bc_get_term_details
Retrieve detailed information about biomedical ontology terms including definitions, synonyms, and hierarchical relationships from verified knowledge bases.
Instructions
Get comprehensive details about a specific ontology term including definition, synonyms, hierarchical relationships.
Returns: dict: Term details with id, label, definition, synonyms, hierarchical info, num_descendants or error message.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| term_id | Yes | Term ID in CURIE format (e.g., 'EFO:0000001', 'GO:0008150') | |
| ontology_id | Yes | Ontology ID where the term is defined (e.g., 'efo', 'go', 'chebi') |
Implementation Reference
- Handler function for bc_get_term_details tool. Decorated with @core_mcp.tool(), fetches term details from OLS API using the provided term_id (CURIE) and ontology_id, returns structured details or error.@core_mcp.tool() def get_term_details( term_id: Annotated[str, Field(description="Term ID in CURIE format (e.g., 'EFO:0000001', 'GO:0008150')")], ontology_id: Annotated[ str, Field(description="Ontology ID where the term is defined (e.g., 'efo', 'go', 'chebi')") ], ) -> Dict[str, Any]: """Get comprehensive details about a specific ontology term including definition, synonyms, hierarchical relationships. Returns: dict: Term details with id, label, definition, synonyms, hierarchical info, num_descendants or error message. """ if not term_id: return {"error": "term_id must be provided"} if not ontology_id: return {"error": "ontology_id must be provided"} # Double URL encode the term IRI import urllib.parse term_iri = f"http://purl.obolibrary.org/obo/{term_id.replace(':', '_')}" encoded_iri = urllib.parse.quote(urllib.parse.quote(term_iri, safe=""), safe="") url = f"https://www.ebi.ac.uk/ols4/api/v2/ontologies/{ontology_id}/entities/{encoded_iri}" try: response = requests.get(url) response.raise_for_status() data = response.json() if not data: return {"error": "Term not found"} # Extract comprehensive term information term_details = { "id": data.get("curie", "").replace(":", "_"), "curie": data.get("curie", ""), "label": data.get("label", ""), "definition": data.get("definition", ""), "synonyms": data.get("synonym", []), "ontology_name": data.get("ontologyName", ""), "ontology_prefix": data.get("ontologyPrefix", ""), "is_defining_ontology": data.get("isDefiningOntology", False), "is_obsolete": data.get("isObsolete", False), "is_preferred_root": data.get("isPreferredRoot", False), "has_hierarchical_children": data.get("hasHierarchicalChildren", False), "has_hierarchical_parents": data.get("hasHierarchicalParents", False), "has_direct_children": data.get("hasDirectChildren", False), "has_direct_parents": data.get("hasDirectParents", False), "num_descendants": data.get("numDescendants", 0), "num_hierarchical_descendants": data.get("numHierarchicalDescendants", 0), "appears_in": data.get("appearsIn", []), "defined_by": data.get("definedBy", []), "imported": data.get("imported", False), } return {"term_details": term_details} except requests.exceptions.RequestException as e: return {"error": f"Failed to fetch term details: {e!s}"}