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GenomesEnsembl REST lookup and xrefs

Ensembl

Ensembl is a genome annotation resource run by EMBL-EBI. It assigns stable gene IDs and places each gene on a named genome assembly. Through ScholarMuse, an agent calls lookup_gene_protein with a gene symbol or an Ensembl gene id and gets the Ensembl ID, biotype and genomic coordinates in the same record as the NCBI Gene and UniProt data.

ScholarMuse tools: lookup_gene_protein. Each successful call uses credits.

Use in my agent

Ask your agent

What are the genomic coordinates of human EGFR, and on which assembly?
Which gene is ENSG00000141510, and what is its biotype?
Give me the Ensembl gene id and strand for zebrafish tp53.

What your agent gets back

Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from Ensembl.

lookup_gene_protein

The tool returns one merged record. These are the parts filled from Ensembl. Field names are paths inside `data`.

ids.ensembl
Ensembl stable gene id
biotype
Gene biotype, for example protein_coding
location.assembly
Genome assembly the coordinates refer to
location.chromosome
Chromosome or sequence region name
location.start
Gene start position
location.end
Gene end position
location.strand
Strand, + or -
links.ensembl
URL of the gene page at Ensembl

What it covers

  • Gene-level annotation: stable gene id, biotype, assembly name, chromosome, start, end and strand.
  • Lookup by gene symbol in a chosen organism, or by Ensembl stable gene id. A version suffix on the id (such as .12) is dropped.
  • When UniProt has no entry for the gene, Ensembl cross-references are used to fill in the NCBI Gene ID and the Swiss-Prot accession.

Limits

  • One gene per call. No transcripts, exons, sequences, variants or homologues are returned.
  • Coordinates are for the assembly Ensembl currently serves and named in location.assembly. Older assemblies cannot be requested.
  • A symbol or id that Ensembl does not recognise is treated as not found, and the record is then built from NCBI Gene and UniProt alone.

How ScholarMuse reaches Ensembl

The connector calls the Ensembl REST API at rest.ensembl.org directly: /lookup/symbol or /lookup/id for the gene, and /xrefs/id when a UniProt or NCBI Gene id still has to be found. No API key is sent.

Responses are cached for up to 7 days, so a change in a new Ensembl release can take that long to appear.

API key: the upstream API can be called without one, so you do not add one.

Licence and attribution

Licence: No restrictions on data use (Ensembl / EMBL-EBI terms of use)

Gene annotation from Ensembl (ensembl.org), EMBL-EBI.

Records that come from Ensembl carry this licence and attribution. When you cite the data in a paper, follow Ensembl's own citation guidance.

Capabilities that use Ensembl

Gene & protein lookupNew

Gene & protein lookup

Life sciences & medicine · NCBI Gene, Ensembl, UniProt +5

Related sources

NCBI GeneUniProtInterProReactomeGTExNCBI GEOSTRING

FAQ

ScholarMuse is not an official Ensembl product. It is one MCP server for academic data, and its lookup_gene_protein tool queries Ensembl. An agent connected to ScholarMuse can use Ensembl without a separate server.

No. The Ensembl API can be called without a key, and ScholarMuse does not ask you for one. You sign in to ScholarMuse once and your agent calls the tool.

The connector calls the Ensembl REST API at rest.ensembl.org directly: /lookup/symbol or /lookup/id for the gene, and /xrefs/id when a UniProt or NCBI Gene id still has to be found. No API key is sent. Responses are cached for up to 7 days, so a change in a new Ensembl release can take that long to appear.

No restrictions on data use (Ensembl / EMBL-EBI terms of use). Attribution: Gene annotation from Ensembl (ensembl.org), EMBL-EBI. Records that come from Ensembl carry this licence and attribution.

Yes. Each successful call to lookup_gene_protein uses credits, and a call that fails is not charged. Current price: Gene & protein lookup, 1 credit / call.