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# 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 ""
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