ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:1166-1214 (handler)

  The main handler function for the 'get_dose_response' tool. It validates input arguments, queries the ChEMBL API for activity data filtered by molecule_chembl_id (and optionally target_chembl_id), processes the response to extract dose-response relevant fields (activity_type, value, units, etc.), and returns formatted JSON output.

  private async handleGetDoseResponse(args: any) {
    if (!args || typeof args.molecule_chembl_id !== 'string') {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid dose response arguments');
    }
  
    try {
      const params: any = {
        molecule_chembl_id: args.molecule_chembl_id,
        limit: 100,
      };
  
      if (args.target_chembl_id) {
        params.target_chembl_id = args.target_chembl_id;
      }
  
      const response = await this.apiClient.get('/activity.json', { params });
      const activities = response.data.activities || [];
  
      // Group activities by assay and extract dose-response data
      const doseResponseData = activities
        .filter((a: any) => a.standard_value !== null && a.standard_type)
        .map((a: any) => ({
          assay_chembl_id: a.assay_chembl_id,
          target_chembl_id: a.target_chembl_id,
          activity_type: a.standard_type,
          value: a.standard_value,
          units: a.standard_units,
          relation: a.standard_relation,
        }));
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify({
              molecule_chembl_id: args.molecule_chembl_id,
              total_measurements: doseResponseData.length,
              dose_response_data: doseResponseData,
            }, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to get dose response: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:564-571 (schema)

  Input schema defining the parameters for the get_dose_response tool: requires molecule_chembl_id (string), optional target_chembl_id (string).

  inputSchema: {
    type: 'object',
    properties: {
      molecule_chembl_id: { type: 'string', description: 'ChEMBL compound ID' },
      target_chembl_id: { type: 'string', description: 'ChEMBL target ID (optional filter)' },
    },
    required: ['molecule_chembl_id'],
  },

• src/index.ts:561-573 (registration)

  Registration of the get_dose_response tool in the ListToolsRequestSchema response, providing the tool name, description, and input schema to MCP clients.

  {
    name: 'get_dose_response',
    description: 'Get dose-response data and activity profiles for compounds',
    inputSchema: {
      type: 'object',
      properties: {
        molecule_chembl_id: { type: 'string', description: 'ChEMBL compound ID' },
        target_chembl_id: { type: 'string', description: 'ChEMBL target ID (optional filter)' },
      },
      required: ['molecule_chembl_id'],
    },
  },
  {

• src/index.ts:773-774 (registration)

  Registration/dispatch of the get_dose_response tool handler in the CallToolRequestSchema switch statement.

  case 'get_dose_response':
    return await this.handleGetDoseResponse(args);