search
Query genetic variant data, gene constraints, and population frequencies from the Genome Aggregation Database. Search by gene symbol, variant ID, or genomic region to access detailed genetic information.
Instructions
Search for genes, variants, or regions in gnomAD
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | Search query (gene symbol, gene ID, variant ID, rsID, etc.) | |
| reference_genome | No | Reference genome (GRCh37 or GRCh38) | GRCh38 |
| dataset | No | Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc.) | gnomad_r4 |
Implementation Reference
- src/index.ts:648-654 (handler)The execution handler for the 'search' tool. It calls the GraphQL API with the searchGene query using the provided query and parsed reference genome.
case "search": result = await makeGraphQLRequest(QUERIES.searchGene, { query: args.query as string, referenceGenome: parseReferenceGenome((args.reference_genome as string) || "GRCh38"), }); formattedResult = result.data?.searchResults || []; break; - src/index.ts:418-437 (schema)Input schema for the 'search' tool, defining parameters like query, reference_genome, and dataset.
inputSchema: { type: "object", properties: { query: { type: "string", description: "Search query (gene symbol, gene ID, variant ID, rsID, etc.)", }, reference_genome: { type: "string", description: "Reference genome (GRCh37 or GRCh38)", default: "GRCh38", }, dataset: { type: "string", description: "Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc.)", default: "gnomad_r4", }, }, required: ["query"], }, - src/index.ts:415-438 (registration)Registration of the 'search' tool in the ListTools response, including name, description, and input schema.
{ name: "search", description: "Search for genes, variants, or regions in gnomAD", inputSchema: { type: "object", properties: { query: { type: "string", description: "Search query (gene symbol, gene ID, variant ID, rsID, etc.)", }, reference_genome: { type: "string", description: "Reference genome (GRCh37 or GRCh38)", default: "GRCh38", }, dataset: { type: "string", description: "Dataset ID (gnomad_r4, gnomad_r3, gnomad_r2_1, etc.)", default: "gnomad_r4", }, }, required: ["query"], }, }, - src/index.ts:65-72 (helper)GraphQL query template 'searchGene' used by the 'search' tool handler to perform the search.
searchGene: ` query SearchGene($query: String!, $referenceGenome: ReferenceGenomeId!) { searchResults(query: $query, referenceGenome: $referenceGenome) { label value: url } } `, - src/index.ts:403-409 (helper)Helper function to parse and validate the reference genome parameter used in the 'search' handler.
function parseReferenceGenome(genome: string): string { const validGenomes = ["GRCh37", "GRCh38"]; if (!validGenomes.includes(genome)) { return "GRCh38"; // Default to GRCh38 } return genome; }