Documentation for GWH API
In order to promote the downloading and sharing of GWH data, we provide a BioProject API, a BioSample API, a Genome API and an Assembly API for each of our released genome assembly in Genome Warehouse.
All of the four APIs share the same base URL (https://ngdc.cncb.ac.cn/gwh/api/public), and have their own database prefix and search terms (ID for Genome, and accession for Assembly, BioProject and BioSample). The output will be in indented JSON format.
The Genome API
URL: https://ngdc.cncb.ac.cn/gwh/api/public/genome/<genome_id>
Parameter: genome_id
Example: https://ngdc.cncb.ac.cn/gwh/api/public/genome/1
Output:
{
"id" : "1",
"organism" : "Taraxacum kok-saghyz",
"organismType" : "Plants",
"taxId" : "333970",
"representativeAssemblyAccession" : "GWHAAAA00000000",
"representativeAssemblyLink" : "https://ngdc.cncb.ac.cn/gwh/api/public/assembly/GWHAAAA00000000",
"representativeAssemblyName" : "TKS",
"representativeAssemblyId" : "1",
"representativeAssemblyLevel" : "Contig",
"otherAssembliesCount" : "0",
"otherAssemblies" : [ ],
"releaseTime" : "2017-09-20 00:00:00"
}
Data source: https://ngdc.cncb.ac.cn/gwh/Genome/1/show
Parameter: genome_id
Example: https://ngdc.cncb.ac.cn/gwh/api/public/genome/1
Output:
{
"id" : "1",
"organism" : "Taraxacum kok-saghyz",
"organismType" : "Plants",
"taxId" : "333970",
"representativeAssemblyAccession" : "GWHAAAA00000000",
"representativeAssemblyLink" : "https://ngdc.cncb.ac.cn/gwh/api/public/assembly/GWHAAAA00000000",
"representativeAssemblyName" : "TKS",
"representativeAssemblyId" : "1",
"representativeAssemblyLevel" : "Contig",
"otherAssembliesCount" : "0",
"otherAssemblies" : [ ],
"releaseTime" : "2017-09-20 00:00:00"
}
Data source: https://ngdc.cncb.ac.cn/gwh/Genome/1/show
The Assembly API
URL: https://ngdc.cncb.ac.cn/gwh/api/public/assembly/<assembly_accession>
Parameter: assembly_accession
Example: https://ngdc.cncb.ac.cn/gwh/api/public/assembly/GWHAAAA00000000
Output:
{
"id" : "1",
"organism" : "Taraxacum kok-saghyz",
"organismType" : "Plants",
"taxId" : "333970",
"assemblyAccession" : "GWHAAAA00000000",
"assemblyName" : "TKS",
"assemblyLevel" : "Contig",
"genomeRepresentation" : "0",
"bioprojectAccession" : "PRJCA000437",
"bioprojectLink" : "https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000437",
"biosampleAccession" : "SAMC012932",
"biosampleLink" : "https://ngdc.cncb.ac.cn/biosample/browse/SAMC012932",
"submitterOrganization" : "State Key Laboratory of Plant Genomics and National Center for Plant Gene Research,Institute of Genetics and Developmental Biology, Chinese Academy of Sciences",
"contacts" : "Tao Lin tlin@genetics.ac.cn
Xia Xu xiuxia@genetics.ac.cn",
"ftpPathDna" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.genome.fasta.gz",
"ftpPathGff" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.gff.gz",
"ftpPathRna" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.RNA.fasta.gz",
"ftpPathCds" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.CDS.fasta.gz",
"ftpPathProtein" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.Protein.faa.gz",
"ftpPathFeature" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.feature.gz",
"releaseTime" : "2017-09-20 00:00:00.0",
"publication": "Tao Lin, et al. Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis. National Science Review. 2018, 5(1): 78- 87. ",
"publicationLink" : "https://doi.org/10.1093/nsr/nwx101"
}
Data source: https://ngdc.cncb.ac.cn/gwh/Assembly/1/show
Parameter: assembly_accession
Example: https://ngdc.cncb.ac.cn/gwh/api/public/assembly/GWHAAAA00000000
Output:
{
"id" : "1",
"organism" : "Taraxacum kok-saghyz",
"organismType" : "Plants",
"taxId" : "333970",
"assemblyAccession" : "GWHAAAA00000000",
"assemblyName" : "TKS",
"assemblyLevel" : "Contig",
"genomeRepresentation" : "0",
"bioprojectAccession" : "PRJCA000437",
"bioprojectLink" : "https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000437",
"biosampleAccession" : "SAMC012932",
"biosampleLink" : "https://ngdc.cncb.ac.cn/biosample/browse/SAMC012932",
"submitterOrganization" : "State Key Laboratory of Plant Genomics and National Center for Plant Gene Research,Institute of Genetics and Developmental Biology, Chinese Academy of Sciences",
"contacts" : "Tao Lin tlin@genetics.ac.cn
Xia Xu xiuxia@genetics.ac.cn",
"ftpPathDna" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.genome.fasta.gz",
"ftpPathGff" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.gff.gz",
"ftpPathRna" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.RNA.fasta.gz",
"ftpPathCds" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.CDS.fasta.gz",
"ftpPathProtein" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.Protein.faa.gz",
"ftpPathFeature" : "https://download.cncb.ac.cn/gwh/Plants/Taraxacum_kok-saghyz_TKS_GWHAAAA00000000/GWHAAAA00000000.feature.gz",
"releaseTime" : "2017-09-20 00:00:00.0",
"publication": "Tao Lin, et al. Genome analysis of Taraxacum kok-saghyz Rodin provides new insights into rubber biosynthesis. National Science Review. 2018, 5(1): 78- 87. ",
"publicationLink" : "https://doi.org/10.1093/nsr/nwx101"
}
Data source: https://ngdc.cncb.ac.cn/gwh/Assembly/1/show
The BioProject API
URL: https://ngdc.cncb.ac.cn/gwh/api/public/bioProject/<BioProject accession>
Parameter: BioProject accession
Example: https://ngdc.cncb.ac.cn/gwh/api/public/bioProject/PRJCA000437
Output:
{
"biomaterialProvider" : "",
"dataTypes" : [ {
"dataTypeId" : 1,
"dataTypeName" : "Whole genome sequencing",
"isOther" : 0
} ],
"description" : "As a potential economic crop for NR production and an ideal model plant for studying rubber biosynthesis, elucidation of the TKS genome will be of great value. In this study, we present a first draft genome of T. kok-saghyz assembled using the PacBio and Illumina sequence data. The assembly has a length of 1.29 Gb (N50 = 100.21 kb), containing 46,731 protein-coding genes. We also present a comprehensive analysis of the genome and the transcriptome, providing new insights into the NR biosynthetic pathways and fundamental information to facilitate the isolation, characterization, and application of key genes in developing new NR-producing.",
"fourLevels" : null,
"listConsortium" : [ ],
"listDataProviders" : [ ],
"listExternalLinks" : [ ],
"listGrants" : [ ],
"listPublication" : [ ],
"listRefProjects" : [ ],
"message" : "SUCCESS",
"prjAccession" : "PRJCA000437",
"releaseTime" : "2018-05-01T00:00:00",
"sampleScope" : {
"isOther" : 0,
"sampleScopeId" : 1,
"sampleScopeName" : "Monoisolate"
},
"submitter" : {
"city" : "Beijing",
"country" : {
"countryId" : 45,
"countryName" : "China"
},
"department" : "Molecular Genetics",
"email" : "tlin@genetics.ac.cn",
"emailSecondary" : "",
"fax" : "",
"firstName" : "Tao",
"lastName" : "Lin",
"middleName" : "",
"organization" : "Institute of Genetics and Development Biology, Chi",
"phone" : "",
"postalCode" : "100101",
"state" : "",
"street" : "Chaoyang District",
"submitOrganizationUrl" : "",
"submitterId" : 2908
},
"taxons" : [ {
"ancestors" : null,
"commonNames" : null,
"genBankCommonName" : null,
"name" : "Taraxacum kok-saghyz",
"ranks" : null,
"synonymNames" : null,
"taxonId" : 333970
} ],
"title" : "Genomic sequence of Taraxacum kok-saghyz Rodin"
}
Data source: https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000437
Parameter: BioProject accession
Example: https://ngdc.cncb.ac.cn/gwh/api/public/bioProject/PRJCA000437
Output:
{
"biomaterialProvider" : "",
"dataTypes" : [ {
"dataTypeId" : 1,
"dataTypeName" : "Whole genome sequencing",
"isOther" : 0
} ],
"description" : "As a potential economic crop for NR production and an ideal model plant for studying rubber biosynthesis, elucidation of the TKS genome will be of great value. In this study, we present a first draft genome of T. kok-saghyz assembled using the PacBio and Illumina sequence data. The assembly has a length of 1.29 Gb (N50 = 100.21 kb), containing 46,731 protein-coding genes. We also present a comprehensive analysis of the genome and the transcriptome, providing new insights into the NR biosynthetic pathways and fundamental information to facilitate the isolation, characterization, and application of key genes in developing new NR-producing.",
"fourLevels" : null,
"listConsortium" : [ ],
"listDataProviders" : [ ],
"listExternalLinks" : [ ],
"listGrants" : [ ],
"listPublication" : [ ],
"listRefProjects" : [ ],
"message" : "SUCCESS",
"prjAccession" : "PRJCA000437",
"releaseTime" : "2018-05-01T00:00:00",
"sampleScope" : {
"isOther" : 0,
"sampleScopeId" : 1,
"sampleScopeName" : "Monoisolate"
},
"submitter" : {
"city" : "Beijing",
"country" : {
"countryId" : 45,
"countryName" : "China"
},
"department" : "Molecular Genetics",
"email" : "tlin@genetics.ac.cn",
"emailSecondary" : "",
"fax" : "",
"firstName" : "Tao",
"lastName" : "Lin",
"middleName" : "",
"organization" : "Institute of Genetics and Development Biology, Chi",
"phone" : "",
"postalCode" : "100101",
"state" : "",
"street" : "Chaoyang District",
"submitOrganizationUrl" : "",
"submitterId" : 2908
},
"taxons" : [ {
"ancestors" : null,
"commonNames" : null,
"genBankCommonName" : null,
"name" : "Taraxacum kok-saghyz",
"ranks" : null,
"synonymNames" : null,
"taxonId" : 333970
} ],
"title" : "Genomic sequence of Taraxacum kok-saghyz Rodin"
}
Data source: https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000437
The BioSample API
URL: https://ngdc.cncb.ac.cn/gwh/api/public/bioProject/<BioSample accession>
Parameter: BioSample accession
Example: https://ngdc.cncb.ac.cn/gwh/api/public/bioSample/SAMC012932
Output:
{
"accession" : "SAMC012932",
"message" : "SUCCESS",
"name" : "Taraxacum kok-saghyz Rodin",
"sampleAttribute" : {
"addAttribute" : null,
"age" : "",
"ageUnit" : "year",
"attributeId" : 9593,
"biomaterialProvider" : "IGDB",
"cellLine" : "",
"cellType" : "",
"collectedBy" : "",
"collectionDate" : null,
"cultivar" : "Taraxacum kok-saghyz Rodin",
"cultureCollection" : "",
"devStage" : "",
"disease" : "",
"diseaseStage" : "",
"genotype" : "",
"geographicLocation" : null,
"growthProtocol" : "",
"heightLength" : null,
"isolationSource" : "",
"latitudeLongitude" : "",
"phenotype" : "",
"population" : "",
"sample" : {
"accession" : null,
"createTime" : null,
"deleteTime" : null,
"experiments" : null,
"isControlled" : null,
"isReleaseImmediately" : null,
"isShared" : null,
"modifyTime" : null,
"name" : null,
"note" : null,
"privateComments" : null,
"prjAccession" : null,
"prjId" : null,
"publicDescription" : null,
"releaseState" : null,
"releaseTime" : null,
"sampleId" : 13668,
"sampleSubmitter" : null,
"sampleType" : null,
"shareCode" : null,
"shareId" : null,
"status" : null,
"submissionId" : "subSAM013668",
"taxon" : null,
"title" : null,
"user" : null
},
"sex" : null,
"specimenVoucher" : "",
"taxon" : {
"ancestors" : null,
"commonNames" : null,
"genBankCommonName" : null,
"name" : "Taraxacum kok-saghyz",
"ranks" : null,
"synonymNames" : null,
"taxonId" : 333970
},
"temperature" : "",
"tissue" : "leaf",
"treatment" : "",
"type" : ""
},
"sampleId" : 13668,
"sampletype" : {
"attributeTable" : "sample_attr_plant",
"sampleTypeId" : 6,
"sampleTypeName" : "Plant sample"
},
"submitter" : {
"city" : "Beijing",
"country" : {
"countryId" : 45,
"countryName" : "China"
},
"department" : "Molecular Genetics",
"email" : "tlin@genetics.ac.cn",
"emailSecondary" : "",
"fax" : "",
"firstName" : "Tao",
"lastName" : "Lin",
"middleName" : "",
"organization" : "Institute of Genetics and Development Biology, Chi",
"phone" : "",
"postalCode" : "100101",
"state" : "",
"street" : "Chaoyang District",
"submitOrganizationUrl" : "",
"submitterId" : 2909
},
"taxon" : {
"ancestors" : [ {
"name" : "cellular organisms",
"ranks" : "no rank",
"taxonId" : 131567
}, {
"name" : "Eukaryota",
"ranks" : "superkingdom",
"taxonId" : 2759
}, {
"name" : "Viridiplantae",
"ranks" : "kingdom",
"taxonId" : 33090
}, {
"name" : "Streptophyta",
"ranks" : "phylum",
"taxonId" : 35493
}, {
"name" : "Streptophytina",
"ranks" : "no rank",
"taxonId" : 131221
}, {
"name" : "Embryophyta",
"ranks" : "no rank",
"taxonId" : 3193
}, {
"name" : "Tracheophyta",
"ranks" : "no rank",
"taxonId" : 58023
}, {
"name" : "Euphyllophyta",
"ranks" : "no rank",
"taxonId" : 78536
}, {
"name" : "Spermatophyta",
"ranks" : "no rank",
"taxonId" : 58024
}, {
"name" : "Magnoliophyta",
"ranks" : "no rank",
"taxonId" : 3398
}, {
"name" : "Mesangiospermae",
"ranks" : "no rank",
"taxonId" : 1437183
}, {
"name" : "eudicotyledons",
"ranks" : "no rank",
"taxonId" : 71240
}, {
"name" : "Gunneridae",
"ranks" : "no rank",
"taxonId" : 91827
}, {
"name" : "Pentapetalae",
"ranks" : "no rank",
"taxonId" : 1437201
}, {
"name" : "asterids",
"ranks" : "subclass",
"taxonId" : 71274
}, {
"name" : "campanulids",
"ranks" : "no rank",
"taxonId" : 91882
}, {
"name" : "Asterales",
"ranks" : "order",
"taxonId" : 4209
}, {
"name" : "Asteraceae",
"ranks" : "family",
"taxonId" : 4210
}, {
"name" : "Cichorioideae",
"ranks" : "subfamily",
"taxonId" : 219120
}, {
"name" : "Cichorieae",
"ranks" : "tribe",
"taxonId" : 219121
}, {
"name" : "Crepidinae",
"ranks" : "subtribe",
"taxonId" : 745067
}, {
"name" : "Taraxacum",
"ranks" : "genus",
"taxonId" : 49743
} ],
"commonNames" : [ ],
"genBankCommonName" : null,
"name" : "Taraxacum kok-saghyz",
"ranks" : "species",
"synonymNames" : [ ],
"taxonId" : 333970
},
"title" : "Genomic sequence of Taraxacum kok-saghyz Rodin",
"userId" : 344
}
Data source: https://ngdc.cncb.ac.cn/biosample/browse/SAMC012932
Parameter: BioSample accession
Example: https://ngdc.cncb.ac.cn/gwh/api/public/bioSample/SAMC012932
Output:
{
"accession" : "SAMC012932",
"message" : "SUCCESS",
"name" : "Taraxacum kok-saghyz Rodin",
"sampleAttribute" : {
"addAttribute" : null,
"age" : "",
"ageUnit" : "year",
"attributeId" : 9593,
"biomaterialProvider" : "IGDB",
"cellLine" : "",
"cellType" : "",
"collectedBy" : "",
"collectionDate" : null,
"cultivar" : "Taraxacum kok-saghyz Rodin",
"cultureCollection" : "",
"devStage" : "",
"disease" : "",
"diseaseStage" : "",
"genotype" : "",
"geographicLocation" : null,
"growthProtocol" : "",
"heightLength" : null,
"isolationSource" : "",
"latitudeLongitude" : "",
"phenotype" : "",
"population" : "",
"sample" : {
"accession" : null,
"createTime" : null,
"deleteTime" : null,
"experiments" : null,
"isControlled" : null,
"isReleaseImmediately" : null,
"isShared" : null,
"modifyTime" : null,
"name" : null,
"note" : null,
"privateComments" : null,
"prjAccession" : null,
"prjId" : null,
"publicDescription" : null,
"releaseState" : null,
"releaseTime" : null,
"sampleId" : 13668,
"sampleSubmitter" : null,
"sampleType" : null,
"shareCode" : null,
"shareId" : null,
"status" : null,
"submissionId" : "subSAM013668",
"taxon" : null,
"title" : null,
"user" : null
},
"sex" : null,
"specimenVoucher" : "",
"taxon" : {
"ancestors" : null,
"commonNames" : null,
"genBankCommonName" : null,
"name" : "Taraxacum kok-saghyz",
"ranks" : null,
"synonymNames" : null,
"taxonId" : 333970
},
"temperature" : "",
"tissue" : "leaf",
"treatment" : "",
"type" : ""
},
"sampleId" : 13668,
"sampletype" : {
"attributeTable" : "sample_attr_plant",
"sampleTypeId" : 6,
"sampleTypeName" : "Plant sample"
},
"submitter" : {
"city" : "Beijing",
"country" : {
"countryId" : 45,
"countryName" : "China"
},
"department" : "Molecular Genetics",
"email" : "tlin@genetics.ac.cn",
"emailSecondary" : "",
"fax" : "",
"firstName" : "Tao",
"lastName" : "Lin",
"middleName" : "",
"organization" : "Institute of Genetics and Development Biology, Chi",
"phone" : "",
"postalCode" : "100101",
"state" : "",
"street" : "Chaoyang District",
"submitOrganizationUrl" : "",
"submitterId" : 2909
},
"taxon" : {
"ancestors" : [ {
"name" : "cellular organisms",
"ranks" : "no rank",
"taxonId" : 131567
}, {
"name" : "Eukaryota",
"ranks" : "superkingdom",
"taxonId" : 2759
}, {
"name" : "Viridiplantae",
"ranks" : "kingdom",
"taxonId" : 33090
}, {
"name" : "Streptophyta",
"ranks" : "phylum",
"taxonId" : 35493
}, {
"name" : "Streptophytina",
"ranks" : "no rank",
"taxonId" : 131221
}, {
"name" : "Embryophyta",
"ranks" : "no rank",
"taxonId" : 3193
}, {
"name" : "Tracheophyta",
"ranks" : "no rank",
"taxonId" : 58023
}, {
"name" : "Euphyllophyta",
"ranks" : "no rank",
"taxonId" : 78536
}, {
"name" : "Spermatophyta",
"ranks" : "no rank",
"taxonId" : 58024
}, {
"name" : "Magnoliophyta",
"ranks" : "no rank",
"taxonId" : 3398
}, {
"name" : "Mesangiospermae",
"ranks" : "no rank",
"taxonId" : 1437183
}, {
"name" : "eudicotyledons",
"ranks" : "no rank",
"taxonId" : 71240
}, {
"name" : "Gunneridae",
"ranks" : "no rank",
"taxonId" : 91827
}, {
"name" : "Pentapetalae",
"ranks" : "no rank",
"taxonId" : 1437201
}, {
"name" : "asterids",
"ranks" : "subclass",
"taxonId" : 71274
}, {
"name" : "campanulids",
"ranks" : "no rank",
"taxonId" : 91882
}, {
"name" : "Asterales",
"ranks" : "order",
"taxonId" : 4209
}, {
"name" : "Asteraceae",
"ranks" : "family",
"taxonId" : 4210
}, {
"name" : "Cichorioideae",
"ranks" : "subfamily",
"taxonId" : 219120
}, {
"name" : "Cichorieae",
"ranks" : "tribe",
"taxonId" : 219121
}, {
"name" : "Crepidinae",
"ranks" : "subtribe",
"taxonId" : 745067
}, {
"name" : "Taraxacum",
"ranks" : "genus",
"taxonId" : 49743
} ],
"commonNames" : [ ],
"genBankCommonName" : null,
"name" : "Taraxacum kok-saghyz",
"ranks" : "species",
"synonymNames" : [ ],
"taxonId" : 333970
},
"title" : "Genomic sequence of Taraxacum kok-saghyz Rodin",
"userId" : 344
}
Data source: https://ngdc.cncb.ac.cn/biosample/browse/SAMC012932