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", ]