openapi: 3.0.3 info: title: ClinicalTrials.gov REST BioSample Genome API description: This API is made available to provide users meta data, statistics, and the most recent version of the clinical trials available on ClinicalTrials.gov. version: 2.0.5 servers: - url: https://clinicaltrials.gov/api/v2 description: This server tags: - name: Genome description: '#### 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. ' paths: /genome/accession/{accessions}/download_summary: get: summary: Get a download summary (preview) of a genome data package by genome assembly accession description: Get a download summary (preview) of a genome data package, including counts and file sizes, in JSON 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: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: array items: type: string examples: example-0: value: GCF_000001405.40 summary: Human reference genome, GRCh38.p14 example-1: value: - GCF_000001405.40 - GCF_000001635.27 summary: Human and mouse reference genomes, GRCh38.p14 and GRCm39 - name: chromosomes description: Only return genomic fasta sequence for the specified chromosomes. in: query required: false schema: type: array items: type: string examples: example-0: value: - '1' - MT summary: Chromosome 1 and mitochondrial genome sequence example-1: value: - X - Y summary: Human sex chromosomes X and Y - name: include_annotation_type description: Specify which sequence, annotation, and report files to include in the data package. The assembly data report is always included, and its inclusion is not affected by this parameter. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2AnnotationForAssemblyType' examples: example-0: value: GENOME_FASTA summary: Include the genome sequence only example-1: value: - GENOME_FASTA - PROT_FASTA - GENOME_GFF - SEQUENCE_REPORT summary: Include genomic and protein sequences, a gff3 annotation file, and the sequence report /genome/download_summary: post: summary: Get a download summary (preview) of a genome data package by genome assembly accession description: Get a downlaod summary (preview) of a genome data package, including counts and file sizes, in JSON format. 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: Tribolium castaneum reference genome, icTRiCast1.1, with genome sequence, annotation and sequence report files value: accessions: - GCF_031307605.1 include_annotation_type: - GENOME_FASTA - GENOME_GFF - SEQUENCE_REPORT /genome/accession/{accessions}/dataset_report: get: summary: Get a genome assembly report by genome assembly accession description: 'Get a genome assembly report by assembly accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' 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 description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: array items: type: string examples: example-0: value: GCF_000001405.40 summary: Human reference genome assembly, GRCh38.p14 example-1: value: - GCF_000001405.40 - GCF_000001635.27 summary: Human and mouse reference genomes, GRCh38.p14 and GRCm39 - name: filters.reference_only description: If true, limit to reference genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to reference genomes example-1: value: false summary: Include all genomes - name: filters.assembly_source description: Limit to either 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: Include all genomes - name: filters.has_annotation description: Limit to annotated genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to annotated genomes example-1: value: false summary: Include all genomes - name: filters.exclude_paired_reports description: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes, including both members of a GenBank/RefSeq pair example-1: value: true summary: Returns the RefSeq copy for GenBank/RefSeq pairs, otherwise returns the GenBank assembly - name: filters.exclude_atypical description: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), 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: Include all genomes example-1: value: true summary: Limit to genomes that are not atypical - name: filters.assembly_version description: Limit to the most recent (current) version of a genome assembly. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' default: current examples: example-0: value: current summary: Limit to the most recent version of a genome assembly example-1: value: all_assemblies summary: Include all genome assemblies - name: filters.assembly_level description: Limit to genomes at the specified [assembly level](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly-level) in: query required: false schema: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' examples: example-0: value: - chromosome - complete_genome summary: Chromosome-level and complete genomes example-1: value: - scaffold - chromosome - complete_genome summary: Scaffold-level genomes and higher - name: filters.first_release_date description: Limit to genomes released on or after the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2024-01-10' summary: January 10th, 2024, in ISO 8601 YYYY-MM-DD format - name: filters.last_release_date description: Limit to genomes released on or before the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2025-01-10' summary: January 10th, 2025, in ISO 8601 YYYY-MM-DD format - name: filters.search_text description: Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name. in: query required: false schema: type: array items: type: string examples: example-0: value: Genome Reference Consortium summary: Limit to genomes that match this submitter name example-1: value: GRCh38 summary: Limit to genomes that match this assembly name example-2: value: C57BL/6J summary: Limit to genomes that match this strain name, a type of infraspecific name - name: filters.is_metagenome_derived description: Exclude or limit to metagenome-assembled genomes (MAGs). in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' examples: example-0: value: metagenome_derived_exclude summary: Exclude metagenome-assembled genomes, or MAGs example-1: value: metagenome_derived_only summary: Limit to metagenome-assembled genomes, or MAGs - name: filters.is_type_material description: If true, limit to genomes derived from type material. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from type material - name: filters.is_ictv_exemplar description: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from an ICTV exemplar - name: filters.exclude_multi_isolate description: If true, exclude genomes that were sequenced as part of large multi-isolate projects. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Exclude genomes that were sequenced as part of large multi-isolate projects - name: filters.type_material_category description: Limit to genomes derived from specific type material categories. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' examples: example-0: value: TYPE_MATERIAL_CLADE summary: Limit to genomes designated as clade exemplar example-1: value: TYPE_MATERIAL_NEOTYPE summary: Limit to genomes derived from neotype material - name: table_fields in: query required: false schema: type: array items: type: string examples: example-0: value: accession summary: Genome assembly accession example-1: value: - accession - assminfo-name summary: Genome assembly accession and name - name: returned_content description: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' examples: example-0: value: ASSM_ACC summary: Return abbreviated report with genome assembly accessions example-1: value: PAIRED_ACC summary: Return abbreviated report with genome assembly accessions and paired assembly information - 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 when the results count exceeds `page size`. Use this token along with previous request 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: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/taxon/{taxons}/dataset_report: get: summary: Get a genome assembly report by taxon description: 'Get a genome assembly report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' 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 ID for human example-1: value: - chimpanzee - eastern gorilla summary: Common names example-2: value: Homo sapiens summary: Scientific name - name: filters.reference_only description: If true, limit to reference genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to reference genomes example-1: value: false summary: Include all genomes - name: filters.assembly_source description: Limit to either 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: Include all genomes - name: filters.has_annotation description: Limit to annotated genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to annotated genomes example-1: value: false summary: Include all genomes - name: filters.exclude_paired_reports description: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes, including both members of a GenBank/RefSeq pair example-1: value: true summary: Returns the RefSeq copy for GenBank/RefSeq pairs, otherwise returns the GenBank assembly - name: filters.exclude_atypical description: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), 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: Include all genomes example-1: value: true summary: Limit to genomes that are not atypical - name: filters.assembly_version description: Limit to the most recent (current) version of a genome assembly. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' default: current examples: example-0: value: current summary: Limit to the most recent version of a genome assembly example-1: value: all_assemblies summary: Include all genome assemblies - name: filters.assembly_level description: Limit to genomes at the specified [assembly level](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly-level) in: query required: false schema: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' examples: example-0: value: - chromosome - complete_genome summary: Chromosome-level and complete genomes example-1: value: - scaffold - chromosome - complete_genome summary: Scaffold-level genomes and higher - name: filters.first_release_date description: Limit to genomes released on or after the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2024-01-10' summary: January 10th, 2024, in ISO 8601 YYYY-MM-DD format - name: filters.last_release_date description: Limit to genomes released on or before the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2025-01-10' summary: January 10th, 2025, in ISO 8601 YYYY-MM-DD format - name: filters.search_text description: Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name. in: query required: false schema: type: array items: type: string examples: example-0: value: Genome Reference Consortium summary: Limit to genomes that match this submitter name example-1: value: GRCh38 summary: Limit to genomes that match this assembly name example-2: value: C57BL/6J summary: Limit to genomes that match this strain name, a type of infraspecific name - name: filters.is_metagenome_derived description: Exclude or limit to metagenome-assembled genomes (MAGs). in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' examples: example-0: value: metagenome_derived_exclude summary: Exclude metagenome-assembled genomes, or MAGs example-1: value: metagenome_derived_only summary: Limit to metagenome-assembled genomes, or MAGs - name: filters.is_type_material description: If true, limit to genomes derived from type material. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from type material - name: filters.is_ictv_exemplar description: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from an ICTV exemplar - name: filters.exclude_multi_isolate description: If true, exclude genomes that were sequenced as part of large multi-isolate projects. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Exclude genomes that were sequenced as part of large multi-isolate projects - name: filters.type_material_category description: Limit to genomes derived from specific type material categories. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' examples: example-0: value: TYPE_MATERIAL_CLADE summary: Limit to genomes designated as clade exemplar example-1: value: TYPE_MATERIAL_NEOTYPE summary: Limit to genomes derived from neotype material - name: tax_exact_match description: If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes. 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: accession summary: Genome assembly accession example-1: value: - accession - assminfo-name summary: Genome assembly accession and name - name: returned_content description: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' examples: example-0: value: ASSM_ACC summary: Return abbreviated report with genome assembly accessions example-1: value: PAIRED_ACC summary: Return abbreviated report with genome assembly accessions and paired assembly information - 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 when the results count exceeds `page size`. Use this token along with previous request 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: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/bioproject/{bioprojects}/dataset_report: get: summary: Get genome assembly reports by BioProject accession description: 'Get genome assembly reports by BioProject accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' 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, limit to reference genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to reference genomes example-1: value: false summary: Include all genomes - name: filters.assembly_source description: Limit to either 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: Include all genomes - name: filters.has_annotation description: Limit to annotated genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to annotated genomes example-1: value: false summary: Include all genomes - name: filters.exclude_paired_reports description: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes, including both members of a GenBank/RefSeq pair example-1: value: true summary: Returns the RefSeq copy for GenBank/RefSeq pairs, otherwise returns the GenBank assembly - name: filters.exclude_atypical description: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), 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: Include all genomes example-1: value: true summary: Limit to genomes that are not atypical - name: filters.assembly_version description: Limit to the most recent (current) version of a genome assembly. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' default: current examples: example-0: value: current summary: Limit to the most recent version of a genome assembly example-1: value: all_assemblies summary: Include all genome assemblies - name: filters.assembly_level description: Limit to genomes at the specified [assembly level](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly-level) in: query required: false schema: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' examples: example-0: value: - chromosome - complete_genome summary: Chromosome-level and complete genomes example-1: value: - scaffold - chromosome - complete_genome summary: Scaffold-level genomes and higher - name: filters.first_release_date description: Limit to genomes released on or after the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2024-01-10' summary: January 10th, 2024, in ISO 8601 YYYY-MM-DD format - name: filters.last_release_date description: Limit to genomes released on or before the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2025-01-10' summary: January 10th, 2025, in ISO 8601 YYYY-MM-DD format - name: filters.search_text description: Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name. in: query required: false schema: type: array items: type: string examples: example-0: value: Genome Reference Consortium summary: Limit to genomes that match this submitter name example-1: value: GRCh38 summary: Limit to genomes that match this assembly name example-2: value: C57BL/6J summary: Limit to genomes that match this strain name, a type of infraspecific name - name: filters.is_metagenome_derived description: Exclude or limit to metagenome-assembled genomes (MAGs). in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' examples: example-0: value: metagenome_derived_exclude summary: Exclude metagenome-assembled genomes, or MAGs example-1: value: metagenome_derived_only summary: Limit to metagenome-assembled genomes, or MAGs - name: filters.is_type_material description: If true, limit to genomes derived from type material. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from type material - name: filters.is_ictv_exemplar description: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from an ICTV exemplar - name: filters.exclude_multi_isolate description: If true, exclude genomes that were sequenced as part of large multi-isolate projects. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Exclude genomes that were sequenced as part of large multi-isolate projects - name: filters.type_material_category description: Limit to genomes derived from specific type material categories. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' examples: example-0: value: TYPE_MATERIAL_CLADE summary: Limit to genomes designated as clade exemplar example-1: value: TYPE_MATERIAL_NEOTYPE summary: Limit to genomes derived from neotype material - name: tax_exact_match description: If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes. 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: accession summary: Genome assembly accession example-1: value: - accession - assminfo-name summary: Genome assembly accession and name - name: returned_content description: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' examples: example-0: value: ASSM_ACC summary: Return abbreviated report with genome assembly accessions example-1: value: PAIRED_ACC summary: Return abbreviated report with genome assembly accessions and paired assembly information - 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 when the results count exceeds `page size`. Use this token along with previous request 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: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/biosample/{biosample_ids}/dataset_report: get: summary: Get genome assembly reports by BioSample accession description: 'Get genome assembly reports by BioSample accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_dataset_reports_by_biosample_id 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: biosample_ids in: path required: true schema: type: array items: type: string examples: example-0: value: SAMN15960293 summary: BioSample Identifier - name: filters.reference_only description: If true, limit to reference genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to reference genomes example-1: value: false summary: Include all genomes - name: filters.assembly_source description: Limit to either 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: Include all genomes - name: filters.has_annotation description: Limit to annotated genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to annotated genomes example-1: value: false summary: Include all genomes - name: filters.exclude_paired_reports description: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes, including both members of a GenBank/RefSeq pair example-1: value: true summary: Returns the RefSeq copy for GenBank/RefSeq pairs, otherwise returns the GenBank assembly - name: filters.exclude_atypical description: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), 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: Include all genomes example-1: value: true summary: Limit to genomes that are not atypical - name: filters.assembly_version description: Limit to the most recent (current) version of a genome assembly. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' default: current examples: example-0: value: current summary: Limit to the most recent version of a genome assembly example-1: value: all_assemblies summary: Include all genome assemblies - name: filters.assembly_level description: Limit to genomes at the specified [assembly level](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly-level) in: query required: false schema: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' examples: example-0: value: - chromosome - complete_genome summary: Chromosome-level and complete genomes example-1: value: - scaffold - chromosome - complete_genome summary: Scaffold-level genomes and higher - name: filters.first_release_date description: Limit to genomes released on or after the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2024-01-10' summary: January 10th, 2024, in ISO 8601 YYYY-MM-DD format - name: filters.last_release_date description: Limit to genomes released on or before the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2025-01-10' summary: January 10th, 2025, in ISO 8601 YYYY-MM-DD format - name: filters.search_text description: Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name. in: query required: false schema: type: array items: type: string examples: example-0: value: Genome Reference Consortium summary: Limit to genomes that match this submitter name example-1: value: GRCh38 summary: Limit to genomes that match this assembly name example-2: value: C57BL/6J summary: Limit to genomes that match this strain name, a type of infraspecific name - name: filters.is_metagenome_derived description: Exclude or limit to metagenome-assembled genomes (MAGs). in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' examples: example-0: value: metagenome_derived_exclude summary: Exclude metagenome-assembled genomes, or MAGs example-1: value: metagenome_derived_only summary: Limit to metagenome-assembled genomes, or MAGs - name: filters.is_type_material description: If true, limit to genomes derived from type material. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from type material - name: filters.is_ictv_exemplar description: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from an ICTV exemplar - name: filters.exclude_multi_isolate description: If true, exclude genomes that were sequenced as part of large multi-isolate projects. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Exclude genomes that were sequenced as part of large multi-isolate projects - name: filters.type_material_category description: Limit to genomes derived from specific type material categories. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' examples: example-0: value: TYPE_MATERIAL_CLADE summary: Limit to genomes designated as clade exemplar example-1: value: TYPE_MATERIAL_NEOTYPE summary: Limit to genomes derived from neotype material - name: tax_exact_match description: If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes. 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: accession summary: Genome assembly accession example-1: value: - accession - assminfo-name summary: Genome assembly accession and name - name: returned_content description: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' examples: example-0: value: ASSM_ACC summary: Return abbreviated report with genome assembly accessions example-1: value: PAIRED_ACC summary: Return abbreviated report with genome assembly accessions and paired assembly information - 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 when the results count exceeds `page size`. Use this token along with previous request 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: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/wgs/{wgs_accessions}/dataset_report: get: summary: Get a genome assembly data report by WGS accession description: 'Get a genome assembly data report by WGS (whole genome shotgun) accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_dataset_reports_by_wgs 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: wgs_accessions description: One or more WGS accessions associated with a genome assembly in: path required: true schema: type: array items: type: string examples: example-0: value: JAXUCZ01 summary: Norway rat (Rattus norvegicus) WGS accession example-1: value: - JAHLSK02 - JAAKGM02 summary: Human WGS accessions - name: filters.reference_only description: If true, limit to reference genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to reference genomes example-1: value: false summary: Include all genomes - name: filters.assembly_source description: Limit to either 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: Include all genomes - name: filters.has_annotation description: Limit to annotated genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to annotated genomes example-1: value: false summary: Include all genomes - name: filters.exclude_paired_reports description: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes, including both members of a GenBank/RefSeq pair example-1: value: true summary: Returns the RefSeq copy for GenBank/RefSeq pairs, otherwise returns the GenBank assembly - name: filters.exclude_atypical description: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), 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: Include all genomes example-1: value: true summary: Limit to genomes that are not atypical - name: filters.assembly_version description: Limit to the most recent (current) version of a genome assembly. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' default: current examples: example-0: value: current summary: Limit to the most recent version of a genome assembly example-1: value: all_assemblies summary: Include all genome assemblies - name: filters.assembly_level description: Limit to genomes at the specified [assembly level](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly-level) in: query required: false schema: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' examples: example-0: value: - chromosome - complete_genome summary: Chromosome-level and complete genomes example-1: value: - scaffold - chromosome - complete_genome summary: Scaffold-level genomes and higher - name: filters.first_release_date description: Limit to genomes released on or after the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2024-01-10' summary: January 10th, 2024, in ISO 8601 YYYY-MM-DD format - name: filters.last_release_date description: Limit to genomes released on or before the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2025-01-10' summary: January 10th, 2025, in ISO 8601 YYYY-MM-DD format - name: filters.search_text description: Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name. in: query required: false schema: type: array items: type: string examples: example-0: value: Genome Reference Consortium summary: Limit to genomes that match this submitter name example-1: value: GRCh38 summary: Limit to genomes that match this assembly name example-2: value: C57BL/6J summary: Limit to genomes that match this strain name, a type of infraspecific name - name: filters.is_metagenome_derived description: Exclude or limit to metagenome-assembled genomes (MAGs). in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' examples: example-0: value: metagenome_derived_exclude summary: Exclude metagenome-assembled genomes, or MAGs example-1: value: metagenome_derived_only summary: Limit to metagenome-assembled genomes, or MAGs - name: filters.is_type_material description: If true, limit to genomes derived from type material. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from type material - name: filters.is_ictv_exemplar description: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from an ICTV exemplar - name: filters.exclude_multi_isolate description: If true, exclude genomes that were sequenced as part of large multi-isolate projects. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Exclude genomes that were sequenced as part of large multi-isolate projects - name: filters.type_material_category description: Limit to genomes derived from specific type material categories. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' examples: example-0: value: TYPE_MATERIAL_CLADE summary: Limit to genomes designated as clade exemplar example-1: value: TYPE_MATERIAL_NEOTYPE summary: Limit to genomes derived from neotype material - name: tax_exact_match description: If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes. 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: accession summary: Genome assembly accession example-1: value: - accession - assminfo-name summary: Genome assembly accession and name - name: returned_content description: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' examples: example-0: value: ASSM_ACC summary: Return abbreviated report with genome assembly accessions example-1: value: PAIRED_ACC summary: Return abbreviated report with genome assembly accessions and paired assembly information - 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 when the results count exceeds `page size`. Use this token along with previous request 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: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/assembly_name/{assembly_names}/dataset_report: get: summary: Get genome assembly reports by assembly name description: 'Get genome assembly reports by assembly name (exact matches only). By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_dataset_reports_by_assembly_name 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: assembly_names description: One or more assembly names (exact match only) in: path required: true schema: type: array items: type: string examples: example-0: value: HanXRQr2.0-SUNRISE summary: Helianthus annuus, or common sunflower, reference genome example-1: value: mCamDro1.pat summary: Camelus dromedarius, or Arabian camel, reference genome - name: filters.reference_only description: If true, limit to reference genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to reference genomes example-1: value: false summary: Include all genomes - name: filters.assembly_source description: Limit to either 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: Include all genomes - name: filters.has_annotation description: Limit to annotated genome assemblies. in: query required: false schema: type: boolean default: false examples: example-0: value: true summary: Limit to annotated genomes example-1: value: false summary: Include all genomes - name: filters.exclude_paired_reports description: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes, including both members of a GenBank/RefSeq pair example-1: value: true summary: Returns the RefSeq copy for GenBank/RefSeq pairs, otherwise returns the GenBank assembly - name: filters.exclude_atypical description: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), 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: Include all genomes example-1: value: true summary: Limit to genomes that are not atypical - name: filters.assembly_version description: Limit to the most recent (current) version of a genome assembly. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' default: current examples: example-0: value: current summary: Limit to the most recent version of a genome assembly example-1: value: all_assemblies summary: Include all genome assemblies - name: filters.assembly_level description: Limit to genomes at the specified [assembly level](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/glossary/#assembly-level) in: query required: false schema: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' examples: example-0: value: - chromosome - complete_genome summary: Chromosome-level and complete genomes example-1: value: - scaffold - chromosome - complete_genome summary: Scaffold-level genomes and higher - name: filters.first_release_date description: Limit to genomes released on or after the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2024-01-10' summary: January 10th, 2024, in ISO 8601 YYYY-MM-DD format - name: filters.last_release_date description: Limit to genomes released on or before the specified date in: query required: false schema: type: string format: date-time examples: example-0: value: '2025-01-10' summary: January 10th, 2025, in ISO 8601 YYYY-MM-DD format - name: filters.search_text description: Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name. in: query required: false schema: type: array items: type: string examples: example-0: value: Genome Reference Consortium summary: Limit to genomes that match this submitter name example-1: value: GRCh38 summary: Limit to genomes that match this assembly name example-2: value: C57BL/6J summary: Limit to genomes that match this strain name, a type of infraspecific name - name: filters.is_metagenome_derived description: Exclude or limit to metagenome-assembled genomes (MAGs). in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' examples: example-0: value: metagenome_derived_exclude summary: Exclude metagenome-assembled genomes, or MAGs example-1: value: metagenome_derived_only summary: Limit to metagenome-assembled genomes, or MAGs - name: filters.is_type_material description: If true, limit to genomes derived from type material. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from type material - name: filters.is_ictv_exemplar description: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Limit to genomes derived from an ICTV exemplar - name: filters.exclude_multi_isolate description: If true, exclude genomes that were sequenced as part of large multi-isolate projects. in: query required: false schema: type: boolean default: false examples: example-0: value: false summary: Include all genomes example-1: value: true summary: Exclude genomes that were sequenced as part of large multi-isolate projects - name: filters.type_material_category description: Limit to genomes derived from specific type material categories. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' examples: example-0: value: TYPE_MATERIAL_CLADE summary: Limit to genomes designated as clade exemplar example-1: value: TYPE_MATERIAL_NEOTYPE summary: Limit to genomes derived from neotype material - name: tax_exact_match description: If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes. 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: accession summary: Genome assembly accession example-1: value: - accession - assminfo-name summary: Genome assembly accession and name - name: returned_content description: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' examples: example-0: value: ASSM_ACC summary: Return abbreviated report with genome assembly accessions example-1: value: PAIRED_ACC summary: Return abbreviated report with genome assembly accessions and paired assembly information - 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 when the results count exceeds `page size`. Use this token along with previous request 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: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/dataset_report: post: summary: Get a genome assembly report description: 'Get a genome assembly report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_dataset_report_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/v2reportsAssemblyDataReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsAssemblyDataReportPage' text/tab-separated-values: schema: type: string requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequest' examples: Single GCF accession example: description: Human reference genome assembly, GRCh38.p14 value: accessions: - GCF_000001405.40 /genome/sequence_accession/{accession}/sequence_assemblies: get: summary: Get a genome assembly accession for a nucleotide sequence accession description: Get a genome assembly accession for a nucleotide sequence accession in JSON format. tags: - Genome operationId: assembly_accessions_for_sequence_accession 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/v2AssemblyAccessions' parameters: - name: accession description: Nucleotide sequence accession associated with a genome assembly in: path required: true schema: type: string examples: example-0: value: NC_000001.11 summary: Human chromosome 1 from GRCh38.p14 /genome/sequence_assemblies: post: summary: Get a genome assembly accession for a nucleotide sequence accession description: Get a genome assembly accession for a nucleotide sequence accession in JSON format. tags: - Genome operationId: assembly_accessions_for_sequence_accession_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/v2AssemblyAccessions' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2SequenceAccessionRequest' examples: Single chromosome accession example: description: Human chromosome 1 from GRCh38.p14 value: accession: NC_000001.11 /genome/accession/{accession}/sequence_reports: get: summary: Get a genome sequence report by genome assembly accession description: 'Get a genome sequence report by genome assembly accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_sequence_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/v2SequenceReportPage' application/vnd.openxmlformats-officedocument.spreadsheetml.sheet: schema: $ref: '#/components/schemas/v2SequenceReportPage' text/tab-separated-values: schema: type: string application/x-ndjson: schema: $ref: '#/components/schemas/v2SequenceReportPage' parameters: - name: accession description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: string examples: example-0: value: GCF_000001635.27 summary: Mouse reference genome assembly, GRCm39 example-1: value: GCF_000001405.40 summary: Human reference genome assembly, GRCh38.p14 - name: chromosomes description: Limit to sequences with the specified chromosome names in: query required: false schema: type: array items: type: string examples: example-0: value: - '1' - MT summary: Chromosome 1 and mitochondrial genome sequence example-1: value: - X - Y summary: Human sex chromosomes X and Y - name: role_filters description: Limit to sequences with the specified "role", where possible roles are `assembled-molecule`, `unlocalized-scaffold`, or `unplaced-scaffold` in: query required: false schema: type: array items: type: string examples: example-0: value: assembled-molecule summary: Assembled sequences - name: table_fields in: query required: false schema: type: array items: type: string examples: example-0: value: - accession - chr-name summary: Genome assembly accession and chromosome name example-1: value: ucsc-style-name summary: Sequence name from the UCSC Genome Browser - name: count_assembly_unplaced description: Include the count of unplaced scaffold sequences in: query required: false schema: type: boolean default: false - name: page_size description: The maximum number of genome assemblies to return. 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 - name: page_token description: A page token is returned when the results count exceeds `page size`. Use this token along with previous request 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: include_tabular_header in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' /genome/sequence_reports: post: summary: Get a genome sequence report by genome assembly accession description: 'Get a genome sequence report by genome assembly accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_sequence_report_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/v2SequenceReportPage' application/vnd.openxmlformats-officedocument.spreadsheetml.sheet: schema: $ref: '#/components/schemas/v2SequenceReportPage' text/tab-separated-values: schema: type: string application/x-ndjson: schema: $ref: '#/components/schemas/v2SequenceReportPage' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblySequenceReportsRequest' examples: Single GCF accession example: description: Human reference genome assembly, GRCh38.p14 value: accession: GCF_000001405.40 /genome/accession/{accessions}/links: get: summary: Get assembly links by genome assembly accession description: Get links to assembly resources by genome assembly accession in JSON format. tags: - Genome operationId: genome_links_by_accession 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/v2AssemblyLinksReply' parameters: - name: accessions description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: array items: type: string examples: example-0: value: GCF_000001405.40 summary: Human reference genome, GRCh38.p14 example-1: value: - GCF_000001405.40 - GCF_000001635.27 summary: Human and mouse reference genomes, GRCh38.p14 and GRCm39 - name: assembly_link_types description: Zero or more assembly link types to retrieve. If no values are provided, all links are retrieved in: query required: false schema: type: array items: $ref: '#/components/schemas/v2AssemblyLinksReplyAssemblyLinkType' /genome/links: post: summary: Get assembly links by genome assembly accession description: Get links to assembly resources by genome assembly accession in JSON format. tags: - Genome operationId: genome_links_by_accession_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/v2AssemblyLinksReply' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblyLinksRequest' examples: Single GCF accession example: description: Human reference genome assembly, GRCh38.p14 value: accessions: - GCF_000001405.40 /genome/taxon/{species_taxon}/checkm_histogram: get: summary: Get CheckM histogram data by species taxon description: Get CheckM histogram data by species taxon. This data is used for rendering CheckM histograms on bacterial genome pages. tags: - Genome operationId: checkm_histogram_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/v2AssemblyCheckMHistogramReply' parameters: - name: species_taxon description: Bacterial species taxonomy ID or taxonomic name in: path required: true schema: type: string examples: example-0: value: '202956' summary: Acinetobacter towneri /genome/checkm_histogram: post: summary: Get CheckM histogram data by species taxon description: Get CheckM histogram data by species taxon. This data is used for rendering CheckM histograms on bacterial genome pages. tags: - Genome operationId: checkm_histogram_by_taxon_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/v2AssemblyCheckMHistogramReply' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblyCheckMHistogramRequest' examples: Single TaxID example: description: Acinetobacter towneri (taxid 202956) value: species_taxon: '202956' /genome/accession/{accessions}/download: get: summary: Get a genome data package by genome assembly accession description: Download a genome data package including sequence, annotation, and a detailed data report by genome assembly accession. tags: - Genome operationId: download_assembly_package responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/zip: schema: format: binary type: string description: Zip compressed stream parameters: - name: accessions description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: array items: type: string examples: example-0: value: GCF_000001405.40 summary: Human reference genome, GRCh38.p14 example-1: value: - GCF_000001405.40 - GCF_000001635.27 summary: Human and mouse reference genomes, GRCh38.p14 and GRCm39 - name: chromosomes description: Only return genomic fasta sequence for the specified chromosomes. in: query required: false schema: type: array items: type: string examples: example-0: value: - '1' - MT summary: Chromosome 1 and mitochondrial genome sequence example-1: value: - X - Y summary: Human sex chromosomes X and Y - name: include_annotation_type description: Specify which sequence, annotation, and report files to include in the data package. The assembly data report is always included, and its inclusion is not affected by this parameter. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2AnnotationForAssemblyType' examples: example-0: value: GENOME_FASTA summary: Include the genome sequence only example-1: value: - GENOME_FASTA - PROT_FASTA - GENOME_GFF - SEQUENCE_REPORT summary: Include genomic and protein sequences, a gff3 annotation file, and the sequence report - name: hydrated description: Specify whether to download a hydrated (with sequence and annotation files included) or dehydrated data package. A dehydrated data package includes the assembly data report and `fetch.txt`, which includes paths to the requested data files on NCBI servers. in: query required: false schema: $ref: '#/components/schemas/v2AssemblyDatasetRequestResolution' examples: example-0: value: DATA_REPORT_ONLY summary: Download a dehydrated data package, which is recommended for large downloads - name: filename description: Output file name. in: query required: false schema: type: string default: ncbi_dataset.zip /genome/download: post: summary: Get a genome data package by genome assembly accession description: Download a genome data package including sequence, annotation, and a detailed data report by genome assembly accession. tags: - Genome operationId: download_assembly_package_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/zip: schema: format: binary type: string description: Zip compressed stream requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblyDatasetRequest' examples: Single GCF accession example: description: Tribolium castaneum reference genome, icTRiCast1.1, with genome sequence, annotation and sequence report files value: accessions: - GCF_031307605.1 include_annotation_type: - GENOME_FASTA - GENOME_GFF - SEQUENCE_REPORT parameters: - name: filename description: Output file name. in: query required: false schema: type: string default: ncbi_dataset.zip /genome/accession/{accession}/annotation_report/download: get: summary: Get a genome annotation data package by genome assembly accession description: Download an annotation data package including sequence and a detailed annotation report by genome assembly accession. tags: - Genome operationId: download_genome_annotation_package responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/zip: schema: format: binary type: string description: Zip compressed stream parameters: - name: accession description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: string examples: example-0: value: GCF_000001635.27 summary: Mouse reference genome assembly, GRCm39 - name: annotation_ids description: Limit to one or more features annotated on the genome by specifying a number corresponding to a row_id (unstable). in: query required: false schema: type: array items: type: string examples: example-0: value: 1 summary: row_id 1 - name: symbols description: Limit to annotated features matching the given gene symbol (case-sensitive). in: query required: false schema: type: array items: type: string examples: example-0: value: Qsox1 summary: Mouse gene Qsox1 - name: locations description: Limit to features annotated at a specific location on the genome, by specifying a chromosome name or accession and optional start-stop range. in: query required: false schema: type: array items: type: string examples: example-0: value: 1:1-1000 summary: Chromosome 1, nucleotides 1-1000 example-1: value: NC_000067.7:3,000,000-4,000,000 summary: Mouse chromosome 1, nucleotides 3,000,000-4,000,000 - name: gene_types description: Limit to features of a specified gene locus type. in: query required: false schema: type: array items: type: string examples: example-0: value: protein-coding summary: Protein-coding genes - name: search_text description: Limit to features that match the specified gene symbol, gene name or protein name. in: query required: false schema: type: array items: type: string examples: example-0: value: kinase summary: Genes matching the term 'kinase' - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' - name: include_annotation_type description: Specify which sequence files to include in the data package. Options include gene (GENOME_FASTA), transcript (RNA_FASTA), and protein (PROT_FASTA) sequences. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GenomeAnnotationRequestAnnotationType' - name: filename description: Output file name. in: query required: false schema: type: string default: ncbi_dataset.zip /genome/annotation_report/download: post: summary: Get a genome annotation data package by genome assembly accession description: Download an annotation data package including sequence and a detailed annotation report by genome assembly accession. tags: - Genome operationId: download_genome_annotation_package_by_post responses: default: description: An unexpected error response. content: text/plain: schema: $ref: '#/components/schemas/rpcStatus' '200': description: A successful response content: application/zip: schema: format: binary type: string description: Zip compressed stream requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GenomeAnnotationRequest' examples: Single GCF accession example: description: Mouse reference genome assembly, GRCm39 value: accession: GCF_000001635.27 parameters: - name: filename description: Output file name. in: query required: false schema: type: string default: ncbi_dataset.zip /genome/accession/{accessions}/check: get: summary: Check the validity of a genome assembly accession description: Check the validity of a genome assembly accession. Output in JSON format. tags: - Genome operationId: check_assembly_availability 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/v2AssemblyDatasetAvailability' parameters: - name: accessions description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: array items: type: string examples: example-0: value: GCF_000001405.40 summary: Human reference genome, GRCh38.p14 example-1: value: - GCF_000001405.40 - GCF_000001635.27 summary: Human and mouse reference genomes, GRCh38.p14 and GRCm39 /genome/check: post: summary: Check the validity of a genome assembly accession description: Check the validity of a genome assembly accession. Output in JSON format. tags: - Genome operationId: check_assembly_availability_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/v2AssemblyDatasetAvailability' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblyDatasetRequest' examples: Single GCF accession example: description: Tribolium castaneum reference genome, icTRiCast1.1, with genome sequence, annotation and sequence report files value: accessions: - GCF_031307605.1 include_annotation_type: - GENOME_FASTA - GENOME_GFF - SEQUENCE_REPORT /genome/accession/{accession}/annotation_report: get: summary: Get genome annotation reports by genome assembly accession description: 'Get genome annotation reports by genome assembly accession, where each report represents a single feature annotated on the genome. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_annotation_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/v2reportsGenomeAnnotationReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGenomeAnnotationReportPage' text/tab-separated-values: schema: type: string parameters: - name: accession description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: string examples: example-0: value: GCF_000001635.27 summary: Mouse reference genome assembly, GRCm39 - name: annotation_ids description: Limit to one or more features annotated on the genome by specifying a number corresponding to a row_id (unstable). in: query required: false schema: type: array items: type: string examples: example-0: value: 1 summary: row_id 1 - name: symbols description: Limit to annotated features matching the given gene symbol (case-sensitive). in: query required: false schema: type: array items: type: string examples: example-0: value: Qsox1 summary: Mouse gene Qsox1 - name: locations description: Limit to features annotated at a specific location on the genome, by specifying a chromosome name or accession and optional start-stop range. in: query required: false schema: type: array items: type: string examples: example-0: value: 1:1-1000 summary: Chromosome 1, nucleotides 1-1000 example-1: value: NC_000067.7:3,000,000-4,000,000 summary: Mouse chromosome 1, nucleotides 3,000,000-4,000,000 - name: gene_types description: Limit to features of a specified gene locus type. in: query required: false schema: type: array items: type: string examples: example-0: value: protein-coding summary: Protein-coding genes - name: search_text description: Limit to features that match the specified gene symbol, gene name or protein name. in: query required: false schema: type: array items: type: string examples: example-0: value: kinase summary: Genes matching the term 'kinase' - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' - name: page_size description: The maximum number of features 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: table_format description: Optional pre-defined template for processing a tabular data request in: query required: false schema: $ref: '#/components/schemas/v2GenomeAnnotationRequestGenomeAnnotationTableFormat' - name: include_tabular_header description: Specify when to include the table header when requesting a tabular report. in: query required: false schema: $ref: '#/components/schemas/v2IncludeTabularHeader' - name: page_token description: A page token is returned when the results count exceeds `page size`. Use this token along with previous request 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 /genome/annotation_report: post: summary: Get genome annotation reports by genome assembly accession description: 'Get genome annotation reports by genome assembly accession, where each report represents a single feature annotated on the genome. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.' tags: - Genome operationId: genome_annotation_report_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/v2reportsGenomeAnnotationReportPage' application/x-ndjson: schema: $ref: '#/components/schemas/v2reportsGenomeAnnotationReportPage' text/tab-separated-values: schema: type: string requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GenomeAnnotationRequest' examples: Single GCF accession example: description: Mouse reference genome assembly, GRCm39 value: accession: GCF_000001635.27 /genome/accession/{accession}/annotation_summary: get: summary: Get genome annotation report summary information by genome assembly accession description: Get genome annotation report summary information by genome assembly accession in JSON format, including chromosome names and gene types. tags: - Genome operationId: annotation_report_facets_by_accession 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/v2GenomeAnnotationTableSummaryReply' parameters: - name: accession description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: string examples: example-0: value: GCF_000001635.27 summary: Mouse reference genome assembly, GRCm39 - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' /genome/annotation_summary: post: summary: Get genome annotation report summary information by genome assembly accession description: Get genome annotation report summary information by genome assembly accession in JSON format, including chromosome names and gene types. tags: - Genome operationId: annotation_report_facets_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/v2GenomeAnnotationTableSummaryReply' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2GenomeAnnotationRequest' examples: Single GCF accession example: description: Mouse reference genome assembly, GRCm39 value: accession: GCF_000001635.27 /genome/accession/{accession}/annotation_report/download_summary: get: summary: Get a download summary (preview) of a genome annotation data package by genome assembly accession description: Get a downlaod summary (preview) of a genome annotation data package, including counts and file sizes, in JSON format. tags: - Genome operationId: genome_annotation_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: accession description: One or more genome assembly accessions, limited to 100 in: path required: true schema: type: string examples: example-0: value: GCF_000001635.27 summary: Mouse reference genome assembly, GRCm39 - name: annotation_ids description: Limit to one or more features annotated on the genome by specifying a number corresponding to a row_id (unstable). in: query required: false schema: type: array items: type: string examples: example-0: value: 1 summary: row_id 1 - name: symbols description: Limit to annotated features matching the given gene symbol (case-sensitive). in: query required: false schema: type: array items: type: string examples: example-0: value: Qsox1 summary: Mouse gene Qsox1 - name: locations description: Limit to features annotated at a specific location on the genome, by specifying a chromosome name or accession and optional start-stop range. in: query required: false schema: type: array items: type: string examples: example-0: value: 1:1-1000 summary: Chromosome 1, nucleotides 1-1000 example-1: value: NC_000067.7:3,000,000-4,000,000 summary: Mouse chromosome 1, nucleotides 3,000,000-4,000,000 - name: gene_types description: Limit to features of a specified gene locus type. in: query required: false schema: type: array items: type: string examples: example-0: value: protein-coding summary: Protein-coding genes - name: search_text description: Limit to features that match the specified gene symbol, gene name or protein name. in: query required: false schema: type: array items: type: string examples: example-0: value: kinase summary: Genes matching the term 'kinase' - name: sort.field in: query required: false schema: type: string - name: sort.direction in: query required: false schema: $ref: '#/components/schemas/v2SortDirection' - name: include_annotation_type description: Specify which sequence files to include in the data package. Options include gene (GENOME_FASTA), transcript (RNA_FASTA), and protein (PROT_FASTA) sequences. in: query required: false schema: type: array items: $ref: '#/components/schemas/v2GenomeAnnotationRequestAnnotationType' /genome/annotation_report/download_summary: post: summary: Get a download summary (preview) of a genome annotation data package by genome assembly accession description: Get a download summary (preview) of a genome annotation data package, including counts and file sizes, by genome assembly accession, in JSON format. tags: - Genome operationId: genome_annotation_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/v2GenomeAnnotationRequest' examples: Single GCF accession example: description: Mouse reference genome assembly, GRCm39 value: accession: GCF_000001635.27 /genome/accession/{accession}/revision_history: get: summary: Get a revision history for a genome assembly by genome assembly accession description: Get a revision history, or list of all versions of a genome assembly, in JSON format. tags: - Genome operationId: assembly_revision_history_by_get 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/v2AssemblyRevisionHistory' parameters: - name: accession description: One genome assembly accession in: path required: true schema: type: string examples: example-0: value: GCF_000001405.40 summary: Human reference genome assembly, GRCh38.p14 /genome/revision_history: post: summary: Get a revision history for a genome assembly by genome assembly accession description: Get a revision history, or list of all versions of a genome assembly, in JSON format. tags: - Genome operationId: assembly_revision_history_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/v2AssemblyRevisionHistory' requestBody: required: true content: application/json: schema: $ref: '#/components/schemas/v2AssemblyRevisionHistoryRequest' examples: Single GCF accession example: description: Human reference genome assembly, GRCh38.p14 value: accession: GCF_000001405.40 components: schemas: v2reportsPairedAssembly: type: object properties: accession: type: string title: The GenColl assembly accession of the GenBank or RefSeq assembly paired with this one status: $ref: '#/components/schemas/v2reportsAssemblyStatus' title: GenColl Assembly status from paired record annotation_name: type: string title: Annotation name from paired record only_genbank: type: string title: Sequences that are only included in the GenBank assembly only_refseq: type: string title: Sequences that are only included in the RefSeq assembly changed: type: string title: Sequences present on both the GenBank and the RefSeq assemblies that have been changed, e.g., contaminated sequence in the GenBank assembly has been replaced with a gap manual_diff: type: string title: Manually curated description of differences between the GenBank and RefSeq assemblies refseq_genbank_are_different: type: boolean title: boolean indication on whether there are any differences between the GenBank and RefSeq assemblies differences: type: string title: Concatenation of all differences between the GenBank and RefSeq assemblies, including manually curated description and other fields v2reportsErrorOrganelleErrorCode: type: string enum: - UNKNOWN_ORGANELLE_ERROR_CODE - INVALID_ORGANELLE_TAXON - NO_ORGANELLES_FOR_ACCESSION default: UNKNOWN_ORGANELLE_ERROR_CODE v2DownloadSummaryAvailableFiles: type: object properties: all_genomic_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' genome_gff: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' genome_gbff: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' rna_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' prot_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' genome_gtf: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' cds_fasta: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' sequence_report: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' annotation_report: $ref: '#/components/schemas/v2DownloadSummaryFileSummary' v2AssemblyDatasetDescriptorsFilter: type: object properties: reference_only: type: boolean title: If true, limit to reference genome assemblies. assembly_source: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource' title: Limit to either RefSeq (GCF_) or GenBank (GCA_) genome assemblies. has_annotation: type: boolean title: Limit to annotated genome assemblies. exclude_paired_reports: type: boolean title: If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned. exclude_atypical: type: boolean title: If true, exclude [atypical genome assemblies](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/policies-annotation/genome-processing/genome_notes/#atypical-assemblies), i.e., genomes that have assembly issues or are otherwise atypical. assembly_version: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion' title: Limit to the most recent (current) version of a genome assembly. assembly_level: type: array items: $ref: '#/components/schemas/v2reportsAssemblyLevel' first_release_date: type: string format: date-time title: Limit to genomes released on or after the specified date last_release_date: type: string format: date-time title: Limit to genomes released on or before the specified date search_text: type: array items: type: string is_metagenome_derived: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter' title: Exclude or limit to metagenome-assembled genomes (MAGs). is_type_material: type: boolean title: If true, limit to genomes derived from type material. is_ictv_exemplar: type: boolean title: If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes). exclude_multi_isolate: type: boolean title: If true, exclude genomes that were sequenced as part of large multi-isolate projects. type_material_category: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory' title: Limit to genomes derived from specific type material categories. v2reportsBioSampleContact: type: object properties: lab: type: string title: Submitter lab name. v2reportsGenomicRegion: type: object properties: gene_range: $ref: '#/components/schemas/v2reportsSeqRangeSet' title: The range of this Gene record on this genomic region. type: $ref: '#/components/schemas/v2reportsGenomicRegionGenomicRegionType' title: Type of genomic region v2reportsSeqRangeSet: type: object properties: accession_version: type: string title: NCBI Accession.version of the sequence range: type: array items: $ref: '#/components/schemas/v2reportsRange' v2AssemblyCheckMHistogramRequest: type: object properties: species_taxon: type: string title: Bacterial species taxonomy ID or taxonomic name v2reportsGeneCounts: type: object properties: total: type: integer title: Total number of annotated genes protein_coding: type: integer title: Count of annotated genes that encode a protein non_coding: type: integer title: Count of transcribed non-coding genes (e.g. lncRNAs, miRNAs, rRNAs, etc...) excludes transcribed pseudogenes pseudogene: type: integer title: Count of transcribed and non-transcribed pseudogenes other: type: integer title: Count of genic region GeneIDs and non-genic regulatory GeneIDs v2reportsTranscript: type: object properties: accession_version: type: string title: RefSeq transcript accession with version name: type: string title: RefSeq transcript name length: type: integer title: RefSeq transcript length in nucleotides cds: $ref: '#/components/schemas/v2reportsSeqRangeSet' genomic_locations: type: array items: $ref: '#/components/schemas/v2reportsGenomicLocation' ensembl_transcript: type: string title: Ensembl transcript accession with version protein: $ref: '#/components/schemas/v2reportsProtein' type: $ref: '#/components/schemas/v2reportsTranscriptTranscriptType' title: Indicates transcript protein-coding potential and whether it was computationally predicted select_category: $ref: '#/components/schemas/v2reportsTranscriptSelectCategory' v2reportsLinkedAssemblyType: type: string enum: - LINKED_ASSEMBLY_TYPE_UNKNOWN - alternate_pseudohaplotype_of_diploid - principal_pseudohaplotype_of_diploid - maternal_haplotype_of_diploid - paternal_haplotype_of_diploid - haplotype_1 - haplotype_2 - haplotype_3 - haplotype_4 - haploid default: LINKED_ASSEMBLY_TYPE_UNKNOWN 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 v2reportsRnaType: type: string enum: - rna_UNKNOWN - premsg - tmRna default: rna_UNKNOWN v2reportsAverageNucleotideIdentityMatchStatus: type: string enum: - BEST_MATCH_STATUS_UNKNOWN - approved_mismatch - below_threshold_match - below_threshold_mismatch - best_match_status - derived_species_match - genus_match - low_coverage - mismatch - status_na - species_match - subspecies_match - synonym_match - lineage_match - below_threshold_lineage_match default: BEST_MATCH_STATUS_UNKNOWN v2AssemblyDatasetRequestResolution: type: string enum: - FULLY_HYDRATED - DATA_REPORT_ONLY default: FULLY_HYDRATED v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter: type: string enum: - METAGENOME_DERIVED_UNSET - metagenome_derived_only - metagenome_derived_exclude default: METAGENOME_DERIVED_UNSET v2AssemblyDatasetAvailability: type: object properties: valid_assemblies: type: array items: type: string invalid_assemblies: type: array items: type: string reason: type: string v2reportsANITypeCategory: type: string enum: - ANI_CATEGORY_UNKNOWN - claderef - category_na - neotype - no_type - pathovar - reftype - suspected_type - synonym - type default: ANI_CATEGORY_UNKNOWN v2reportsFeatureCounts: type: object properties: gene_counts: $ref: '#/components/schemas/v2reportsGeneCounts' title: Counts of gene types v2GenomeAnnotationRequest: type: object properties: accession: type: string title: One or more genome assembly accessions, limited to 100 annotation_ids: type: array items: type: string symbols: type: array items: type: string locations: type: array items: type: string gene_types: type: array items: type: string search_text: type: array items: type: string sort: type: array items: $ref: '#/components/schemas/v2SortField' include_annotation_type: type: array items: $ref: '#/components/schemas/v2GenomeAnnotationRequestAnnotationType' page_size: type: integer title: The maximum number of features 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. table_fields: type: array items: type: string table_format: $ref: '#/components/schemas/v2GenomeAnnotationRequestGenomeAnnotationTableFormat' title: Optional pre-defined template for processing a tabular data request include_tabular_header: $ref: '#/components/schemas/v2IncludeTabularHeader' title: Specify when to include the table header when requesting a tabular report. page_token: type: string title: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved. v2reportsGeneType: type: string enum: - UNKNOWN - tRNA - rRNA - snRNA - scRNA - snoRNA - PROTEIN_CODING - PSEUDO - TRANSPOSON - miscRNA - ncRNA - BIOLOGICAL_REGION - OTHER default: UNKNOWN title: 'NB: GeneType values match Entrez Gene' v2DownloadSummaryHydrated: type: object properties: estimated_file_size_mb: type: integer url: type: string cli_download_command_line: type: string protobufAny: type: object properties: type_url: type: string value: type: string format: byte rpcStatus: type: object properties: code: type: integer format: int32 message: type: string details: type: array items: $ref: '#/components/schemas/protobufAny' v2reportsAssemblyDataReport: type: object properties: accession: type: string title: The GenColl assembly accession current_accession: type: string title: The latest GenColl assembly accession for this revision chain paired_accession: type: string title: The GenBank or RefSeq assembly accession paired with this assembly source_database: $ref: '#/components/schemas/v2reportsSourceDatabase' title: Source of the accession. The paired accession, if it exists, is from the other database. organism: $ref: '#/components/schemas/v2reportsOrganism' assembly_info: $ref: '#/components/schemas/v2reportsAssemblyInfo' title: Metadata for the genome assembly submission assembly_stats: $ref: '#/components/schemas/v2reportsAssemblyStats' title: Global statistics for the genome assembly organelle_info: type: array items: $ref: '#/components/schemas/v2reportsOrganelleInfo' additional_submitters: type: array items: $ref: '#/components/schemas/v2reportsAdditionalSubmitter' annotation_info: $ref: '#/components/schemas/v2reportsAnnotationInfo' title: Metadata and statistics for the genome assembly annotation, when available wgs_info: $ref: '#/components/schemas/v2reportsWGSInfo' title: Metadata pertaining to the Whole Genome Shotgun (WGS) record for the genome assemblies that are complete genomes. Those that are clone-based do not have WGS-master records. type_material: $ref: '#/components/schemas/v2reportsTypeMaterial' checkm_info: $ref: '#/components/schemas/v2reportsCheckM' title: Metadata on the completeness and contamination of this assembly average_nucleotide_identity: $ref: '#/components/schemas/v2reportsAverageNucleotideIdentity' v2reportsBioSampleAttribute: type: object properties: name: type: string value: type: string v2reportsAdditionalSubmitter: type: object properties: genbank_accession: type: string title: genbank accession of extra sequence refseq_accession: type: string title: genbank accession of extra sequence chr_name: type: string title: chromosome name molecule_type: type: string title: molecule type submitter: type: string title: Name of submitter bioproject_accession: type: string title: Bioproject accession v2reportsAssemblyRevision: type: object properties: genbank_accession: type: string refseq_accession: type: string assembly_name: type: string assembly_level: $ref: '#/components/schemas/v2reportsAssemblyLevel' release_date: type: string submission_date: type: string sequencing_technology: type: string identical: type: boolean title: Are the RefSeq and GenBank revisions identical? v2AssemblyCheckMHistogramReplyHistogramInterval: type: object properties: start_pos: type: number format: float title: Starting position for this interval stop_pos: type: number format: float title: ending position for this interval count: type: number format: float title: number of elements in this interval v2reportsAverageNucleotideIdentityTaxonomyCheckStatus: type: string enum: - TAXONOMY_CHECK_STATUS_UNKNOWN - OK - Failed - Inconclusive default: TAXONOMY_CHECK_STATUS_UNKNOWN v2AssemblyAccessions: type: object properties: accessions: type: array items: type: string v2GenomeAnnotationTableSummaryReply: type: object properties: accession: type: string title: Assembly from which available values are taken chromosomes: type: array items: type: string gene_types: type: array items: type: string empty_columns: type: array items: type: string v2reportsCheckM: type: object properties: checkm_marker_set: type: string title: What taxonomic group is used as the basis for comparison with this assembly with regards to checkM values checkm_species_tax_id: type: integer title: The species-level taxid for this assemblies checkM dataset checkm_marker_set_rank: type: string title: CheckM taxonomic rank of checkm_marker_set checkm_version: type: string title: CheckM software version completeness: type: number format: float title: What percent complete is this assembly contamination: type: number format: float title: What is the contamination percentage for this assembly completeness_percentile: type: number format: float title: The percent of assemblies under the taxonomic grouping 'checkm_marker_set' that this assembly is as-or-more complete than. v2AssemblyLinksRequest: type: object properties: accessions: type: array items: type: string assembly_link_types: type: array items: $ref: '#/components/schemas/v2AssemblyLinksReplyAssemblyLinkType' v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory: type: string enum: - NONE - TYPE_MATERIAL - TYPE_MATERIAL_CLADE - TYPE_MATERIAL_NEOTYPE - TYPE_MATERIAL_REFTYPE - PATHOVAR_TYPE - TYPE_MATERIAL_SYN default: NONE v2reportsTypeMaterial: type: object properties: type_label: type: string type_display_text: type: string v2reportsGenomeAnnotationReportMatch: type: object properties: annotation: $ref: '#/components/schemas/v2reportsGenomeAnnotation' query: type: array items: type: string warning: $ref: '#/components/schemas/v2reportsWarning' errors: type: array items: $ref: '#/components/schemas/v2reportsError' row_id: type: string v2reportsGenomeAnnotation: type: object properties: gene_id: type: string format: uint64 title: NCBI GeneID symbol: type: string title: Gene symbol description: type: string title: Gene name name: type: string tax_id: type: string format: uint64 title: NCBI Taxonomy ID for the organism taxname: type: string title: Taxonomic name of the organism common_name: type: string title: Common name of the organism type: $ref: '#/components/schemas/v2reportsGeneType' title: Deprecated gene_type: type: string title: Gene locus type rna_type: $ref: '#/components/schemas/v2reportsRnaType' orientation: $ref: '#/components/schemas/v2reportsOrientation' locus_tag: type: string reference_standards: type: array items: $ref: '#/components/schemas/v2reportsGenomicRegion' genomic_regions: type: array items: $ref: '#/components/schemas/v2reportsGenomicRegion' transcripts: type: array items: $ref: '#/components/schemas/v2reportsTranscript' proteins: type: array items: $ref: '#/components/schemas/v2reportsProtein' chromosomes: type: array items: type: string swiss_prot_accessions: type: array items: type: string ensembl_gene_ids: type: array items: type: string omim_ids: type: array items: type: string synonyms: type: array items: type: string annotations: type: array items: $ref: '#/components/schemas/v2reportsAnnotation' v2DownloadSummaryFileSummary: type: object properties: file_count: type: integer size_mb: type: number format: float v2AssemblySequenceReportsRequest: type: object properties: accession: type: string title: One or more genome assembly accessions, limited to 100 chromosomes: type: array items: type: string role_filters: type: array items: type: string table_fields: type: array items: type: string count_assembly_unplaced: type: boolean title: Include the count of unplaced scaffold sequences page_size: type: integer title: The maximum number of genome assemblies to return. Maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results. page_token: type: string title: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved. include_tabular_header: $ref: '#/components/schemas/v2IncludeTabularHeader' table_format: type: string title: Optional pre-defined template for processing a tabular data request v2reportsAssemblyInfo: type: object properties: assembly_level: type: string title: The level at which a genome has been assembled assembly_status: $ref: '#/components/schemas/v2reportsAssemblyStatus' title: The GenColl assembly status paired_assembly: $ref: '#/components/schemas/v2reportsPairedAssembly' title: Metadata from the GenBank or RefSeq assembly paired with this one assembly_name: type: string title: The assembly submitter's name for the genome assembly, when provided. Otherwise, a default name in the form ASM#####v# is assigned assembly_long_name: type: string assembly_type: type: string title: Chromosome content of the submitted genome assembly bioproject_lineage: type: array items: $ref: '#/components/schemas/v2reportsBioProjectLineage' bioproject_accession: type: string submission_date: type: string title: Date the assembly was submitted to NCBI (being replaced by release date - should maintain until most CLI users upgrade) release_date: type: string title: Date the assembly was made available by NCBI. This field is not returned by versions of the datasets Command Line Interface (CLI) program < 15. description: type: string title: Long description for this genome submitter: type: string title: The submitting consortium or organization. Full submitter information is available in the BioProject refseq_category: type: string title: The RefSeq Category, if present, indicates whether the assembly is a reference genome synonym: type: string title: Genome name ascribed to this assembly by the UC Santa Cruz genome browser linked_assembly: type: string title: The accession.version and designation (principal or alternate pseudohaplotype) of a paired genome assembly derived from the same diploid individual linked_assemblies: type: array items: $ref: '#/components/schemas/v2reportsLinkedAssembly' atypical: $ref: '#/components/schemas/v2reportsAtypicalInfo' title: Information on atypical genomes - genomes that have assembly issues or are otherwise atypical genome_notes: type: array items: type: string sequencing_tech: type: string title: Sequencing technology used to sequence this genome assembly_method: type: string title: Genome assembly method grouping_method: type: string biosample: $ref: '#/components/schemas/v2reportsBioSampleDescriptor' title: NCBI BioSample from which the sequences in the genome assembly were obtained. blast_url: type: string title: URL to blast page for this assembly comments: type: string title: Freeform comments suppression_reason: type: string title: The reason for the assembly is suppressed, for suppressed assemblies diploid_role: $ref: '#/components/schemas/v2reportsLinkedAssemblyType' v2reportsBioSampleId: type: object properties: db: type: string label: type: string value: type: string v2reportsAssemblyDataReportPage: type: object properties: reports: type: array items: $ref: '#/components/schemas/v2reportsAssemblyDataReport' content_type: $ref: '#/components/schemas/v2reportsContentType' 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' v2AssemblyCheckMHistogramReply: type: object properties: species_taxid: type: integer histogram_intervals: type: array items: $ref: '#/components/schemas/v2AssemblyCheckMHistogramReplyHistogramInterval' v2reportsErrorTaxonomyErrorCode: type: string enum: - UNKNOWN_TAXONOMY_ERROR_CODE - INVALID_TAXONOMY_TAXON default: UNKNOWN_TAXONOMY_ERROR_CODE v2reportsLineageOrganism: type: object properties: tax_id: type: integer title: NCBI Taxonomy identifier name: type: string title: Scientific name v2reportsGenomicRegionGenomicRegionType: type: string enum: - UNKNOWN - REFSEQ_GENE - PSEUDOGENE - BIOLOGICAL_REGION - OTHER default: UNKNOWN v2reportsMessage: type: object properties: error: $ref: '#/components/schemas/v2reportsError' warning: $ref: '#/components/schemas/v2reportsWarning' v2reportsOrganelleInfo: type: object properties: assembly_name: type: string title: Name of associated nuclear assembly infraspecific_name: type: string title: The strain, breed, cultivar or ecotype of the organism from which the sequences in the assembly were derived bioproject: type: array items: type: string description: type: string title: Long description of the organelle genome total_seq_length: type: string format: uint64 title: Sequence length of the organelle genome submitter: type: string title: Name of submitter 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' v2SequenceReportPage: type: object properties: reports: type: array items: $ref: '#/components/schemas/v2reportsSequenceInfo' total_count: type: integer title: The total count of available datasets (ignoring the cutoff parameter). Only provided for the first page of results (when `page_token` is empty in the request). 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. v2reportsMaturePeptide: type: object properties: accession_version: type: string name: type: string length: type: integer v2DownloadSummaryDehydrated: type: object properties: estimated_file_size_mb: type: integer url: type: string cli_download_command_line: type: string cli_rehydrate_command_line: type: string v2AssemblyDatasetDescriptorsFilterAssemblyVersion: type: string enum: - current - all_assemblies default: current title: The assembly status - current (latest), or all assemblies, which adds replaced and suppressed v2AssemblyDatasetRequest: type: object properties: accessions: type: array items: type: string chromosomes: type: array items: type: string include_annotation_type: type: array items: $ref: '#/components/schemas/v2AnnotationForAssemblyType' hydrated: $ref: '#/components/schemas/v2AssemblyDatasetRequestResolution' title: Specify whether to download a hydrated (with sequence and annotation files included) or dehydrated data package. A dehydrated data package includes the assembly data report and `fetch.txt`, which includes paths to the requested data files on NCBI servers. include_tsv: type: boolean title: Set to true to include a TSV representation of the data-report. v2GenomeAnnotationRequestAnnotationType: type: string enum: - DEFAULT - GENOME_FASTA - RNA_FASTA - PROT_FASTA default: DEFAULT v2reportsOrientation: type: string enum: - none - plus - minus default: none v2AnnotationForAssemblyType: type: string enum: - DEFAULT - GENOME_GFF - GENOME_GBFF - RNA_FASTA - PROT_FASTA - GENOME_GTF - CDS_FASTA - GENOME_FASTA - SEQUENCE_REPORT default: DEFAULT v2AssemblyLinksReply: type: object properties: assembly_links: type: array items: $ref: '#/components/schemas/v2AssemblyLinksReplyAssemblyLink' v2reportsRange: type: object properties: begin: type: string format: uint64 title: Sequence start position end: type: string format: uint64 title: Sequence stop position orientation: $ref: '#/components/schemas/v2reportsOrientation' title: Direction relative to the genome order: type: integer title: The position of this sequence in a group of sequences ribosomal_slippage: type: integer title: When ribosomal slippage is desired, fill out slippage amount between this and previous range. 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 v2reportsBioSampleDescriptor: type: object properties: accession: type: string last_updated: type: string publication_date: type: string submission_date: type: string sample_ids: type: array items: $ref: '#/components/schemas/v2reportsBioSampleId' description: $ref: '#/components/schemas/v2reportsBioSampleDescription' owner: $ref: '#/components/schemas/v2reportsBioSampleOwner' models: type: array items: type: string bioprojects: type: array items: $ref: '#/components/schemas/v2reportsBioProject' package: type: string attributes: type: array items: $ref: '#/components/schemas/v2reportsBioSampleAttribute' status: $ref: '#/components/schemas/v2reportsBioSampleStatus' 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: Geographic 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 v2AssemblyDatasetReportsRequestContentType: type: string enum: - COMPLETE - ASSM_ACC - PAIRED_ACC default: COMPLETE v2AssemblyRevisionHistory: type: object properties: assembly_revisions: type: array items: $ref: '#/components/schemas/v2reportsAssemblyRevision' total_count: type: integer v2reportsGenomeAnnotationReportPage: type: object properties: reports: type: array items: $ref: '#/components/schemas/v2reportsGenomeAnnotationReportMatch' messages: type: array items: $ref: '#/components/schemas/v2reportsMessage' total_count: type: integer title: The total count of available genes (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. v2reportsANIMatch: type: object properties: assembly: type: string title: Accession of the submitted organism best match type-strain assembly or best match type-strain assembly organism_name: type: string title: Taxonomic name of the submitted organism or best match type-strain organism category: $ref: '#/components/schemas/v2reportsANITypeCategory' title: Type category ani: type: number format: float title: Percent average nucleotide identity assembly_coverage: type: number format: float title: Percent coverage of the query assembly by the submitted organism or best match type assembly type_assembly_coverage: type: number format: float title: Percent coverage of the submitted organism or best match type assembly by the query assembly v2SortDirection: type: string enum: - SORT_DIRECTION_UNSPECIFIED - SORT_DIRECTION_ASCENDING - SORT_DIRECTION_DESCENDING default: SORT_DIRECTION_UNSPECIFIED v2reportsWarningReplacedId: type: object properties: requested: type: string returned: type: string v2AssemblyDatasetDescriptorsFilterAssemblySource: type: string enum: - all - refseq - genbank default: all v2reportsLinkedAssembly: type: object properties: linked_assembly: type: string title: The linked assembly accession assembly_type: $ref: '#/components/schemas/v2reportsLinkedAssemblyType' title: The linked assembly type v2AssemblyLinksReplyAssemblyLinkType: type: string enum: - DEFAULT - GDV_LINK - FTP_LINK - ASSEMBLY_PUBMED - BLAST_LINK - ASSEMBLY_NUCCORE_REFSEQ - ASSEMBLY_NUCCORE_GENBANK - CGV_LINK default: DEFAULT title: Types of assembly links that may be returned v2reportsAnnotationInfo: type: object properties: name: type: string title: Annotation name provider: type: string title: Source of the annotation release_date: type: string title: Annotation release date report_url: type: string title: Annotation report web address stats: $ref: '#/components/schemas/v2reportsFeatureCounts' busco: $ref: '#/components/schemas/v2reportsBuscoStat' method: type: string title: Software tools used to calculate annotation pipeline: type: string title: NCBI annotation pipeline used to calculate annotation software_version: type: string title: NCBI annotation pipeline software version status: type: string title: Type of annotation release_version: type: string v2reportsBioSampleStatus: type: object properties: status: type: string when: type: string v2AssemblyDatasetReportsRequest: type: object properties: taxons: type: array items: type: string bioprojects: type: array items: type: string biosample_ids: type: array items: type: string assembly_names: type: array items: type: string wgs_accessions: type: array items: type: string accessions: type: array items: type: string filters: $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilter' tax_exact_match: type: boolean title: If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes. chromosomes: type: array items: type: string table_fields: type: array items: type: string returned_content: $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType' title: Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information. page_size: type: integer title: 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. page_token: type: string title: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved. sort: type: array items: $ref: '#/components/schemas/v2SortField' include_tabular_header: $ref: '#/components/schemas/v2IncludeTabularHeader' title: Specify when to include the table header when requesting a tabular report. table_format: type: string title: Optional pre-defined template for processing a tabular data request v2reportsContentType: type: string enum: - COMPLETE - ASSM_ACC - PAIRED_ACC default: COMPLETE v2AssemblyLinksReplyAssemblyLink: type: object properties: accession: type: string title: The matching assembly accession assembly_link_type: $ref: '#/components/schemas/v2AssemblyLinksReplyAssemblyLinkType' title: The type of link resource_link: type: string title: A link to the resource linked_identifiers: type: array items: type: string v2SequenceAccessionRequest: type: object properties: accession: type: string title: Nucleotide sequence accession associated with a genome assembly v2reportsAssemblyStats: type: object properties: total_number_of_chromosomes: type: integer title: Count of nuclear chromosomes, organelles and plasmids in a submitted genome assembly total_sequence_length: type: string format: uint64 title: Total sequence length of the nuclear genome including unplaced and unlocalized sequences total_ungapped_length: type: string format: uint64 title: Total length of all top-level sequences ignoring gaps. Any stretch of 10 or more Ns in a sequence is treated like a gap number_of_contigs: type: integer title: Total number of sequence contigs in the assembly. Any stretch of 10 or more Ns in a sequence is treated as a gap between two contigs in a scaffold when counting contigs and calculating contig N50 & L50 values contig_n50: type: integer title: Length such that sequence contigs of this length or longer include half the bases of the assembly contig_l50: type: integer title: Number of sequence contigs that are longer than, or equal to, the N50 length and therefore include half the bases of the assembly number_of_scaffolds: type: integer title: Number of scaffolds including placed, unlocalized, unplaced, alternate loci and patch scaffolds scaffold_n50: type: integer title: Length such that scaffolds of this length or longer include half the bases of the assembly scaffold_l50: type: integer title: Number of scaffolds that are longer than, or equal to, the N50 length and therefore include half the bases of the assembly gaps_between_scaffolds_count: type: integer title: Number of unspanned gaps between scaffolds number_of_component_sequences: type: integer title: Total number of component WGS or clone sequences in the assembly atgc_count: type: string format: uint64 title: The number of AT and GC base-pairs in the assembly gc_count: type: string format: uint64 title: The number of GC base-pairs in the assembly gc_percent: type: number format: float title: The percentage of GC base-pairs in the assembly genome_coverage: type: string title: Genome assembly coverage number_of_organelles: type: integer title: number of organelles 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 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 v2reportsAverageNucleotideIdentity: type: object properties: taxonomy_check_status: $ref: '#/components/schemas/v2reportsAverageNucleotideIdentityTaxonomyCheckStatus' title: Indicates whether the ANI result is consistent with the submitted organism match_status: $ref: '#/components/schemas/v2reportsAverageNucleotideIdentityMatchStatus' title: Indicates the specific type of ANI result that supports the Taxonomy check status submitted_organism: type: string title: Taxonomic name of the query assembly submitted_species: type: string title: Species name of the query assembly category: $ref: '#/components/schemas/v2reportsANITypeCategory' title: Category of type or validated assembly submitted_ani_match: $ref: '#/components/schemas/v2reportsANIMatch' best_ani_match: $ref: '#/components/schemas/v2reportsANIMatch' comment: type: string title: Additional information about the ANI result v2reportsBioProjectLineage: type: object properties: bioprojects: type: array items: $ref: '#/components/schemas/v2reportsBioProject' v2reportsBuscoStat: type: object properties: busco_lineage: type: string title: BUSCO Lineage busco_ver: type: string title: BUSCO Version complete: type: number format: float title: 'BUSCO score: Complete' single_copy: type: number format: float title: 'BUSCO score: Single Copy' duplicated: type: number format: float title: 'BUSCO score: Duplicated' fragmented: type: number format: float title: 'BUSCO score: Fragmented' missing: type: number format: float title: 'BUSCO score: Missing' total_count: type: string format: uint64 title: 'BUSCO score: Total Count' v2SortField: type: object properties: field: type: string direction: $ref: '#/components/schemas/v2SortDirection' 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 v2reportsAssemblyStatus: type: string enum: - ASSEMBLY_STATUS_UNKNOWN - current - previous - suppressed - retired default: ASSEMBLY_STATUS_UNKNOWN v2reportsWGSInfo: type: object properties: wgs_project_accession: type: string title: WGS project accession master_wgs_url: type: string title: WGS project Nucleotide web address wgs_contigs_url: type: string title: WGS project Sequence set browser web address v2reportsTranscriptTranscriptType: type: string enum: - UNKNOWN - PROTEIN_CODING - NON_CODING - PROTEIN_CODING_MODEL - NON_CODING_MODEL default: UNKNOWN v2reportsGenomicLocation: type: object properties: genomic_accession_version: type: string sequence_name: type: string genomic_range: $ref: '#/components/schemas/v2reportsRange' exons: type: array items: $ref: '#/components/schemas/v2reportsRange' v2reportsBioSampleOwner: type: object properties: name: type: string contacts: type: array items: $ref: '#/components/schemas/v2reportsBioSampleContact' v2reportsSourceDatabase: type: string enum: - SOURCE_DATABASE_UNSPECIFIED - SOURCE_DATABASE_GENBANK - SOURCE_DATABASE_REFSEQ default: SOURCE_DATABASE_UNSPECIFIED v2DownloadSummary: type: object properties: record_count: type: integer title: The number of records for the requested filter. assembly_count: type: integer title: For backwards compatability with old VirusDatasetSummary resource_updated_on: type: string format: date-time title: The latest date on which the resource was updated. hydrated: $ref: '#/components/schemas/v2DownloadSummaryHydrated' dehydrated: $ref: '#/components/schemas/v2DownloadSummaryDehydrated' errors: type: array items: $ref: '#/components/schemas/v2reportsError' messages: type: array items: $ref: '#/components/schemas/v2reportsMessage' available_files: $ref: '#/components/schemas/v2DownloadSummaryAvailableFiles' v2reportsErrorVirusErrorCode: type: string enum: - UNKNOWN_VIRUS_ERROR_CODE default: UNKNOWN_VIRUS_ERROR_CODE v2GenomeAnnotationRequestGenomeAnnotationTableFormat: type: string enum: - NO_TABLE - SUMMARY - PRODUCT default: NO_TABLE v2reportsAssemblyLevel: type: string enum: - chromosome - scaffold - contig - complete_genome default: chromosome title: 'The level of the genome assembly: Chromosome, Scaffold, Contig or Complete Genome' 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 v2AssemblyRevisionHistoryRequest: type: object properties: accession: type: string title: One genome assembly accession v2reportsBioSampleDescription: type: object properties: title: type: string organism: $ref: '#/components/schemas/v2reportsOrganism' comment: type: string v2reportsProtein: type: object properties: accession_version: type: string title: RefSeq protein accession with version name: type: string title: Protein name length: type: integer title: Protein length in amino acids isoform_name: type: string title: Protein isoform name ensembl_protein: type: string title: Ensembl protein accession with version mature_peptides: type: array items: $ref: '#/components/schemas/v2reportsMaturePeptide' v2IncludeTabularHeader: type: string enum: - INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY - INCLUDE_TABULAR_HEADER_ALWAYS - INCLUDE_TABULAR_HEADER_NEVER default: INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY v2reportsAtypicalInfo: type: object properties: is_atypical: type: boolean title: If true there are assembly issues or the assembly is in some way non-standard warnings: type: array items: type: string v2reportsAnnotation: type: object properties: assembly_accession: type: string title: Genome assembly accession assembly_name: type: string title: Genome assembly name annotation_name: type: string title: Genome annotation name annotation_release_date: type: string title: Genome annotation release date genomic_locations: type: array items: $ref: '#/components/schemas/v2reportsGenomicLocation' v2reportsSequenceInfo: type: object properties: assembly_accession: type: string title: The genome assembly accession chr_name: type: string title: The name of the associated chromosome. The name "Un" indicates that the chromosome is unknown. ucsc_style_name: type: string title: Name ascribed to this sequence by the UC Santa Cruz genome browser sort_order: type: integer title: A sort order value assigned to the sequence assigned_molecule_location_type: type: string title: The type of molecule represented by the sequence refseq_accession: type: string title: The RefSeq accession of the sequence assembly_unit: type: string title: Name of the assembly unit, or set of sequences that comprise the assembly. length: type: integer title: The length of the sequence in nucleotides genbank_accession: type: string title: The GenBank accession of the sequence gc_count: type: string format: uint64 title: The number of GC base-pairs in the chromosome gc_percent: type: number format: float title: The percentage of GC base-pairs in the chromosome unlocalized_count: type: integer title: Number of scaffolds that are unlocalized on a given chromosome assembly_unplaced_count: type: integer title: Number of unplaced scaffolds for a given assembly accession role: type: string sequence_name: type: string title: The sequence name v2reportsErrorGeneErrorCode: type: string enum: - UNKNOWN_GENE_ERROR_CODE - INCOMPLETE_LOOKUP_SYMBOL - INVALID_TAXON_GENE_ARGUMENT default: UNKNOWN_GENE_ERROR_CODE v2reportsTranscriptSelectCategory: type: string enum: - SELECT_UNKNOWN - REFSEQ_SELECT - MANE_SELECT - MANE_PLUS_CLINICAL default: SELECT_UNKNOWN externalDocs: description: Introduction on clinicaltrials.gov url: https://clinicaltrials.gov/data-about-studies/learn-about-api