BioContextAI Knowledgebase MCP

Instructions

Implementation Reference

• src/biocontext_kb/core/interpro/_get_interpro_entry.py:9-91 (handler)

  Handler function decorated with @core_mcp.tool() implementing the logic to fetch InterPro entry details from EBI API, including optional interactions, pathways, and cross-references. The tool is named 'get_interpro_entry' in core_mcp but prefixed to 'bc_get_interpro_entry' in the main server.

  @core_mcp.tool()
  def get_interpro_entry(
      interpro_id: Annotated[
          str,
          Field(description="InterPro ID (e.g., 'IPR000001')"),
      ],
      include_interactions: Annotated[
          bool,
          Field(description="Include protein-protein interactions data"),
      ] = False,
      include_pathways: Annotated[
          bool,
          Field(description="Include pathway information"),
      ] = False,
      include_cross_references: Annotated[
          bool,
          Field(description="Include cross-references to other databases"),
      ] = False,
  ) -> dict:
      """Get InterPro entry details (family, domain, or functional site). Returns metadata from member databases like PFAM, PROSITE.
  
      Returns:
          dict: Entry metadata including name, type, description, member databases, optionally interactions/pathways/cross-references or error message.
      """
      # Validate InterPro ID format
      interpro_id = interpro_id.upper().strip()
      if not interpro_id.startswith("IPR") or len(interpro_id) != 9:
          return {"error": "Invalid InterPro ID format. Expected format: IPR000001"}
  
      base_url = f"https://www.ebi.ac.uk/interpro/api/entry/interpro/{interpro_id}"
  
      # Build query parameters for additional data
      params = {}
      extra_fields = []
  
      if include_cross_references:
          extra_fields.append("cross_references")
  
      if extra_fields:
          params["extra_fields"] = ",".join(extra_fields)
  
      try:
          # Get basic entry information
          response = requests.get(base_url, params=params)
          response.raise_for_status()
  
          entry_data = response.json()
  
          if not entry_data.get("metadata"):
              return {"error": f"No data found for InterPro entry {interpro_id}"}
  
          result = entry_data["metadata"]
  
          # Optionally fetch interactions data
          if include_interactions:
              try:
                  interactions_url = f"{base_url}?interactions"
                  interactions_response = requests.get(interactions_url)
                  if interactions_response.status_code == 200:
                      interactions_data = interactions_response.json()
                      result["interactions"] = interactions_data.get("results", [])
              except Exception:
                  result["interactions"] = {"error": "Could not fetch interactions data"}
  
          # Optionally fetch pathways data
          if include_pathways:
              try:
                  pathways_url = f"{base_url}?pathways"
                  pathways_response = requests.get(pathways_url)
                  if pathways_response.status_code == 200:
                      pathways_data = pathways_response.json()
                      result["pathways"] = pathways_data.get("results", [])
              except Exception:
                  result["pathways"] = {"error": "Could not fetch pathways data"}
  
          return result
  
      except requests.exceptions.HTTPError as e:
          if e.response.status_code == 404:
              return {"error": f"InterPro entry {interpro_id} not found"}
          return {"error": f"HTTP error: {e}"}
      except Exception as e:
          return {"error": f"Exception occurred: {e!s}"}

• src/biocontext_kb/app.py:35-40 (registration)

  Registers tools from core_mcp (named 'BC', slugified to 'bc') into the main mcp_app by importing the server with prefix 'bc', resulting in tool name 'bc_get_interpro_entry'.

  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/_server.py:3-6 (registration)

  Defines core_mcp FastMCP server instance named 'BC', which provides the namespace for tool registration via @core_mcp.tool(). Tools are later prefixed with 'bc_'.

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

• src/biocontext_kb/core/interpro/__init__.py:1-9 (helper)

  Exports the get_interpro_entry tool function for use in the module namespace.

  from ._get_interpro_entry import get_interpro_entry
  from ._get_protein_domains import get_protein_domains
  from ._search_interpro_entries import search_interpro_entries
  
  __all__ = [
      "get_interpro_entry",
      "get_protein_domains",
      "search_interpro_entries",
  ]