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# genesis/api_clients/bioportal_api.py
import requests
from typing import List, Dict, Optional
BIOPORTAL_BASE_URL = "https://data.bioontology.org"
BIOPORTAL_API_KEY = None # Load from secrets in Hugging Face or local .env
def search_term(term: str, ontologies: Optional[List[str]] = None, max_results: int = 20) -> List[Dict]:
"""
Search BioPortal for a term across one or more ontologies.
If no ontologies specified, searches all available ones.
"""
headers = {"Authorization": f"apikey token={BIOPORTAL_API_KEY}"}
params = {
"q": term,
"pagesize": max_results
}
if ontologies:
params["ontologies"] = ",".join(ontologies)
r = requests.get(f"{BIOPORTAL_BASE_URL}/search", headers=headers, params=params)
r.raise_for_status()
data = r.json()
results = []
for result in data.get("collection", []):
results.append({
"pref_label": result.get("prefLabel"),
"definition": result.get("definition", ["No definition found"])[0],
"synonyms": result.get("synonym", []),
"ontology": result.get("links", {}).get("ontology"),
"iri": result.get("@id"),
"score": result.get("score", 0)
})
return results
def get_concept_details(ontology_acronym: str, concept_id: str) -> Dict:
"""
Fetch detailed metadata for a specific ontology concept.
"""
headers = {"Authorization": f"apikey token={BIOPORTAL_API_KEY}"}
r = requests.get(f"{BIOPORTAL_BASE_URL}/ontologies/{ontology_acronym}/classes/{concept_id}",
headers=headers)
r.raise_for_status()
data = r.json()
return {
"pref_label": data.get("prefLabel"),
"definition": data.get("definition", ["No definition found"])[0],
"synonyms": data.get("synonym", []),
"properties": data.get("properties", {}),
"relations": data.get("links", {})
}
def map_to_ontologies(term: str, ontologies: List[str]) -> Dict[str, List[str]]:
"""
Map a given term to equivalent terms in multiple ontologies.
Returns a dictionary mapping ontology → list of equivalent labels.
"""
results = search_term(term, ontologies=ontologies)
mapping = {}
for res in results:
onto_name = res.get("ontology", "Unknown")
if onto_name not in mapping:
mapping[onto_name] = []
mapping[onto_name].append(res.get("pref_label"))
return mapping
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