get_external_references
Retrieve cross-references from UniProt entries to external databases like PDB, EMBL, and RefSeq by providing an accession number.
Instructions
Links to other databases (PDB, EMBL, RefSeq, etc.)
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| accession | Yes | UniProt accession number |
Implementation Reference
- src/index.ts:1697-1737 (handler)The handler function for the 'get_external_references' tool. It validates the accession input, fetches the UniProtKB entry via API, extracts cross-references (uniProtKBCrossReferences), categorizes them by database (PDB, EMBL, RefSeq, Ensembl, GO), and returns structured JSON.
private async handleGetExternalReferences(args: any) { if (!isValidProteinInfoArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid external references arguments'); } try { const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, { params: { format: 'json' }, }); const protein = response.data; const externalRefs = { accession: protein.primaryAccession, allReferences: protein.uniProtKBCrossReferences || [], pdbReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'PDB') || [], emblReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'EMBL') || [], refseqReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'RefSeq') || [], ensemblReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'Ensembl') || [], goReferences: protein.uniProtKBCrossReferences?.filter((ref: any) => ref.database === 'GO') || [], }; return { content: [ { type: 'text', text: JSON.stringify(externalRefs, null, 2), }, ], }; } catch (error) { return { content: [ { type: 'text', text: `Error fetching external references: ${error instanceof Error ? error.message : 'Unknown error'}`, }, ], isError: true, }; } } - src/index.ts:774-775 (registration)Registers and dispatches the 'get_external_references' tool call to its handler within the CallToolRequestSchema switch statement.
return this.handleGetExternalReferences(args); case 'get_literature_references': - src/index.ts:653-662 (schema)Tool metadata and input schema definition returned by ListToolsRequestSchema, specifying the name, description, and required 'accession' parameter.
name: 'get_external_references', description: 'Links to other databases (PDB, EMBL, RefSeq, etc.)', inputSchema: { type: 'object', properties: { accession: { type: 'string', description: 'UniProt accession number' }, }, required: ['accession'], }, }, - src/index.ts:79-89 (helper)Input validation helper function used by the get_external_references handler to validate the accession argument.
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)) ); };