PubChem MCP Server

Instructions

Implementation Reference

• src/index.ts:1148-1150 (handler)

  The main handler function for executing the 'get_compound_bioactivities' tool. Currently implemented as a placeholder that returns a 'not yet implemented' message.

  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 defining the parameters for the 'get_compound_bioactivities' tool: requires 'cid', optional 'activity_outcome'.

  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:600-611 (registration)

  Tool registration in the ListToolsRequestSchema handler, including name, description, and input 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'],
    },
  },

• src/index.ts:784-785 (registration)

  Dispatch registration in the main CallToolRequestSchema switch statement that calls the handler.

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