{"error": f"BioPortal error: {e}"}]