OLS MCP Server

Instructions

Implementation Reference

• src/ols_mcp_server/server.py:110-124 (handler)

  The handler function for the get_ontology_info tool. It makes an API request to the OLS API using the ontology_id parameter, parses the response, validates it against the OntologyInfo Pydantic model, and returns the validated data or an error message.

  @mcp.tool()
  async def get_ontology_info(
      ontology_id: Annotated[str, "Ontology identifier (e.g., 'efo', 'go', 'mondo')"]
  ) -> OntologyInfo | str:
      """Get detailed information about a specific ontology."""
      url = f"{OLS_BASE_URL}/api/v2/ontologies/{ontology_id}"
      
      try:
          response = await client.get(url)
          response.raise_for_status()
          data = response.json()
          return OntologyInfo.model_validate(data)
          
      except httpx.HTTPError as e:
          return f"Error getting ontology info: {str(e)}"

• src/ols_mcp_server/models.py:4-15 (schema)

  Pydantic BaseModel defining the structure and validation for the OntologyInfo response returned by the get_ontology_info tool.

  class OntologyInfo(BaseModel):
      id: str = Field(..., description="Unique identifier for the ontology", alias="ontologyId")
      title: str = Field(..., description="Name of the ontology")
      version: Optional[str] = Field(None, description="Version of the ontology")
      description: Optional[str] = Field(None, description="Description of the ontology")
      domain: Optional[str] = Field(None, description="Domain of the ontology")
      homepage: Optional[HttpUrl] = Field(None, description="URL for the ontology")
      preferred_prefix: Optional[str] = Field(None, description="Preferred prefix for the ontology", alias="preferredPrefix")
      number_of_terms: Optional[int] = Field(None, description="Number of terms in the ontology")
      number_of_classes: Optional[int] = Field(None, description="Number of classes in the ontology", alias="numberOfClasses")
      repository: Optional[HttpUrl] = Field(None, description="Repository URL for the ontology")