GeneOntology MCP Server

Instructions

Implementation Reference

• src/index.ts:495-556 (handler)

  The main handler function that validates the GO identifier format using regex, normalizes it, queries the QuickGO API to check existence, and returns detailed validation results.

  private async handleValidateGoId(args: any) {
    if (!isValidTermArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'GO ID is required');
    }
  
    try {
      const termId = this.normalizeGoId(args.id);
  
      // Check format
      const isValidFormat = /^GO:\d{7}$/.test(termId);
  
      let exists = false;
      let termInfo = null;
  
      if (isValidFormat) {
        try {
          const response = await this.quickGoClient.get(`/ontology/go/terms/${termId}`);
          termInfo = response.data.results?.[0];
          exists = !!termInfo;
        } catch (e) {
          exists = false;
        }
      }
  
      const validation = {
        input_id: args.id,
        normalized_id: termId,
        valid_format: isValidFormat,
        exists: exists,
        term_info: exists ? {
          name: termInfo?.name,
          namespace: termInfo?.aspect === 'F' ? 'molecular_function' :
                    termInfo?.aspect === 'P' ? 'biological_process' : 'cellular_component',
          obsolete: termInfo?.isObsolete || false
        } : null,
        format_rules: {
          pattern: 'GO:NNNNNNN',
          example: 'GO:0008150',
          description: 'GO identifiers consist of "GO:" followed by exactly 7 digits'
        }
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(validation, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error validating GO ID: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:317-323 (schema)

  Defines the input schema for the validate_go_id tool, requiring a single 'id' string parameter.

  inputSchema: {
    type: 'object',
    properties: {
      id: { type: 'string', description: 'GO identifier to validate' },
    },
    required: ['id'],
  },

• src/index.ts:314-324 (registration)

  Registers the validate_go_id tool in the ListToolsRequestSchema response, including name, description, and input schema.

  {
    name: 'validate_go_id',
    description: 'Validate GO identifier format and check if term exists',
    inputSchema: {
      type: 'object',
      properties: {
        id: { type: 'string', description: 'GO identifier to validate' },
      },
      required: ['id'],
    },
  },

• src/index.ts:347-348 (registration)

  Dispatches calls to the validate_go_id tool to its handler function in the CallToolRequestSchema switch statement.

  case 'validate_go_id':
    return this.handleValidateGoId(args);

• src/index.ts:361-369 (helper)

  Helper function used by the handler to normalize GO IDs to the standard 'GO:NNNNNNN' format.

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