GTEx MCP Server

Instructions

Implementation Reference

• src/handlers/reference-handlers.ts:519-640 (handler)

  The primary handler function implementing the get_tissue_info tool. Fetches tissue site details from the API, handles errors, filters by tissueIds if provided, formats comprehensive output with identifiers, sample summaries, eQTL data, and statistics.
  async getTissueInfo(args: any) { const result = await this.apiClient.getTissueSiteDetails(args.datasetId || 'gtex_v8'); if (result.error) { return { content: [{ type: "text", text: `Error retrieving tissue information: ${result.error}` }], isError: true }; } const tissues = result.data || []; if (tissues.length === 0) { return { content: [{ type: "text", text: "No tissue information available." }] }; } let output = `**GTEx Tissue Information**\n`; output += `Dataset: ${tissues[0]?.datasetId}\n`; output += `Total tissues: ${tissues.length}\n\n`; // Filter tissues if specific ones requested let displayTissues = tissues; if (args.tissueIds && Array.isArray(args.tissueIds)) { displayTissues = tissues.filter(t => args.tissueIds.includes(t.tissueSiteDetailId)); if (displayTissues.length === 0) { return { content: [{ type: "text", text: `No tissues found matching: ${args.tissueIds.join(', ')}` }] }; } } // Sort by tissue name const sortedTissues = displayTissues.sort((a, b) => a.tissueSiteDetail.localeCompare(b.tissueSiteDetail)); sortedTissues.forEach((tissue, index) => { if (displayTissues.length === 1) { output += `### ${tissue.tissueSiteDetail}\n`; } else { output += `${(index + 1).toString().padStart(2)}. **${tissue.tissueSiteDetail}** (${tissue.tissueSiteDetailId})\n`; } if (displayTissues.length === 1) { output += `**Identifiers:**\n`; output += ` • Tissue ID: ${tissue.tissueSiteDetailId}\n`; output += ` • Abbreviation: ${tissue.tissueSiteDetailAbbr}\n`; output += ` • Sampling Site: ${tissue.samplingSite}\n`; output += ` • Ontology ID: ${tissue.ontologyId}\n`; if (tissue.ontologyIri) { output += ` • Ontology IRI: ${tissue.ontologyIri}\n`; } output += `\n**Visual Properties:**\n`; output += ` • Color (hex): ${tissue.colorHex}\n`; output += ` • Color (RGB): ${tissue.colorRgb}\n`; output += `\n**Data Availability:**\n`; output += ` • Has eGenes: ${tissue.hasEGenes ? 'Yes' : 'No'}\n`; output += ` • Has sGenes: ${tissue.hasSGenes ? 'Yes' : 'No'}\n`; output += ` • Mapped in HubMAP: ${tissue.mappedInHubmap ? 'Yes' : 'No'}\n`; if (tissue.hasEGenes) { output += ` • eGene count: ${tissue.eGeneCount.toLocaleString()}\n`; } if (tissue.hasSGenes) { output += ` • sGene count: ${tissue.sGeneCount.toLocaleString()}\n`; } output += ` • Expressed genes: ${tissue.expressedGeneCount.toLocaleString()}\n`; // RNA-seq samples const rnaSamples = tissue.rnaSeqSampleSummary; output += `\n**RNA-seq Samples:**\n`; output += ` • Total: ${rnaSamples.totalCount}\n`; output += ` • Female: ${rnaSamples.female.count} (age: ${rnaSamples.female.ageMin}-${rnaSamples.female.ageMax}, mean: ${rnaSamples.female.ageMean.toFixed(1)})\n`; output += ` • Male: ${rnaSamples.male.count} (age: ${rnaSamples.male.ageMin}-${rnaSamples.male.ageMax}, mean: ${rnaSamples.male.ageMean.toFixed(1)})\n`; // eQTL samples const eqtlSamples = tissue.eqtlSampleSummary; output += `\n**eQTL Samples:**\n`; output += ` • Total: ${eqtlSamples.totalCount}\n`; output += ` • Female: ${eqtlSamples.female.count} (age: ${eqtlSamples.female.ageMin}-${eqtlSamples.female.ageMax}, mean: ${eqtlSamples.female.ageMean.toFixed(1)})\n`; output += ` • Male: ${eqtlSamples.male.count} (age: ${eqtlSamples.male.ageMin}-${eqtlSamples.male.ageMax}, mean: ${eqtlSamples.male.ageMean.toFixed(1)})\n`; } else { // Brief format for multiple tissues const totalSamples = tissue.rnaSeqSampleSummary.totalCount; const eGeneInfo = tissue.hasEGenes ? `, ${tissue.eGeneCount} eGenes` : ''; const sGeneInfo = tissue.hasSGenes ? `, ${tissue.sGeneCount} sGenes` : ''; output += ` ${totalSamples} samples${eGeneInfo}${sGeneInfo}\n`; } }); if (displayTissues.length > 1) { // Summary statistics const totalSamples = displayTissues.reduce((sum, t) => sum + t.rnaSeqSampleSummary.totalCount, 0); const totalEGenes = displayTissues.reduce((sum, t) => sum + (t.hasEGenes ? t.eGeneCount : 0), 0); const totalSGenes = displayTissues.reduce((sum, t) => sum + (t.hasSGenes ? t.sGeneCount : 0), 0); output += `\n**Summary:**\n`; output += ` • Total RNA-seq samples: ${totalSamples.toLocaleString()}\n`; output += ` • Total eGenes: ${totalEGenes.toLocaleString()}\n`; output += ` • Total sGenes: ${totalSGenes.toLocaleString()}\n`; output += ` • Tissues with eQTL data: ${displayTissues.filter(t => t.hasEGenes).length}\n`; output += ` • Tissues with sQTL data: ${displayTissues.filter(t => t.hasSGenes).length}\n`; } return { content: [{ type: "text", text: output }] }; }
• src/index.ts:448-460 (schema)

  Tool schema definition including input schema for parameters like datasetId and optional tissueIds.
  name: "get_tissue_info", description: "Get information about GTEx tissues and sample counts", inputSchema: { type: "object", properties: { datasetId: { type: "string", description: "GTEx dataset ID (default: gtex_v8)", default: "gtex_v8" } } } },
• src/index.ts:734-738 (registration)

  Registration and dispatch logic in the main request handler that maps the 'get_tissue_info' tool name to the referenceHandlers.getTissueInfo method.
  if (name === "get_tissue_info") { return await referenceHandlers.getTissueInfo({ datasetId: args?.datasetId }); }