get_literature_references
Retrieve scientific publications and citations for UniProt protein entries using accession numbers to support research validation and literature review.
Instructions
Associated publications and citations
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| accession | Yes | UniProt accession number |
Implementation Reference
- src/index.ts:1739-1776 (handler)The handler function that implements the core logic for the 'get_literature_references' tool. It validates input, fetches the UniProt protein entry via API, extracts the references array and PubMed cross-references, and formats the response.
private async handleGetLiteratureReferences(args: any) { if (!isValidProteinInfoArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid literature references arguments'); } try { const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, { params: { format: 'json' }, }); const protein = response.data; const literatureInfo = { accession: protein.primaryAccession, references: protein.references || [], pubmedReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'PubMed') || [], citationCount: protein.references?.length || 0, }; return { content: [ { type: 'text', text: JSON.stringify(literatureInfo, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error fetching literature references: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } } - src/index.ts:664-673 (registration)Tool registration entry in the ListToolsRequestSchema response, defining the tool name, description, and input schema (schema).
name: 'get_literature_references', description: 'Associated publications and citations', inputSchema: { type: 'object', properties: { accession: { type: 'string', description: 'UniProt accession number' }, }, required: ['accession'], }, }, - src/index.ts:776-776 (registration)Dispatch case in the CallToolRequestSchema handler switch statement that routes tool calls to the specific handler.
return this.handleGetLiteratureReferences(args); - src/index.ts:79-89 (helper)Helper validation function for input arguments requiring a UniProt accession, used by the get_literature_references handler and others.
const isValidProteinInfoArgs = ( args: any ): args is { accession: string; format?: string } => { return ( typeof args === 'object' && args !== null && typeof args.accession === 'string' && args.accession.length > 0 && (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format)) ); };