PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1129-1146 (handler)

  The main handler function that implements the get_assay_info tool. It fetches detailed assay information from the PubChem API using the provided AID and returns the 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:590-598 (schema)

  The input schema definition for the get_assay_info tool, specifying that it requires a numeric 'aid' parameter (PubChem Assay ID).

  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)

  The switch case in the tool request handler that routes calls to 'get_assay_info' to the handleGetAssayInfo method.

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