bc_get_go_terms_by_gene
Retrieve Gene Ontology terms associated with specific genes to understand their biological functions, processes, and cellular components using structured vocabularies.
Instructions
Search OLS for Gene Ontology (GO) terms related to a gene name using structured vocabularies.
Returns: dict: GO terms with go_terms array containing id, label, description, type or error message.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene_name | Yes | Gene name or symbol to search for (e.g., 'TP53', 'BRCA1') | |
| size | No | Maximum number of results to return | |
| exact_match | No | Whether to perform exact match search |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Implementation Reference
- The core handler function for the 'bc_get_go_terms_by_gene' tool. It queries the OLS API with the gene name filtered to the 'go' ontology, extracts GO-prefixed terms, and formats them into a 'go_terms' list with id, label, description, ontology_name, and type.
@core_mcp.tool() def get_go_terms_by_gene( gene_name: Annotated[str, Field(description="Gene name or symbol to search for (e.g., 'TP53', 'BRCA1')")], size: Annotated[ int, Field(description="Maximum number of results to return"), ] = 10, exact_match: Annotated[ bool, Field(description="Whether to perform exact match search"), ] = False, ) -> Dict[str, Any]: """Search OLS for Gene Ontology (GO) terms related to a gene name using structured vocabularies. Returns: dict: GO terms with go_terms array containing id, label, description, type or error message. """ if not gene_name: return {"error": "gene_name must be provided"} url = "https://www.ebi.ac.uk/ols4/api/v2/entities" params = { "search": gene_name, "size": str(size), "lang": "en", "exactMatch": str(exact_match).lower(), "includeObsoleteEntities": "false", "ontologyId": "go", } def starts_with_go_prefix(curie: str) -> bool: """Check if the curie starts with GO prefix.""" return curie.startswith("GO:") try: response = requests.get(url, params=params) response.raise_for_status() data = response.json() # Check that at least one item is in elements with GO prefix if not data.get("elements") or not any( starts_with_go_prefix(str(element.get("curie", ""))) for element in data["elements"] ): return {"error": "No GO terms found"} # Extract GO terms and their information go_terms = [ { "id": element["curie"].replace(":", "_"), "label": element["label"], "description": element.get("description", ""), "ontology_name": element.get("ontologyName", ""), "type": element.get("type", ""), } for element in data["elements"] if starts_with_go_prefix(str(element.get("curie", ""))) ] return {"go_terms": go_terms} except requests.exceptions.RequestException as e: return {"error": f"Failed to fetch GO terms: {e!s}"} - src/biocontext_kb/core/ols/__init__.py:5-5 (registration)Explicit import of the handler function into the OLS module namespace.
from ._get_go_terms_by_gene import get_go_terms_by_gene - src/biocontext_kb/core/__init__.py:12-12 (registration)Wildcard import of OLS tools into the core_mcp FastMCP server namespace, registering 'get_go_terms_by_gene' as 'bc_get_go_terms_by_gene' due to server prefix.
from .ols import * - src/biocontext_kb/core/ols/_get_go_terms_by_gene.py:6-6 (registration)Import of the core_mcp server instance used for the @tool decorator to register the function.
from biocontext_kb.core._server import core_mcp