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National Institutes of Health (NIH)

National Institutes of Health (NIH) Genome API

#### Options to download assembled genome data, including the associated sequence, annotation and metadata.These genome services allow you to get genome metadata as a data report or download genome, transcript and protein sequence, annotation and metadata as a genome data package, for assembled genomes.

Documentation Provider Profile APIs.io OpenAPI GitHub

National Institutes of Health (NIH) Genome API is one of 15 APIs that National Institutes of Health (NIH) publishes on the APIs.io network, described by a machine-readable OpenAPI specification.

Tagged areas include Genome. The published artifact set on APIs.io includes an OpenAPI specification and API documentation.

This API exposes 31 operations across 31 paths, and defines 105 schemas. It is described by OpenAPI 3.0.3, at version 2.0.5.

Requests are made against a single base URL, https://clinicaltrials.gov/api/v2.

31 operations 31 paths 105 schemas 18 GET13 POST

Metadata

The identity and technical contract details declared by the specification.

Specification
OpenAPI 3.0.3
API Version
2.0.5
Base URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
Resource Areas
1

Paths & Operations 31

Across 31 paths, the API surfaces 31 operations — 18 GET, 13 POST. Each is listed below with its method, path, parameters, and response codes.

Genome 31

Options to download assembled genome data, including the associated sequence, annotation and metadata. These genome services allow you to get genome metadata as a data report or d…

GET
/genome/accession/{accessions}/download_summary
Get a download summary (preview) of a genome data package by genome assembly accession
genome_download_summary 3 params → default200
POST
/genome/download_summary
Get a download summary (preview) of a genome data package by genome assembly accession
genome_download_summary_by_post body → default200
GET
/genome/accession/{accessions}/dataset_report
Get a genome assembly report by genome assembly accession
genome_dataset_report 23 params → default200
GET
/genome/taxon/{taxons}/dataset_report
Get a genome assembly report by taxon
genome_dataset_reports_by_taxon 24 params → default200
GET
/genome/bioproject/{bioprojects}/dataset_report
Get genome assembly reports by BioProject accession
genome_dataset_reports_by_bioproject 24 params → default200
GET
/genome/biosample/{biosample_ids}/dataset_report
Get genome assembly reports by BioSample accession
genome_dataset_reports_by_biosample_id 24 params → default200
GET
/genome/wgs/{wgs_accessions}/dataset_report
Get a genome assembly data report by WGS accession
genome_dataset_reports_by_wgs 24 params → default200
GET
/genome/assembly_name/{assembly_names}/dataset_report
Get genome assembly reports by assembly name
genome_dataset_reports_by_assembly_name 24 params → default200
POST
/genome/dataset_report
Get a genome assembly report
genome_dataset_report_by_post body → default200
GET
/genome/sequence_accession/{accession}/sequence_assemblies
Get a genome assembly accession for a nucleotide sequence accession
assembly_accessions_for_sequence_accession 1 param → default200
POST
/genome/sequence_assemblies
Get a genome assembly accession for a nucleotide sequence accession
assembly_accessions_for_sequence_accession_by_post body → default200
GET
/genome/accession/{accession}/sequence_reports
Get a genome sequence report by genome assembly accession
genome_sequence_report 8 params → default200
POST
/genome/sequence_reports
Get a genome sequence report by genome assembly accession
genome_sequence_report_by_post body → default200
GET
/genome/accession/{accessions}/links
Get assembly links by genome assembly accession
genome_links_by_accession 2 params → default200
POST
/genome/links
Get assembly links by genome assembly accession
genome_links_by_accession_by_post body → default200
GET
/genome/taxon/{species_taxon}/checkm_histogram
Get CheckM histogram data by species taxon
checkm_histogram_by_taxon 1 param → default200
POST
/genome/checkm_histogram
Get CheckM histogram data by species taxon
checkm_histogram_by_taxon_by_post body → default200
GET
/genome/accession/{accessions}/download
Get a genome data package by genome assembly accession
download_assembly_package 5 params → default200
POST
/genome/download
Get a genome data package by genome assembly accession
download_assembly_package_post 1 param body → default200
GET
/genome/accession/{accession}/annotation_report/download
Get a genome annotation data package by genome assembly accession
download_genome_annotation_package 10 params → default200
POST
/genome/annotation_report/download
Get a genome annotation data package by genome assembly accession
download_genome_annotation_package_by_post 1 param body → default200
GET
/genome/accession/{accessions}/check
Check the validity of a genome assembly accession
check_assembly_availability 1 param → default200
POST
/genome/check
Check the validity of a genome assembly accession
check_assembly_availability_post body → default200
GET
/genome/accession/{accession}/annotation_report
Get genome annotation reports by genome assembly accession
genome_annotation_report 12 params → default200
POST
/genome/annotation_report
Get genome annotation reports by genome assembly accession
genome_annotation_report_by_post body → default200
GET
/genome/accession/{accession}/annotation_summary
Get genome annotation report summary information by genome assembly accession
annotation_report_facets_by_accession 3 params → default200
POST
/genome/annotation_summary
Get genome annotation report summary information by genome assembly accession
annotation_report_facets_by_post body → default200
GET
/genome/accession/{accession}/annotation_report/download_summary
Get a download summary (preview) of a genome annotation data package by genome assembly accession
genome_annotation_download_summary 9 params → default200
POST
/genome/annotation_report/download_summary
Get a download summary (preview) of a genome annotation data package by genome assembly accession
genome_annotation_download_summary_by_post body → default200
GET
/genome/accession/{accession}/revision_history
Get a revision history for a genome assembly by genome assembly accession
assembly_revision_history_by_get 1 param → default200
POST
/genome/revision_history
Get a revision history for a genome assembly by genome assembly accession
assembly_revision_history_by_post body → default200

Schemas 105

The contract defines 105 schemas that model the data the API accepts and returns. The most detailed are v2reportsBioSampleDescriptor (38 properties), v2reportsAssemblyInfo (26 properties), v2reportsGenomeAnnotation (22 properties), v2reportsAssemblyStats (16 properties). Each schema is shown below with its type and property counts.

v2reportsPairedAssembly
object
9 properties
v2reportsErrorOrganelleErrorCode
string
v2DownloadSummaryAvailableFiles
object
9 properties
v2AssemblyDatasetDescriptorsFilter
object
15 properties
v2reportsBioSampleContact
object
1 property
v2reportsGenomicRegion
object
2 properties
v2reportsSeqRangeSet
object
2 properties
v2AssemblyCheckMHistogramRequest
object
1 property
v2reportsGeneCounts
object
5 properties
v2reportsTranscript
object
9 properties
v2reportsLinkedAssemblyType
string
v2reportsInfraspecificNames
object
6 properties
v2reportsRnaType
string
v2reportsAverageNucleotideIdentityMatchStatus
string
v2AssemblyDatasetRequestResolution
string
v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter
string
v2AssemblyDatasetAvailability
object
3 properties
v2reportsANITypeCategory
string
v2reportsFeatureCounts
object
1 property
v2GenomeAnnotationRequest
object
13 properties
v2reportsGeneType
string
v2DownloadSummaryHydrated
object
3 properties
protobufAny
object
2 properties
rpcStatus
object
3 properties
v2reportsAssemblyDataReport
object
14 properties
v2reportsBioSampleAttribute
object
2 properties
v2reportsAdditionalSubmitter
object
6 properties
v2reportsAssemblyRevision
object
8 properties
v2AssemblyCheckMHistogramReplyHistogramInterval
object
3 properties
v2reportsAverageNucleotideIdentityTaxonomyCheckStatus
string
v2AssemblyAccessions
object
1 property
v2GenomeAnnotationTableSummaryReply
object
4 properties
v2reportsCheckM
object
7 properties
v2AssemblyLinksRequest
object
2 properties
v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory
string
v2reportsTypeMaterial
object
2 properties
v2reportsGenomeAnnotationReportMatch
object
5 properties
v2reportsGenomeAnnotation
object
22 properties
v2DownloadSummaryFileSummary
object
2 properties
v2AssemblySequenceReportsRequest
object
9 properties
v2reportsAssemblyInfo
object
26 properties
v2reportsBioSampleId
object
3 properties
v2reportsAssemblyDataReportPage
object
5 properties
v2AssemblyCheckMHistogramReply
object
2 properties
v2reportsErrorTaxonomyErrorCode
string
v2reportsLineageOrganism
object
2 properties
v2reportsGenomicRegionGenomicRegionType
string
v2reportsMessage
object
2 properties
v2reportsOrganelleInfo
object
6 properties
v2reportsOrganism
object
8 properties
v2SequenceReportPage
object
3 properties
v2reportsMaturePeptide
object
3 properties
v2DownloadSummaryDehydrated
object
4 properties
v2AssemblyDatasetDescriptorsFilterAssemblyVersion
string
v2AssemblyDatasetRequest
object
5 properties
v2GenomeAnnotationRequestAnnotationType
string
v2reportsOrientation
string
v2AnnotationForAssemblyType
string
v2AssemblyLinksReply
object
1 property
v2reportsRange
object
5 properties
v2reportsError
object
8 properties
v2reportsBioSampleDescriptor
object
38 properties
v2AssemblyDatasetReportsRequestContentType
string
v2AssemblyRevisionHistory
object
2 properties
v2reportsGenomeAnnotationReportPage
object
4 properties
v2reportsANIMatch
object
6 properties
v2SortDirection
string
v2reportsWarningReplacedId
object
2 properties
v2AssemblyDatasetDescriptorsFilterAssemblySource
string
v2reportsLinkedAssembly
object
2 properties
v2AssemblyLinksReplyAssemblyLinkType
string
v2reportsAnnotationInfo
object
11 properties
v2reportsBioSampleStatus
object
2 properties
v2AssemblyDatasetReportsRequest
object
16 properties
v2reportsContentType
string
v2AssemblyLinksReplyAssemblyLink
object
4 properties
v2SequenceAccessionRequest
object
1 property
v2reportsAssemblyStats
object
16 properties
v2reportsWarningGeneWarningCode
string
v2reportsWarning
object
5 properties
v2reportsAverageNucleotideIdentity
object
8 properties
v2reportsBioProjectLineage
object
1 property
v2reportsBuscoStat
object
8 properties
v2SortField
object
2 properties
v2reportsErrorAssemblyErrorCode
string
v2reportsAssemblyStatus
string
v2reportsWGSInfo
object
3 properties
v2reportsTranscriptTranscriptType
string
v2reportsGenomicLocation
object
4 properties
v2reportsBioSampleOwner
object
2 properties
v2reportsSourceDatabase
string
v2DownloadSummary
object
8 properties
v2reportsErrorVirusErrorCode
string
v2GenomeAnnotationRequestGenomeAnnotationTableFormat
string
v2reportsAssemblyLevel
string
v2reportsBioProject
object
4 properties
v2AssemblyRevisionHistoryRequest
object
1 property
v2reportsBioSampleDescription
object
3 properties
v2reportsProtein
object
6 properties
v2IncludeTabularHeader
string
v2reportsAtypicalInfo
object
2 properties
v2reportsAnnotation
object
5 properties
v2reportsSequenceInfo
object
15 properties
v2reportsErrorGeneErrorCode
string
v2reportsTranscriptSelectCategory
string

Specification

The full machine-readable OpenAPI contract behind this narrative.

Source

nih-genome-api-openapi.yml Raw ↑

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National Institutes of Health (NIH) BioSample API
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National Institutes of Health (NIH) Gene API
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National Institutes of Health (NIH) Organelle API
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#Genome
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API Details
ID
nih:nih-genome-api
Base URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
Docs
https://www.ncbi.nlm.nih.gov/home/develop/api/
Provider
National Institutes of Health (NIH)
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