UniProt MCP Server

Instructions

Implementation Reference

• src/uniprot_mcp_server/server.py:185-205 (handler)

  Executes the get_batch_protein_info tool by iterating over the list of accessions, fetching protein information for each using the fetch_protein_info helper, handling errors, and returning a JSON-formatted list of results.

  elif name == "get_batch_protein_info":
      accessions = arguments.get("accessions", [])
      if not accessions:
          raise ValueError("At least one accession No. is required")
  
      results = []
      for accession in accessions:
          try:
              protein_info = await fetch_protein_info(accession)
              results.append(protein_info)
          except httpx.HTTPError as e:
              results.append(
                  {
                      "accession": accession,
                      "error": f"Failed to fetch data: {str(e)}",
                  }
              )
  
      return [
          TextContent(type="text", text=json.dumps(results, indent=2))
      ]

• src/uniprot_mcp_server/server.py:95-109 (registration)

  Registers the get_batch_protein_info tool in the MCP server's list_tools handler, including its name, description, and input schema requiring a list of accessions.

  Tool(
      name="get_batch_protein_info",
      description="Get protein information for multiple accession No.",
      inputSchema={
          "type": "object",
          "properties": {
              "accessions": {
                  "type": "array",
                  "items": {"type": "string"},
                  "description": "List of UniProt accession No.",
              }
          },
          "required": ["accessions"],
      },
  ),

• src/uniprot_mcp_server/server.py:112-166 (helper)

  Core helper function that fetches detailed protein information (name, function, sequence, length, organism) from the UniProt API for a single accession, with caching support. Used by both get_protein_info and get_batch_protein_info.

  async def fetch_protein_info(accession: str) -> ProteinInfo:
      """Fetch protein information from UniProt API with caching."""
      # Check cache first
      cached_data = self.cache.get(accession)
      if cached_data:
          logger.info(f"Cache hit for {accession}")
          return cached_data
  
      logger.info(f"Fetching data for {accession}")
      async with httpx.AsyncClient() as client:
          response = await client.get(
              f"{API_BASE_URL}/{accession}",
              headers={"Accept": "application/json"},
          )
          response.raise_for_status()
          data = response.json()
  
          # Extract relevant information
          protein_info: ProteinInfo = {
              "accession": accession,
              "protein_name": data.get("proteinDescription", {})
              .get("recommendedName", {})
              .get("fullName", {})
              .get("value", "Unknown"),
              "function": [],
              "sequence": "",
              "length": 0,
              "organism": "Unknown",
          }
  
          # Extract function information safely
          for comment in data.get("comments", []):
              if comment.get("commentType") == "FUNCTION":
                  texts = comment.get("texts", [])
                  if texts:
                      protein_info["function"].extend(
                          [text.get("value", "") for text in texts]
                      )
  
          # Add sequence information
          seq_info = data.get("sequence", {})
          org_info = data.get("organism", {})
  
          protein_info.update(
              {
                  "sequence": seq_info.get("value", ""),
                  "length": seq_info.get("length", 0),
                  "organism": org_info.get("scientificName", "Unknown"),
              }
          )
  
          # Cache the result
          self.cache.set(accession, protein_info)
          return protein_info

• src/uniprot_mcp_server/server.py:21-30 (schema)

  TypedDict schema defining the structure of protein information returned by the tools.

  class ProteinInfo(TypedDict):
      """Type definition for protein information."""
  
      accession: str
      protein_name: str
      function: list[str]
      sequence: str
      length: int
      organism: str