OpenTargets MCP Server

Instructions

Implementation Reference

• src/index.ts:510-564 (handler)

  The handler function that validates input, executes a GraphQL query to fetch disease-associated targets from Open Targets, processes the top 10 targets into a summary, and returns the result as JSON text.

  private async handleGetDiseaseTargetsSummary(args: any) {
    if (!isValidIdArgs(args) && !args.diseaseId) {
      throw new McpError(ErrorCode.InvalidParams, 'Disease ID is required');
    }
  
    try {
      const diseaseId = args.diseaseId || args.id;
  
      const query = `query GetDiseaseTargetsSummary($efoId: String!) { disease(efoId: $efoId) { id name associatedTargets { count rows { target { id approvedSymbol approvedName } score } } } }`;
  
      const response = await this.graphqlClient.post('', {
        query,
        variables: {
          efoId: diseaseId,
          size: args.size || 50
        }
      });
  
      const diseaseData = response.data.data?.disease;
      const associations = diseaseData?.associatedTargets;
  
      const summary = {
        diseaseId,
        diseaseName: diseaseData?.name,
        totalTargets: associations?.count || 0,
        topTargets: associations?.rows?.slice(0, 10).map((assoc: any) => ({
          targetId: assoc.target.id,
          targetSymbol: assoc.target.approvedSymbol,
          targetName: assoc.target.approvedName,
          associationScore: assoc.score,
          datatypeScores: assoc.datatypeScores,
        })) || [],
        fullResults: response.data,
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(summary, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error getting disease targets summary: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:250-262 (schema)

  The tool registration entry defining the name, description, and input schema (diseaseId required, optional minScore and size). Note: minScore is defined but not used in handler.

  {
    name: 'get_disease_targets_summary',
    description: 'Get overview of all targets associated with a disease',
    inputSchema: {
      type: 'object',
      properties: {
        diseaseId: { type: 'string', description: 'Disease EFO ID' },
        minScore: { type: 'number', description: 'Minimum association score (0-1)', minimum: 0, maximum: 1 },
        size: { type: 'number', description: 'Number of targets to return (1-500, default: 50)', minimum: 1, maximum: 500 },
      },
      required: ['diseaseId'],
    },
  },

• src/index.ts:298-299 (registration)

  The switch case in the request handler that dispatches calls to this tool to its handler method.

  case 'get_disease_targets_summary':
    return this.handleGetDiseaseTargetsSummary(args);

• src/index.ts:240-286 (registration)

  The server.setTools call registering all tools including this one (full tools array spans lines ~190-285).

          type: 'object',
          properties: {
            targetId: { type: 'string', description: 'Target Ensembl gene ID' },
            diseaseId: { type: 'string', description: 'Disease EFO ID' },
            minScore: { type: 'number', description: 'Minimum association score (0-1)', minimum: 0, maximum: 1 },
            size: { type: 'number', description: 'Number of results to return (1-500, default: 25)', minimum: 1, maximum: 500 },
          },
          required: [],
        },
      },
      {
        name: 'get_disease_targets_summary',
        description: 'Get overview of all targets associated with a disease',
        inputSchema: {
          type: 'object',
          properties: {
            diseaseId: { type: 'string', description: 'Disease EFO ID' },
            minScore: { type: 'number', description: 'Minimum association score (0-1)', minimum: 0, maximum: 1 },
            size: { type: 'number', description: 'Number of targets to return (1-500, default: 50)', minimum: 1, maximum: 500 },
          },
          required: ['diseaseId'],
        },
      },
      {
        name: 'get_target_details',
        description: 'Get comprehensive target information',
        inputSchema: {
          type: 'object',
          properties: {
            id: { type: 'string', description: 'Target Ensembl gene ID' },
          },
          required: ['id'],
        },
      },
      {
        name: 'get_disease_details',
        description: 'Get comprehensive disease information',
        inputSchema: {
          type: 'object',
          properties: {
            id: { type: 'string', description: 'Disease EFO ID' },
          },
          required: ['id'],
        },
      },
    ],
  }));