Create ncbi.py

mcp/ncbi.py

@@ -0,0 +1,35 @@
+# mcp/ncbi.py
+"""
+NCBI E-utilities helpers – Gene, Protein, ClinVar, MeSH.
+"""
+
+import os
+import httpx
+from typing import List, Dict
+
+NCBI_KEY = os.getenv("BIO_KEY")  # optional but increases rate limits
+BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
+
+async def _get(endpoint: str, params: Dict) -> Dict:
+    if NCBI_KEY:
+        params["api_key"] = NCBI_KEY
+    async with httpx.AsyncClient(timeout=20) as client:
+        r = await client.get(f"{BASE}{endpoint}", params=params)
+        r.raise_for_status()
+        return r.json() if r.headers["Content-Type"].startswith("application/json") else r.text
+
+# ---------- Public helpers ----------
+async def search_gene(term: str, retmax: int = 5) -> List[Dict]:
+    """Return basic gene info (ID + name/symbol) by search term."""
+    data = await _get("esearch.fcgi", {"db": "gene", "term": term, "retmode": "json", "retmax": retmax})
+    ids = data["esearchresult"]["idlist"]
+    if not ids:
+        return []
+    summary = await _get("esummary.fcgi", {"db": "gene", "id": ",".join(ids), "retmode": "json"})
+    return list(summary["result"].values())[1:]  # first key is 'uids'
+
+async def get_mesh_definition(term: str) -> str:
+    """Return MeSH term definition (first record)."""
+    text = await _get("esummary.fcgi", {"db": "mesh", "term": term, "retmode": "json", "retmax": 1})
+    recs = list(text["result"].values())[1:]
+    return recs[0].get("ds_meshterms", [""])[0] if recs else ""