BioOntology MCP Server

Instructions

Implementation Reference

• src/index.ts:1042-1075 (handler)

  The handler function for the 'get_class_info' tool. Validates arguments, makes an API request to BioOntology.org for the specified ontology class, and returns the JSON response or error.

  private async handleGetClassInfo(args: any) {
    if (!isValidGetClassInfoArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid class info arguments');
    }
  
    try {
      const params: any = {
        apikey: this.apiKey,
      };
  
      if (args.include) params.include = args.include;
  
      const response = await this.apiClient.get(`/ontologies/${args.ontology}/classes/${encodeURIComponent(args.class_id)}`, { params });
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } catch (error: any) {
      return {
        content: [
          {
            type: 'text',
            text: `Error fetching class info: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:204-216 (schema)

  Type guard function that validates the input arguments for the get_class_info tool, ensuring ontology and class_id are non-empty strings, and include is optional string.

  const isValidGetClassInfoArgs = (
    args: any
  ): args is { ontology: string; class_id: string; include?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.ontology === 'string' &&
      args.ontology.length > 0 &&
      typeof args.class_id === 'string' &&
      args.class_id.length > 0 &&
      (args.include === undefined || typeof args.include === 'string')
    );
  };

• src/index.ts:655-667 (registration)

  Tool registration in the ListToolsRequestSchema handler, defining the name, description, and detailed inputSchema for get_class_info.

  {
    name: 'get_class_info',
    description: 'Get detailed information about a specific ontology class',
    inputSchema: {
      type: 'object',
      properties: {
        ontology: { type: 'string', description: 'Ontology acronym' },
        class_id: { type: 'string', description: 'Class ID/URI (URL-encoded if necessary)' },
        include: { type: 'string', description: 'Comma-separated attributes to include (e.g., prefLabel,definition,parents,children)' },
      },
      required: ['ontology', 'class_id'],
    },
  },

• src/index.ts:717-718 (registration)

  Dispatch case in the CallToolRequestSchema switch statement that routes calls to the get_class_info handler.

  case 'get_class_info':
    return this.handleGetClassInfo(args);