BioContextAI Knowledgebase MCP

Instructions

Implementation Reference

• src/biocontext_kb/core/ols/_get_available_ontologies.py:8-80 (handler)

  The handler function that implements the logic to retrieve all available ontologies from the OLS API, paginating through results and extracting metadata. Registered as an MCP tool via @core_mcp.tool() decorator.

  @core_mcp.tool()
  def get_available_ontologies() -> Dict[str, Any]:
      """Query OLS for all available ontologies with their metadata. Use this first to discover available ontologies.
  
      Returns:
          dict: Ontologies list with id, name, description, prefix, homepage, number of terms, status or error message.
      """
      url = "https://www.ebi.ac.uk/ols4/api/v2/ontologies"
  
      try:
          # First request to get total count
          params = {
              "size": "100",  # OLS now limits to 100 elements per page
              "page": "0",
              "lang": "en",
          }
  
          response = requests.get(url, params=params)
          response.raise_for_status()
  
          data = response.json()
  
          if not data.get("elements"):
              return {"error": "No ontologies found"}
  
          ontologies: list[Dict[str, Any]] = []
          total_elements = data.get("totalElements", 0)
          total_pages = (total_elements + 99) // 100  # Ceiling division
  
          # Iterate through all pages
          for page in range(total_pages):
              params["page"] = str(page)
              response = requests.get(url, params=params)
              response.raise_for_status()
  
              data = response.json()
  
              # Extract ontology information
              page_ontologies = [
                  {
                      "id": element.get("ontologyId", ""),
                      "name": element.get("label", ""),
                      "description": element.get("definition", ""),
                      "prefix": element.get("ontologyPrefix", ""),
                      "base_uri": element.get("baseUri", ""),
                      "homepage": element.get("homepage", ""),
                      "mailing_list": element.get("mailingList", ""),
                      "number_of_terms": element.get("numberOfTerms", 0),
                      "number_of_properties": element.get("numberOfProperties", 0),
                      "number_of_individuals": element.get("numberOfIndividuals", 0),
                      "last_loaded": element.get("lastLoaded", ""),
                      "status": element.get("status", ""),
                  }
                  for element in data.get("elements", [])
              ]
  
              ontologies.extend(page_ontologies)
  
          # Sort by ontology ID for consistency
          ontologies.sort(key=lambda x: x["id"])
  
          return {
              "ontologies": ontologies,
              "total_ontologies": total_elements,
              "page_info": {
                  "total_pages": total_pages,
                  "num_elements": len(ontologies),
              },
          }
  
      except requests.exceptions.RequestException as e:
          return {"error": f"Failed to fetch available ontologies: {e!s}"}

• src/biocontext_kb/core/_server.py:1-6 (registration)

  Defines the core_mcp FastMCP server instance named 'BC', to which all core tools including get_available_ontologies are registered via decorators.

  from fastmcp import FastMCP
  
  core_mcp = FastMCP(  # type: ignore
      "BC",
      instructions="Provides access to biomedical knowledge bases.",
  )

• src/biocontext_kb/app.py:34-40 (registration)

  Registers the core_mcp server (containing get_available_ontologies) into the main BioContextAI MCP app with prefix 'bc' (slugify('BC')), making the tool available as 'bc_get_available_ontologies'.

  logger.info("Setting up MCP server...")
  for mcp in [core_mcp, *(await get_openapi_mcps())]:
      await mcp_app.import_server(
          mcp,
          slugify(mcp.name),
      )
  logger.info("MCP server setup complete.")

• src/biocontext_kb/core/ols/__init__.py:1-19 (helper)

  Re-exports the get_available_ontologies function for convenient import in core/__init__.py.

  from ._get_available_ontologies import get_available_ontologies
  from ._get_cell_ontology_terms import get_cell_ontology_terms
  from ._get_chebi_terms_by_chemical import get_chebi_terms_by_chemical
  from ._get_efo_id_by_disease_name import get_efo_id_by_disease_name
  from ._get_go_terms_by_gene import get_go_terms_by_gene
  from ._get_term_details import get_term_details
  from ._get_term_hierarchical_children import get_term_hierarchical_children
  from ._search_ontology_terms import search_ontology_terms
  
  __all__ = [
      "get_available_ontologies",
      "get_cell_ontology_terms",
      "get_chebi_terms_by_chemical",
      "get_efo_id_by_disease_name",
      "get_go_terms_by_gene",
      "get_term_details",
      "get_term_hierarchical_children",
      "search_ontology_terms",
  ]