get_tissue_expression
Retrieve tissue-specific protein expression data from the Human Protein Atlas to analyze where genes are active in the human body.
Instructions
Get tissue-specific expression data for a protein
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gene | Yes | Gene symbol | |
| format | No | Output format (default: json) |
Implementation Reference
- src/index.ts:893-919 (handler)The main handler function that executes the 'get_tissue_expression' tool. Validates input using isValidGeneArgs, fetches tissue expression data via fetchTissueExpression, formats as JSON text response, and handles errors.
private async handleGetTissueExpression(args: any) { if (!isValidGeneArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid gene arguments'); } try { const result = await this.fetchTissueExpression(args.gene); return { content: [ { type: 'text', text: JSON.stringify(result, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error fetching tissue expression: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } } - src/index.ts:748-751 (helper)Helper function that performs the actual API query for tissue expression data by calling searchProteins with specific tissue-related columns.
private async fetchTissueExpression(gene: string): Promise<any> { const columns = ['g', 'eg', 'rnats', 'rnatd', 'rnatss', 't_RNA_adipose_tissue', 't_RNA_adrenal_gland', 't_RNA_brain', 't_RNA_breast', 't_RNA_colon', 't_RNA_heart_muscle', 't_RNA_kidney', 't_RNA_liver', 't_RNA_lung', 't_RNA_ovary', 't_RNA_pancreas', 't_RNA_prostate', 't_RNA_skeletal_muscle', 't_RNA_skin_1', 't_RNA_spleen', 't_RNA_stomach_1', 't_RNA_testis', 't_RNA_thyroid_gland']; return this.searchProteins(gene, 'json', columns, 1); } - src/index.ts:485-495 (registration)Tool registration entry in the tools array passed to server.setTools(), including name, description, and input schema.
name: 'get_tissue_expression', description: 'Get tissue-specific expression data for a protein', inputSchema: { type: 'object', properties: { gene: { type: 'string', description: 'Gene symbol' }, format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' }, }, required: ['gene'], }, }, - src/index.ts:676-677 (registration)Switch case in the CallToolRequest handler that routes 'get_tissue_expression' calls to the handleGetTissueExpression method.
case 'get_tissue_expression': return this.handleGetTissueExpression(args); - src/index.ts:487-494 (schema)Input schema defining parameters for the tool: required 'gene' string and optional 'format' enum.
inputSchema: { type: 'object', properties: { gene: { type: 'string', description: 'Gene symbol' }, format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' }, }, required: ['gene'], },