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datasets.openapi.yaml
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openapi: 3.0.1
info:
title: NCBI Datasets API
version: v2
description: '### NCBI Datasets is a resource that lets you easily gather data from
NCBI.
The Datasets version 2 API is still in alpha, and we''re updating it often to add new functionality,
iron out bugs and enhance usability.
For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/),
and retrieve the individual data files at a later time.
'
servers:
- url: https://api.ncbi.nlm.nih.gov/datasets/v2
- url: https://dev.ncbi.nlm.nih.gov/datasets/v2
tags:
- name: Genome
description: '#### Options to explore, summarize and download assembled genomes,
including the associated sequence, metadata and annotation.
These genome services allow you to explore genome [assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly). For
a set of genomes of interest, identified by either assembly accession or taxonomic
subtree, you can generate a summary, determine the package size, and download.
'
- name: Gene
description: '#### Options to explore, summarize and download sequences and metadata
for genes and their associated transcripts and proteins.
These gene services allow you explore [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/),
and for genes of interest, identified by either gene-id, symbol or RefSeq sequence
accession, download a data package including metadata (tabular and [JSON Lines](https://jsonlines.org/)
formats), transcript and protein sequence in FASTA format.
'
- name: Prokaryote
description: '#### Options to explore, summarize and download sequences and metadata
for prokaryote genes and their associated proteins.
These gene services allow you to explore prokaryotic gene data by RefSeq protein
sequence accession and download a data package including metadata for the gene
including all genomic annotations as [JSON Lines](https://jsonlines.org/) format,
gene and protein sequences in FASTA format.
'
- name: Virus
description: '#### Get metadata or a zip archive containing a virus genome
or coronavirus protein dataset.
The following files are optionally available for virus genome and/or protein
datasets:
* genomic.fna (genomic sequences in FASTA format)
* cds.fna (nucleotide coding sequences in FASTA format)
* protein.faa (protein sequences in FASTA format)
* annotation_report.jsonl (annotation report in [JSON Lines](https://jsonlines.org/) format)
* biosample_report.jsonl (biosample report in [JSON Lines](https://jsonlines.org/) format)
The following files are always included in coronavirus genome and protein datasets:
* data_report.jsonl (data report with viral metadata in JSON lines format)
* virus_dataset.md (README containing details on sequence file data content and
other information)
* dataset_catalog.json (a list of files and file types included in the dataset)
You may also request a tab-delimited table of metadata that describes the available
virus genome and protein data.
Virus genome datasets are available for all viruses, including SARS-CoV-2.
Various parameters may be used for filtering and specifying the contents of the genome dataset.
Protein datasets are available for SARS-CoV-2 only.
'
- name: Version
description: "#### Retrieve the current version of all services. \nServices follow\
\ [Semantic Versioning 2.0.0 Schema](https://semver.org/spec/v2.0.0.html).\n"
- name: Taxonomy
description: '#### Options to explore taxonomic metadata and relationships.
These taxonomic services allow you to browse taxonomic metadata in addition to retrieving
parent lineages and filtered sets of child nodes for any given set of taxonomic identifiers.
'
externalDocs:
description: Interactively explore genome assembly datasets
url: https://www.ncbi.nlm.nih.gov/datasets/genomes/
security:
- ApiKeyAuthHeader: []
paths:
/genome/accession/{accessions}/download_summary:
get:
summary: Preview genome dataset download
description: 'Get a download summary by accession in a JSON output format.'
tags:
- Genome
operationId: genome_download_summary
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/v2DownloadSummary'
parameters:
- name: accessions
description: 'NCBI genome assembly accessions'
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: GCF_000001405.40
summary: Human
example-1:
value:
- GCF_000001405.40
- GCF_000001635.27
summary: Human and Mouse
- name: chromosomes
description: 'The default setting is all chromosome. Specify individual chromosome by string (1,2,MT or chr1,chr2.chrMT). Unplaced sequences are treated like their own chromosome (''Un''). The filter only applies to fasta sequence.'
in: query
required: false
schema:
type: array
items:
type: string
examples:
example-0:
value:
- 1
- 2
- 3
- X
- Y
- MT
summary: Selected chromosomes #1
example-1:
value:
- X
- Y
summary: Human sex chromosomes
- name: include_annotation_type
description: 'Select additional types of annotation to include in the data package. If unset, no annotation is provided.'
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2AnnotationForAssemblyType'
examples:
example-0:
value:
- GENOME_FASTA
- PROT_FASTA
- RNA_FASTA
summary: Genomic, Transcript & Protein Sequence
example-1:
value:
- GENOME_GFF
- GENOME_GBFF
- GENOME_GTF
- PROT_FASTA
- RNA_FASTA
- CDS_FASTA, SEQUENCE_REPORT
summary: All
/genome/download_summary:
post:
summary: Preview genome dataset download by POST
description: 'The ''GET'' version of download summary is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request.'
tags:
- Genome
operationId: genome_download_summary_by_post
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/v2DownloadSummary'
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/v2AssemblyDatasetRequest'
examples:
Single GCF accession example:
description: GCF Accession (just one)
value:
accessions:
- GCF_000001405.40
/genome/accession/{accessions}/dataset_report:
get:
summary: Get dataset reports by accessions
description: 'Get dataset reports by accessions. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
tags:
- Genome
operationId: genome_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/v2reportsAssemblyDataReportPage'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsAssemblyDataReportPage'
text/tab-separated-values:
schema:
type: string
parameters:
- name: accessions
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: GCF_000001405.40
summary: Human
example-1:
value:
- GCF_000001405.40
- GCF_000001635.27
summary: Human and Mouse
- name: filters.reference_only
description: 'If true, only return reference and representative (GCF_ and GCA_) genome assemblies.'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: true
summary: Limit to reference & representative genomes
example-1:
value: false
summary: Include reference and non-reference genomes
- name: filters.assembly_source
description: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
default: all
examples:
example-0:
value: refseq
summary: Limit to RefSeq genomes
example-1:
value: genbank
summary: Limit to GenBank genomes
example-2:
value: all
summary: All genomes
- name: filters.has_annotation
description: 'Return only annotated genome assemblies'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: true
summary: Limit to annotated assemblies
example-1:
value: false
summary: Return all assemblies
- name: filters.exclude_paired_reports
description: 'For paired (GCA/GCF) records, only return the primary record'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all assemblies
example-1:
value: true
summary: Only return single record for GCA/GCF pairs
- name: filters.exclude_atypical
description: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones that are atypical
example-1:
value: true
summary: Only return genomes that have not been classified as atypical
- name: filters.assembly_version
description: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
default: current
examples:
example-0:
value: current
summary: Only return current assemblies
example-1:
value: all_assemblies
summary: Return all assemblies, including suppressed and replaced
- name: filters.assembly_level
description: 'Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.'
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2reportsAssemblyLevel'
examples:
example-0:
value:
- chromosome
- complete_genome
summary: Chromosome and complete genome
example-1:
value:
- scaffold
- chromosome
- complete_genome
summary: Scaffold and higher
- name: filters.first_release_date
description: 'Only return genome assemblies that were released on or after the specified date By default, do not filter.'
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: 01/10/2015
summary: Jan 10, 2015
- name: filters.last_release_date
description: 'Only return genome assemblies that were released on or before to the specified date By default, do not filter.'
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: 01/10/2021
summary: Jan 10, 2021
- name: filters.search_text
description: 'Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter'
in: query
required: false
schema:
type: array
items:
type: string
examples:
example-0:
value: Genome Reference Consortium
summary: Genome Reference Consortium
example-1:
value: GRCh38
summary: GRCh38
example-2:
value: C57BL/6J
summary: C57BL/6J
- name: filters.is_metagenome_derived
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter'
examples:
example-0:
value: metagenome_derived_exclude
summary: Exclude metagenome derived assemblies
example-1:
value: metagenome_derived_only
summary: Return only metagenome derived assemblies
- name: filters.is_type_material
description: 'If true, include only type materials'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones of type materials
example-1:
value: true
summary: Only return genomes that are classified as type materials
- name: filters.is_ictv_exemplar
description: 'If true, include only ICTV Exemplars'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones of type ICTV exemplar
example-1:
value: true
summary: Only return genomes that are classified as ICTV exemplar
- name: filters.exclude_multi_isolate
description: 'If true, exclude large multi-isolate projects'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones of large multi-isolate projects
example-1:
value: true
summary: Exclude genomes that are classified as large multi-isolate projects
- name: filters.type_material_category
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory'
examples:
example-0:
value: TYPE_MATERIAL
summary: A Type Material with no classification
example-1:
value: TYPE_MATERIAL_CLADE
summary: A Type Material of the Clade classification
example-2:
value: TYPE_MATERIAL_NEOTYPE
summary: A Type Material of the Neotype classification
- name: tax_exact_match
description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
in: query
required: false
schema:
type: boolean
default: false
- name: table_fields
in: query
required: false
schema:
type: array
items:
type: string
examples:
example-0:
value:
- assminfo-accession
- assminfo-name
summary: Genome Accession and Name
example-1:
value: assminfo-accession
summary: Just accession
- name: returned_content
description: 'Return either assembly accessions, or complete assembly reports'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType'
- name: page_size
description: 'The maximum number of genome assembly reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
in: query
required: false
schema:
type: integer
default: 20
- name: page_token
description: 'A page token is returned from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
in: query
required: false
schema:
type: string
- name: sort.field
in: query
required: false
schema:
type: string
- name: sort.direction
in: query
required: false
schema:
$ref: '#/components/schemas/v2SortDirection'
- name: include_tabular_header
description: 'Whether this request for tabular data should include the header row'
in: query
required: false
schema:
$ref: '#/components/schemas/v2IncludeTabularHeader'
/genome/taxon/{taxons}/dataset_report:
get:
summary: Get dataset reports by taxons
description: 'Get dataset reports by taxons. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
tags:
- Genome
operationId: genome_dataset_reports_by_taxon
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/v2reportsAssemblyDataReportPage'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsAssemblyDataReportPage'
text/tab-separated-values:
schema:
type: string
parameters:
- name: taxons
description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: 9606
summary: NCBI Taxonomy Identifier
example-1:
value:
- chimpanzee
- eastern gorilla
summary: Common Names
example-2:
value: Homo sapiens
summary: Scientific Name
- name: filters.reference_only
description: 'If true, only return reference and representative (GCF_ and GCA_) genome assemblies.'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: true
summary: Limit to reference & representative genomes
example-1:
value: false
summary: Include reference and non-reference genomes
- name: filters.assembly_source
description: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
default: all
examples:
example-0:
value: refseq
summary: Limit to RefSeq genomes
example-1:
value: genbank
summary: Limit to GenBank genomes
example-2:
value: all
summary: All genomes
- name: filters.has_annotation
description: 'Return only annotated genome assemblies'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: true
summary: Limit to annotated assemblies
example-1:
value: false
summary: Return all assemblies
- name: filters.exclude_paired_reports
description: 'For paired (GCA/GCF) records, only return the primary record'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all assemblies
example-1:
value: true
summary: Only return single record for GCA/GCF pairs
- name: filters.exclude_atypical
description: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones that are atypical
example-1:
value: true
summary: Only return genomes that have not been classified as atypical
- name: filters.assembly_version
description: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
default: current
examples:
example-0:
value: current
summary: Only return current assemblies
example-1:
value: all_assemblies
summary: Return all assemblies, including suppressed and replaced
- name: filters.assembly_level
description: 'Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.'
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2reportsAssemblyLevel'
examples:
example-0:
value:
- chromosome
- complete_genome
summary: Chromosome and complete genome
example-1:
value:
- scaffold
- chromosome
- complete_genome
summary: Scaffold and higher
- name: filters.first_release_date
description: 'Only return genome assemblies that were released on or after the specified date By default, do not filter.'
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: 01/10/2015
summary: Jan 10, 2015
- name: filters.last_release_date
description: 'Only return genome assemblies that were released on or before to the specified date By default, do not filter.'
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: 01/10/2021
summary: Jan 10, 2021
- name: filters.search_text
description: 'Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter'
in: query
required: false
schema:
type: array
items:
type: string
examples:
example-0:
value: Genome Reference Consortium
summary: Genome Reference Consortium
example-1:
value: GRCh38
summary: GRCh38
example-2:
value: C57BL/6J
summary: C57BL/6J
- name: filters.is_metagenome_derived
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter'
examples:
example-0:
value: metagenome_derived_exclude
summary: Exclude metagenome derived assemblies
example-1:
value: metagenome_derived_only
summary: Return only metagenome derived assemblies
- name: filters.is_type_material
description: 'If true, include only type materials'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones of type materials
example-1:
value: true
summary: Only return genomes that are classified as type materials
- name: filters.is_ictv_exemplar
description: 'If true, include only ICTV Exemplars'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones of type ICTV exemplar
example-1:
value: true
summary: Only return genomes that are classified as ICTV exemplar
- name: filters.exclude_multi_isolate
description: 'If true, exclude large multi-isolate projects'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones of large multi-isolate projects
example-1:
value: true
summary: Exclude genomes that are classified as large multi-isolate projects
- name: filters.type_material_category
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory'
examples:
example-0:
value: TYPE_MATERIAL
summary: A Type Material with no classification
example-1:
value: TYPE_MATERIAL_CLADE
summary: A Type Material of the Clade classification
example-2:
value: TYPE_MATERIAL_NEOTYPE
summary: A Type Material of the Neotype classification
- name: tax_exact_match
description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
in: query
required: false
schema:
type: boolean
default: false
- name: table_fields
in: query
required: false
schema:
type: array
items:
type: string
examples:
example-0:
value:
- assminfo-accession
- assminfo-name
summary: Genome Accession and Name
example-1:
value: assminfo-accession
summary: Just accession
- name: returned_content
description: 'Return either assembly accessions, or complete assembly reports'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType'
- name: page_size
description: 'The maximum number of genome assembly reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
in: query
required: false
schema:
type: integer
default: 20
- name: page_token
description: 'A page token is returned from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
in: query
required: false
schema:
type: string
- name: sort.field
in: query
required: false
schema:
type: string
- name: sort.direction
in: query
required: false
schema:
$ref: '#/components/schemas/v2SortDirection'
- name: include_tabular_header
description: 'Whether this request for tabular data should include the header row'
in: query
required: false
schema:
$ref: '#/components/schemas/v2IncludeTabularHeader'
/genome/bioproject/{bioprojects}/dataset_report:
get:
summary: Get dataset reports by bioproject
description: 'Get dataset reports by bioprojects. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
tags:
- Genome
operationId: genome_dataset_reports_by_bioproject
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/v2reportsAssemblyDataReportPage'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsAssemblyDataReportPage'
text/tab-separated-values:
schema:
type: string
parameters:
- name: bioprojects
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: PRJNA489243
summary: Vertebrate Genomes Project
example-1:
value: PRJNA31257
summary: Human Genome Project
- name: filters.reference_only
description: 'If true, only return reference and representative (GCF_ and GCA_) genome assemblies.'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: true
summary: Limit to reference & representative genomes
example-1:
value: false
summary: Include reference and non-reference genomes
- name: filters.assembly_source
description: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
default: all
examples:
example-0:
value: refseq
summary: Limit to RefSeq genomes
example-1:
value: genbank
summary: Limit to GenBank genomes
example-2:
value: all
summary: All genomes
- name: filters.has_annotation
description: 'Return only annotated genome assemblies'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: true
summary: Limit to annotated assemblies
example-1:
value: false
summary: Return all assemblies
- name: filters.exclude_paired_reports
description: 'For paired (GCA/GCF) records, only return the primary record'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all assemblies
example-1:
value: true
summary: Only return single record for GCA/GCF pairs
- name: filters.exclude_atypical
description: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
in: query
required: false
schema:
type: boolean
default: false
examples:
example-0:
value: false
summary: Return all selected genomes, including ones that are atypical
example-1:
value: true
summary: Only return genomes that have not been classified as atypical
- name: filters.assembly_version
description: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
in: query
required: false
schema:
$ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
default: current
examples:
example-0:
value: current
summary: Only return current assemblies
example-1:
value: all_assemblies
summary: Return all assemblies, including suppressed and replaced
- name: filters.assembly_level
description: 'Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.'
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2reportsAssemblyLevel'
examples:
example-0:
value:
- chromosome
- complete_genome
summary: Chromosome and complete genome