genesis/api_clients/bioportal_api.py

# genesis/api_clients/bioportal_api.py
import os
import requests
from typing import List, Dict, Optional

BIOPORTAL_API_KEY = os.getenv("BIOPORTAL_API_KEY")  # From your Hugging Face secrets or .env
BIOPORTAL_BASE = "https://data.bioontology.org"

HEADERS = {
    "Authorization": f"apikey token={BIOPORTAL_API_KEY}"
}

def search_ontology(term: str, ontology: Optional[str] = None, max_results: int = 10) -> List[Dict]:
    """
    Search BioPortal for a given term, optionally within a specific ontology.
    """
    params = {
        "q": term,
        "pagesize": max_results
    }
    if ontology:
        params["ontology"] = ontology
    
    r = requests.get(f"{BIOPORTAL_BASE}/search", params=params, headers=HEADERS)
    r.raise_for_status()
    data = r.json()
    
    results = []
    for item in data.get("collection", []):
        results.append({
            "label": item.get("prefLabel"),
            "definition": item.get("definition"),
            "synonyms": item.get("synonym", []),
            "ontology": item.get("links", {}).get("ontology"),
            "iri": item.get("@id"),
            "cui": item.get("cui", None),
            "semantic_types": item.get("semanticType", [])
        })
    return results

def get_term_details(ontology_acronym: str, term_id: str) -> Dict:
    """
    Get detailed information about a specific term in an ontology.
    """
    encoded_term_id = term_id.replace(":", "%3A").replace("/", "%2F")
    r = requests.get(
        f"{BIOPORTAL_BASE}/ontologies/{ontology_acronym}/classes/{encoded_term_id}",
        headers=HEADERS
    )
    r.raise_for_status()
    return r.json()

def map_to_ontologies(term: str) -> List[Dict]:
    """
    Search multiple ontologies for mappings of a term.
    """
    params = {
        "q": term,
        "include": "mappings"
    }
    r = requests.get(f"{BIOPORTAL_BASE}/search", params=params, headers=HEADERS)
    r.raise_for_status()
    data = r.json()
    
    mappings = []
    for item in data.get("collection", []):
        for mapping in item.get("mappings", []):
            mappings.append({
                "source": mapping.get("source"),
                "target": mapping.get("target"),
                "relation": mapping.get("relation")
            })
    return mappings