openapi: 3.0.1
info:
  title: NCBI Datasets API
  version: v2
  description: '### NCBI Datasets is a resource that lets you easily gather data from
      NCBI.

      The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.

    '
servers:
- url: https://api.ncbi.nlm.nih.gov/datasets/v2
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.

    '
- name: Gene
  description: '#### Options to download gene data, including the
    associated sequence and metadata.

    These gene services allow you to get gene metadata as a data report or download gene, transcript
    and protein sequence, and metadata, as a gene data package, for all genes in NCBI Gene.

    '
- name: Prokaryote
  description: '#### Options to download prokaryote gene data, including the associated
    sequence and metadata.

    These gene services allow you to download gene and protein sequence, and metadata as a prokaryote
    gene data package, for prokaryotic [RefSeq non-redundant proteins](https://www.ncbi.nlm.nih.gov/refseq/about/nonredundantproteins/).

    '
- name: Virus
  description: '#### Options to download virus genome data, including the
    associated sequence and metadata.

    These virus services allow you to get virus genome metadata as a data report or download genome and protein
    sequence, and metadata, as a virus data package, for virus GenBank genomes.
    '

- name: Version
  description: '#### Retrieve the current version of all NCBI Datasets services.

    NCBI Datasets services follow the [Semantic Versioning 2.0.0 Schema](https://semver.org/spec/v2.0.0.html).
    '

- name: Taxonomy
  description: '#### Options to download taxonomy data.

    These taxonomy services allow you to get taxonomy data as a data report or download taxonomy
    data as a taxonomy data package, for taxonomic nodes in NCBI Taxonomy.

    '

- name: BioSample
  description: '#### Options to download BioSample data.

    This BioSample service allows you to get BioSample data as a data report.

    '

- name: Organelle
  description: '#### Options to download RefSeq organelle genome data, including the associated sequence and metadata.

    These organelle services allow you to get RefSeq organelle genome metadata as a data report or download gene,
    transcript and protein sequence, and metadata, as an organelle data package, for RefSeq organelle genomes.

    '

externalDocs:
  description: Interactively explore genome assembly datasets
  url: https://www.ncbi.nlm.nih.gov/datasets/genomes/
security:
- ApiKeyAuthHeader: []
paths:
  /genome/accession/{accessions}/download_summary:
    get:
      summary: 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"
  /biosample/accession/{accessions}/biosample_report:
    get:
      summary: Get BioSample dataset reports by accession(s)
      description: 'Get BioSample dataset reports by accession(s). By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
      tags:
        - BioSample
      operationId: BioSample_dataset_report
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2reportsBioSampleDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsBioSampleDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: SAMN15960293
            summary: Animal sample from Gallus gallus, bGalGal3
          example-1:
            value: SAMN12629504
            summary: Animal sample from Carcharodon carcharias
  /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
  /gene/id/{gene_ids}/download:
    get:
      summary: Get a gene data package by GeneID
      description: 'Download a gene data package including sequence, annotation and data reports, as a compressed zip archive, by GeneID.'
      tags:
        - Gene
      operationId: download_gene_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: gene_ids
        description: 'One or more NCBI GeneIDs'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: Human IL21, interleukin 21
          example-1:
            value:
              - 59067
              - 50615
            summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor
      - name: include_annotation_type
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
        examples:
          example-0:
            value:
              - FASTA_RNA
              - FASTA_PROTEIN
            summary: Include RNA and protein sequence files
          example-1:
            value:
              - FASTA_CDS
              - FASTA_5P_UTR
              - FASTA_3P_UTR
            summary: Include coding sequence, and 5' and 3' UTRs
      - name: accession_filter
        description: 'Limit the contents of the sequence files and tabular product report to the specified RNA and protein accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NM_021803.4
            summary: Human IL21 MANE Select transcript
      - name: aux_report
        description: 'Specify additional report files to include in the data package. The gene 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/v2GeneDatasetRequestGeneDatasetReportType'
        examples:
          example-0:
            value: PRODUCT_REPORT
            summary: Add the gene product report
      - name: tabular_reports
        description: 'Specify which tabular report files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
        examples:
          example-0:
            value:
              - DATASET_REPORT
              - PRODUCT_REPORT
            summary: Include tabular gene and gene product reports
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /gene/download:
    post:
      summary: Get a gene data package
      description: 'Download a gene data package including sequence, annotation and data reports, as a compressed zip archive.'
      tags:
        - Gene
      operationId: download_gene_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/v2GeneDatasetRequest'
            examples:
              Multiple GeneID examples:
                description: Human interleukin 21 and interleukin 21 receptor genes, with RNA and protein sequence files, and both gene and product reports
                value:
                  gene_ids:
                  - 59067
                  - 50615
                  include_annotation_type:
                  - FASTA_RNA
                  - FASTA_PROTEIN
                  aux_report:
                  - DATASET_REPORT
                  - PRODUCT_REPORT
      parameters:
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /protein/accession/{accessions}/download:
    get:
      summary: Get a prokaryote gene data package by RefSeq protein accession
      description: 'Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.'
      tags:
        - Prokaryote
      operationId: download_prokaryote_gene_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 RefSeq non-redundant protein accessions (preceded by `WP_`)'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: WP_015878339.1
            summary: DNA-deoxyinosine glycosylase
          example-1:
            value: WP_001040085.1
            summary: type II CRISPR RNA-guided endonuclease Cas9
      - name: include_annotation_type
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
        examples:
          example-0:
            value: FASTA_GENE
            summary: Include gene sequence file, which includes gene sequences for all genomes on which the protein is annotated
          example-1:
            value:
              - FASTA_GENE
              - FASTA_PROTEIN
            summary: Include gene and protein sequence files
      - name: gene_flank_config.length
        in: query
        required: false
        schema:
          type: integer
      - name: taxon
        description: 'Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.'
        in: query
        required: false
        schema:
          type: string
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /protein/accession/download:
    post:
      summary: Get a prokaryote gene data package by RefSeq protein accession
      description: 'Download a prokaryote gene data package including sequence, annotation and data reports by RefSeq non-redundant protein accession.'
      tags:
        - Prokaryote
      operationId: download_prokaryote_gene_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/v2ProkaryoteGeneRequest'
            examples:
              Multiple Prokaryote (WP_) accessions example:
                description: DNA-deoxyinosine glycosylase (WP_015878339.1) and type II CRISPR RNA-guided endonuclease Cas9 (WP_001040085.1), with gene and protein sequence files
                value:
                  accessions:
                  - WP_015878339.1
                  - WP_001040085.1
                  include_annotation_type:
                  - FASTA_GENE
                  - FASTA_PROTEIN
      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
  /taxonomy/taxon/{tax_ids}/download:
    get:
      summary: Get a taxonomy data package by Taxonomy ID
      description: 'Download a taxonomy data package, including taxonomy and names reports, as a compressed zip archive.'
      tags:
        - Taxonomy
      operationId: download_taxonomy_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: tax_ids
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
              - 9606
              - 10090
            summary: NCBI Taxonomy IDs for human and mouse
      - name: aux_reports
        description: 'Specify additional report files to include in the data package. The taxonomy report is always included, and its inclusion is not affected by this parameter.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyDatasetRequestTaxonomyReportType'
        examples:
          example-0:
            value:
              - NAMES_REPORT
              - TAXONOMY_SUMMARY
            summary: Add the names report (JSON Lines format) and taxonomy summary (TSV) files.
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /taxonomy/download:
    post:
      summary: Get a taxonomy data package by Taxonomy ID
      description: 'Download a taxonomy data package, including taxonomy and names reports, as a compressed zip archive.'
      tags:
        - Taxonomy
      operationId: download_taxonomy_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/v2TaxonomyDatasetRequest'
            examples:
              Multiple TaxID examples:
                description: Taxonomy report, names report, and taxonomy summary table for human and mouse
                value:
                  tax_ids:
                  - 9606
                  - 10090
                  aux_reports:
                   - NAMES_REPORT
                   - TAXONOMY_SUMMARY
      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
  /organelle/accession/{accessions}/download:
    get:
      summary: Get an organelle data package by nucleotide accession
      description: 'Download an organelle data package including sequence, annotation, and detailed data reports as a compressed zip archive.'
      tags:
        - Organelle
      operationId: download_organelle_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: 'NCBI organelle assembly accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_001643.1
            summary: Chimpanzee mitochondrial genome
          example-1:
            value:
              - NC_001643.1
              - NC_002082.1
            summary: Chimpanzee and common Gibbon mitochondrial genomes
      - name: include_annotation_type
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2AnnotationForOrganelleType'
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /organelle/download:
    post:
      summary: Get an organelle data package
      description: 'Download an organelle data package including sequence, annotation, and detailed data reports as a compressed zip archive.'
      tags:
        - Organelle
      operationId: download_organelle_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/v2OrganelleDownloadRequest'
            examples:
              Single organelle accession example:
                description: Organelle accession (just one)
                value:
                  accessions:
                    - NC_001643.1
      parameters:
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /version:
    get:
      summary: Retrieve service version
      description: 'Retrieve the latest version of the Datasets services.'
      tags:
        - Version
      operationId: version
      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/v2VersionReply'
  /gene/id/{gene_ids}:
    get:
      deprecated: true
      summary: Get gene reports by GeneID
      description: 'Get a gene summary by GeneID. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
      tags:
        - Gene
      operationId: gene_reports_by_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: gene_ids
        description: 'One or more NCBI GeneIDs'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: Human IL21, interleukin 21
          example-1:
            value:
              - 59067
              - 50615
            summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor
      - name: locus_tags
        description: 'Gene locus tags'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: b0001
            summary: E. coli thrL, thr operon leader peptide
          example-1:
            value:
              - YER095W
              - YML032C
            summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - 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_size
        description: 'The maximum number of gene 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: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/accession/{accessions}:
    get:
      deprecated: true
      summary: Get gene metadata by RefSeq Accession
      description: 'Get a gene summary by RefSeq Accession. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
      tags:
        - Gene
      operationId: gene_metadata_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: accessions
        description: 'One or more RefSeq nucleotide or protein accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NM_021803.4
            summary: Human interleukin 21 mRNA
          example-1:
            value:
              - NP_068575.1
              - NP_851564.1
            summary: Human interleukin 21 and interleukin 21 receptor proteins
      - name: locus_tags
        description: 'Gene locus tags'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: b0001
            summary: E. coli thrL, thr operon leader peptide
          example-1:
            value:
              - YER095W
              - YML032C
            summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - 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_size
        description: 'The maximum number of gene 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: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/symbol/{symbols}/taxon/{taxon}:
    get:
      deprecated: true
      summary: Get gene metadata by gene symbol
      description: 'Get a gene summary by by gene symbol. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
      tags:
        - Gene
      operationId: gene_metadata_by_tax_and_symbol
      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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: symbols
        description: 'One or more gene symbols'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: GNAS
            summary: Human GNAS, GNAS complex locus
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: locus_tags
        description: 'Gene locus tags'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: b0001
            summary: E. coli thrL, thr operon leader peptide
          example-1:
            value:
              - YER095W
              - YML032C
            summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - 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_size
        description: 'The maximum number of gene 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: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/taxon/{taxon}:
    get:
      deprecated: true
      summary: Get gene reports by taxonomic identifier
      description: 'Get a gene summary for a specified NCBI Taxonomy ID or name (common or scientific). By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
      tags:
        - Gene
      operationId: gene_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: locus_tags
        description: 'Gene locus tags'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: b0001
            summary: E. coli thrL, thr operon leader peptide
          example-1:
            value:
              - YER095W
              - YML032C
            summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene:
    post:
      deprecated: true
      summary: Get gene metadata as JSON
      description: 'Get a gene summary. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)'
      tags:
        - Gene
      operationId: gene_metadata_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GeneDatasetReportsRequest'
            examples:
              Multiple GeneID examples:
                description: Human interleukin 21 and interleukin 21 receptor genes
                value:
                  gene_ids:
                  - 59067
                  - 50615
  /gene/id/{gene_ids}/dataset_report:
    get:
      summary: Get a gene data report by GeneID
      description: 'Get a gene data report by GeneID. 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:
        - Gene
      operationId: gene_dataset_reports_by_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: gene_ids
        description: 'One or more NCBI GeneIDs'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: Human IL21, interleukin 21
          example-1:
            value:
              - 59067
              - 50615
            summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/accession/{accessions}/dataset_report:
    get:
      summary: Get a gene data report by RefSeq nucleotide or protein accession
      description: 'Get a gene data report by RefSeq nucleotide or protein 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:
        - Gene
      operationId: gene_dataset_report_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: accessions
        description: 'One or more RefSeq nucleotide or protein accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NM_021803.4
            summary: Human interleukin 21 mRNA
          example-1:
            value:
              - NP_068575.1
              - NP_851564.1
            summary: Human interleukin 21 and interleukin 21 receptor proteins
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/symbol/{symbols}/taxon/{taxon}/dataset_report:
    get:
      summary: Get a gene data report by symbol and taxon
      description: 'Get a gene data report by gene symbol and 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:
        - Gene
      operationId: gene_dataset_report_by_tax_and_symbol
      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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: symbols
        description: 'One or more gene symbols'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: GNAS
            summary: Human GNAS, GNAS complex locus
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /gene/taxon/{taxon}/dataset_report:
    get:
      summary: Get a gene data report by taxon
      description: 'Get a gene data 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:
        - Gene
      operationId: gene_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /gene/locus_tag/{locus_tags}/dataset_report:
    get:
      summary: Get a gene data report by locus tag
      description: 'Get a gene data report by gene locus tag. 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:
        - Gene
      operationId: gene_dataset_reports_by_locus_tag
      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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: locus_tags
        description: 'Gene locus tags'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: b0001
            summary: E. coli thrL, thr operon leader peptide
          example-1:
            value:
              - YER095W
              - YML032C
            summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
  /gene/dataset_report:
    post:
      summary: Get a gene data report
      description: 'Get a gene data 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:
        - Gene
      operationId: gene_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GeneDatasetReportsRequest'
            examples:
              Multiple GeneID examples:
                description: Human interleukin 21 and interleukin 21 receptor genes
                value:
                  gene_ids:
                  - 59067
                  - 50615
  /gene/id/{gene_ids}/product_report:
    get:
      summary: Get a gene product report by GeneID
      description: 'Get a gene product report by GeneID. 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:
        - Gene
      operationId: gene_product_reports_by_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: gene_ids
        description: 'One or more NCBI GeneIDs'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: Human IL21, interleukin 21
          example-1:
            value:
              - 59067
              - 50615
            summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/accession/{accessions}/product_report:
    get:
      summary: Get a gene product report by RefSeq nucleotide or protein accession
      description: 'Get a gene product report by RefSeq nucleotide or protein 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:
        - Gene
      operationId: gene_product_report_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        description: 'One or more RefSeq nucleotide or protein accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NM_021803.4
            summary: Human interleukin 21 mRNA
          example-1:
            value:
              - NP_068575.1
              - NP_851564.1
            summary: Human interleukin 21 and interleukin 21 receptor proteins
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
  /gene/symbol/{symbols}/taxon/{taxon}/product_report:
    get:
      summary: Get a gene product report by symbol and taxon
      description: 'Get a gene product report by symbol and 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:
        - Gene
      operationId: gene_product_report_by_tax_and_symbol
      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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: symbols
        description: 'One or more gene symbols'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: GNAS
            summary: Human GNAS, GNAS complex locus
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /gene/taxon/{taxon}/product_report:
    get:
      summary: Get a gene product report by taxon
      description: 'Get a gene product 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:
        - Gene
      operationId: gene_product_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: tax_search_subtree
        description: 'If true, include genes from taxonomic ranks below the requested taxon.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /gene/locus_tag/{locus_tags}/product_report:
    get:
      summary: Get a gene product report by locus tag
      description: 'Get a gene product report by gene locus tag. 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:
        - Gene
      operationId: gene_product_reports_by_locus_tags
      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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: locus_tags
        description: 'Gene locus tags'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: b0001
            summary: E. coli thrL, thr operon leader peptide
          example-1:
            value:
              - YER095W
              - YML032C
            summary: Saccharomyces cerevisiae recombinases, RAD51 and RAD52
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [Create a table from the gene data reports](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/gene-data-reports/). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: summary
            summary: This template, valid for both gene report types, specifies a basic set of fields available from the report
          example-1:
            value: gene-ontology
            summary: This template, only valid for the gene data report, specifies fields that describe gene ontology information
      - 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_size
        description: 'The maximum number of gene 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: query
        description: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: Gene name or description
      - name: types
        description: 'Limit to genes matching the specified gene type.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Protein coding genes
          example-1:
            value: ncRNA
            summary: Non-coding RNA genes, including microRNAs, long non-coding RNAs and other types of non-coding RNA genes
          example-2:
            value: PSEUDO
            summary: Pseudogenes
      - name: accession_filter
        description: 'Filter tabular product report to only include the selected accessions. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_001407959.1
              - NM_001408458.1
            summary: Human BRCA1 transcripts, encoding isoforms 78 and 116, respectively
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
  /gene/product_report:
    post:
      summary: Get a gene product report
      description: 'Get a gene product 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:
        - Gene
      operationId: gene_product_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/v2reportsGeneDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsGeneDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GeneDatasetReportsRequest'
            examples:
              Multiple GeneID examples:
                description: Human interleukin 21 and interleukin 21 receptor genes
                value:
                  gene_ids:
                  - 59067
                  - 50615
  /gene/id/{gene_ids}/download_summary:
    get:
      summary: Get a download summary of a gene data package by GeneID
      description: 'Get a download summary of a gene data package, including counts and estimated package size, in JSON format.'
      tags:
        - Gene
      operationId: gene_download_summary_by_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/v2DownloadSummary'
      parameters:
      - name: gene_ids
        description: 'One or more NCBI GeneIDs'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: Human IL21, interleukin 21
          example-1:
            value:
              - 59067
              - 50615
            summary: Human IL21 and IL21R, interleukin 21 and interleukin 21 receptor
      - name: include_annotation_type
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
        examples:
          example-0:
            value:
              - FASTA_RNA
              - FASTA_PROTEIN
            summary: Include RNA and protein sequence files
          example-1:
            value:
              - FASTA_CDS
              - FASTA_5P_UTR
              - FASTA_3P_UTR
            summary: Include coding sequence, and 5' and 3' UTRs
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: fasta_filter
        description: 'Limit the FASTA sequences in the datasets package to these transcript and protein accessions (deprecated)'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: accession_filter
        description: 'Limit the contents of the sequence files and tabular product report to the specified RNA and protein accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NM_021803.4
            summary: Human IL21 MANE Select transcript
      - name: aux_report
        description: 'Specify additional report files to include in the data package. The gene 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/v2GeneDatasetRequestGeneDatasetReportType'
        examples:
          example-0:
            value: PRODUCT_REPORT
            summary: Add the gene product report
      - name: tabular_reports
        description: 'Specify which tabular report files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
        examples:
          example-0:
            value:
              - DATASET_REPORT
              - PRODUCT_REPORT
            summary: Include tabular gene and gene product reports
  /gene/download_summary:
    post:
      summary: Get a download summary of a gene data package
      description: 'Get a download summary of a gene data package, including counts and estimated package size, in JSON format.'
      tags:
        - Gene
      operationId: gene_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/v2GeneDatasetRequest'
            examples:
              Multiple GeneID examples:
                description: Human interleukin 21 and interleukin 21 receptor genes, with RNA and protein sequence files, and both gene and product reports
                value:
                  gene_ids:
                  - 59067
                  - 50615
                  include_annotation_type:
                  - FASTA_RNA
                  - FASTA_PROTEIN
                  aux_report:
                  - DATASET_REPORT
                  - PRODUCT_REPORT
  /gene/taxon/{taxon}/counts:
    get:
      summary: Get gene counts by taxon
      description: 'Get gene counts by taxon in JSON format.'
      tags:
        - Gene
      operationId: gene_counts_for_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/v2GeneCountsByTaxonReply'
      parameters:
      - name: taxon
        description: 'Taxon for provided gene symbol'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value: human
            summary: Common name
          example-2:
            value: Homo sapiens
            summary: Scientific name
  /gene/taxon/counts:
    post:
      summary: Get gene counts by taxon
      description: 'Get gene counts by taxon in JSON format.'
      tags:
        - Gene
      operationId: gene_counts_for_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/v2GeneCountsByTaxonReply'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GeneCountsByTaxonRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: "9606"
  /gene/id/{gene_id}/orthologs:
    get:
      summary: Get a gene data report for a gene ortholog set by GeneID
      description: 'Get a gene data report for a gene ortholog set by GeneID in JSON format.'
      tags:
        - Gene
      operationId: gene_orthologs_by_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/v2reportsGeneDataReportPage'
      parameters:
      - name: gene_id
        description: 'One or more NCBI GeneIDs'
        in: path
        required: true
        schema:
          type: integer
        examples:
          example-0:
            value: 2778
            summary: Human GNAS, GNAS complex locus
          example-1:
            value: 2
            summary: Human A2M, alpha-2-macroglobulin
      - name: returned_content
        description: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrthologRequestContentType'
        examples:
          example-0:
            value: IDS_ONLY
            summary: Return abbreviated report with GeneIDs
          example-1:
            value: COUNTS_ONLY
            summary: Return abbreviated report with GeneIDs, transcript and protein counts
      - name: taxon_filter
        description: 'Limit to genes from the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - "9606"
              - "10090"
            summary: NCBI Taxonomy IDs for human and mouse
          example-1:
            value: house mouse
            summary: Common name
          example-2:
            value: Homo sapiens
            summary: Scientific name
      - name: page_size
        description: 'The maximum number of gene 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
  /gene/orthologs:
    post:
      summary: Get a gene data report for a gene ortholog set by GeneID
      description: 'Get a gene data report for a gene ortholog set by GeneID in JSON format.'
      tags:
        - Gene
      operationId: gene_orthologs_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/v2reportsGeneDataReportPage'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2OrthologRequest'
            examples:
              Single GeneID example:
                description: Primate gene orthologs of the human gene, GNAS complex locus
                value:
                  gene_id: 2778
                  taxon_filter:
                   - primates
  /gene/id/{gene_ids}/links:
    get:
      summary: Get gene links by GeneID
      description: 'Get links to available gene resources in JSON format.'
      tags:
        - Gene
      operationId: gene_links_by_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/v2GeneLinksReply'
      parameters:
      - name: gene_ids
        description: 'One or more NCBI GeneIDs, limited to 100'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: Human IL21, interleukin 21
          example-1:
            value:
              - 59067
              - 50615
            summary: Human IL21 and ILR21R, interleukin 21 and interleukin 21 receptor
  /gene/links:
    post:
      summary: Get gene links by GeneID
      description: 'Get links to available gene resources in JSON format.'
      tags:
        - Gene
      operationId: gene_links_by_id_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/v2GeneLinksReply'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GeneLinksRequest'
            examples:
              Multiple GeneID examples:
                description: Human interleukin 21 and interleukin 21 receptor genes
                value:
                  gene_ids:
                  - 59067
                  - 50615
  /gene/taxon/{taxon}/annotation/{annotation_name}/chromosome_summary:
    get:
      summary: Get gene counts per chromosome by taxon and annotation name
      description: 'Get gene counts per chromosome by taxon and annotation name in JSON format.'
      tags:
        - Gene
      operationId: gene_chromosome_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/v2GeneChromosomeSummaryReply'
      parameters:
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank, with an anntoated genome'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9117"
            summary: NCBI Taxonomy ID for Grus americana
          example-1:
            value: Whooping crane
            summary: Common Name
          example-2:
            value: Grus americana
            summary: Scientific Name
      - name: annotation_name
        description: 'Annotation name corresponding to the provided taxon'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: GCF_028858705.1-RS_2023_03
            summary: NCBI Grus americana Annotation Release GCF_028858705.1-RS_2023_03
  /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"
  /organelle/accessions/{accessions}/dataset_report:
    get:
      summary: Get an organelle data report by nucleotide accession
      description: 'Get an organelle data report in JSON format.'
      tags:
        - Organelle
      operationId: organelle_datareport_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/v2reportsOrganelleDataReports'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsOrganelleDataReports'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        description: 'One or more organelle nucleotide accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_001643.1
            summary: Chimpanzee mitochondrial genome
          example-1:
            value:
              - NC_001643.1
              - NC_002082.1
            summary: Chimpanzee and common gibbon mitochondrial genomes
      - name: organelle_types
        description: 'Limit results to the specified organelle types.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsOrganelleType'
      - name: first_release_date
        description: 'Limit results to organelle genomes released on or after the specified date.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2015-01-10"
            summary: Jan 10, 2015, in ISO 8601 YYYY-MM-DD format
      - name: last_release_date
        description: 'Limit results to organelle genomes released on or before the specified date.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2021-01-10"
            summary: Jan 10, 2021, in ISO 8601 YYYY-MM-DD format
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
      - name: returned_content
        description: 'Return complete organelle reports or nucleotide accessions only.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganelleMetadataRequestContentType'
        examples:
          example-0:
            value: ASSM_ACC
            summary: Return nucleotide accessions only
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganelleMetadataRequestOrganelleTableFormat'
        examples:
          example-0:
            value: SUMMARY
            summary: This template specifies a basic set of fields available from the organelle report
      - 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'
  /organelle/taxon/{taxons}/dataset_report:
    get:
      summary: Get an organelle data report by taxon
      description: 'Get an organelle data report  in JSON format.'
      tags:
        - Organelle
      operationId: organelle_datareport_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/v2reportsOrganelleDataReports'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsOrganelleDataReports'
            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: "9443"
            summary: Primate organelle genomes
          example-1:
            value:
              - "9606"
              - "10090"
            summary: Human and mouse organelle genomes
      - name: organelle_types
        description: 'Limit results to the specified organelle types.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsOrganelleType'
      - name: first_release_date
        description: 'Limit results to organelle genomes released on or after the specified date.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2015-01-10"
            summary: Jan 10, 2015, in ISO 8601 YYYY-MM-DD format
      - name: last_release_date
        description: 'Limit results to organelle genomes released on or before the specified date.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2021-01-10"
            summary: Jan 10, 2021, in ISO 8601 YYYY-MM-DD format
      - name: tax_exact_match
        description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
      - name: returned_content
        description: 'Return complete organelle reports or nucleotide accessions only.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganelleMetadataRequestContentType'
        examples:
          example-0:
            value: ASSM_ACC
            summary: Return nucleotide accessions only
      - name: page_size
        description: 'The maximum number of organelle assemblies 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
      - name: page_token
        description: 'A page token is returned from an `OrganelleMetadata` call with more than `page_size` results. Use this token, along with the previous `OrganelleMetadata` 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: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganelleMetadataRequestOrganelleTableFormat'
        examples:
          example-0:
            value: SUMMARY
            summary: This template specifies a basic set of fields available from the organelle report
      - 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'
  /organelle/dataset_report:
    post:
      summary: Get an organelle data report
      description: 'Get an organelle data report in JSON format.'
      tags:
        - Organelle
      operationId: organelle_datareport_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/v2reportsOrganelleDataReports'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsOrganelleDataReports'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2OrganelleMetadataRequest'
            examples:
              Single TaxID example:
                description: Primate organelle genomes
                value:
                  taxons:
                    - "9443"
  /taxonomy/taxon/{taxons}:
    get:
      deprecated: true
      summary: Use taxonomic identifiers to get taxonomic metadata
      description: 'Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_metadata
      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/v2TaxonomyMetadataResponse'
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
              - human
              - house mouse
            summary: Common names
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific names
      - name: returned_content
        description: 'Return complete taxonomy reports, Taxonomy IDs only, or reports without assembly and gene counts (metadata).'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
        examples:
          example-0:
            value: TAXIDS
            summary: Return Taxonomy IDs only
          example-1:
            value: METADATA
            summary: Return abbreviated taxonomy report without genome assembly and gene counts
      - name: page_size
        description: 'The maximum number of taxons 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: 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
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
        examples:
          example-0:
            value: SUMMARY
            summary: This template specifies a basic set of fields available from the taxonomy report
      - name: children
        description: 'If true, return results for child taxa.'
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: 'Limit results to taxa of the specified ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy:
    post:
      deprecated: true
      summary: Get taxonomy metadata by taxon
      description: 'Get taxonomy metadata by taxon in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_metadata_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/v2TaxonomyMetadataResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            examples:
              Multiple TaxID and common name examples:
                description: NCBI Taxonomy ID for human and common name for Mus musculus
                value:
                  taxons:
                  - "9606"
                  - house mouse
  /taxonomy/taxon/{taxons}/dataset_report:
    get:
      summary: Get a taxonomy data report by taxon
      description: 'Get a taxonomy data 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:
        - Taxonomy
      operationId: taxonomy_data_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/v2reportsTaxonomyDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
              - human
              - house mouse
            summary: Common names
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific names
      - name: returned_content
        description: 'Return complete taxonomy reports, Taxonomy IDs only, or reports without assembly and gene counts (metadata).'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
        examples:
          example-0:
            value: TAXIDS
            summary: Return Taxonomy IDs only
          example-1:
            value: METADATA
            summary: Return abbreviated taxonomy report without genome assembly and gene counts
      - name: page_size
        description: 'The maximum number of taxons 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: 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
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
        examples:
          example-0:
            value: SUMMARY
            summary: This template specifies a basic set of fields available from the taxonomy report
      - name: children
        description: 'If true, return results for child taxa.'
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: 'Limit results to taxa of the specified ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy/dataset_report:
    post:
      summary: Get a taxonomy data report by taxon
      description: 'Get a taxonomy data 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:
        - Taxonomy
      operationId: taxonomy_data_report_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/v2reportsTaxonomyDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            examples:
              Multiple TaxID and common name examples:
                description: NCBI Taxonomy ID for human and common name for Mus musculus
                value:
                  taxons:
                  - "9606"
                  - house mouse
  /taxonomy/taxon/{taxons}/name_report:
    get:
      summary: Get a taxonomy names report by taxon
      description: 'Get a taxonomy names report, including common names and other synonyms, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_names
      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/v2reportsTaxonomyNamesDataReportPage'
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
              - human
              - house mouse
            summary: Common names
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific names
      - name: page_size
        description: 'The maximum number of taxons 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: children
        description: 'If true, return results for child taxa.'
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: 'Limit results to taxa of the specified ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy/name_report:
    post:
      summary: Get a taxonomy names report by taxon
      description: 'Get a taxonomy names report, including common names and other synonyms, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_names_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/v2reportsTaxonomyNamesDataReportPage'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            examples:
              Multiple TaxID and common name examples:
                description: NCBI Taxonomy ID for human and common name for Mus musculus
                value:
                  taxons:
                  - "9606"
                  - house mouse
  /taxonomy/taxon/{tax_id}/related_ids:
    get:
      summary: Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
      description: 'Get child nodes, and optionally parent nodes, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_related_ids
      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/v2TaxonomyTaxIdsPage'
      parameters:
      - name: tax_id
        in: path
        required: true
        schema:
          type: integer
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
      - name: include_lineage
        description: 'If true, include parent nodes'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: ranks
        description: 'Limit to taxonomic nodes from the given ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
      - name: page_size
        description: 'The maximum number of taxids 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
  /taxonomy/related_ids:
    post:
      summary: Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
      description: 'Get child nodes, and optionally parent nodes, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_related_ids_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/v2TaxonomyTaxIdsPage'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyRelatedIdRequest'
            examples:
              Single TaxID example:
                description: Child and parent nodes for human
                value:
                  tax_id: 9606
                  include_lineage: true
  /taxonomy/taxon/{taxons}/filtered_subtree:
    get:
      summary: Get a filtered taxonomic subtree by taxon
      description: 'Get a filtered taxonomic subtree, including parent and child nodes, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_filtered_subtree
      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/v2TaxonomyFilteredSubtreeResponse'
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
              - human
              - mouse
            summary: Common Name
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific Name
      - name: specified_limit
        description: 'Limit to specified species'
        in: query
        required: false
        schema:
          type: boolean
      - name: exclude_extinct
        description: 'Limit to species that are not extinct'
        in: query
        required: false
        schema:
          type: boolean
      - name: levels
        description: 'Number of taxonomic levels to return with a valid range of 1-5. Values above 5 will return 5 levels and if level is 0 or not specified, 1 level will be returned.'
        in: query
        required: false
        schema:
          type: integer
      - name: rank_limits
        description: 'Limit to the provided ranks.  If empty, accept any rank.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
      - name: include_incertae_sedis
        description: 'Include nodes with ranks not in ''rank_limits'' if their names meet criteria for incertae sedis (of unknown origin).'
        in: query
        required: false
        schema:
          type: boolean
  /taxonomy/filtered_subtree:
    post:
      summary: Get a filtered taxonomic subtree by taxon
      description: 'Get a filtered taxonomic subtree, including parent and child nodes, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_filtered_subtree_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/v2TaxonomyFilteredSubtreeResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeRequest'
            examples:
              Multiple TaxID example:
                description: NCBI Taxonomy IDs for human and mouse
                value:
                  taxons:
                  - "9606"
                  - "10090"
  /taxonomy/taxon_suggest/{taxon_query}:
    get:
      summary: Get a list of taxonomy names and IDs by partial taxonomic name
      description: 'Get a list of taxonomy names and IDs in JSON format.'
      tags:
        - Taxonomy
      operationId: tax_name_query
      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/v2SciNameAndIds'
      parameters:
      - name: taxon_query
        description: 'Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: hum
            summary: Partial taxonomic name for human
      - name: tax_rank_filter
        description: 'Optionally return results for taxonomic ranks above species using `higher_taxon`'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxRankFilter'
          default: species
      - name: taxon_resource_filter
        description: 'Limit to taxonomy nodes with gene, genome or organelle data'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxonResourceFilter'
          default: TAXON_RESOURCE_FILTER_ALL
        examples:
          example-0:
            value: TAXON_RESOURCE_FILTER_GENOME
            summary: Limit to nodes with genome data
          example-1:
            value: TAXON_RESOURCE_FILTER_GENE
            summary: Limit to nodes with gene data
      - name: exact_match
        description: 'If true, only return results that exactly match the provided taxonomic name'
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /taxonomy/taxon_suggest:
    post:
      summary: Get a list of taxonomy names and IDs by partial taxonomic name
      description: 'Get a list of taxonomy names and IDs in JSON format.'
      tags:
        - Taxonomy
      operationId: tax_name_query_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/v2SciNameAndIds'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2OrganismQueryRequest'
            examples:
              Incomplete taxon name example:
                description: Partial taxonomic name for human
                value:
                  taxon_query: "hum"
  /taxonomy/taxon/{taxon}/links:
    get:
      summary: Get external links by Taxonomy ID
      description: 'Get external links associated with a given taxon in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_links
      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/v2TaxonomyLinksResponse'
      parameters:
      - name: taxon
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
  /taxonomy/links:
    post:
      summary: Get external links by Taxonomy ID
      description: 'Get external links associated with a given taxon in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_links_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/v2TaxonomyLinksResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyLinksRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: "9606"
  /taxonomy/taxon/{taxon}/image:
    get:
      summary: Get a taxonomy image by taxon
      description: 'Get an image associated with the specified taxon. By default, in JPEG format, but also available in PNG (accept: image/png), TIFF (accept: accept: image/tiff), and SVG+XML (accept: image/svg+xml) formats.'
      tags:
        - Taxonomy
      operationId: taxonomy_image
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            image/jpeg:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/png:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/gif:
              schema:
                $ref: '#/components/schemas/v2HttpBody'
            image/tiff:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/svg+xml:
              schema:
                format: binary
                type: string
                description: SVG Image stream
      parameters:
      - name: taxon
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
      - name: image_size
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2ImageSize'
  /taxonomy/image:
    post:
      summary: Get a taxonomy image by taxon
      description: 'Get an image associated with the specified taxon. By default, in JPEG format, but also available in PNG (accept: image/png), TIFF (accept: accept: image/tiff), and SVG+XML (accept: image/svg+xml) formats.'
      tags:
        - Taxonomy
      operationId: taxonomy_image_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            image/jpeg:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/png:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/tiff:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/svg+xml:
              schema:
                format: binary
                type: string
                description: SVG Image stream
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyImageRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: "9606"
  /taxonomy/taxon/{taxon}/image/metadata:
    get:
      summary: Get taxonomy image metadata by Taxonomy ID
      description: 'Get taxonomy image metadata, including the image URL and license information, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_image_metadata
      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/v2TaxonomyImageMetadataResponse'
      parameters:
      - name: taxon
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "9606"
            summary: NCBI Taxonomy ID for human
  /taxonomy/image/metadata:
    post:
      summary: Get taxonomy image metadata by Taxonomy ID
      description: 'Get taxonomy image metadata, including the image URL and license information, in JSON format.'
      tags:
        - Taxonomy
      operationId: taxonomy_image_metadata_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/v2TaxonomyImageMetadataResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyImageMetadataRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: "9606"
  /virus/taxon/{taxon}/genome:
    get:
      summary: Get a download summary of a virus genome data package by taxon
      description: 'Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.'
      tags:
        - Virus
      operationId: virus_genome_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 nucleotide sequence accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_038294.1
            summary: Betacoronavirus England 1 isolate H123990006, complete genome
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "1335626"
            summary: NCBI Taxonomy ID for MERS, Middle East respiratory syndrome-related coronavirus
          example-1:
            value: "2697049"
            summary: NCBI Taxonomy ID for SARS-CoV-2
          example-2:
            value: "197911"
            summary: NCBI Taxonomy ID for the genus Alphainfluenzavirus
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: Inclue all genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specified geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: include_sequence
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Include genomic, CDS, and protein sequence files
      - name: aux_report
        description: 'Specify which report files to include in the data package. The virus 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/v2VirusDatasetReportType'
        examples:
          example-0:
            value: BIOSAMPLE
            summary: Include the BioSample report
  /virus/genome:
    post:
      summary: Get a download summary of a virus genome data package
      description: 'Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.'
      tags:
        - Virus
      operationId: virus_genome_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/v2VirusDatasetRequest'
            examples:
              Single Virus accession example:
                description: Betacoronavirus England 1 isolate H123990006, complete genome
                value:
                  accessions:
                    - NC_038294.1
  /virus/taxon/sars2/protein/{proteins}:
    get:
      summary: Get a download summary of a SARS-CoV-2 protein data package by protein name
      description: 'Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.'
      tags:
        - Virus
      operationId: sars2_protein_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: proteins
        description: 'One or more SARS-CoV-2 protein names'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: spike protein
            summary: SARS-CoV-2 spike protein
          example-1:
            value:
              - spike protein
              - envelope protein
              - RdRp
            summary: SARS-CoV-2 spike, envelope, and RNA-dependent RNA polymerase proteins
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Both GenBank & RefSeq genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: All genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes with the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specififed geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: include_sequence
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - CDS
              - PROTEIN
            summary: Include CDS and proetin sequence files
      - name: aux_report
        description: 'Specify which report files to include in the data package. The virus 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/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Include the annotation report
  /virus/taxon/sars2/protein:
    post:
      summary: Get a download summary of a SARS-CoV-2 protein data package by protein name
      description: 'Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.'
      tags:
        - Virus
      operationId: sars2_protein_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/v2Sars2ProteinDatasetRequest'
            examples:
              SARS-CoV-2 virus RefSeq protein example:
                description: SARS-CoV-2 spike surface glycoprotein (RefSeq)
                value:
                  proteins:
                   - spike
                  refseq_only: true
                  include_sequence:
                   - PROTEIN
  /virus/taxon/{taxon}/genome/table:
    get:
      deprecated: true
      summary: Get virus genome metadata in a tabular format
      description: 'Get virus genome metadata in tabular format for virus genomes by taxon.'
      tags:
        - Virus
      operationId: virus_genome_table
      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/v2TabularOutput'
      parameters:
      - name: accessions
        description: 'One or more nucleotide sequence accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_038294.1
            summary: Betacoronavirus England 1 isolate H123990006, complete genome
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "1335626"
            summary: NCBI Taxonomy ID for MERS, Middle East respiratory syndrome-related coronavirus
          example-1:
            value: "2697049"
            summary: NCBI Taxonomy ID for SARS-CoV-2
          example-2:
            value: "197911"
            summary: NCBI Taxonomy ID for the genus Alphainfluenzavirus
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: Inclue all genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specified geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: table_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusTableField'
        examples:
          example-0:
            value:
              - protein_accession
              - protein_name
            summary: SARS-CoV-2 protein accession and name
      - name: include_sequence
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Include genomic, CDS, and protein sequence files
      - name: aux_report
        description: 'Specify which report files to include in the data package. The virus 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/v2VirusDatasetReportType'
        examples:
          example-0:
            value: BIOSAMPLE
            summary: Include the BioSample report
      - name: format
        description: 'Choose download format (tsv, csv or jsonl)'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TableFormat'
          default: tsv
        examples:
          example-0:
            value: tsv
            summary: TSV
          example-1:
            value: csv
            summary: CSV
          example-2:
            value: jsonl
            summary: JSON Lines
  /virus/taxon/sars2/protein/{proteins}/table:
    get:
      summary: Get SARS-CoV-2 protein metadata in a tabular format by protein name
      description: 'Get SARS-CoV-2 protein metadata in a tabular format by protein name.'
      tags:
        - Virus
      operationId: sars2_protein_table
      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/v2TabularOutput'
      parameters:
      - name: proteins
        description: 'One or more SARS-CoV-2 protein names'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: spike protein
            summary: SARS-CoV-2 spike protein
          example-1:
            value:
              - spike protein
              - envelope protein
              - RdRp
            summary: SARS-CoV-2 spike, envelope, and RNA-dependent RNA polymerase proteins
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Both GenBank & RefSeq genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: All genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes with the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specififed geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: table_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusTableField'
        examples:
          example-0:
            value:
              - protein_accession
              - protein_name
            summary: Protein accession and name
      - name: format
        description: 'Specify output format'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TableFormat'
          default: tsv
        examples:
          example-0:
            value: tsv
            summary: TSV, tabular format
          example-1:
            value: jsonl
            summary: JSON Lines format
  /virus/taxon/{taxon}/dataset_report:
    get:
      summary: Get a virus data report by taxon
      description: 'Get a virus data 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:
        - Virus
      operationId: virus_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/v2reportsVirusDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsVirusDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "1335626"
            summary: NCBI Taxonomy ID for MERS, Middle East respiratory syndrome-related coronavirus
          example-1:
            value: "2697049"
            summary: NCBI Taxonomy ID for SARS-CoV-2
          example-2:
            value: "197911"
            summary: NCBI Taxonomy ID for the genus Alphainfluenzavirus
      - name: filter.refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: filter.annotated_only
        description: 'If true, limit results to annotated genomes.'
        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: filter.released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: filter.pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: filter.geo_location
        description: 'Limit to genomes collected from the specified geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: filter.usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: returned_content
        description: 'Return complete virus reports or nucleotide accessions only'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2VirusDataReportRequestContentType'
      - name: table_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - accession
              - is-complete
              - is-annotated
            summary: Virus Data Report Fields
      - name: page_size
        description: 'The maximum number of virus data 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
  /virus/accession/{accessions}/dataset_report:
    get:
      summary: Get a virus data report by nucleotide accession
      description: 'Get a virus data report by nucleotide 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:
        - Virus
      operationId: virus_reports_by_acessions
      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/v2reportsVirusDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsVirusDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        description: 'One or more nucleotide sequence accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_038294.1
            summary: Betacoronavirus England 1 isolate H123990006, complete genome
      - name: filter.refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: filter.annotated_only
        description: 'If true, limit results to annotated genomes.'
        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: filter.released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: filter.pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: filter.geo_location
        description: 'Limit to genomes collected from the specified geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: filter.usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: returned_content
        description: 'Return complete virus reports or nucleotide accessions only'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2VirusDataReportRequestContentType'
      - name: table_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - accession
              - is-complete
              - is-annotated
            summary: Virus Data Report Fields
      - name: page_size
        description: 'The maximum number of virus data 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
  /virus:
    post:
      summary: Get a virus data report
      description: 'Get a virus data 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:
        - Virus
      operationId: virus_reports_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/v2reportsVirusDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsVirusDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2VirusDataReportRequest'
            examples:
              RefSeq Virus TaxID example:
                description: Middle East repiratory syndrome-related coronavirus, RefSeq genomes
                value:
                  filter: 
                   taxons:
                   - "1335626"
                   refseq_only: true
  /virus/taxon/{taxon}/annotation_report:
    get:
      summary: Get a virus annotation report by taxon
      description: 'Get virus annotation 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:
        - Virus
      operationId: virus_annotation_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/v2reportsVirusAnnotationReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsVirusAnnotationReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "1335626"
            summary: MERS
          example-1:
            value: "2697049"
            summary: SARS-COV-2
          example-2:
            value: "11118"
            summary: Coronaviridae
      - name: filter.refseq_only
        description: 'If true, limit to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: filter.annotated_only
        description: 'If true, limit to annotated genomes.'
        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: filter.released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: filter.pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: filter.geo_location
        description: 'Limit to genomes collected from the specififed geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: filter.usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - accession
              - gene-cds-name
              - gene-cds-nuc-fasta-range-start
              - gene-cds-nuc-fasta-range-stop
            summary: Virus genome nucleotide accession, gene CDS name, and annotated location
      - name: page_size
        description: 'The maximum number of virus data 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
  /virus/accession/{accessions}/annotation_report:
    get:
      summary: Get a virus annotation report by nucleotide accession
      description: 'Get a virus annotation report by nucleotide accesion. 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:
        - Virus
      operationId: virus_annotation_reports_by_acessions
      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/v2reportsVirusAnnotationReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsVirusAnnotationReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        description: 'One or more nucleotide sequence accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_038294.1
            summary: Betacoronavirus England 1 isolate H123990006, complete genome
      - name: filter.refseq_only
        description: 'If true, limit to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: filter.annotated_only
        description: 'If true, limit to annotated genomes.'
        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: filter.released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: filter.host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: filter.pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: filter.geo_location
        description: 'Limit to genomes collected from the specififed geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: filter.usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: table_fields
        description: 'Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - accession
              - gene-cds-name
              - gene-cds-nuc-fasta-range-start
              - gene-cds-nuc-fasta-range-stop
            summary: Virus genome nucleotide accession, gene CDS name, and annotated location
      - name: page_size
        description: 'The maximum number of virus data 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
  /virus/annotation_report:
    post:
      summary: Get a virus annotation report
      description: 'Get a virus annotation 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:
        - Virus
      operationId: virus_annotation_reports_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/v2reportsVirusAnnotationReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsVirusAnnotationReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2VirusAnnotationReportRequest'
            examples:
              RefSeq Virus TaxID example:
                description: Middle East repiratory syndrome-related coronavirus, RefSeq genomes
                value:
                  filter: 
                   taxons:
                   - "1335626"
                   refseq_only: true
  /virus/accession/{accessions}/check:
    get:
      summary: Check the validity of a virus genome nucleotide accession
      description: 'Check the validity of a virus genome nucleotide accession. Output in JSON format.'
      tags:
        - Virus
      operationId: virus_accession_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/v2VirusAvailability'
      parameters:
      - name: accessions
        description: 'virus accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_038294.1
            summary: Betacoronavirus England 1 isolate H123990006, complete genome
  /virus/check:
    post:
      summary: Check the validity of a virus genome nucleotide accession
      description: 'Check the validity of a virus genome nucleotide accession. Output in JSON format.'
      tags:
        - Virus
      operationId: virus_accession_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/v2VirusAvailability'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2VirusAvailabilityRequest'
            examples:
              Single Virus accession example:
                description: Betacoronavirus England 1 isolate H123990006, complete genome
                value:
                  accessions:
                    - NC_038294.1
  /virus/taxon/{taxon}/genome/download:
    get:
      summary: Get a virus genome data package by taxon
      description: 'Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.'
      tags:
        - Virus
      operationId: virus_genome_download
      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: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: "1335626"
            summary: NCBI Taxonomy ID for MERS, Middle East respiratory syndrome-related coronavirus
          example-1:
            value: "2697049"
            summary: NCBI Taxonomy ID for SARS-CoV-2
          example-2:
            value: "197911"
            summary: NCBI Taxonomy ID for the genus Alphainfluenzavirus
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: Inclue all genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specified geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: include_sequence
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Include genomic, CDS, and protein sequence files
      - name: aux_report
        description: 'Specify which report files to include in the data package. The virus 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/v2VirusDatasetReportType'
        examples:
          example-0:
            value: BIOSAMPLE
            summary: Include the BioSample report
      - name: use_psg
        description: 'Experimental approach to retrieving sequence data.'
        in: query
        required: false
        schema:
          type: boolean
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /virus/accession/{accessions}/genome/download:
    get:
      summary: Get a virus genome data package by nucleotide accession
      description: 'Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.'
      tags:
        - Virus
      operationId: virus_genome_download_accession
      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 nucleotide sequence accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_038294.1
            summary: Betacoronavirus England 1 isolate H123990006, complete genome
      - name: taxons
        description: 'NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: "1335626"
            summary: MERS
          example-1:
            value: "2697049"
            summary: SARS-COV-2
          example-2:
            value: "11118"
            summary: Coronaviridae
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Include both RefSeq and GenBank genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: Inclue all genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specified geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: include_sequence
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Include genomic, CDS, and protein sequence files
      - name: aux_report
        description: 'Specify which report files to include in the data package. The virus 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/v2VirusDatasetReportType'
        examples:
          example-0:
            value: BIOSAMPLE
            summary: Include the BioSample report
      - name: use_psg
        description: 'Experimental approach to retrieving sequence data.'
        in: query
        required: false
        schema:
          type: boolean
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /virus/genome/download:
    post:
      summary: Get a virus genome data package
      description: 'Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.'
      tags:
        - Virus
      operationId: virus_genome_download_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/v2VirusDatasetRequest'
            examples:
              Single Virus accession example:
                description: Betacoronavirus England 1 isolate H123990006, complete genome
                value:
                  accessions:
                    - NC_038294.1
      parameters:
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /virus/taxon/sars2/protein/{proteins}/download:
    get:
      summary: Get a SARS-CoV-2 protein data package by protein name
      description: 'Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report by protein name.'
      tags:
        - Virus
      operationId: sars2_protein_download
      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: proteins
        description: 'One or more SARS-CoV-2 protein names'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: spike protein
            summary: SARS-CoV-2 spike protein
          example-1:
            value:
              - spike protein
              - envelope protein
              - RdRp
            summary: SARS-CoV-2 spike, envelope, and RNA-dependent RNA polymerase proteins
      - name: refseq_only
        description: 'If true, limit results to RefSeq genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to RefSeq genomes
          example-1:
            value: false
            summary: Both GenBank & RefSeq genomes
      - name: annotated_only
        description: 'If true, limit results to annotated genomes.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated genomes
          example-1:
            value: false
            summary: All genomes
      - name: released_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: "2025-01-15"
            summary: January 15th, 2025, in ISO 8601 YYYY-MM-DD format
      - name: host
        description: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value: Felis catus
            summary: Scientific name for domestic cat
      - name: pangolin_classification
        description: 'Limit to SARS-CoV-2 genomes with the specified Pango lineage.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: LP.8.1
            summary: SARS-CoV-2 Pango lineage LP.8.1
      - name: geo_location
        description: 'Limit to genomes collected from the specififed geographic location.'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: Asia
            summary: Asia
      - name: usa_state
        description: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: CA
            summary: California
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'Limit to genomes designated as complete, as defined by the submitter.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to complete genomes
          example-1:
            value: false
            summary: All genomes
      - name: include_sequence
        description: 'Specify which sequence files to include in the data package.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - CDS
              - PROTEIN
            summary: Include CDS and proetin sequence files
      - name: aux_report
        description: 'Specify which report files to include in the data package. The virus 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/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Include the annotation report
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /virus/taxon/sars2/protein/download:
    post:
      summary: Get a SARS-CoV-2 protein data package
      description: 'Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.'
      tags:
        - Virus
      operationId: sars2_protein_download_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/v2Sars2ProteinDatasetRequest'
            examples:
              SARS-CoV-2 virus RefSeq protein example:
                description: SARS-CoV-2 spike surface glycoprotein (RefSeq)
                value:
                  proteins:
                   - spike
                  refseq_only: true
                  include_sequence:
                   - PROTEIN
      parameters:
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /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:
  securitySchemes:
    ApiKeyAuth:
      type: apiKey
      in: query
      name: api_key
    ApiKeyAuthHeader:
      type: apiKey
      in: header
      name: api-key
  schemas:
    v2Accessions:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
    v2AssemblyAccessions:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
    v2AssemblyCheckMHistogramReply:
      type: object
      properties:
        species_taxid:
          type: integer
        histogram_intervals:
          type: array
          items:
            $ref: '#/components/schemas/v2AssemblyCheckMHistogramReplyHistogramInterval'
    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'
    v2AssemblyCheckMHistogramRequest:
      type: object
      properties:
        species_taxon:
          type: string
          title: 'Bacterial species taxonomy ID or taxonomic name'
    v2AssemblyDataReportDraftRequest:
      type: object
      properties:
        accession:
          type: string
    v2AssemblyDatasetAvailability:
      type: object
      properties:
        valid_assemblies:
          type: array
          items:
            type: string
        invalid_assemblies:
          type: array
          items:
            type: string
        reason:
          type: string
    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.'
    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'
    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.'
    v2AssemblyLinksReply:
      type: object
      properties:
        assembly_links:
          type: array
          items:
            $ref: '#/components/schemas/v2AssemblyLinksReplyAssemblyLink'
    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
    v2AssemblyLinksRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        assembly_link_types:
          type: array
          items:
            $ref: '#/components/schemas/v2AssemblyLinksReplyAssemblyLinkType'
    v2AssemblyRevisionHistory:
      type: object
      properties:
        assembly_revisions:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAssemblyRevision'
        total_count:
          type: integer
    v2AssemblyRevisionHistoryRequest:
      type: object
      properties:
        accession:
          type: string
          title: 'One genome assembly accession'
    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'
    v2BioSampleDatasetReportsRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
    v2BiocollectionsSortField:
      type: object
      properties:
        field:
          type: string
        direction:
          $ref: '#/components/schemas/v2SortDirection'
    v2DatasetRequest:
      type: object
      properties:
        genome_v2:
          $ref: '#/components/schemas/v2AssemblyDatasetRequest'
        gene_v2:
          $ref: '#/components/schemas/v2GeneDatasetRequest'
        virus_v2:
          $ref: '#/components/schemas/v2VirusDatasetRequest'
    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'
    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'
    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
    v2DownloadSummaryFileSummary:
      type: object
      properties:
        file_count:
          type: integer
        size_mb:
          type: number
          format: float
    v2DownloadSummaryHydrated:
      type: object
      properties:
        estimated_file_size_mb:
          type: integer
        url:
          type: string
        cli_download_command_line:
          type: string
    v2ElementFlankConfig:
      type: object
      properties:
        length:
          type: integer
    v2GeneChromosomeSummaryReply:
      type: object
      properties:
        gene_chromosome_summaries:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneChromosomeSummaryReplyGeneChromosomeSummary'
    v2GeneChromosomeSummaryReplyGeneChromosomeSummary:
      type: object
      properties:
        name:
          type: string
        count:
          type: integer
        accession:
          type: string
    v2GeneChromosomeSummaryRequest:
      type: object
      properties:
        taxon:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank, with an anntoated genome'
        annotation_name:
          type: string
          title: 'Annotation name corresponding to the provided taxon'
    v2GeneCountsByTaxonReply:
      type: object
      properties:
        report:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneCountsByTaxonReplyGeneTypeAndCount'
    v2GeneCountsByTaxonReplyGeneTypeAndCount:
      type: object
      properties:
        gene_type:
          type: string
        count:
          type: integer
    v2GeneCountsByTaxonRequest:
      type: object
      properties:
        taxon:
          type: string
          title: 'Taxon for provided gene symbol'
    v2GeneDatasetReportsRequest:
      type: object
      properties:
        returned_content:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
          title: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        gene_ids:
          type: array
          items:
            type: integer
        accessions:
          type: array
          items:
            type: string
        symbols_for_taxon:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestSymbolsForTaxon'
        taxon:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at'
        locus_tags:
          type: array
          items:
            type: string
        table_fields:
          type: array
          items:
            type: string
        table_format:
          type: string
          title: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        include_tabular_header:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
          title: 'Specify when to include the table header when requesting a tabular report.'
        page_size:
          type: integer
          title: 'The maximum number of gene 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.'
        query:
          type: string
          title: 'Limit to genes that match the specified gene symbol, name (description), alias, locus tag or protein name.'
        types:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        accession_filter:
          type: array
          items:
            type: string
        tax_search_subtree:
          type: boolean
          title: 'If true, include genes from taxonomic ranks below the requested taxon.'
        sort:
          type: array
          items:
            $ref: '#/components/schemas/v2SortField'
    v2GeneDatasetReportsRequestSymbolsForTaxon:
      type: object
      properties:
        symbols:
          type: array
          items:
            type: string
        taxon:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific, any taxonomic rank) for the provided gene symbol'
    v2GeneDatasetRequest:
      type: object
      properties:
        gene_ids:
          type: array
          items:
            type: integer
        include_annotation_type:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
        returned_content:
          $ref: '#/components/schemas/v2GeneDatasetRequestContentType'
          title: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        fasta_filter:
          type: array
          items:
            type: string
        accession_filter:
          type: array
          items:
            type: string
        aux_report:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
        tabular_reports:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
        table_fields:
          type: array
          items:
            type: string
        table_report_type:
          $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
          title: 'Specify the report from which the table fields will be taken. This is currently deprecated - use tabular_reports instead.'
    v2GeneLinksReply:
      type: object
      properties:
        gene_links:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneLinksReplyGeneLink'
    v2GeneLinksReplyGeneLink:
      type: object
      properties:
        gene_id:
          type: integer
          title: 'The matching gene id'
        gene_link_type:
          $ref: '#/components/schemas/v2GeneLinksReplyGeneLinkType'
          title: 'The type of link, e.g. gdv link or ortholog set'
        resource_link:
          type: string
          title: 'A link to a gene resource'
        resource_id:
          type: string
          title: 'A resource ID, provided if gene-id is not used for the link, e.g. the ortholog id.'
    v2GeneLinksRequest:
      type: object
      properties:
        gene_ids:
          type: array
          items:
            type: integer
    v2GenePubmedIdsRequest:
      type: object
      properties:
        gene_ids:
          type: integer
    v2GenePubmedIdsResponse:
      type: object
      properties:
        pubmed_ids:
          type: array
          items:
            type: integer
    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.'
    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
    v2GetBiocollectionsRequest:
      type: object
      properties:
        collection_ids:
          type: array
          items:
            type: string
        page_size:
          type: integer
          title: 'The maximum number of biocollection reports to return. Default is 1000 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 returned from a prior call with more than `page_size` results. Use this token with the same request parameters to retrieve the next page. When `page_token` is empty, all results have been retrieved.'
        sort:
          type: array
          items:
            $ref: '#/components/schemas/v2BiocollectionsSortField'
    v2HttpBody:
      type: object
      properties:
        content_type:
          type: string
          title: 'The HTTP Content-Type header value specifying the content type of the body.'
        data:
          type: string
          format: byte
          title: 'The HTTP request/response body as raw binary.'
    v2MicroBiggeDatasetRequest:
      type: object
      properties:
        opaque_solr_query:
          type: string
        files:
          type: array
          items:
            $ref: '#/components/schemas/v2MicroBiggeDatasetRequestFileType'
        element_flank_config:
          $ref: '#/components/schemas/v2ElementFlankConfig'
    v2OrganelleDownloadRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        exclude_sequence:
          type: boolean
          title: 'If true, exclude the genome sequence from the data package.'
        include_annotation_type:
          type: array
          items:
            $ref: '#/components/schemas/v2AnnotationForOrganelleType'
    v2OrganelleMetadataRequest:
      type: object
      properties:
        taxons:
          type: array
          items:
            type: string
        accessions:
          type: array
          items:
            type: string
        organelle_types:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsOrganelleType'
        first_release_date:
          type: string
          format: date-time
          title: 'Limit results to organelle genomes released on or after the specified date.'
        last_release_date:
          type: string
          format: date-time
          title: 'Limit results to organelle genomes released on or before the specified date.'
        tax_exact_match:
          type: boolean
          title: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
        sort:
          type: array
          items:
            $ref: '#/components/schemas/v2OrganelleSort'
        returned_content:
          $ref: '#/components/schemas/v2OrganelleMetadataRequestContentType'
          title: 'Return complete organelle reports or nucleotide accessions only.'
        page_size:
          type: integer
          title: 'The maximum number of organelle assemblies 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 from an `OrganelleMetadata` call with more than `page_size` results. Use this token, along with the previous `OrganelleMetadata` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        table_format:
          $ref: '#/components/schemas/v2OrganelleMetadataRequestOrganelleTableFormat'
          title: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        include_tabular_header:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
          title: 'Specify when to include the table header when requesting a tabular report.'
    v2OrganelleSort:
      type: object
      properties:
        field:
          type: string
        direction:
          $ref: '#/components/schemas/v2SortDirection'
    v2OrganismQueryRequest:
      type: object
      properties:
        organism_query:
          type: string
        taxon_query:
          type: string
          title: 'Taxonomy ID or name (common or scientific) at any taxonomic rank'
        tax_rank_filter:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxRankFilter'
          title: 'Optionally return results for taxonomic ranks above species using `higher_taxon`'
        taxon_resource_filter:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxonResourceFilter'
          title: 'Limit to taxonomy nodes with gene, genome or organelle data'
        exact_match:
          type: boolean
          title: 'If true, only return results that exactly match the provided taxonomic name'
    v2OrthologRequest:
      type: object
      properties:
        gene_id:
          type: integer
          title: 'One or more NCBI GeneIDs'
        returned_content:
          $ref: '#/components/schemas/v2OrthologRequestContentType'
          title: 'Return complete gene reports, or abbreviated reports with either GeneIDs only or GeneIDs, transcript and protein counts.'
        taxon_filter:
          type: array
          items:
            type: string
        page_size:
          type: integer
          title: 'The maximum number of gene 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.'
    v2ProkaryoteGeneRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        include_annotation_type:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
        gene_flank_config:
          $ref: '#/components/schemas/v2ProkaryoteGeneRequestGeneFlankConfig'
        taxon:
          type: string
          title: 'Limit gene sequences and the genome assemblies described by the [annotation report file](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/data-reports/prokaryote-gene-location/) to the specified NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank.'
    v2ProkaryoteGeneRequestGeneFlankConfig:
      type: object
      properties:
        length:
          type: integer
    v2PubmedList:
      type: object
      properties:
        pubmed_ids:
          type: array
          items:
            type: integer
    v2RefGeneCatalogDatasetRequest:
      type: object
      properties:
        opaque_solr_query:
          type: string
        files:
          type: array
          items:
            $ref: '#/components/schemas/v2RefGeneCatalogDatasetRequestFileType'
        element_flank_config:
          $ref: '#/components/schemas/v2ElementFlankConfig'
    v2Sars2ProteinDatasetRequest:
      type: object
      properties:
        proteins:
          type: array
          items:
            type: string
        refseq_only:
          type: boolean
          title: 'If true, limit results to RefSeq genomes.'
        annotated_only:
          type: boolean
          title: 'If true, limit results to annotated genomes.'
        released_since:
          type: string
          format: date-time
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        pangolin_classification:
          type: string
          title: 'Limit to SARS-CoV-2 genomes with the specified Pango lineage.'
        geo_location:
          type: string
          title: 'Limit to genomes collected from the specififed geographic location.'
        usa_state:
          type: string
          title: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        complete_only:
          type: boolean
          title: 'Limit to genomes designated as complete, as defined by the submitter.'
        table_fields:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusTableField'
        include_sequence:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        aux_report:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        format:
          $ref: '#/components/schemas/v2TableFormat'
          title: 'Specify output format'
    v2SciNameAndIds:
      type: object
      properties:
        sci_name_and_ids:
          type: array
          items:
            $ref: '#/components/schemas/v2SciNameAndIdsSciNameAndId'
    v2SciNameAndIdsSciNameAndId:
      type: object
      properties:
        sci_name:
          type: string
          title: 'Scientific name'
        tax_id:
          type: string
          format: uint64
          title: 'NCBI Taxonomy ID'
        common_name:
          type: string
          title: 'Common name'
        matched_term:
          type: string
          title: 'Matched term'
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
          title: 'Rank'
        group_name:
          type: string
          title: 'Group name (blast group)'
    v2SeqRange:
      type: object
      properties:
        accession:
          type: string
          title: 'NCBI Accession.version of the sequence'
        begin:
          type: string
          format: uint64
        end:
          type: string
          format: uint64
        orientation:
          $ref: '#/components/schemas/v2reportsOrientation'
    v2SeqReply:
      type: object
      properties:
        accession:
          type: string
          title: 'Accession.version of the retrieved sequence'
        seq_length:
          type: string
          format: uint64
          title: 'Total length of the sequence (not just the amount retrieved)'
        mol_type:
          $ref: '#/components/schemas/v2MolType'
          title: 'Molecule type - dna, rna, protein'
        defline:
          type: string
          title: 'Defline for the retrieved sequence data'
        sequence:
          type: string
          title: 'The retrieved sequence (includes line-breaks)'
    v2SequenceAccessionRequest:
      type: object
      properties:
        accession:
          type: string
          title: 'Nucleotide sequence accession associated with a genome assembly'
    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.'
    v2SequenceRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        include_all_versions:
          type: boolean
          title: 'When true, include previous versions as well as the latest. Default behavior when this field is omitted is to return latest version only (i.e., `include_all_versions` defaults to false).'
    v2SleepReply:
      type: object
      properties:
        reply:
          type: string
    v2SleepRequest:
      type: object
      properties:
        sleep_msec:
          type: integer
        error_rate:
          type: number
          format: float
          title: 'From 0 to 100, chance of an error'
    v2SortField:
      type: object
      properties:
        field:
          type: string
        direction:
          $ref: '#/components/schemas/v2SortDirection'
    v2TabularOutput:
      type: object
      properties:
        data:
          type: string
    v2TaxonomyDatasetRequest:
      type: object
      properties:
        tax_ids:
          type: array
          items:
            type: integer
        aux_reports:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyDatasetRequestTaxonomyReportType'
    v2TaxonomyFilteredSubtreeRequest:
      type: object
      properties:
        taxons:
          type: array
          items:
            type: string
        specified_limit:
          type: boolean
          title: 'Limit to specified species'
        exclude_extinct:
          type: boolean
          title: 'Limit to species that are not extinct'
        levels:
          type: integer
          title: 'Number of taxonomic levels to return with a valid range of 1-5. Values above 5 will return 5 levels and if level is 0 or not specified, 1 level will be returned.'
        rank_limits:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
        include_incertae_sedis:
          type: boolean
          title: 'Include nodes with ranks not in ''rank_limits'' if their names meet criteria for incertae sedis (of unknown origin).'
    v2TaxonomyFilteredSubtreeResponse:
      type: object
      properties:
        root_nodes:
          type: array
          items:
            type: integer
        edges:
          $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdgesEntry'
        warnings:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsWarning'
        errors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsError'
    v2TaxonomyFilteredSubtreeResponseEdge:
      type: object
      properties:
        visible_children:
          type: array
          items:
            type: integer
        children_status:
          $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdgeChildStatus'
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
        scientific_name:
          type: string
        curator_common_name:
          type: string
        assembly_count:
          type: integer
    v2TaxonomyFilteredSubtreeResponseEdgesEntry:
      description: A map.
      properties:
        default:
          $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdge'
      additionalProperties:
        $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdge'
    v2TaxonomyImageMetadataRequest:
      type: object
      properties:
        taxon:
          type: string
    v2TaxonomyImageMetadataResponse:
      type: object
      properties:
        tax_id:
          type: string
        src:
          type: string
        license:
          type: string
        attribution:
          type: string
        source:
          type: string
        image_sizes:
          type: array
          items:
            $ref: '#/components/schemas/v2ImageSize'
        format:
          type: string
        license_url:
          type: string
    v2TaxonomyImageRequest:
      type: object
      properties:
        taxon:
          type: string
        image_size:
          $ref: '#/components/schemas/v2ImageSize'
    v2TaxonomyLinksRequest:
      type: object
      properties:
        taxon:
          type: string
    v2TaxonomyLinksResponse:
      type: object
      properties:
        tax_id:
          type: string
        encyclopedia_of_life:
          type: string
        global_biodiversity_information_facility:
          type: string
        inaturalist:
          type: string
        viralzone:
          type: string
        wikipedia:
          type: string
        generic_links:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyLinksResponseGenericLink'
    v2TaxonomyLinksResponseGenericLink:
      type: object
      properties:
        link_name:
          type: string
        link_url:
          type: string
    v2TaxonomyMatch:
      type: object
      properties:
        warnings:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsWarning'
        errors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsError'
        query:
          type: array
          items:
            type: string
        taxonomy:
          $ref: '#/components/schemas/v2TaxonomyNode'
    v2TaxonomyMetadataRequest:
      type: object
      properties:
        taxons:
          type: array
          items:
            type: string
        returned_content:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
          title: 'Return complete taxonomy reports, Taxonomy IDs only, or reports without assembly and gene counts (metadata).'
        page_size:
          type: integer
          title: 'The maximum number of taxons 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.'
        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.'
        table_format:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
          title: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        children:
          type: boolean
          title: 'If true, return results for child taxa.'
        ranks:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
    v2TaxonomyMetadataResponse:
      type: object
      properties:
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        taxonomy_nodes:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyMatch'
    v2TaxonomyNode:
      type: object
      properties:
        tax_id:
          type: integer
          title: 'NCBI Taxonomy identifier'
        organism_name:
          type: string
          title: 'Scientific name'
        common_name:
          type: string
          title: 'Common name'
        genbank_common_name:
          type: string
          title: 'GenBank common name'
        acronyms:
          type: array
          items:
            type: string
        genbank_acronym:
          type: string
          title: 'GenBank acronym'
        blast_name:
          type: string
          title: 'blast name for organism'
        lineage:
          type: array
          items:
            type: integer
        children:
          type: array
          items:
            type: integer
        descendent_with_described_species_names_count:
          type: integer
          title: 'The number of descendants (grand total) that are specified.'
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
          title: 'The rank of the organism.  An enumerated set of values.'
        has_described_species_name:
          type: boolean
          title: 'If the taxonomy node has a proper species name'
        counts:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyNodeCountByType'
        min_ord:
          type: integer
          title: 'ordinal values for any node are the full range of the ordinal values in the subtree underneath this node, and are used for faster range-based lookups'
        max_ord:
          type: integer
        extinct:
          type: boolean
          title: 'True if organism is extinct'
        genomic_moltype:
          type: string
          title: 'genomic molecule type (dsDNA, ssDNA, ssDNA(-), ssRNA)'
    v2TaxonomyNodeCountByType:
      type: object
      properties:
        type:
          $ref: '#/components/schemas/v2reportsCountType'
        count:
          type: integer
    v2TaxonomyRelatedIdRequest:
      type: object
      properties:
        tax_id:
          type: integer
        include_lineage:
          type: boolean
          title: 'If true, include parent nodes'
        include_subtree:
          type: boolean
          title: 'This field is deprecated because all requests include the subtree, so it has no effect'
        ranks:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
        page_size:
          type: integer
          title: 'The maximum number of taxids 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.'
    v2TaxonomyTaxIdsPage:
      type: object
      properties:
        tax_ids:
          type: array
          items:
            type: integer
        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.'
    v2VersionReply:
      type: object
      properties:
        version:
          type: string
        major_ver:
          type: integer
        minor_ver:
          type: integer
        patch_ver:
          type: integer
    v2VirusAnnotationFilter:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        taxon:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        taxons:
          type: array
          items:
            type: string
        refseq_only:
          type: boolean
          title: 'If true, limit to RefSeq genomes.'
        annotated_only:
          type: boolean
          title: 'If true, limit to annotated genomes.'
        released_since:
          type: string
          format: date-time
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        pangolin_classification:
          type: string
          title: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        geo_location:
          type: string
          title: 'Limit to genomes collected from the specififed geographic location.'
        usa_state:
          type: string
          title: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        complete_only:
          type: boolean
          title: 'Limit to genomes designated as complete, as defined by the submitter.'
    v2VirusAnnotationReportRequest:
      type: object
      properties:
        filter:
          $ref: '#/components/schemas/v2VirusAnnotationFilter'
        table_fields:
          type: array
          items:
            type: string
        table_format:
          type: string
          title: 'Optional pre-defined template for processing a tabular data request'
        page_size:
          type: integer
          title: 'The maximum number of virus data 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.'
    v2VirusAvailability:
      type: object
      properties:
        valid_accessions:
          type: array
          items:
            type: string
        invalid_accessions:
          type: array
          items:
            type: string
        message:
          type: string
    v2VirusAvailabilityRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
    v2VirusDataReportRequest:
      type: object
      properties:
        filter:
          $ref: '#/components/schemas/v2VirusDatasetFilter'
          title: 'All the supported filters for virus requests'
        returned_content:
          $ref: '#/components/schemas/v2VirusDataReportRequestContentType'
          title: 'Return complete virus reports or nucleotide accessions only'
        table_fields:
          type: array
          items:
            type: string
        table_format:
          type: string
          title: 'Optional pre-defined template for processing a tabular data request'
        page_size:
          type: integer
          title: 'The maximum number of virus data 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.'
    v2VirusDatasetFilter:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        taxon:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        taxons:
          type: array
          items:
            type: string
        refseq_only:
          type: boolean
          title: 'If true, limit results to RefSeq genomes.'
        annotated_only:
          type: boolean
          title: 'If true, limit results to annotated genomes.'
        released_since:
          type: string
          format: date-time
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        pangolin_classification:
          type: string
          title: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        geo_location:
          type: string
          title: 'Limit to genomes collected from the specified geographic location.'
        usa_state:
          type: string
          title: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        complete_only:
          type: boolean
          title: 'Limit to genomes designated as complete, as defined by the submitter.'
    v2VirusDatasetRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
        taxon:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        taxons:
          type: array
          items:
            type: string
        refseq_only:
          type: boolean
          title: 'If true, limit results to RefSeq genomes.'
        annotated_only:
          type: boolean
          title: 'If true, limit results to annotated genomes.'
        released_since:
          type: string
          format: date-time
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).'
        pangolin_classification:
          type: string
          title: 'Limit to SARS-CoV-2 genomes from the specified Pango lineage.'
        geo_location:
          type: string
          title: 'Limit to genomes collected from the specified geographic location.'
        usa_state:
          type: string
          title: 'Limit to genomes collected from the specified U.S. state (two-letter abbreviation).'
        complete_only:
          type: boolean
          title: 'Limit to genomes designated as complete, as defined by the submitter.'
        table_fields:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusTableField'
        include_sequence:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        aux_report:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        format:
          $ref: '#/components/schemas/v2TableFormat'
          title: 'Choose download format (tsv, csv or jsonl)'
        use_psg:
          type: boolean
          title: 'Experimental approach to retrieving sequence data.'
    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'
    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'
    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'
    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
    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'
    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'
    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'
    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?'
    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'
    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
    v2reportsAuthor:
      type: object
      properties:
        name:
          type: string
          title: 'Author names.'
        affiliation:
          type: string
          title: 'Author affiliation'
    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'
    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
    v2reportsBioProjectLineage:
      type: object
      properties:
        bioprojects:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioProject'
    v2reportsBioSampleAttribute:
      type: object
      properties:
        name:
          type: string
        value:
          type: string
    v2reportsBioSampleContact:
      type: object
      properties:
        lab:
          type: string
          title: 'Submitter lab name.'
    v2reportsBioSampleDataReport:
      type: object
      properties:
        accession:
          type: string
          title: 'BioSample Accession identifier'
        last_updated:
          type: string
          title: 'When the biosample object was last updated.'
        publication_date:
          type: string
          title: 'BioSample object publication date.'
        submission_date:
          type: string
          title: 'BioSample object submission date.'
        sample_ids:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioSampleId'
        description:
          $ref: '#/components/schemas/v2reportsBioSampleDescription'
          title: 'BioSample description.'
        owner:
          $ref: '#/components/schemas/v2reportsBioSampleOwner'
          title: 'BioSample owner.'
        models:
          type: array
          items:
            type: string
        bioprojects:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioProject'
        package:
          type: string
          title: 'Package identifier.'
        attributes:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioSampleAttribute'
        status:
          $ref: '#/components/schemas/v2reportsBioSampleStatus'
          title: 'Current status of the object.'
        age:
          type: string
          title: 'Age at the time of sampling'
        biomaterial_provider:
          type: string
          title: 'Name and address of the lab or PI'
        breed:
          type: string
          title: 'Breed name'
        collected_by:
          type: string
          title: 'Name of persons or institute who collected the sample'
        collection_date:
          type: string
          title: 'Date on which the sample was collected'
        cultivar:
          type: string
          title: 'Cultivated variety of plant'
        dev_stage:
          type: string
          title: 'Developmental stage at the time of sampling'
        ecotype:
          type: string
          title: 'Population within a given species adapted to a local habitat'
        geo_loc_name:
          type: string
          title: 'Geographical origin of the sample'
        host:
          type: string
          title: 'The natural host to the organism'
        host_disease:
          type: string
          title: 'Name of relevant disease'
        identified_by:
          type: string
          title: 'Name of the taxonomist who identified the specimen'
        ifsac_category:
          type: string
          title: 'Interagency Food Safety Analytics Collaboration (IFSAC) category'
        isolate:
          type: string
          title: 'Description of the specific individual from which the sample was derived'
        isolate_name_alias:
          type: string
          title: 'Other IDs associated with this isolate'
        isolation_source:
          type: string
          title: 'Source of the sample'
        lat_lon:
          type: string
          title: 'Geogrpahic coordinates of the location where the sample was collected'
        project_name:
          type: string
          title: 'Name of the project'
        sample_name:
          type: string
          title: 'Sample name in source database'
        serovar:
          type: string
          title: 'Taxonomic name below subspecies. Same as serotype.'
        sex:
          type: string
          title: 'Physical sex of sampled organism'
        source_type:
          type: string
          title: 'Controlled vocabulary describing the isolation source'
        strain:
          type: string
          title: 'Strain name'
        sub_species:
          type: string
          title: 'Sub-species taxonomic name'
        tissue:
          type: string
          title: 'Type of tissue from which the sample was derived'
        serotype:
          type: string
          title: 'Taxonomic name below subspecies. Same as serovar'
    v2reportsBioSampleDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioSampleDataReport'
        total_count:
          type: integer
          title: 'The total count of available datasets (ignoring the page_size parameter).'
        next_page_token:
          type: string
          title: 'A token that can be sent as `page_token` to retrieve the next page. If this field is omitted, there are no subsequent pages.'
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
    v2reportsBioSampleDescription:
      type: object
      properties:
        title:
          type: string
        organism:
          $ref: '#/components/schemas/v2reportsOrganism'
        comment:
          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'
    v2reportsBioSampleId:
      type: object
      properties:
        db:
          type: string
        label:
          type: string
        value:
          type: string
    v2reportsBioSampleOwner:
      type: object
      properties:
        name:
          type: string
        contacts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioSampleContact'
    v2reportsBioSampleStatus:
      type: object
      properties:
        status:
          type: string
        when:
          type: string
    v2reportsBiocollection:
      type: object
      properties:
        bio_collection_id:
          type: string
          format: int64
          title: 'Stable numeric identifier for the biocollection in NameBank.'
        code:
          type: string
          title: 'Canonical collection code as provided by the source institution.'
        ncbi_unique_code:
          type: string
          title: 'NCBI-normalized unique collection code used for cross-source lookup.'
        name:
          type: string
          title: 'Human-readable collection name.'
        type:
          type: string
          title: 'Collection type from NameBank (e.g., museum, culture collection)'
        comments:
          type: string
          title: 'Any additional comments'
    v2reportsBiocollectionInstitution:
      type: object
      properties:
        name:
          type: string
          title: 'Human-readable institution name.'
        country:
          type: string
          title: 'Country where the institution is located.'
        address:
          type: string
          title: 'Mailing or street address for the institution.'
        url:
          type: string
          title: 'Institution website URL.'
        comments:
          type: string
          title: 'Additional notes about the institution.'
        bio_collections:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBiocollection'
    v2reportsBiocollectionsReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGetBiocollectionsReport'
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        total_count:
          type: integer
          title: 'The total count of available biocollection reports (ignoring page_size) for the full 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.'
    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'
    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.'
    v2reportsClassification:
      type: object
      properties:
        superkingdom:
          $ref: '#/components/schemas/v2reportsTaxData'
        kingdom:
          $ref: '#/components/schemas/v2reportsTaxData'
        phylum:
          $ref: '#/components/schemas/v2reportsTaxData'
        class:
          $ref: '#/components/schemas/v2reportsTaxData'
        order:
          $ref: '#/components/schemas/v2reportsTaxData'
        family:
          $ref: '#/components/schemas/v2reportsTaxData'
        genus:
          $ref: '#/components/schemas/v2reportsTaxData'
        species:
          $ref: '#/components/schemas/v2reportsTaxData'
        domain:
          $ref: '#/components/schemas/v2reportsTaxData'
          title: 'NOTE: These are out of order'
        realm:
          $ref: '#/components/schemas/v2reportsTaxData'
        acellular_root:
          $ref: '#/components/schemas/v2reportsTaxData'
    v2reportsConservedDomain:
      type: object
      properties:
        accession:
          type: string
          title: 'cdd accession'
        name:
          type: string
        range:
          $ref: '#/components/schemas/v2reportsRange'
          title: 'range on the protein'
    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
    v2reportsFeatureCounts:
      type: object
      properties:
        gene_counts:
          $ref: '#/components/schemas/v2reportsGeneCounts'
          title: 'Counts of gene types'
    v2reportsFunctionalSite:
      type: object
      properties:
        name:
          type: string
          title: 'the name of this functional site'
        type:
          type: string
          title: 'function type'
        specific:
          type: boolean
          title: 'Whether this is a specific site'
        completeness:
          type: number
          format: float
          title: 'The fraction of residues mapped to the protein sequence'
        source_accession:
          type: string
          title: 'The accession of domain that defines this functional site'
        location:
          type: array
          items:
            type: integer
    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'
    v2reportsGeneDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneReportMatch'
        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.'
    v2reportsGeneDescriptor:
      type: object
      properties:
        gene_id:
          type: string
          format: uint64
          title: 'NCBI Gene ID'
        symbol:
          type: string
          title: 'Gene symbol'
        description:
          type: string
          title: 'Gene name'
        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: 'Type of gene'
        rna_type:
          $ref: '#/components/schemas/v2reportsRnaType'
        orientation:
          $ref: '#/components/schemas/v2reportsOrientation'
          title: 'Direction of the gene relative to the genome coordinates'
        reference_standards:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGenomicRegion'
        genomic_regions:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGenomicRegion'
        chromosomes:
          type: array
          items:
            type: string
        nomenclature_authority:
          $ref: '#/components/schemas/v2reportsNomenclatureAuthority'
        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
        alternate_names:
          type: array
          items:
            type: string
        replaced_gene_id:
          type: string
          format: uint64
          title: 'The NCBI Gene ID for the gene that was merged into the current gene record'
        annotations:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAnnotation'
        transcript_count:
          type: integer
          title: 'Number of transcripts encoded by the gene'
        protein_count:
          type: integer
          title: 'Number of proteins encoded by the gene'
        transcript_type_counts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTranscriptTypeCount'
        gene_groups:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneGroup'
        summary:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneSummary'
        gene_ontology:
          $ref: '#/components/schemas/v2reportsGeneOntology'
        locus_tag:
          type: string
        map_locations:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMapLocation'
    v2reportsGeneGroup:
      type: object
      properties:
        id:
          type: string
          title: 'Gene group identifier, currently these only include gene ortholog sets'
        method:
          type: string
          title: 'Method used to calculate the gene group, currently this only includes "NCBI Ortholog"'
    v2reportsGeneNeighbor:
      type: object
      properties:
        gene_id:
          type: string
          format: uint64
          title: 'NCBI Gene ID'
        symbol:
          type: string
          title: 'Gene symbol'
        description:
          type: string
          title: 'Gene name'
        gene_type:
          $ref: '#/components/schemas/v2reportsGeneType'
          title: 'Type of gene'
        genomic_range:
          $ref: '#/components/schemas/v2reportsRange'
          title: 'Location range and orientation of gene'
    v2reportsGeneNeighborGenomicLocation:
      type: object
      properties:
        genomic_location:
          $ref: '#/components/schemas/v2reportsGenomicLocation'
        gene_neighbors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneNeighbor'
    v2reportsGeneNeighborsAnnotation:
      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/v2reportsGeneNeighborGenomicLocation'
    v2reportsGeneNeighborsDescriptor:
      type: object
      properties:
        tax_id:
          type: string
          format: uint64
          title: 'NCBI Taxonomy ID for the organism'
        gene_id:
          type: string
          format: uint64
          title: 'NCBI Gene ID'
        symbol:
          type: string
          title: 'Gene symbol'
        description:
          type: string
          title: 'Gene name'
        gene_type:
          $ref: '#/components/schemas/v2reportsGeneType'
          title: 'Type of gene'
        annotations:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneNeighborsAnnotation'
    v2reportsGeneNeighborsReports:
      type: object
      properties:
        genes:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneNeighborsDescriptor'
    v2reportsGeneOntology:
      type: object
      properties:
        assigned_by:
          type: string
          title: 'The database that made the annotation'
        molecular_functions:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsProcessMetadata'
        biological_processes:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsProcessMetadata'
        cellular_components:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsProcessMetadata'
    v2reportsGeneReportMatch:
      type: object
      properties:
        gene:
          $ref: '#/components/schemas/v2reportsGeneDescriptor'
        product:
          $ref: '#/components/schemas/v2reportsProductDescriptor'
        query:
          type: array
          items:
            type: string
        warnings:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsWarning'
        warning:
          $ref: '#/components/schemas/v2reportsWarning'
        errors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsError'
    v2reportsGeneSummary:
      type: object
      properties:
        source:
          type: string
          title: 'Source of the gene summary'
        description:
          type: string
          title: 'Gene summary text itself that describes the gene'
        date:
          type: string
          title: 'Date that the gene summary was last updated'
    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'
    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
    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.'
    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'
    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'
    v2reportsGetBiocollectionsReport:
      type: object
      properties:
        institution:
          $ref: '#/components/schemas/v2reportsBiocollectionInstitution'
          title: 'A single institution and its collections. Each report contains exactly one institution record and the list of biocollections owned by that institution.'
    v2reportsInfraspecificName:
      type: object
      properties:
        strain:
          type: string
          title: 'A specific genetic variant or lineage within a species.'
        substrain:
          type: string
          title: 'A subdivision of a strain.'
        variety:
          type: string
          title: 'A taxonomic rank below species.'
        serotype:
          type: string
          title: 'A distinct variation within a species of bacteria or virus based on surface antigens.'
        serogroup:
          type: string
          title: 'A group of serotypes.'
        biotype:
          type: string
          title: 'A group of organisms sharing a specific genetic makeup, often referring to physiological characteristics.'
        isolate:
          type: string
          title: 'An organism obtained from a specific source, typically indicating a particular collection event.'
        forma:
          type: string
          title: 'A taxonomic rank below variety.'
        forma_specialis:
          type: string
          title: 'A taxonomic rank for parasitic fungi or bacteria that are adapted to specific hosts.'
        ecotype:
          type: string
          title: 'A genetically distinct geographical variety or population within a species.'
        teleomorph:
          type: string
          title: 'The sexual reproductive stage of a fungus.'
        breed:
          type: string
          title: 'A domesticated group within a species'
    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'
    v2reportsIsolate:
      type: object
      properties:
        name:
          type: string
          title: 'BioSample harmonized attribute names https://www.ncbi.nlm.nih.gov/biosample/docs/attributes/'
        source:
          type: string
          title: 'Source material from which the viral specimen was isolated'
        collection_date:
          type: string
          title: 'The collection date for the sample from which the viral nucleotide sequence was derived'
    v2reportsLineageOrganism:
      type: object
      properties:
        tax_id:
          type: integer
          title: 'NCBI Taxonomy identifier'
        name:
          type: string
          title: 'Scientific name'
    v2reportsLinkedAssembly:
      type: object
      properties:
        linked_assembly:
          type: string
          title: 'The linked assembly accession'
        assembly_type:
          $ref: '#/components/schemas/v2reportsLinkedAssemblyType'
          title: 'The linked assembly type'
    v2reportsMapLocation:
      type: object
      properties:
        map_type:
          $ref: '#/components/schemas/v2reportsMapLocationMapType'
          title: 'Type of mapping; can be "Cytogenetic" or "Genetic"'
        map_value:
          type: string
          title: 'Location of the gene in mapping coordinates'
    v2reportsMaturePeptide:
      type: object
      properties:
        accession_version:
          type: string
        name:
          type: string
        length:
          type: integer
    v2reportsMessage:
      type: object
      properties:
        error:
          $ref: '#/components/schemas/v2reportsError'
        warning:
          $ref: '#/components/schemas/v2reportsWarning'
    v2reportsNameAndAuthority:
      type: object
      properties:
        name:
          type: string
          title: 'This could be the scientific name, common name, synonym, etc. depending on the context.'
        authority:
          type: string
          title: 'The authority that this name was created by. The authority is typically represented by the author(s) name and the year in which it was published.'
        type_strains:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyTypeMaterial'
        curator_synonym:
          type: string
          title: 'The primary synonym of the scientific name.'
        homotypic_synonyms:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsNameAndAuthority'
        heterotypic_synonyms:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsNameAndAuthority'
        other_synonyms:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsNameAndAuthority'
        informal_names:
          type: array
          items:
            type: string
        basionym:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: 'The originally described name, no longer in use. Attached to the type material and species description.'
        publications:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsNameAndAuthorityPublication'
        notes:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsNameAndAuthorityNote'
        formal:
          type: boolean
          title: 'Indicates whether the name is formal (i.e. compliant)'
    v2reportsNameAndAuthorityNote:
      type: object
      properties:
        name:
          type: string
          title: 'Name of the notation.'
        note:
          type: string
          title: 'Note text.'
        note_classifier:
          $ref: '#/components/schemas/v2reportsNameAndAuthorityNoteClassifier'
          title: 'Note classification'
    v2reportsNameAndAuthorityPublication:
      type: object
      properties:
        name:
          type: string
          title: 'Name of the publication (article, book, etc.).'
        citation:
          type: string
          title: 'Citation to the publication.'
        pmid:
          type: string
          format: uint64
    v2reportsNomenclatureAuthority:
      type: object
      properties:
        authority:
          type: string
          title: 'The nomenclature authority for this gene record'
        identifier:
          type: string
          title: 'The nomenclature authority identifier for this gene record'
    v2reportsOrganelle:
      type: object
      properties:
        description:
          $ref: '#/components/schemas/v2reportsOrganelleType'
        genbank:
          $ref: '#/components/schemas/v2reportsSequenceInformation'
        refseq:
          $ref: '#/components/schemas/v2reportsSequenceInformation'
        organism:
          $ref: '#/components/schemas/v2reportsOrganism'
          title: 'Taxon for the organelle'
        bioprojects:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsBioProject'
        biosample:
          $ref: '#/components/schemas/v2reportsOrganelleBiosample'
          title: 'The associated BioSample.'
        gene_counts:
          $ref: '#/components/schemas/v2reportsOrganelleGeneCounts'
        length:
          type: integer
          title: 'Genome length'
        topology:
          $ref: '#/components/schemas/v2reportsOrganelleTopology'
        gene_count:
          type: integer
    v2reportsOrganelleBiosample:
      type: object
      properties:
        accession:
          type: string
          title: 'BioSample Accession identifier'
    v2reportsOrganelleDataReports:
      type: object
      properties:
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsOrganelle'
        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.'
    v2reportsOrganelleGeneCounts:
      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'
        rrna:
          type: integer
          title: 'Count of ribosomal RNAs'
        trna:
          type: integer
          title: 'Count of transfer RNAs'
        lncrna:
          type: integer
          title: 'Count of long, non-coding RNAs'
    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'
    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'
    v2reportsProcessMetadata:
      type: object
      properties:
        name:
          type: string
          title: 'Gene ontology term name'
        go_id:
          type: string
          title: 'Gene ontology identifier'
        evidence_code:
          type: string
          title: 'Indicates how the annotation is supported'
        qualifier:
          type: string
          title: 'Explicitly link gene products to GO terms'
        reference:
          $ref: '#/components/schemas/v2reportsReference'
          title: 'Source of evidence supporting the GO annotation'
    v2reportsProductDescriptor:
      type: object
      properties:
        gene_id:
          type: string
          format: uint64
          title: 'NCBI Gene ID'
        symbol:
          type: string
          title: 'gene symbol'
        description:
          type: string
          title: 'gene name'
        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: 'Type of gene'
        rna_type:
          $ref: '#/components/schemas/v2reportsRnaType'
          title: 'Type of RNA'
        transcripts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTranscript'
        transcript_count:
          type: integer
          title: 'Number of transcripts encoded by the gene'
        protein_count:
          type: integer
          title: 'Number of proteins encoded by the gene'
        transcript_type_counts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTranscriptTypeCount'
    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'
    v2reportsProteinConservedDomain:
      type: object
      properties:
        accession:
          type: string
          title: 'Domain family or superfamily accession, like ''cd01234'' or ''cl01234'''
        name:
          type: string
          title: 'The short name of the domain family'
        description:
          type: string
          title: 'The description for the domain/superfamily (defline)'
        start:
          type: integer
          title: 'The start coordinate of the annotation on the query sequence'
        stop:
          type: integer
          title: 'The stop coordination (inclusive) of the annotation on the query protein'
        specific:
          type: boolean
          title: 'Whether this hit is specific for a particular model'
        partial:
          type: boolean
          title: 'Whether this domain is fully aligned to the protein'
        evalue:
          type: number
          format: float
          title: 'The Expect Value of the alignment between query sequence and the domain consensus'
        bit_score:
          type: number
          format: float
          title: 'The bit_score of the alignment between query sequence and the domain consensus'
    v2reportsProteinDataReport:
      type: object
      properties:
        accession:
          type: string
          title: 'Protein accession, as input'
        description:
          type: string
          title: 'Protein name as in defline'
        length:
          type: integer
          title: 'Length of the protein'
        gene_id:
          type: integer
          title: 'Gene ID associated with the protein'
        identical_protein_group:
          type: integer
          title: 'Non-redundent protein group ID, aka IPG/PIG'
        tax_id:
          type: integer
          title: 'Taxonomy ID'
        conserved_domains:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsProteinConservedDomain'
        functional_sites:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsFunctionalSite'
        protein_families:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsProteinFamily'
    v2reportsProteinDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsProteinDataReport'
    v2reportsProteinFamily:
      type: object
      properties:
        method:
          type: string
          title: 'The method used to assign the protein family'
        identifier:
          type: integer
          title: 'The numeric ID of the model assigned to the protein using the particular method'
        name:
          type: string
          title: 'The name of the assigned model'
        description:
          type: string
          title: 'The more detailed description of the assigned model'
        type:
          type: string
          title: 'Sub-category specific to this method'
    v2reportsPublication:
      type: object
      properties:
        pmid:
          type: integer
          title: 'PubMed identifier'
        title:
          type: string
          title: 'Publication title'
        date:
          type: string
          title: 'Publication date'
        authors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAuthor'
    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.'
    v2reportsReference:
      type: object
      properties:
        pmids:
          type: array
          items:
            type: string
            format: uint64
    v2reportsSampleInfo:
      type: object
      properties:
        clone:
          type: string
          title: 'Name for the clone or subculture from which the sample was taken.'
        subclone:
          type: string
          title: 'Name for the derived clone or subculture from which the sample was taken.'
        haplotype:
          type: string
          title: 'Name of the haplotype.'
        genotype:
          type: string
          title: 'Observed genotype.'
        sex:
          type: string
          title: 'Physical sex of sampled organism.'
        cell_line:
          type: string
          title: 'Name of the cell line.'
        cell_type:
          type: string
          title: 'Type of cell of the sample or from which the sample was obtained.'
        tissue:
          type: string
          title: 'Tissue from which the sample was derived.'
        clone_lib:
          type: string
          title: 'Formal identifier that points to source institute and clone library identifier.'
        dev_stage:
          type: string
          title: 'Developmental stage at the time of sampling.'
        lab_host:
          type: string
          title: 'Scientific name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.'
        tissue_lib:
          type: string
          title: 'Formal identifier that points to source institute and tissue library identifier.'
        geo_loc_name:
          type: string
          title: 'Geographical origin of the sample.'
        environmental_sample:
          type: boolean
          title: 'True when the sample is environmental.'
        isolation_source:
          type: string
          title: 'Source of the sample.'
        lat_lon:
          type: string
          title: 'Geographic coordinates of the location where the sample was collected.'
        collection_date:
          type: string
          title: 'Date on which the sample was collected.'
        collected_by:
          type: string
          title: 'Name of persons or institute who collected the sample.'
        identified_by:
          type: string
          title: 'Name of the taxonomist who identified the specimen.'
        metagenomic:
          type: boolean
          title: 'True when the sample is metagenomic.'
        mating_type:
          type: string
          title: 'Mating type of the sampled organism.'
        phenotype:
          type: string
          title: 'Phenotype of sampled organism.'
        altitude:
          type: string
          title: 'The altitude of the sample above sea level.'
        metagenome_name:
          type: string
          title: 'Name of the metagenome.'
        metagenome_taxid:
          type: integer
          title: 'NCBI taxonomy identifier for the metagenome.'
    v2reportsSeqRangeSet:
      type: object
      properties:
        accession_version:
          type: string
          title: 'NCBI Accession.version of the sequence'
        range:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRange'
    v2reportsSeqRangeSetFasta:
      type: object
      properties:
        seq_id:
          type: string
          title: 'Seq_id may include location info in addition to a sequence accession'
        accession_version:
          type: string
          title: 'Accession and version of the viral nucleotide sequence'
        title:
          type: string
        sequence_hash:
          type: string
          title: 'Unique identifier for identical sequences'
        range:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRange'
    v2reportsSequenceDataReport:
      type: object
      properties:
        accession:
          type: string
          title: 'Sequence accession requested by the user (typically accession.version).'
        organism_name:
          type: string
          title: 'Scientific organism name associated with this sequence.'
        length:
          type: integer
          title: 'Sequence length measured in the units field.'
        units:
          type: string
          title: 'Units for sequence length, for example "nucleotides" or "amino acids".'
        molecule_type:
          type: string
          title: 'Molecule type such as "ss-RNA", "mRNA", or "protein".'
        database_provider:
          type: string
          title: 'Upstream source database for this record, for example "RefSeq".'
        description:
          type: string
          title: 'Human-readable sequence definition line.'
        source_mrna:
          type: string
          title: 'Source mRNA accession when this report describes a protein sequence.'
        publication_date:
          type: string
          title: 'Initial release/publication date in ISO-8601 format.'
        latest_update_date:
          type: string
          title: 'Most recent update date in ISO-8601 format.'
        tax_id:
          type: integer
          title: 'NCBI Taxonomy identifier for this rank.'
        submissions:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsSubmission'
        publications:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsPublication'
        bioproject_accession:
          type: string
          title: 'NCBI BioProject accession linked to this sequence record.'
        biosample_accessions:
          type: array
          items:
            type: string
        origin_type:
          $ref: '#/components/schemas/v2reportsSequenceDataReportOriginType'
          title: 'Biological context regarding how the material for the sequence originated.'
        specimen_voucher:
          $ref: '#/components/schemas/v2reportsSpecimenVoucher'
          title: 'Specimen voucher information for this sequence record.'
        infraspecific_names:
          $ref: '#/components/schemas/v2reportsInfraspecificName'
          title: 'Infraspecific Names'
        sample_info:
          $ref: '#/components/schemas/v2reportsSampleInfo'
          title: 'Sample Info'
    v2reportsSequenceDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsSequenceDataReport'
        total_count:
          type: integer
          title: 'Total number of reports available across all pages.'
    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'
    v2reportsSequenceInformation:
      type: object
      properties:
        accession:
          type: string
          title: 'The accession.version of the organelle genomic nucleotide sequence.'
        submission_date:
          type: string
          title: 'Date record was submitted to GenBank or Curated into RefSeq (ISO 8601)'
        submitter:
          type: string
          title: 'The submitter, e.g. NCBI Genome Project for RefSeq'
    v2reportsSpecimenVoucher:
      type: object
      properties:
        id:
          type: string
          title: 'Specimen voucher identifier.'
        biocollection_code:
          type: string
          title: 'Institution code for the specimen voucher.'
    v2reportsSubmission:
      type: object
      properties:
        date:
          type: string
          title: 'Submission date'
        institution:
          type: string
          title: 'Submitting institution or organization.'
        address:
          type: string
          title: 'Submitter mailing address or contact address.'
        names:
          type: array
          items:
            type: string
    v2reportsTaxData:
      type: object
      properties:
        name:
          type: string
          title: 'Taxonomic name'
        id:
          type: integer
          title: 'NCBI Taxonomy identifier'
    v2reportsTaxonomyDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyReportMatch'
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        total_count:
          type: integer
          title: 'The total count of available taxons - deprecated because it not supported for multiple-page results.'
        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.'
    v2reportsTaxonomyNamesDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyNamesReportMatch'
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        total_count:
          type: integer
          title: 'The total count of available taxons - deprecated because it not supported for multiple-page results.'
        next_page_token:
          type: string
          title: 'A page token.  A token that can be used in a future request as `page_token` to retrieve the next page. If this field is emtpy then there are no subsequent pages available.'
    v2reportsTaxonomyNamesDescriptor:
      type: object
      properties:
        tax_id:
          type: string
          format: uint64
          title: 'NCBI Taxonomy identifier'
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
          title: 'The taxonomic rank of the taxonomic node.'
        current_scientific_name:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: 'The currently accepted name chosen out of all synonyms for the taxonomic node.'
        group_name:
          type: string
          title: 'Group name for the species.'
        curator_common_name:
          type: string
          title: 'The canonical common name.'
        other_common_names:
          type: array
          items:
            type: string
        general_notes:
          type: array
          items:
            type: string
        links_from_type:
          type: string
          title: 'TBD'
        citations:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyNamesDescriptorCitation'
        current_scientific_name_is_formal:
          type: boolean
          title: 'Specify if the current scientific name is considered ''formal'' or not.'
    v2reportsTaxonomyNamesDescriptorCitation:
      type: object
      properties:
        full_citation:
          type: string
        short_citation:
          type: string
        pmid:
          type: string
          format: uint64
    v2reportsTaxonomyNamesReportMatch:
      type: object
      properties:
        taxonomy:
          $ref: '#/components/schemas/v2reportsTaxonomyNamesDescriptor'
          title: 'Detailed taxonomic information related to the requested node.'
        query:
          type: array
          items:
            type: string
        warning:
          $ref: '#/components/schemas/v2reportsWarning'
          title: 'Warnings associated with this request.  Any warning associated with this request.  This is represented by a Warning object which is separately documented.'
        errors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsError'
    v2reportsTaxonomyNode:
      type: object
      properties:
        tax_id:
          type: integer
          title: 'NCBI Taxonomy identifier'
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
          title: 'The taxonomic rank of the taxonomic node.'
        current_scientific_name:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: 'The currently accepted name chosen out of all synonyms for the taxonomic node.'
        basionym:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: 'The originally described name, no longer in use. Attached to the type material and species description.'
        curator_common_name:
          type: string
          title: 'The canonical common name.'
        group_name:
          type: string
          title: 'A common name describing large, well-known taxa.'
        has_type_material:
          type: boolean
          title: 'A boolean that indicates whether or not type material is available for the species.'
        classification:
          $ref: '#/components/schemas/v2reportsClassification'
          title: 'A subset of parent nodes including well-established ranks.'
        parents:
          type: array
          items:
            type: integer
        children:
          type: array
          items:
            type: integer
        counts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyNodeCountByType'
        genomic_moltype:
          type: string
          title: 'Genomic molecule type (dsDNA, ssDNA, ssDNA(-), ssRNA)'
        current_scientific_name_is_formal:
          type: boolean
          title: 'Specify if the current scientific name is considered ''formal'' or not.'
        secondary_tax_ids:
          type: array
          items:
            type: integer
        extinct:
          type: boolean
          title: 'True if organism is extinct'
    v2reportsTaxonomyNodeCountByType:
      type: object
      properties:
        type:
          $ref: '#/components/schemas/v2reportsCountType'
        count:
          type: integer
    v2reportsTaxonomyReportMatch:
      type: object
      properties:
        taxonomy:
          $ref: '#/components/schemas/v2reportsTaxonomyNode'
        query:
          type: array
          items:
            type: string
        warning:
          $ref: '#/components/schemas/v2reportsWarning'
        errors:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsError'
    v2reportsTaxonomyTypeMaterial:
      type: object
      properties:
        type_strain_name:
          type: string
          title: 'The strain name of the type material.'
        type_strain_id:
          type: string
          title: 'The strain ID of the type material.'
        bio_collection_id:
          type: string
          title: 'The biocollection ID of the type material.'
        bio_collection_name:
          type: string
          title: 'The biocollection name of the type material.'
        collection_type:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsCollectionType'
        type_class:
          type: string
          title: 'Type material classification.'
    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'
    v2reportsTranscriptTypeCount:
      type: object
      properties:
        type:
          $ref: '#/components/schemas/v2reportsTranscriptTranscriptType'
          title: 'Type of transcript'
        count:
          type: integer
          title: 'Number of transcripts of a particular type'
    v2reportsTypeMaterial:
      type: object
      properties:
        type_label:
          type: string
        type_display_text:
          type: string
    v2reportsVirusAnnotationReport:
      type: object
      properties:
        accession:
          type: string
        isolate_name:
          type: string
        genes:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsVirusGene'
    v2reportsVirusAnnotationReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsVirusAnnotationReport'
        total_count:
          type: integer
          title: 'The total count of available assemblies (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.'
    v2reportsVirusAssembly:
      type: object
      properties:
        accession:
          type: string
          title: 'The accession.version of the viral nucleotide sequence. Includes both GenBank and RefSeq accessions'
        is_complete:
          type: boolean
        is_annotated:
          type: boolean
          title: 'The viral genome has been annotated by either the submitter (GenBank) or by NCBI (RefSeq)'
        isolate:
          $ref: '#/components/schemas/v2reportsIsolate'
        source_database:
          type: string
          title: 'Indicates if the source of the viral nucleotide record is from a GenBank submitter or from NCBI-derived curation (RefSeq)'
        protein_count:
          type: integer
          title: 'The total count of annotated proteins including both proteins and polyproteins but not processed mature peptides'
        host:
          $ref: '#/components/schemas/v2reportsOrganism'
          title: 'Taxon from which the virus sample was isolated'
        virus:
          $ref: '#/components/schemas/v2reportsOrganism'
          title: 'Viral taxon'
        bioprojects:
          type: array
          items:
            type: string
        location:
          $ref: '#/components/schemas/v2reportsVirusAssemblyCollectionLocation'
        update_date:
          type: string
          title: 'Date the viral nucleotide accession was last updated in NCBI Virus'
        release_date:
          type: string
          title: 'Date the viral nucleotide accession was first released in NCBI Virus'
        nucleotide_completeness:
          type: string
          title: 'Value describing if the of the viral nucleotide sequence represents a complete or partial genome'
        completeness:
          $ref: '#/components/schemas/v2reportsVirusAssemblyCompleteness'
          title: 'Indicates whether the viral nucleotide sequence represents a complete or partial genome'
        length:
          type: integer
          title: 'Length of the viral nucleotide sequence'
        gene_count:
          type: integer
          title: 'Total count of genes annotated on the viral nucleotide sequence'
        mature_peptide_count:
          type: integer
          title: 'Total count of processed mature peptides annotated on the viral nucleotide sequence'
        biosample:
          type: string
          title: 'Associated Biosample accessions'
        mol_type:
          type: string
          title: 'ICTV (International Committee on Taxonomy of Viruses) viral classification based on nucleic acid composition, strandedness and method of replication'
        nucleotide:
          $ref: '#/components/schemas/v2reportsSeqRangeSetFasta'
          title: 'The whole genomic nucleotide record of the CDS feature.'
        purpose_of_sampling:
          $ref: '#/components/schemas/v2reportsPurposeOfSampling'
          title: 'SARS-CoV-2 only, indicates whether the sequence was collected randomly for epedimiology studies'
        sra_accessions:
          type: array
          items:
            type: string
        submitter:
          $ref: '#/components/schemas/v2reportsVirusAssemblySubmitterInfo'
          title: 'Name, affiliation, and country of the submitter(s)'
        lab_host:
          type: string
          title: 'This sequence is from viruses passaged in this host'
        is_lab_host:
          type: boolean
          title: 'If true, this sequence is from viruses passaged in a laboratory'
        is_vaccine_strain:
          type: boolean
          title: 'If true, this sequence is derived from a virus used as a vaccine or potential vaccine'
        segment:
          type: string
          title: 'The virus segment'
    v2reportsVirusAssemblyCollectionLocation:
      type: object
      properties:
        geographic_location:
          type: string
          title: 'Country of virus specimen collection'
        geographic_region:
          type: string
          title: 'Region of virus specimen collection'
        usa_state:
          type: string
          title: 'Two letter abbreviation of the state of the virus specifime collection (if United States)'
    v2reportsVirusAssemblySubmitterInfo:
      type: object
      properties:
        names:
          type: array
          items:
            type: string
        affiliation:
          type: string
          title: 'The submitter''s organization and/or institution'
        country:
          type: string
          title: 'The country representing the submitter''s affilation'
    v2reportsVirusDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsVirusAssembly'
        total_count:
          type: integer
          title: 'The total count of available assemblies (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.'
    v2reportsVirusGene:
      type: object
      properties:
        name:
          type: string
        gene_id:
          type: integer
        nucleotide:
          $ref: '#/components/schemas/v2reportsSeqRangeSetFasta'
          title: 'The interval on the genomic nucleotide record of the CDS feature.'
        cds:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsVirusPeptide'
    v2reportsVirusPeptide:
      type: object
      properties:
        accession:
          type: string
          title: 'Protein accession and version'
        name:
          type: string
          title: 'Protein name'
        other_names:
          type: array
          items:
            type: string
        nucleotide:
          $ref: '#/components/schemas/v2reportsSeqRangeSetFasta'
          title: 'The interval on the genomic nucleotide record of this mature-peptide feature'
        protein:
          $ref: '#/components/schemas/v2reportsSeqRangeSetFasta'
          title: 'The full polyprotein record or interval on the polyprotein for mature-peptide features'
        pdb_ids:
          type: array
          items:
            type: string
        cdd:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsConservedDomain'
        uni_prot_kb:
          $ref: '#/components/schemas/v2reportsVirusPeptideUniProtId'
          title: 'UniProt identifier'
        mature_peptide:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsVirusPeptide'
        protein_completeness:
          $ref: '#/components/schemas/v2reportsVirusPeptideViralPeptideCompleteness'
          title: 'Protein completeness'
    v2reportsVirusPeptideUniProtId:
      type: object
      properties:
        id:
          type: string
          title: 'UniProt ID'
        name:
          type: string
          title: 'UniProt name'
    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'
    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
    v2reportsWarningReplacedId:
      type: object
      properties:
        requested:
          type: string
        returned:
          type: string
    ncbieukgenev2GeneIdRequest:
      type: object
      properties:
        gene_ids:
          type: array
          items:
            type: integer
    ncbigsupgcolv2AssemblyAccessionsReply:
      type: object
      properties:
        accession:
          type: array
          items:
            type: string
    ncbigsupgcolv2AssemblyCheckMHistogramRequest:
      type: object
      properties:
        tax_id:
          type: integer
          title: 'species level'
    ncbigsupgcolv2AssemblyDataReportDraftRequest:
      type: object
      properties:
        accession:
          type: string
        _bypass_cache:
          type: string
          title: 'buf:lint:ignore FIELD_LOWER_SNAKE_CASE'
    ncbigsupgcolv2AssemblyDataReportsRequest:
      type: object
      properties:
        accessions:
          type: array
          items:
            type: string
    ncbigsupgcolv2SequenceAccessionRequest:
      type: object
      properties:
        accession:
          type: string
          title: 'Could be WGS or sequence accession'
    ncbiprotddv2ChainFootprint:
      type: object
      properties:
        query_from:
          type: integer
        query_to:
          type: integer
        dependent_from:
          type: integer
        dependent_to:
          type: integer
    ncbiprotddv2ParsedAbstract:
      type: object
      properties:
        pmid:
          type: integer
          title: 'The pubmed ID of the article'
        title:
          type: string
          title: 'Title of the article'
        authors:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2ParsedAbstractAuthor'
        epub:
          $ref: '#/components/schemas/ncbiprotddv2ParsedAbstractEpub'
          title: 'Electronic publication information'
        abstract_text:
          type: string
          title: 'Body of the abstract'
    ncbiprotddv2ParsedAbstractAuthor:
      type: object
      properties:
        surname:
          type: string
          title: 'Author''s surname'
        given_name_initials:
          type: string
          title: 'Abbreviated initials of the author''s given name'
    ncbiprotddv2ParsedAbstractEpub:
      type: object
      properties:
        journal:
          type: string
          title: 'Name of the journal'
        year:
          type: integer
          title: 'Year of publication'
        volume:
          type: integer
          title: 'Volume of publication'
        pages:
          type: string
          title: 'Pages of publication'
    ncbiprotddv2PubmedAbstractRequest:
      type: object
      properties:
        pmid:
          type: integer
          title: 'The pubmed ID of the article'
    ncbiprotddv2QueryStructureDefinition:
      type: object
      properties:
        sdid:
          type: integer
          title: 'Structure Domain ID: Unique ID for mmdb_id + chain_id + domain_number'
        mmdb_id:
          type: integer
          title: 'The MMDB ID of the structure'
        pdb_id:
          type: string
          title: 'The PDB ID of the structure'
        description:
          type: string
          title: 'Description of the structure'
        chain_id:
          type: string
          title: 'Chain name. I.e. AA'
        domain_number:
          type: integer
          title: 'Domain Number 0 is the entire chain'
        from:
          type: integer
          title: 'Domain start interval residue number.'
        to:
          type: integer
          title: 'Domain end interval residue number.'
    ncbiprotddv2SdidRequest:
      type: object
      properties:
        sdid:
          type: integer
          title: 'Structure Domain ID'
    ncbiprotddv2SimilarStructureReport:
      type: object
      properties:
        sdid:
          type: integer
          title: 'Structure Domain ID'
        structure_title:
          type: string
          title: 'PDB Structure Title'
        protein_chain_name:
          type: string
          title: 'Protein Chain Name'
        chain_id:
          type: string
          title: 'Chain ID'
        domain_number:
          type: integer
          title: 'Domain Number 0 is the entire chain'
        mmdb_id:
          type: integer
          title: 'The MMDB ID of the structure'
        pdb_id:
          type: string
          title: 'The PDB ID of the structure'
        vast_score:
          $ref: '#/components/schemas/ncbiprotddv2VastScore'
        align_id:
          type: integer
          title: 'Alignment Id'
        superkingdom_id:
          type: integer
          title: 'Superkingdom ID'
        tax_id:
          type: integer
          title: 'NCBI Taxonomy ID'
        footprints:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2ChainFootprint'
    ncbiprotddv2SimilarStructureReportPage:
      type: object
      properties:
        similar_structures:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2SimilarStructureReport'
        next_page_token:
          type: string
        total_count:
          type: integer
    ncbiprotddv2SimilarStructureRequest:
      type: object
      properties:
        sdid:
          type: string
        page_token:
          type: string
          title: 'Only needed for paging GetSimilarStructures RPC'
        redundancy_level:
          $ref: '#/components/schemas/ncbiprotddv2RedundancyLevel'
          title: 'Sort and filter fields here. Redundancy Level'
        sort_by:
          $ref: '#/components/schemas/ncbiprotddv2SortById'
        hits_per_page:
          type: integer
        sort_direction:
          $ref: '#/components/schemas/v2SortDirection'
    ncbiprotddv2StructureDataReport:
      type: object
      properties:
        pdb_id:
          type: string
          title: 'The PDB ID of the structure'
        mmdb_id:
          type: integer
          title: 'The MMDB ID of the structure'
        is_obsolete:
          type: boolean
          title: 'Marks the structure as obsolete'
        publication_pmid:
          type: array
          items:
            type: integer
        deposition_date:
          type: string
          title: 'YYYY-MM-DD formatted date of publication Example: "2023-10-01"'
        update_date:
          type: string
          title: 'YYYY-MM-DD formatted last date updated'
        experiment:
          $ref: '#/components/schemas/ncbiprotddv2StructureDataReportExperiment'
          title: 'relevant experiment data'
        chains:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2StructureDataReportBiounitChain'
        ligand_chains:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2StructureDataReportLigandChain'
        asymmetric_chains:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2StructureDataReportBiounitChain'
        asymmetric_ligands:
          type: array
          items:
            $ref: '#/components/schemas/ncbiprotddv2StructureDataReportLigandChain'
        title:
          type: string
    ncbiprotddv2StructureDataReportBiounitChain:
      type: object
      properties:
        chain_id:
          type: string
          title: 'Chain name. I.e. AA'
        tax_id:
          type: integer
          title: 'taxonomy id'
        kind:
          $ref: '#/components/schemas/ncbiprotddv2StructureDataReportKind'
          title: 'Kind of molecule. DNA, RNA, Protein, etc.'
        molecule_group:
          type: integer
          title: 'Which group of identical chains does this chain belong to'
        sdid:
          type: integer
          title: 'Unique structure identifier of the chain'
    ncbiprotddv2StructureDataReportExperiment:
      type: object
      properties:
        experimental_method:
          type: string
          title: 'The experimental method used to characterize the protein structure. I.e. x-ray diffraction, etc.'
        resolution:
          type: number
          format: float
          title: 'The resolution (in Angstroms) of a protein structure resolved by diffraction or electron microscopy.'
    ncbiprotddv2StructureDataReportLigandChain:
      type: object
      properties:
        chain_id:
          type: string
          title: 'Chain name. I.e. ZINC ION'
        kind:
          $ref: '#/components/schemas/ncbiprotddv2StructureDataReportKind'
          title: 'Kind of molecule. DNA, RNA, Protein, etc.'
        sid:
          type: integer
          title: 'Unique substance identifier'
        sdid:
          type: integer
          title: 'Unique structure identifiers'
    ncbiprotddv2StructureRequest:
      type: object
      properties:
        pdb_id:
          type: string
          title: 'The PDB ID of the structure'
        mmdb_id:
          type: integer
          title: 'The MMDB ID of the structure'
    ncbiprotddv2VastScore:
      type: object
      properties:
        vast_score:
          type: number
          format: float
          title: 'Vast Similarity Score as computed by the VAST algorithm'
        align_length:
          type: integer
          title: 'Alignment Length'
        pct_identity:
          type: number
          format: float
          title: 'Percentage Sequence Identity'
        rmsd:
          type: number
          format: float
          title: 'Root Mean Square Deviation in Angstroms'
        p_value:
          type: number
          format: float
          title: 'Statistical Significance of the similarity'
    
    v2AnnotationForAssemblyType:
      type: string
      enum:
        - DEFAULT
        - GENOME_GFF
        - GENOME_GBFF
        - RNA_FASTA
        - PROT_FASTA
        - GENOME_GTF
        - CDS_FASTA
        - GENOME_FASTA
        - SEQUENCE_REPORT
      default: DEFAULT
    
    v2AnnotationForOrganelleType:
      type: string
      enum:
        - DEFAULT
        - GENOME_FASTA
        - CDS_FASTA
        - PROTEIN_FASTA
      default: DEFAULT
    
    v2AssemblyDatasetDescriptorsFilterAssemblySource:
      type: string
      enum:
        - all
        - refseq
        - genbank
      default: all
    
    v2AssemblyDatasetDescriptorsFilterAssemblyVersion:
      type: string
      enum:
        - current
        - all_assemblies
      default: current
      title: 'The assembly status - current (latest), or all assemblies, which adds replaced and suppressed'
    
    v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter:
      type: string
      enum:
        - METAGENOME_DERIVED_UNSET
        - metagenome_derived_only
        - metagenome_derived_exclude
      default: METAGENOME_DERIVED_UNSET
    
    v2AssemblyDatasetDescriptorsFilterTypeMaterialCategory:
      type: string
      enum:
        - NONE
        - TYPE_MATERIAL
        - TYPE_MATERIAL_CLADE
        - TYPE_MATERIAL_NEOTYPE
        - TYPE_MATERIAL_REFTYPE
        - PATHOVAR_TYPE
        - TYPE_MATERIAL_SYN
      default: NONE
    
    v2AssemblyDatasetReportsRequestContentType:
      type: string
      enum:
        - COMPLETE
        - ASSM_ACC
        - PAIRED_ACC
      default: COMPLETE
    
    v2AssemblyDatasetRequestResolution:
      type: string
      enum:
        - FULLY_HYDRATED
        - DATA_REPORT_ONLY
      default: FULLY_HYDRATED
    
    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'
    
    v2CatalogApiVersion:
      type: string
      enum:
        - UNKNOWN
        - V1
        - V2
      default: UNKNOWN
    
    v2Fasta:
      type: string
      enum:
        - FASTA_UNSPECIFIED
        - FASTA_GENE
        - FASTA_RNA
        - FASTA_PROTEIN
        - FASTA_GENE_FLANK
        - FASTA_CDS
        - FASTA_5P_UTR
        - FASTA_3P_UTR
      default: FASTA_UNSPECIFIED
    
    v2FileFileType:
      type: string
      enum:
        - UNKNOWN
        - FASTA
        - GFF3
        - DATA_REPORT
        - ANNOTATION_REPORT
        - GENOMIC_NUCLEOTIDE_FASTA
        - PROTEIN_FASTA
        - GENBANK_FLAT_FILE
        - GENPEPT_FLAT_FILE
        - README
        - PDB_FILE
        - CDS_NUCLEOTIDE_FASTA
        - RNA_NUCLEOTIDE_FASTA
        - DATA_TABLE
        - SEQUENCE_REPORT
        - GTF
        - PROKARYOTE_GENE_DATA_REPORT
        - PROKARYOTE_GENE_LOCATION_DATA_REPORT
        - GENOMIC_NUCLEOTIDE_WITH_FLANK_FASTA
        - BIOSAMPLE_REPORT
        - CATALOG
        - TAXONOMY_NAMES_REPORT
      default: UNKNOWN
    
    v2GeneDatasetReportsRequestContentType:
      type: string
      enum:
        - COMPLETE
        - IDS_ONLY
        - COUNTS_ONLY
      default: COMPLETE
      title: 'Specify a specific group of values to be returned for dataset reports. These options do not apply to product reports.'
    
    v2GeneDatasetRequestContentType:
      type: string
      enum:
        - COMPLETE
        - IDS_ONLY
      default: COMPLETE
    
    v2GeneDatasetRequestGeneDatasetReportType:
      type: string
      enum:
        - DATASET_REPORT
        - PRODUCT_REPORT
      default: DATASET_REPORT
    
    v2GeneLinksReplyGeneLinkType:
      type: string
      enum:
        - DEFAULT
        - GENE_LINK
        - GDV_LINK
        - ORTHOLOG_LINK
        - MCGV_LINK
      default: DEFAULT
      title: 'Types of gene links that may be returned'
    
    v2GeneType:
      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'
    
    v2GenomeAnnotationRequestAnnotationType:
      type: string
      enum:
        - DEFAULT
        - GENOME_FASTA
        - RNA_FASTA
        - PROT_FASTA
      default: DEFAULT
    
    v2GenomeAnnotationRequestGenomeAnnotationTableFormat:
      type: string
      enum:
        - NO_TABLE
        - SUMMARY
        - PRODUCT
      default: NO_TABLE
    
    v2ImageSize:
      type: string
      enum:
        - UNSPECIFIED
        - SMALL
        - MEDIUM
      default: UNSPECIFIED
    
    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
    
    v2MicroBiggeDatasetRequestFileType:
      type: string
      enum:
        - element_fasta
        - element_flank_fasta
        - contig_fasta
        - protein_fasta
      default: FILE_TYPE_UNSPECIFIED
    
    v2MolType:
      type: string
      enum:
        - MOL_UNSPECIFIED
        - MOL_DNA
        - MOL_RNA
        - MOL_PROTEIN
        - MOL_NA
      default: MOL_UNSPECIFIED
    
    v2OrganelleMetadataRequestContentType:
      type: string
      enum:
        - COMPLETE
        - ASSM_ACC
      default: COMPLETE
    
    v2OrganelleMetadataRequestOrganelleTableFormat:
      type: string
      enum:
        - ORGANELLE_TABLE_FORMAT_NO_TABLE
        - SUMMARY
      default: ORGANELLE_TABLE_FORMAT_NO_TABLE
    
    v2OrganismQueryRequestTaxRankFilter:
      type: string
      enum:
        - species
        - higher_taxon
      default: species
    
    v2OrganismQueryRequestTaxonResourceFilter:
      type: string
      enum:
        - TAXON_RESOURCE_FILTER_ALL
        - TAXON_RESOURCE_FILTER_GENOME
        - TAXON_RESOURCE_FILTER_GENE
        - TAXON_RESOURCE_FILTER_ORGANELLE
      default: TAXON_RESOURCE_FILTER_ALL
    
    v2OrthologRequestContentType:
      type: string
      enum:
        - COMPLETE
        - IDS_ONLY
      default: COMPLETE
    
    v2RefGeneCatalogDatasetRequestFileType:
      type: string
      enum:
        - FILE_TYPE_NUCLEOTIDE
        - FILE_TYPE_NUCLEOTIDE_WITH_FLANK
        - FILE_TYPE_PROTEIN
      default: FILE_TYPE_UNSPECIFIED
    
    v2SortDirection:
      type: string
      enum:
        - SORT_DIRECTION_UNSPECIFIED
        - SORT_DIRECTION_ASCENDING
        - SORT_DIRECTION_DESCENDING
      default: SORT_DIRECTION_UNSPECIFIED
    
    v2TableFormat:
      type: string
      enum:
        - tsv
        - csv
        - jsonl
      default: tsv
    
    v2TaxonomyDatasetRequestTaxonomyReportType:
      type: string
      enum:
        - TAXONOMY_SUMMARY
        - NAMES_REPORT
      default: TAXONOMY_SUMMARY
    
    v2TaxonomyFilteredSubtreeResponseEdgeChildStatus:
      type: string
      enum:
        - UNSPECIFIED
        - HAS_MORE_CHILDREN
        - NO_VISIBLE_CHILDREN
        - ONLY_UNSPECIFIED_CHILDREN
      default: UNSPECIFIED
      title: 'HAS_MORE_CHILDREN means there are children of a valid rank that are not unspecified NO_VISIBLE_CHILDREN means there are no children at all, not even unspecified children ONLY_UNSPECIFIED_CHILDREN Means that there are children, but those children are all unspecified (e.g. environmental samples)'
    
    v2TaxonomyMetadataRequestContentType:
      type: string
      enum:
        - COMPLETE
        - TAXIDS
        - METADATA
      default: COMPLETE
    
    v2TaxonomyMetadataRequestTableFormat:
      type: string
      enum:
        - SUMMARY
      default: SUMMARY
      title: 'Optional pre-defined template for processing a tabular data request'
    
    v2ViralSequenceType:
      type: string
      enum:
        - GENOME
        - CDS
        - PROTEIN
        - NONE
      default: GENOME
    
    v2VirusDataReportRequestContentType:
      type: string
      enum:
        - COMPLETE
        - ACCESSIONS_ONLY
      default: COMPLETE
      title: 'Specify a specific group of values to be returned, currently either all fields or accessions only'
    
    v2VirusDatasetReportType:
      type: string
      enum:
        - DATASET_REPORT
        - ANNOTATION
        - BIOSAMPLE_REPORT
      default: DATASET_REPORT
    
    v2VirusTableField:
      type: string
      enum:
        - unspecified
        - nucleotide_accession
        - species_tax_id
        - species_name
        - genus
        - family
        - nucleotide_length
        - isolate_name
        - sequence_type
        - nuc_completeness
        - geo_location
        - us_state
        - host_name
        - host_tax_id
        - collection_date
        - bioproject
        - biosample
        - polyprotein_name
        - protein_name
        - protein_accession
        - protein_synonym
        - cds_span
      default: unspecified
    
    v2reportsANITypeCategory:
      type: string
      enum:
        - ANI_CATEGORY_UNKNOWN
        - claderef
        - category_na
        - neotype
        - no_type
        - pathovar
        - reftype
        - suspected_type
        - synonym
        - type
      default: ANI_CATEGORY_UNKNOWN
    
    v2reportsAssemblyLevel:
      type: string
      enum:
        - chromosome
        - scaffold
        - contig
        - complete_genome
      default: chromosome
      title: 'The level of the genome assembly: Chromosome, Scaffold, Contig or Complete Genome'
    
    v2reportsAssemblyStatus:
      type: string
      enum:
        - ASSEMBLY_STATUS_UNKNOWN
        - current
        - previous
        - suppressed
        - retired
      default: ASSEMBLY_STATUS_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
    
    v2reportsAverageNucleotideIdentityTaxonomyCheckStatus:
      type: string
      enum:
        - TAXONOMY_CHECK_STATUS_UNKNOWN
        - OK
        - Failed
        - Inconclusive
      default: TAXONOMY_CHECK_STATUS_UNKNOWN
    
    v2reportsCollectionType:
      type: string
      enum:
        - no_collection_type
        - collection_culture_collection
        - specimen_voucher
      default: no_collection_type
    
    v2reportsContentType:
      type: string
      enum:
        - COMPLETE
        - ASSM_ACC
        - PAIRED_ACC
      default: COMPLETE
    
    v2reportsCountType:
      type: string
      enum:
        - COUNT_TYPE_UNSPECIFIED
        - COUNT_TYPE_ASSEMBLY
        - COUNT_TYPE_GENE
        - COUNT_TYPE_tRNA
        - COUNT_TYPE_rRNA
        - COUNT_TYPE_snRNA
        - COUNT_TYPE_scRNA
        - COUNT_TYPE_snoRNA
        - COUNT_TYPE_PROTEIN_CODING
        - COUNT_TYPE_PSEUDO
        - COUNT_TYPE_TRANSPOSON
        - COUNT_TYPE_miscRNA
        - COUNT_TYPE_ncRNA
        - COUNT_TYPE_BIOLOGICAL_REGION
        - COUNT_TYPE_OTHER
        - COUNT_TYPE_ORGANELLE
      default: COUNT_TYPE_UNSPECIFIED
    
    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
    
    v2reportsErrorGeneErrorCode:
      type: string
      enum:
        - UNKNOWN_GENE_ERROR_CODE
        - INCOMPLETE_LOOKUP_SYMBOL
        - INVALID_TAXON_GENE_ARGUMENT
      default: UNKNOWN_GENE_ERROR_CODE
    
    v2reportsErrorOrganelleErrorCode:
      type: string
      enum:
        - UNKNOWN_ORGANELLE_ERROR_CODE
        - INVALID_ORGANELLE_TAXON
        - NO_ORGANELLES_FOR_ACCESSION
      default: UNKNOWN_ORGANELLE_ERROR_CODE
    
    v2reportsErrorTaxonomyErrorCode:
      type: string
      enum:
        - UNKNOWN_TAXONOMY_ERROR_CODE
        - INVALID_TAXONOMY_TAXON
      default: UNKNOWN_TAXONOMY_ERROR_CODE
    
    v2reportsErrorVirusErrorCode:
      type: string
      enum:
        - UNKNOWN_VIRUS_ERROR_CODE
      default: UNKNOWN_VIRUS_ERROR_CODE
    
    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'
    
    v2reportsGenomicRegionGenomicRegionType:
      type: string
      enum:
        - UNKNOWN
        - REFSEQ_GENE
        - PSEUDOGENE
        - BIOLOGICAL_REGION
        - OTHER
      default: UNKNOWN
    
    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
    
    v2reportsMapLocationMapType:
      type: string
      enum:
        - Unknown
        - Cytogenetic
        - Genetic
      default: Unknown
    
    v2reportsNameAndAuthorityNoteClassifier:
      type: string
      enum:
        - no_authority_classifier
        - effective_name
        - nomen_approbbatum
        - ictv_accepted
      default: no_authority_classifier
      title: 'Class of authority  If the authority has any special classification, such as having been effectively and validly published or having been included in an approved list.'
    
    v2reportsOrganelleTopology:
      type: string
      enum:
        - TOPOLOGY_UNKNOWN
        - Circular
        - Linear
        - Tandem
      default: TOPOLOGY_UNKNOWN
    
    v2reportsOrganelleType:
      type: string
      enum:
        - ORGANELLE_TYPE_UNKNOWN
        - Mitochondrion
        - Chloroplast
        - Plastid
        - Kinetoplast
        - Apicoplast
        - Chromatophore
        - Cyanelle
      default: ORGANELLE_TYPE_UNKNOWN
    
    v2reportsOrientation:
      type: string
      enum:
        - none
        - plus
        - minus
      default: none
    
    v2reportsProkaryoteGeneLocationCompleteness:
      type: string
      enum:
        - complete
        - partial
      default: complete
    
    v2reportsPurposeOfSampling:
      type: string
      enum:
        - PURPOSE_OF_SAMPLING_UNKNOWN
        - PURPOSE_OF_SAMPLING_BASELINE_SURVEILLANCE
      default: PURPOSE_OF_SAMPLING_UNKNOWN
    
    v2reportsRankType:
      type: string
      enum:
        - NO_RANK
        - SUPERKINGDOM
        - DOMAIN
        - REALM
        - KINGDOM
        - SUBKINGDOM
        - SUPERPHYLUM
        - SUBPHYLUM
        - PHYLUM
        - CLADE
        - SUPERCLASS
        - CLASS
        - SUBCLASS
        - INFRACLASS
        - COHORT
        - SUBCOHORT
        - SUPERORDER
        - ORDER
        - SUBORDER
        - INFRAORDER
        - PARVORDER
        - SUPERFAMILY
        - FAMILY
        - SUBFAMILY
        - GENUS
        - SUBGENUS
        - SPECIES_GROUP
        - SPECIES_SUBGROUP
        - SPECIES
        - SUBSPECIES
        - TRIBE
        - SUBTRIBE
        - FORMA
        - VARIETAS
        - STRAIN
        - SECTION
        - SUBSECTION
        - PATHOGROUP
        - SUBVARIETY
        - GENOTYPE
        - SEROTYPE
        - ISOLATE
        - MORPH
        - SERIES
        - FORMA_SPECIALIS
        - SEROGROUP
        - BIOTYPE
        - ACELLULAR_ROOT
        - CELLULAR_ROOT
      default: NO_RANK
      title: 'Rank level'
    
    v2reportsRnaType:
      type: string
      enum:
        - rna_UNKNOWN
        - premsg
        - tmRna
      default: rna_UNKNOWN
    
    v2reportsSequenceDataReportOriginType:
      type: string
      enum:
        - unknown
        - natural
        - naturally_occurring_mutant
        - artificially_mutagenized
        - artificially_engineered
        - purely_synthetic
        - other
      default: unknown
    
    v2reportsSourceDatabase:
      type: string
      enum:
        - SOURCE_DATABASE_UNSPECIFIED
        - SOURCE_DATABASE_GENBANK
        - SOURCE_DATABASE_REFSEQ
      default: SOURCE_DATABASE_UNSPECIFIED
    
    v2reportsTranscriptSelectCategory:
      type: string
      enum:
        - SELECT_UNKNOWN
        - REFSEQ_SELECT
        - MANE_SELECT
        - MANE_PLUS_CLINICAL
      default: SELECT_UNKNOWN
    
    v2reportsTranscriptTranscriptType:
      type: string
      enum:
        - UNKNOWN
        - PROTEIN_CODING
        - NON_CODING
        - PROTEIN_CODING_MODEL
        - NON_CODING_MODEL
      default: UNKNOWN
    
    v2reportsVirusAssemblyCompleteness:
      type: string
      enum:
        - UNKNOWN
        - COMPLETE
        - PARTIAL
      default: UNKNOWN
    
    v2reportsVirusPeptideViralPeptideCompleteness:
      type: string
      enum:
        - UNKNOWN
        - COMPLETE
        - PARTIAL
      default: UNKNOWN
    
    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
    
    ncbigsupgcolv2ChromosomeLocation:
      type: string
      enum:
        - LOCATION_UNKNOWN
        - APICOPLAST
        - CHLOROPLAST
        - CHROMATOPHORE
        - CHROMOPLAST
        - CYANELLE
        - HYDROGENOSOME
        - KINETOPLAST
        - LEUCOPLAST
        - MACRONUCLEAR
        - MITOCHONDRION
        - NUCLEARPROKARYOTE
        - NUCLEOMORPH
        - OTHER_LOCATION
        - PLASTID
        - PROPLASTID
        - PROVIRALPROPHAGE
        - VIRIONPHAGE
        - VIROID
      default: LOCATION_UNKNOWN
      title: 'Represents the location information for a chromosome'
    
    ncbigsupgcolv2ChromosomeType:
      type: string
      enum:
        - TYPE_UNKNOWN
        - CHROMOSOME
        - EXTRACHROM
        - LINKAGEGROUP
        - OTHER_TYPE
        - PLASMID
        - SEGMENT
      default: TYPE_UNKNOWN
      title: 'Represents the type information for a chromosome'
    
    ncbiprotddv2RedundancyLevel:
      type: string
      enum:
        - NOT_SPECIFIED
        - ALL_SEQUENCES
        - LOW
        - MEDIUM
        - HIGH
      default: NOT_SPECIFIED
    
    ncbiprotddv2SortById:
      type: string
      enum:
        - NONE
        - VAST_SCORE
        - P_VALUE
        - RMSD
        - ALIGNMENT_LENGTH
        - PCT_IDENTITY
        - ACCESSION
        - SDID
        - ALIGNMENT_ID
        - PDB_ID
        - CHAIN_NAME
        - DOMAIN_NUMBER
        - DESCRIPTION
        - TAXONOMY_ID
        - SUPERKINGDOM_ID
        - DOMAIN_NAME
      default: NONE
      title: 'Corresponds to sort @sortBy options in PubVast.dbo.getVastSimilarStructures stored procedure'
    
    ncbiprotddv2StructureDataReportKind:
      type: string
      enum:
        - DNA
        - RNA
        - PROTEIN
        - OTHER_BIOPOLYMER
        - SOLVENT
        - OTHER_NONPOLYMER
        - OTHER
      default: DNA
      title: 'Kind of molecule. DNA, RNA, Protein, etc.'
    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'