Spaces:
Sleeping
Sleeping
File size: 2,689 Bytes
1c6cb4b 7b3f817 cdc75a8 98d71a3 1c6cb4b 98d71a3 1087a21 98d71a3 a9daa10 98d71a3 1087a21 98d71a3 1087a21 98d71a3 cdc75a8 98d71a3 7b3f817 a9daa10 98d71a3 a9daa10 98d71a3 a9daa10 98d71a3 cdc75a8 1c6cb4b 7b3f817 98d71a3 1087a21 98d71a3 1087a21 cdc75a8 98d71a3 cdc75a8 98d71a3 a9daa10 98d71a3 a9daa10 cdc75a8 98d71a3 cdc75a8 98d71a3 7b3f817 98d71a3 7b3f817 98d71a3 7b3f817 98d71a3 cdc75a8 98d71a3 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 |
# genesis/api_clients/umls_api.py
import os
import requests
from typing import Dict, List, Optional
# UMLS API
UMLS_BASE = "https://uts-ws.nlm.nih.gov/rest"
UMLS_API_KEY = os.getenv("UMLS_API_KEY") # Add this to your Hugging Face secrets or .env
if not UMLS_API_KEY:
raise EnvironmentError("UMLS_API_KEY is missing. Add it to your environment variables or Hugging Face secrets.")
# UMLS requires ticket-granting service for authentication
def get_tgt() -> str:
"""
Obtain a Ticket Granting Ticket (TGT) for UMLS authentication.
"""
r = requests.post("https://utslogin.nlm.nih.gov/cas/v1/api-key", data={"apikey": UMLS_API_KEY})
r.raise_for_status()
from xml.etree import ElementTree
root = ElementTree.fromstring(r.text)
return root.attrib.get("action")
def get_service_ticket(tgt: str) -> str:
"""
Get a single-use service ticket for API requests.
"""
r = requests.post(tgt, data={"service": "http://umlsks.nlm.nih.gov"})
r.raise_for_status()
return r.text
def search_umls(query: str, max_results: int = 10) -> List[Dict]:
"""
Search UMLS Metathesaurus for a term and return CUIs and names.
"""
tgt = get_tgt()
ticket = get_service_ticket(tgt)
params = {"string": query, "ticket": ticket, "pageSize": max_results}
r = requests.get(f"{UMLS_BASE}/search/current", params=params)
r.raise_for_status()
results = r.json().get("result", {}).get("results", [])
return [
{
"ui": item.get("ui"),
"name": item.get("name"),
"rootSource": item.get("rootSource")
}
for item in results if item.get("ui") != "NONE"
]
def get_concept_details(cui: str) -> Dict:
"""
Get full details for a given CUI (Concept Unique Identifier).
Includes synonyms, definitions, and mappings.
"""
tgt = get_tgt()
ticket = get_service_ticket(tgt)
r = requests.get(f"{UMLS_BASE}/content/current/CUI/{cui}", params={"ticket": ticket})
r.raise_for_status()
return r.json().get("result", {})
def map_between_ontologies(cui: str) -> List[Dict]:
"""
Given a CUI, return cross-ontology mappings (e.g., SNOMED → MeSH → ICD).
"""
tgt = get_tgt()
ticket = get_service_ticket(tgt)
r = requests.get(f"{UMLS_BASE}/crosswalk/current/source/{cui}", params={"ticket": ticket})
r.raise_for_status()
return r.json().get("result", [])
def normalize_term(term: str) -> Optional[Dict]:
"""
Normalize a free-text biomedical term to its canonical CUI and return metadata.
"""
matches = search_umls(term, max_results=1)
return matches[0] if matches else None
|