Unofficial PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1148-1150 (handler)

  The handler function that executes the 'get_compound_bioactivities' tool logic. Currently implemented as a placeholder indicating that full bioactivity search is not yet implemented.

  private async handleGetCompoundBioactivities(args: any) {
    return { content: [{ type: 'text', text: JSON.stringify({ message: 'Bioactivity search not yet implemented', args }, null, 2) }] };
  }

• src/index.ts:603-610 (schema)

  Input schema definition for the 'get_compound_bioactivities' tool, specifying parameters like CID and optional activity outcome filter.

  inputSchema: {
    type: 'object',
    properties: {
      cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
      activity_outcome: { type: 'string', enum: ['active', 'inactive', 'inconclusive', 'all'], description: 'Filter by activity outcome (default: all)' },
    },
    required: ['cid'],
  },

• src/index.ts:784-785 (registration)

  Registration and dispatch case in the main CallToolRequestSchema switch statement that routes calls to the handler.

  case 'get_compound_bioactivities':
    return await this.handleGetCompoundBioactivities(args);

• src/index.ts:600-610 (registration)

  Tool registration entry in the ListToolsRequestSchema response, including name, description, and schema.

  {
    name: 'get_compound_bioactivities',
    description: 'Get all bioassay results and activities for a compound',
    inputSchema: {
      type: 'object',
      properties: {
        cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        activity_outcome: { type: 'string', enum: ['active', 'inactive', 'inconclusive', 'all'], description: 'Filter by activity outcome (default: all)' },
      },
      required: ['cid'],
    },