/uniprot/proteomes

POST /api/uniprot/proteomes

Price: 5 credits

Get a UniProt proteome record by its UP identifier

How to use it

Resolves the protein set UniProt holds for one genome assembly of one organism. An organism can have several proteomes, one of which is marked `Reference proteome` in `proteome_type`, so pick by that rather than assuming one per species. `components` lists the chromosomes and plasmids with their own protein counts, and `busco_report` is the completeness assessment of the assembly rather than of UniProt's annotation. Use the id as `proteome` on uniprot/proteins/search to list the entries themselves - this endpoint returns the record, not its proteins.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• proteome string required — UniProt proteome identifier (examples: "UP000005640", "UP000000589", "UP000000625"; minLength: 1)

Response

• @type string (default: "UniprotProteome")
• id string required
• description string (default: "")
• proteome_type string (default: "")
• strain string (default: "")
• superkingdom string (default: "")
• taxonomy object nullable
  • @type string (default: "UniprotTaxonNode")
  • taxon_id integer nullable
  • scientific_name string (default: "")
  • common_name string (default: "")
  • mnemonic string (default: "")
  • rank string (default: "")
  • synonyms array (default: [])
  • is_hidden boolean nullable
• panproteome_taxon_id integer nullable
• taxon_lineage array (default: [])
  • @type string (default: "UniprotTaxonNode")
  • taxon_id integer nullable
  • scientific_name string (default: "")
  • common_name string (default: "")
  • mnemonic string (default: "")
  • rank string (default: "")
  • synonyms array (default: [])
  • is_hidden boolean nullable
• components array (default: [])
  • @type string (default: "UniprotProteomeComponent")
  • name string (default: "")
  • description string (default: "")
  • protein_count integer nullable
  • genome_annotation_source string (default: "")
  • cross_references array (default: [])
• citations array (default: [])
  • @type string (default: "UniprotProteomeCitation")
  • citation_id string (default: "")
  • citation_type string (default: "")
  • citation_title string (default: "")
  • authors array (default: [])
  • authoring_group array (default: [])
  • journal string (default: "")
  • submission_database string (default: "")
  • publication_date string (default: "")
  • volume string (default: "")
  • first_page string (default: "")
  • last_page string (default: "")
  • pubmed_id string (default: "")
  • doi string (default: "")
• annotation_score number nullable
• busco_report object nullable
  • @type string (default: "UniprotBuscoReport")
  • complete integer nullable
  • complete_single integer nullable
  • complete_duplicated integer nullable
  • fragmented integer nullable
  • missing integer nullable
  • total integer nullable
  • lineage_db string (default: "")
  • score number nullable
• cpd_report object nullable
  • @type string (default: "UniprotCpdReport")
  • status string (default: "")
  • confidence number nullable
  • proteome_count integer nullable
  • average_cdss number nullable
  • std_cdss number nullable
• genome_assembly_id string (default: "")
• genome_assembly_level string (default: "")
• genome_assembly_source string (default: "")
• genome_assembly_url string (default: "")
• genome_annotation_source string (default: "")
• genome_annotation_url string (default: "")
• gene_count integer nullable
• protein_count integer nullable
• reviewed_protein_count integer nullable
• unreviewed_protein_count integer nullable
• isoform_protein_count integer nullable
• modified_date string (default: "")
• url string (default: "")

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 — Proteome not found 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.