OpenTargets MCP Server

Instructions

Implementation Reference

• src/index.ts:313-371 (handler)

  The handler function that implements the core logic of the 'search_targets' tool: validates input, executes a GraphQL query to the Open Targets API to search for targets, limits results based on size parameter, and returns formatted JSON response.

  private async handleSearchTargets(args: any) {
    if (!isValidTargetSearchArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid target search arguments');
    }
  
    try {
      const query = `
        query SearchTargets($queryString: String!) {
          search(queryString: $queryString, entityNames: ["target"]) {
            hits {
              id
              name
              description
              entity
            }
          }
        }
      `;
  
      const response = await this.graphqlClient.post('', {
        query,
        variables: {
          queryString: args.query
        }
      });
  
      // Limit results on client side
      const hits = response.data.data?.search?.hits || [];
      const limitedHits = hits.slice(0, args.size || 25);
      const result = {
        ...response.data,
        data: {
          search: {
            hits: limitedHits,
            total: hits.length
          }
        }
      };
  
      return {
        content: [
          {
            type: 'text',
            text: JSON.stringify(result, null, 2),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error searching targets: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:213-221 (schema)

  JSON Schema defining the input parameters for the 'search_targets' tool, including required 'query' string and optional 'size' and 'format'.

  inputSchema: {
    type: 'object',
    properties: {
      query: { type: 'string', description: 'Search query (gene symbol, name, description)' },
      size: { type: 'number', description: 'Number of results to return (1-500, default: 25)', minimum: 1, maximum: 500 },
      format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
    },
    required: ['query'],
  },

• src/index.ts:210-222 (registration)

  Registration of the 'search_targets' tool in the ListTools response, specifying name, description, and input schema.

  {
    name: 'search_targets',
    description: 'Search for therapeutic targets by gene symbol, name, or description',
    inputSchema: {
      type: 'object',
      properties: {
        query: { type: 'string', description: 'Search query (gene symbol, name, description)' },
        size: { type: 'number', description: 'Number of results to return (1-500, default: 25)', minimum: 1, maximum: 500 },
        format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
      },
      required: ['query'],
    },
  },

• src/index.ts:292-293 (registration)

  Switch case in CallToolRequest handler that dispatches calls to 'search_targets' to the handleSearchTargets method.

  case 'search_targets':
    return this.handleSearchTargets(args);

• src/index.ts:16-25 (helper)

  Type guard and validation helper function used by the handler to validate input arguments for 'search_targets'.

  const isValidTargetSearchArgs = (args: any): args is { query: string; size?: number; format?: string } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      typeof args.query === 'string' &&
      args.query.length > 0 &&
      (args.size === undefined || (typeof args.size === 'number' && args.size > 0 && args.size <= 500)) &&
      (args.format === undefined || ['json', 'tsv'].includes(args.format))
    );
  };