ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:1033-1059 (handler)

  The handler function for the 'search_by_uniprot' tool. It validates the uniprot_id argument, queries the ChEMBL target/search API with the UniProt ID, and returns the JSON response.

  private async handleSearchByUniprot(args: any) {
    if (!args || typeof args.uniprot_id !== 'string') {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid UniProt arguments');
    }
  
    try {
      const response = await this.apiClient.get('/target/search.json', {
        params: {
          q: args.uniprot_id,
          limit: args.limit || 25,
        },
      });
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to search by UniProt: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }

• src/index.ts:499-506 (schema)

  Input schema definition for the 'search_by_uniprot' tool, specifying uniprot_id as required string and optional limit.

  inputSchema: {
    type: 'object',
    properties: {
      uniprot_id: { type: 'string', description: 'UniProt accession number' },
      limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 },
    },
    required: ['uniprot_id'],
  },

• src/index.ts:496-507 (registration)

  Registration of the 'search_by_uniprot' tool in the ListTools response, including name, description, and input schema.

  {
    name: 'search_by_uniprot',
    description: 'Find ChEMBL targets by UniProt accession',
    inputSchema: {
      type: 'object',
      properties: {
        uniprot_id: { type: 'string', description: 'UniProt accession number' },
        limit: { type: 'number', description: 'Number of results to return (1-1000, default: 25)', minimum: 1, maximum: 1000 },
      },
      required: ['uniprot_id'],
    },
  },

• src/index.ts:762-763 (registration)

  Dispatch/registration in the CallToolRequestSchema switch statement that routes to the handler.

  case 'search_by_uniprot':
    return await this.handleSearchByUniprot(args);