get_tissue_info

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
    });
  }