PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1129-1146 (handler)

  The handler function that executes the tool logic: fetches detailed bioassay information from PubChem API using the provided AID and returns formatted JSON response.

  private async handleGetAssayInfo(args: any) {
    try {
      const response = await this.apiClient.get(`/assay/aid/${args.aid}/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:592-598 (schema)

  Input schema validating the required 'aid' parameter as a number representing the PubChem Assay ID.

  inputSchema: {
    type: 'object',
    properties: {
      aid: { type: 'number', description: 'PubChem Assay ID (AID)' },
    },
    required: ['aid'],
  },

• src/index.ts:590-599 (registration)

  Tool registration in the MCP server's tools list, defining name, description, and input schema.

    name: 'get_assay_info',
    description: 'Get detailed information for a specific bioassay by AID',
    inputSchema: {
      type: 'object',
      properties: {
        aid: { type: 'number', description: 'PubChem Assay ID (AID)' },
      },
      required: ['aid'],
    },
  },

• src/index.ts:782-783 (registration)

  Dispatch registration in the switch statement of the CallToolRequestHandler, routing 'get_assay_info' calls to the handler method.

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