ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:1113-1124 (handler)

  The core handler function that implements the logic for the 'get_assay_info' tool. It validates the input chembl_id and fetches detailed assay information from the ChEMBL API.

  private async handleGetAssayInfo(args: any) {
    if (!isValidChemblIdArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid arguments');
    }
  
    try {
      const response = await this.apiClient.get(`/assay/${args.chembl_id}.json`);
      return { content: [{ type: 'text', text: JSON.stringify(response.data, null, 2) }] };
    } catch (error) {
      throw new McpError(ErrorCode.InternalError, `Failed to get assay info: ${error instanceof Error ? error.message : 'Unknown error'}`);
    }
  }

• src/index.ts:536-545 (schema)

  The tool's metadata including name, description, and input schema definition, provided in response to ListToolsRequest.

    name: 'get_assay_info',
    description: 'Get detailed information for a specific assay by ChEMBL assay ID',
    inputSchema: {
      type: 'object',
      properties: {
        chembl_id: { type: 'string', description: 'ChEMBL assay ID (e.g., CHEMBL1217643)' },
      },
      required: ['chembl_id'],
    },
  },

• src/index.ts:769-770 (registration)

  Dispatches calls to the 'get_assay_info' tool handler within the CallToolRequestSchema request handler.

  case 'get_assay_info':
    return await this.handleGetAssayInfo(args);

• src/index.ts:90-99 (helper)

  Type guard and validation function for chembl_id arguments, used by get_assay_info and similar tools.

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

• src/index.ts:309-330 (registration)

  Related resource handler for assay data (chembl://assay/{id}), which performs identical API fetch as the tool.

  // Handle assay info requests
  const assayMatch = uri.match(/^chembl:\/\/assay\/([A-Z0-9]+)$/);
  if (assayMatch) {
    const chemblId = assayMatch[1];
    try {
      const response = await this.apiClient.get(`/assay/${chemblId}.json`);
      return {
        contents: [
          {
            uri: request.params.uri,
            mimeType: 'application/json',
            text: JSON.stringify(response.data, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to fetch assay ${chemblId}: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }