BioContextAI Knowledgebase MCP

Instructions

Implementation Reference

• src/biocontext_kb/core/uniprot/_get_uniprot_protein_info.py:9-87 (handler)

  The handler function `get_uniprot_protein_info` for the tool, decorated with `@core_mcp.tool()`, which queries the UniProt REST API to retrieve protein information based on ID, name, gene symbol, species, and includes references optionally.
  @core_mcp.tool() def get_uniprot_protein_info( protein_id: Annotated[ Optional[str], Field(description="Protein accession number (e.g., 'P04637')"), ] = None, protein_name: Annotated[ Optional[str], Field(description="Protein name to search for (e.g., 'P53')"), ] = None, gene_symbol: Annotated[ Optional[str], Field(description="Gene symbol to search for (e.g., 'TP53')"), ] = None, species: Annotated[ Optional[str], Field(description="Taxonomy ID (e.g., '10090') or species name"), ] = None, include_references: Annotated[ bool, Field(description="Include references and cross-references in response"), ] = False, ) -> dict: """Retrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol. Returns: dict: Protein information with accession, proteinDescription, genes, organism, sequence, functions, keywords, references or error message. """ base_url = "https://rest.uniprot.org/uniprotkb/search" # Ensure at least one search parameter was provided if not protein_id and not protein_name and not gene_symbol: return {"error": "At least one of protein_id or protein_name or gene_symbol must be provided."} query_parts = [] if protein_id: query_parts.append(f"accession:{protein_id}") elif protein_name: query_parts.append(f"protein_name:{protein_name}") elif gene_symbol: query_parts.append(f"gene:{gene_symbol}") if species: species = str(species).strip() # Try to determine if it's a taxonomy ID (numeric) or a name if species.isdigit(): query_parts.append(f"organism_id:{species}") else: query_parts.append(f'taxonomy_name:"{species}"') query = " AND ".join(query_parts) params: dict[str, str | int] = { "query": query, "format": "json", } try: response = requests.get(base_url, params=params) response.raise_for_status() result = response.json() if not result.get("results"): return {"error": "No results found for the given query."} first_result = result["results"][0] # Remove references and cross-references by default to reduce response size if not include_references: first_result.pop("references", None) first_result.pop("uniProtKBCrossReferences", None) return first_result except Exception as e: return {"error": f"Exception occurred: {e!s}"}
• src/biocontext_kb/app.py:35-39 (registration)

  Registration of the `core_mcp` server (containing the uniprot tool) into the main `mcp_app` with namespace prefix `slugify('BC') = 'bc'`, resulting in the tool name `bc_get_uniprot_protein_info`.
  for mcp in [core_mcp, *(await get_openapi_mcps())]: await mcp_app.import_server( mcp, slugify(mcp.name), )
• src/biocontext_kb/core/_server.py:3-6 (registration)

  Definition of `core_mcp` FastMCP server instance named 'BC', into which tools like `get_uniprot_protein_info` are registered via `@tool()` decorators, later namespaced as 'bc_'.
  core_mcp = FastMCP( # type: ignore "BC", instructions="Provides access to biomedical knowledge bases.", )
• src/biocontext_kb/core/uniprot/_get_uniprot_protein_info.py:10-31 (schema)

  Pydantic schema definition for the tool inputs using Annotated and Field for protein_id, protein_name, gene_symbol, species, and include_references.
  def get_uniprot_protein_info( protein_id: Annotated[ Optional[str], Field(description="Protein accession number (e.g., 'P04637')"), ] = None, protein_name: Annotated[ Optional[str], Field(description="Protein name to search for (e.g., 'P53')"), ] = None, gene_symbol: Annotated[ Optional[str], Field(description="Gene symbol to search for (e.g., 'TP53')"), ] = None, species: Annotated[ Optional[str], Field(description="Taxonomy ID (e.g., '10090') or species name"), ] = None, include_references: Annotated[ bool, Field(description="Include references and cross-references in response"), ] = False, ) -> dict:
• src/biocontext_kb/core/uniprot/__init__.py:1-7 (helper)

  Exports the `get_uniprot_protein_info` function, allowing it to be imported into the core module for registration.
  from ._get_uniprot_id_by_protein_symbol import get_uniprot_id_by_protein_symbol from ._get_uniprot_protein_info import get_uniprot_protein_info __all__ = [ "get_uniprot_id_by_protein_symbol", "get_uniprot_protein_info", ]