GeneOntology MCP Server

Instructions

Implementation Reference

• src/index.ts:431-493 (handler)

  The core handler function that implements the logic for the 'get_go_term' tool. It validates the input arguments, normalizes the GO term ID, queries the QuickGO API, processes the response data into a structured format, and returns the result as MCP content or an error response.

  private async handleGetGoTerm(args: any) {
    if (!isValidTermArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'GO term ID is required');
    }
  
    try {
      const termId = this.normalizeGoId(args.id);
      const response = await this.quickGoClient.get(`/ontology/go/terms/${termId}`);
  
      const termInfo = response.data.results?.[0];
      if (!termInfo) {
        return {
          content: [
            {
              type: 'text',
              text: JSON.stringify({
                error: `GO term not found: ${termId}`,
                suggestion: 'Check the GO ID format (e.g., GO:0008150) or search for the term first'
              }, null, 2),
            },
          ],
          isError: true,
        };
      }
  
      const detailedTerm = {
        id: termInfo.id,
        name: termInfo.name,
        definition: {
          text: termInfo.definition?.text || 'No definition available',
          references: termInfo.definition?.xrefs || []
        },
        namespace: termInfo.aspect === 'F' ? 'molecular_function' :
                  termInfo.aspect === 'P' ? 'biological_process' : 'cellular_component',
        obsolete: termInfo.isObsolete || false,
        replaced_by: termInfo.replacedBy || [],
        consider: termInfo.consider || [],
        synonyms: termInfo.synonyms || [],
        xrefs: termInfo.xrefs || [],
        url: `https://www.ebi.ac.uk/QuickGO/term/${termInfo.id}`,
        amigo_url: `http://amigo.geneontology.org/amigo/term/${termInfo.id}`
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(detailedTerm, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error fetching GO term: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:303-313 (registration)

  The tool registration entry in the ListToolsRequestSchema handler, defining the name, description, and input schema for 'get_go_term'.

  {
    name: 'get_go_term',
    description: 'Get detailed information for a specific GO term',
    inputSchema: {
      type: 'object',
      properties: {
        id: { type: 'string', description: 'GO term identifier (e.g., GO:0008150)' },
      },
      required: ['id'],
    },
  },

• src/index.ts:84-91 (schema)

  Type guard function used to validate the input arguments for the 'get_go_term' tool, ensuring the required 'id' field is a non-empty string.

  const isValidTermArgs = (args: any): args is { id: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.id === 'string' &&
      args.id.length > 0
    );
  };

• src/index.ts:345-346 (registration)

  The switch case in the CallToolRequestSchema handler that routes calls to the 'get_go_term' tool to its handler function.

  case 'get_go_term':
    return this.handleGetGoTerm(args);

• src/index.ts:361-369 (helper)

  Helper function used by the handler to normalize GO term IDs, adding 'GO:' prefix if missing and the input matches 7 digits.

  private normalizeGoId(id: string): string {
    if (id.startsWith('GO:')) {
      return id;
    }
    if (/^\d{7}$/.test(id)) {
      return `GO:${id}`;
    }
    return id;
  }