Ensembl

live BiologyScience

Ensembl REST — vertebrate genomes, gene annotations, sequences, comparative genomics, variation. Keyless.

7 tools
0ms auth
free tier 50 calls/day

Tools

lookup

"Ensembl gene info for [ENSG...]" / "look up [Ensembl ID]" / "fetch [ENST.../ENSE.../ENSP...]" — fetch metadata for an Ensembl stable ID (gene / transcript / exon / translation). Returns name, biotype

No parameters required.

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lookup_symbol

"What's the Ensembl ID for [gene symbol]" / "look up [gene] in Ensembl" / "BRCA1 / TP53 / BRAF Ensembl info" / "find gene [symbol] in [species]" — look up a gene by symbol within a species (e.g. speci

No parameters required.

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xrefs

"What's the UniProt / HGNC / RefSeq ID for [gene]" / "cross-references for [gene symbol]" — external database IDs (UniProt, RefSeq, HGNC, Entrez, OMIM, etc.) for a gene symbol. Use to map between bio-

No parameters required.

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sequence

"DNA / cDNA / CDS / protein sequence of [gene]" / "FASTA for [Ensembl ID]" / "get sequence of [transcript]" — sequence by Ensembl stable ID. Type defaults to "genomic"; pass "cdna", "cds", or "protein

No parameters required.

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homology

"What's the mouse / rat / zebrafish ortholog of [human gene]" / "ortholog of [gene] in [species]" / "homologs of [gene]" — orthologs and paralogs for a gene across species. Use for cross-species compa

No parameters required.

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variation

"What is [rsID]" / "look up SNP [rs...]" / "variant info for [rsN]" — fetch a genetic variation record by ID (e.g. rs56116432). Returns alleles, genomic location, clinical significance, gene mappings.

No parameters required.

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vep

"What's the effect of [variant]" / "predict consequences of [genomic change]" / "VEP for [chrom:pos]" — Variant Effect Predictor for a specified region + allele. Returns consequences (missense, synony

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash 
curl -X POST https://gateway.pipeworx.io/ensembl/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash 
curl -X POST https://gateway.pipeworx.io/ensembl/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"lookup","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript 
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("lookup", {});
ask_pipeworx 
// Or ask in plain English:
const answer = await px.ask("ensembl rest — vertebrate genomes, gene annotations, sequences, comparative genomics, variation");