/genbank/biosamples

POST /api/genbank/biosamples

Price: 1 credit

Get an NCBI BioSample record by accession or uid

How to use it

Resolves the biological sample a sequencing submission was made from. Accepts the SAMN/SAMEA/SAMD accession or the numeric uid. The descriptive payload lives in `attributes` - a free-form name/value list whose keys differ per submission `package`, with `harmonized_name` giving NCBI's normalised key where one exists - so read host, tissue, isolation source, collection date and geography from there rather than expecting dedicated fields. `identifiers` carries the sample's accessions in SRA, GEO and other archives, which is how you cross to those.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• id string required — BioSample accession or the numeric BioSample uid (examples: "SAMN02797621", "SAMD00000001", "2797621"; minLength: 1)

Response

• @type string (default: "GenbankBioSample")
• id string required
• accession string (default: "")
• sample_title string (default: "")
• description string (default: "")
• organism string (default: "")
• organism_name string (default: "")
• taxid string (default: "")
• infraspecies string (default: "")
• package string (default: "")
• models array (default: [])
• organization string (default: "")
• owner string (default: "")
• owner_abbreviation string (default: "")
• owner_url string (default: "")
• contacts array (default: [])
• access string (default: "")
• status string (default: "")
• status_date string (default: "")
• publication_date string (default: "")
• modification_date string (default: "")
• submission_date string (default: "")
• identifiers array (default: [])
  • @type string (default: "GenbankBioSampleIdentifier")
  • database string required
  • value string required
  • label string (default: "")
  • is_primary boolean (default: false)
• attributes array (default: [])
  • @type string (default: "GenbankBioSampleAttribute")
  • name string required
  • value string required
  • harmonized_name string (default: "")
  • display_name string (default: "")
• links array (default: [])
  • @type string (default: "GenbankBioSampleLink")
  • link_type string required
  • target string (default: "")
  • label string (default: "")
  • value 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 — BioSample 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.