#### Options to download BioSample data. This BioSample service allows you to get BioSample data as a data report.
openapi: 3.0.1
info:
title: NCBI Datasets BioSample API
version: v2
description: '### NCBI Datasets is a resource that lets you easily gather data from NCBI.
The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
'
servers:
- url: https://api.ncbi.nlm.nih.gov/datasets/v2
security:
- ApiKeyAuthHeader: []
tags:
- name: BioSample
description: '#### Options to download BioSample data.
This BioSample service allows you to get BioSample data as a data report.
'
paths:
/biosample/accession/{accessions}/biosample_report:
get:
summary: Get BioSample dataset reports by accession(s)
description: 'Get BioSample dataset reports by accession(s). By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
tags:
- BioSample
operationId: BioSample_dataset_report
responses:
default:
description: An unexpected error response.
content:
text/plain:
schema:
$ref: '#/components/schemas/rpcStatus'
'200':
description: A successful response
content:
application/json:
schema:
$ref: '#/components/schemas/v2reportsBioSampleDataReportPage'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsBioSampleDataReportPage'
text/tab-separated-values:
schema:
type: string
parameters:
- name: accessions
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: SAMN15960293
summary: Animal sample from Gallus gallus, bGalGal3
example-1:
value: SAMN12629504
summary: Animal sample from Carcharodon carcharias
components:
schemas:
v2reportsInfraspecificNames:
type: object
properties:
breed:
type: string
title: A homogenous group of animals within a domesticated species
cultivar:
type: string
title: A variety of plant within a species produced and maintained by cultivation
ecotype:
type: string
title: A population or subspecies occupying a distinct habitat
isolate:
type: string
title: The individual isolate from which the sequences in the genome assembly were derived
sex:
type: string
title: Physical sex of sampled organism
strain:
type: string
title: A genetic variant, subtype or culture within a species
v2reportsBioSampleStatus:
type: object
properties:
status:
type: string
when:
type: string
v2reportsWarning:
type: object
properties:
gene_warning_code:
$ref: '#/components/schemas/v2reportsWarningGeneWarningCode'
reason:
type: string
message:
type: string
replaced_id:
$ref: '#/components/schemas/v2reportsWarningReplacedId'
unrecognized_identifier:
type: string
v2reportsBioSampleId:
type: object
properties:
db:
type: string
label:
type: string
value:
type: string
v2reportsBioSampleOwner:
type: object
properties:
name:
type: string
contacts:
type: array
items:
$ref: '#/components/schemas/v2reportsBioSampleContact'
v2reportsErrorGeneErrorCode:
type: string
enum:
- UNKNOWN_GENE_ERROR_CODE
- INCOMPLETE_LOOKUP_SYMBOL
- INVALID_TAXON_GENE_ARGUMENT
default: UNKNOWN_GENE_ERROR_CODE
v2reportsOrganism:
type: object
properties:
tax_id:
type: integer
title: NCBI Taxonomy identifier
sci_name:
type: string
title: Scientific name
organism_name:
type: string
title: Scientific name
common_name:
type: string
title: Common name
lineage:
type: array
items:
$ref: '#/components/schemas/v2reportsLineageOrganism'
strain:
type: string
pangolin_classification:
type: string
infraspecific_names:
$ref: '#/components/schemas/v2reportsInfraspecificNames'
v2reportsBioSampleAttribute:
type: object
properties:
name:
type: string
value:
type: string
v2reportsErrorAssemblyErrorCode:
type: string
enum:
- UNKNOWN_ASSEMBLY_ERROR_CODE
- INVALID_BIOPROJECT_IDS
- NO_ASSEMBLIES_FOR_BIOPROJECTS
- INVALID_TAXON
- MISSING_SEARCH_FIELD
- INVALID_BIOSAMPLE_IDS
- NO_ASSEMBLIES_FOR_BIOSAMPLE_IDS
- NO_ASSEMBLIES_FOR_ASSEMBLY_NAMES
- INVALID_WGS_ACCESSIONS
- NO_ASSEMBLIES_FOR_WGS_ACCESSIONS
default: UNKNOWN_ASSEMBLY_ERROR_CODE
v2reportsBioSampleDescription:
type: object
properties:
title:
type: string
organism:
$ref: '#/components/schemas/v2reportsOrganism'
comment:
type: string
v2reportsErrorVirusErrorCode:
type: string
enum:
- UNKNOWN_VIRUS_ERROR_CODE
default: UNKNOWN_VIRUS_ERROR_CODE
v2reportsErrorTaxonomyErrorCode:
type: string
enum:
- UNKNOWN_TAXONOMY_ERROR_CODE
- INVALID_TAXONOMY_TAXON
default: UNKNOWN_TAXONOMY_ERROR_CODE
rpcStatus:
type: object
properties:
code:
type: integer
format: int32
message:
type: string
details:
type: array
items:
$ref: '#/components/schemas/protobufAny'
v2reportsBioSampleDataReportPage:
type: object
properties:
reports:
type: array
items:
$ref: '#/components/schemas/v2reportsBioSampleDataReport'
total_count:
type: integer
title: The total count of available datasets (ignoring the page_size parameter).
next_page_token:
type: string
title: A token that can be sent as `page_token` to retrieve the next page. If this field is omitted, there are no subsequent pages.
messages:
type: array
items:
$ref: '#/components/schemas/v2reportsMessage'
v2reportsError:
type: object
properties:
assembly_error_code:
$ref: '#/components/schemas/v2reportsErrorAssemblyErrorCode'
gene_error_code:
$ref: '#/components/schemas/v2reportsErrorGeneErrorCode'
organelle_error_code:
$ref: '#/components/schemas/v2reportsErrorOrganelleErrorCode'
virus_error_code:
$ref: '#/components/schemas/v2reportsErrorVirusErrorCode'
taxonomy_error_code:
$ref: '#/components/schemas/v2reportsErrorTaxonomyErrorCode'
reason:
type: string
message:
type: string
invalid_identifiers:
type: array
items:
type: string
v2reportsBioSampleDataReport:
type: object
properties:
accession:
type: string
title: BioSample Accession identifier
last_updated:
type: string
title: When the biosample object was last updated.
publication_date:
type: string
title: BioSample object publication date.
submission_date:
type: string
title: BioSample object submission date.
sample_ids:
type: array
items:
$ref: '#/components/schemas/v2reportsBioSampleId'
description:
$ref: '#/components/schemas/v2reportsBioSampleDescription'
title: BioSample description.
owner:
$ref: '#/components/schemas/v2reportsBioSampleOwner'
title: BioSample owner.
models:
type: array
items:
type: string
bioprojects:
type: array
items:
$ref: '#/components/schemas/v2reportsBioProject'
package:
type: string
title: Package identifier.
attributes:
type: array
items:
$ref: '#/components/schemas/v2reportsBioSampleAttribute'
status:
$ref: '#/components/schemas/v2reportsBioSampleStatus'
title: Current status of the object.
age:
type: string
title: Age at the time of sampling
biomaterial_provider:
type: string
title: Name and address of the lab or PI
breed:
type: string
title: Breed name
collected_by:
type: string
title: Name of persons or institute who collected the sample
collection_date:
type: string
title: Date on which the sample was collected
cultivar:
type: string
title: Cultivated variety of plant
dev_stage:
type: string
title: Developmental stage at the time of sampling
ecotype:
type: string
title: Population within a given species adapted to a local habitat
geo_loc_name:
type: string
title: Geographical origin of the sample
host:
type: string
title: The natural host to the organism
host_disease:
type: string
title: Name of relevant disease
identified_by:
type: string
title: Name of the taxonomist who identified the specimen
ifsac_category:
type: string
title: Interagency Food Safety Analytics Collaboration (IFSAC) category
isolate:
type: string
title: Description of the specific individual from which the sample was derived
isolate_name_alias:
type: string
title: Other IDs associated with this isolate
isolation_source:
type: string
title: Source of the sample
lat_lon:
type: string
title: Geogrpahic coordinates of the location where the sample was collected
project_name:
type: string
title: Name of the project
sample_name:
type: string
title: Sample name in source database
serovar:
type: string
title: Taxonomic name below subspecies. Same as serotype.
sex:
type: string
title: Physical sex of sampled organism
source_type:
type: string
title: Controlled vocabulary describing the isolation source
strain:
type: string
title: Strain name
sub_species:
type: string
title: Sub-species taxonomic name
tissue:
type: string
title: Type of tissue from which the sample was derived
serotype:
type: string
title: Taxonomic name below subspecies. Same as serovar
v2reportsLineageOrganism:
type: object
properties:
tax_id:
type: integer
title: NCBI Taxonomy identifier
name:
type: string
title: Scientific name
v2reportsMessage:
type: object
properties:
error:
$ref: '#/components/schemas/v2reportsError'
warning:
$ref: '#/components/schemas/v2reportsWarning'
v2reportsWarningGeneWarningCode:
type: string
enum:
- UNKNOWN_GENE_WARNING_CODE
- ACCESSION_VERSION_MISMATCH
- REPLACED_GENE_ID
- DISCONTINUED_GENE_ID
- UNRECOGNIZED_GENE_ID
- UNRECOGNIZED_GENE_SYMBOL
- UNRECOGNIZED_ACCESSION
- UNRECOGNIZED_TAX_TOKEN
- NO_GENE_ANNOTATION_FOUND
- ABOVE_SPECIES_TAXON
default: UNKNOWN_GENE_WARNING_CODE
v2reportsErrorOrganelleErrorCode:
type: string
enum:
- UNKNOWN_ORGANELLE_ERROR_CODE
- INVALID_ORGANELLE_TAXON
- NO_ORGANELLES_FOR_ACCESSION
default: UNKNOWN_ORGANELLE_ERROR_CODE
v2reportsBioSampleContact:
type: object
properties:
lab:
type: string
title: Submitter lab name.
v2reportsBioProject:
type: object
properties:
accession:
type: string
title: BioProject accession
title:
type: string
title: Title of the BioProject provided by the submitter
parent_accession:
type: string
parent_accessions:
type: array
items:
type: string
protobufAny:
type: object
properties:
type_url:
type: string
value:
type: string
format: byte
v2reportsWarningReplacedId:
type: object
properties:
requested:
type: string
returned:
type: string
securitySchemes:
ApiKeyAuth:
type: apiKey
in: query
name: api_key
ApiKeyAuthHeader:
type: apiKey
in: header
name: api-key
externalDocs:
description: Interactively explore genome assembly datasets
url: https://www.ncbi.nlm.nih.gov/datasets/genomes/