ChEMBL MCP Server

Instructions

Implementation Reference

• src/index.ts:1062-1097 (handler)

  The handler function for the 'get_target_pathways' tool. It validates the input target_chembl_id, fetches target data from ChEMBL API, extracts pathway information from cross-references (filtering Reactome, KEGG, WikiPathways), and returns formatted JSON.

  private async handleGetTargetPathways(args: any) {
    if (!args || typeof args.target_chembl_id !== 'string') {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid target pathways arguments');
    }
  
    try {
      // Get target information which includes pathway data
      const targetResponse = await this.apiClient.get(`/target/${args.target_chembl_id}.json`);
      const target = targetResponse.data;
  
      // Extract pathway information from target data
      const pathways = {
        target_chembl_id: args.target_chembl_id,
        target_name: target.pref_name,
        target_type: target.target_type,
        cross_references: target.cross_references || [],
        pathways: (target.cross_references || []).filter((ref: any) =>
          ref.xref_src === 'Reactome' || ref.xref_src === 'KEGG' || ref.xref_src === 'WikiPathways'
        ),
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(pathways, null, 2),
          },
        ],
      };
    } catch (error) {
      throw new McpError(
        ErrorCode.InternalError,
        `Failed to get target pathways: ${error instanceof Error ? error.message : 'Unknown error'}`
      );
    }
  }

• src/index.ts:509-518 (schema)

  The tool schema definition in the list of tools returned by ListToolsRequestSchema, including name, description, and input schema requiring 'target_chembl_id'.

    name: 'get_target_pathways',
    description: 'Get biological pathways associated with a target',
    inputSchema: {
      type: 'object',
      properties: {
        target_chembl_id: { type: 'string', description: 'ChEMBL target ID' },
      },
      required: ['target_chembl_id'],
    },
  },

• src/index.ts:764-765 (registration)

  The registration/dispatch case in the CallToolRequestSchema handler's switch statement that routes calls to the handleGetTargetPathways function.

  case 'get_target_pathways':
    return await this.handleGetTargetPathways(args);