/ensembl/genes/xrefs

POST /api/ensembl/genes/xrefs

Price: 5 credits

List the external database cross-references Ensembl holds for a gene, transcript or translation

How to use it

This is how an Ensembl stable id is translated into an identifier from another resource - UniProt, HGNC, RefSeq, Entrez and the rest - so use `database` when only one of them is wanted. By default only the cross-references hanging off the id itself come back, which for a gene is around ten databases, HGNC, EntrezGene, Uniprot_gn, GeneCards, MIM_GENE and Reactome_gene among them; RefSeq, GO, PDB and the reviewed UniProt entries hang off the transcripts and translations below it and need `all_levels`. A symbol is not accepted here: resolve it through ensembl/genes first.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• gene string required — Ensembl stable id of a gene, transcript or translation (examples: "ENSG00000139618", "ENST00000380152"; minLength: 1)
• all_levels boolean — Also return the cross-references attached to the transcripts and translations below the gene, not only those on the gene itself (default: false)
• database string nullable — Keep only cross-references to this database; a trailing % matches a prefix (examples: "Uniprot%", "HGNC", "EntrezGene"; minLength: 1)
• count integer required — Max number of cross-references to return (min: 1)

Response

• @type string (default: "EnsemblXref")
• primary_id string required
• display_id string (default: "")
• database string (default: "")
• database_display_name string (default: "")
• description string (default: "")
• version string (default: "")
• info_type string (default: "")
• info_text string (default: "")
• synonyms array (default: [])
• linkage_types array (default: [])
• cigar_line string (default: "")
• evalue number nullable
• score number nullable
• ensembl_start integer nullable
• ensembl_end integer nullable
• ensembl_identity number nullable
• xref_start integer nullable
• xref_end integer nullable
• xref_identity number nullable

Errors

• 422 — The request body did not validate Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — The entity was not found, or a precondition failed Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.