datasets.openapi.yaml

openapi: 3.0.1
info:
  title: NCBI Datasets API
  version: v2alpha
  description: '### NCBI Datasets is a resource that lets you easily gather data from
      NCBI.

      The Datasets version 2 API is still in alpha, and we''re updating it often to add new functionality,
      iron out bugs and enhance usability.

      For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/),
      and retrieve the individual data files at a later time.

    '
servers:
- url: https://api.ncbi.nlm.nih.gov/datasets/v2alpha
- url: https://dev.ncbi.nlm.nih.gov/datasets/v2alpha
tags:
- name: Genome
  description: '#### Options to explore, summarize and download assembled genomes,
    including the associated sequence, metadata and annotation.

    These genome services allow you to explore [assembled genomes](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/gca-and-gcf-explained/).  For
    a set of genomes of interest, identified by either assembly accession or taxonomic
    subtree, you can generate a summary, determine the package size, and download.

    '
- name: Gene
  description: '#### Options to explore, summarize and download sequences and metadata
    for genes and their associated transcripts and proteins.

    These gene services allow you explore [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/),
    and for genes of interest, identified by either gene-id, symbol or RefSeq sequence
    accession, download a data package including metadata (tabular and [JSON Lines](https://jsonlines.org/)
    formats), transcript and protein sequence in FASTA format.

    '
- name: Prokaryote
  description: '#### Options to explore, summarize and download sequences and metadata
    for prokaryote genes and their associated proteins.

    These gene services allow you to explore prokaryotic gene data by RefSeq protein
    sequence accession and download a data package including metadata for the gene
    including all genomic annotations as [JSON Lines](https://jsonlines.org/) format,
    gene and protein sequences in FASTA format.

    '
- name: Virus
  description: '#### Get metadata or a zip archive containing a virus genome
    or coronavirus protein dataset.

    The following files are optionally available for virus genome and/or protein
    datasets:

    * genomic.fna (genomic sequences in FASTA format)

    * cds.fna (nucleotide coding sequences in FASTA format)

    * protein.faa (protein sequences in FASTA format)

    * annotation_report.jsonl (annotation report in [JSON Lines](https://jsonlines.org/) format)

    * biosample_report.jsonl (biosample report in [JSON Lines](https://jsonlines.org/) format)


    The following files are always included in coronavirus genome and protein datasets:

    * data_report.jsonl (data report with viral metadata in JSON lines format)

    * virus_dataset.md (README containing details on sequence file data content and
    other information)

    * dataset_catalog.json (a list of files and file types included in the dataset)


    You may also request a tab-delimited table of metadata that describes the available
    virus genome and protein data.

    Virus genome datasets are available for all viruses, including SARS-CoV-2.
    Various parameters may be used for filtering and specifying the contents of the genome dataset.

    Protein datasets are available for SARS-CoV-2 only.
    '

- name: Version
  description: "#### Retrieve the current version of all services.  \nServices follow\
    \ [Semantic Versioning 2.0.0 Schema](https://semver.org/spec/v2.0.0.html).\n"


- name: Taxonomy
  description: '#### Options to explore taxonomic metadata and relationships.

    These taxonomic services allow you to browse taxonomic metadata in addition to retrieving
    parent lineages and filtered sets of child nodes for any given set of taxonomic identifiers.

    '

externalDocs:
  description: Interactively explore genome assembly datasets
  url: https://www.ncbi.nlm.nih.gov/datasets/genomes/
security:
- ApiKeyAuthHeader: []
paths:
  /genome/accession/{accessions}/download_summary:
    get:
      summary: Preview genome dataset download
      description: 'Get a download summary by accession in a JSON output format.'
      tags:
        - Genome
      operationId: genome_download_summary
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2DownloadSummary'
      parameters:
      - name: accessions
        description: 'NCBI genome assembly accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - GCF_000001405.40
              - GCF_000001635.27
            summary: Human and Mouse
          example-1:
            value: GCF_000001405.40
            summary: Human
      - name: chromosomes
        description: 'The default setting is all chromosome. Specify individual chromosome by string (1,2,MT or chr1,chr2.chrMT). Unplaced sequences are treated like their own chromosome (''Un''). The filter only applies to fasta sequence.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - 1
              - 2
              - 3
              - X
              - Y
              - MT
            summary: Selected chromosomes #1
          example-1:
            value:
              - X
              - Y
            summary: Human sex chromosomes
      - name: include_annotation_type
        description: 'Select additional types of annotation to include in the data package.  If unset, no annotation is provided.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2AnnotationForAssemblyType'
        examples:
          example-0:
            value:
              - GENOME_FASTA
              - PROT_FASTA
              - RNA_FASTA
            summary: Genomic, Transcript & Protein Sequence
          example-1:
            value:
              - GENOME_GFF
              - GENOME_GBFF
              - GENOME_GTF
              - PROT_FASTA
              - RNA_FASTA
              - CDS_FASTA, SEQUENCE_REPORT
            summary: All
      - name: _exp_debug_values
        description: 'Supports debugging, e.g. by controlling data download speeds'
        in: query
        required: false
        schema:
          type: string
  /genome/download_summary:
    post:
      summary: Preview genome dataset download by POST
      description: 'The ''GET'' version of download summary is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions).  The POST operation is provided to allow users to supply a larger number of accessions in a single request.'
      tags:
        - Genome
      operationId: genome_download_summary_by_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2DownloadSummary'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2AssemblyDatasetRequest'
            example:
              accessions:
              - GCF_000001405.40
  /genome/accession/{accessions}/dataset_report:
    get:
      summary: Get dataset reports by accessions
      description: 'Get dataset reports by accessions.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - GCF_000001405.40
              - GCF_000001635.27
            summary: Human and Mouse
          example-1:
            value: GCF_000001405.40
            summary: Human
      - name: filters.reference_only
        description: 'If true, only return reference and representative (GCF_ and GCA_) genome assemblies.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to reference & representative genomes
          example-1:
            value: false
            summary: Include reference and non-reference genomes
      - name: filters.assembly_source
        description: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
          default: all
        examples:
          example-0:
            value: refseq
            summary: Limit to RefSeq genomes
          example-1:
            value: genbank
            summary: Limit to GenBank genomes
          example-2:
            value: all
            summary: All genomes
      - name: filters.has_annotation
        description: 'Return only annotated genome assemblies'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated assemblies
          example-1:
            value: false
            summary: Return all assemblies
      - name: filters.exclude_paired_reports
        description: 'For paired (GCA/GCF) records, only return the primary record'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all assemblies
          example-1:
            value: true
            summary: Only return single record for GCA/GCF pairs
      - name: filters.exclude_atypical
        description: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones that are atypical
          example-1:
            value: true
            summary: Only return genomes that have not been classified as atypical
      - name: filters.assembly_version
        description: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
          default: current
        examples:
          example-0:
            value: current
            summary: Only return current assemblies
          example-1:
            value: all_assemblies
            summary: Return all assemblies, including suppressed and replaced
      - name: filters.assembly_level
        description: 'Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAssemblyLevel'
        examples:
          example-0:
            value:
              - chromosome
              - complete_genome
            summary: Chromosome and complete genome
          example-1:
            value:
              - scaffold
              - chromosome
              - complete_genome
            summary: Scaffold and higher
      - name: filters.first_release_date
        description: 'Only return genome assemblies that were released on or after the specified date By default, do not filter.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 01/10/2015
            summary: Jan 10, 2015
      - name: filters.last_release_date
        description: 'Only return genome assemblies that were released on or before to the specified date By default, do not filter.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 01/10/2021
            summary: Jan 10, 2021
      - name: filters.search_text
        description: 'Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: Genome Reference Consortium
            summary: Genome Reference Consortium
          example-1:
            value: GRCh38
            summary: GRCh38
          example-2:
            value: C57BL/6J
            summary: C57BL/6J
      - name: filters.is_metagenome_derived
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter'
        examples:
          example-0:
            value: metagenome_derived_exclude
            summary: Exclude metagenome derived assemblies
          example-1:
            value: metagenome_derived_only
            summary: Return only metagenome derived assemblies
      - name: filters.is_type_material
        description: 'If true, include only type materials'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of type materials
          example-1:
            value: true
            summary: Only return genomes that are classified as type materials
      - name: filters.is_ictv_exemplar
        description: 'If true, include only ICTV Exemplars'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of type ICTV exemplar
          example-1:
            value: true
            summary: Only return genomes that are classified as ICTV exemplar
      - name: filters.exclude_multi_isolate
        description: 'If true, exclude large multi-isolate projects'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of large multi-isolate projects
          example-1:
            value: true
            summary: Exclude genomes that are classified as large multi-isolate projects
      - name: tax_exact_match
        description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: table_fields
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - assminfo-accession
              - assminfo-name
            summary: Genome Accession and Name
          example-1:
            value: assminfo-accession
            summary: Just accession
      - name: returned_content
        description: 'Return either assembly accessions, or complete assembly reports'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType'
      - name: page_size
        description: 'The maximum number of genome assembly reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: page_token
        description: 'A page token is returned from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
  /genome/taxon/{taxons}/dataset_report:
    get:
      summary: Get dataset reports by taxons
      description: 'Get dataset reports by taxons.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: taxons
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy Identifier
          example-1:
            value:
              - chimpanzee
              - eastern gorilla
            summary: Common Names
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: filters.reference_only
        description: 'If true, only return reference and representative (GCF_ and GCA_) genome assemblies.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to reference & representative genomes
          example-1:
            value: false
            summary: Include reference and non-reference genomes
      - name: filters.assembly_source
        description: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
          default: all
        examples:
          example-0:
            value: refseq
            summary: Limit to RefSeq genomes
          example-1:
            value: genbank
            summary: Limit to GenBank genomes
          example-2:
            value: all
            summary: All genomes
      - name: filters.has_annotation
        description: 'Return only annotated genome assemblies'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated assemblies
          example-1:
            value: false
            summary: Return all assemblies
      - name: filters.exclude_paired_reports
        description: 'For paired (GCA/GCF) records, only return the primary record'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all assemblies
          example-1:
            value: true
            summary: Only return single record for GCA/GCF pairs
      - name: filters.exclude_atypical
        description: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones that are atypical
          example-1:
            value: true
            summary: Only return genomes that have not been classified as atypical
      - name: filters.assembly_version
        description: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
          default: current
        examples:
          example-0:
            value: current
            summary: Only return current assemblies
          example-1:
            value: all_assemblies
            summary: Return all assemblies, including suppressed and replaced
      - name: filters.assembly_level
        description: 'Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAssemblyLevel'
        examples:
          example-0:
            value:
              - chromosome
              - complete_genome
            summary: Chromosome and complete genome
          example-1:
            value:
              - scaffold
              - chromosome
              - complete_genome
            summary: Scaffold and higher
      - name: filters.first_release_date
        description: 'Only return genome assemblies that were released on or after the specified date By default, do not filter.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 01/10/2015
            summary: Jan 10, 2015
      - name: filters.last_release_date
        description: 'Only return genome assemblies that were released on or before to the specified date By default, do not filter.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 01/10/2021
            summary: Jan 10, 2021
      - name: filters.search_text
        description: 'Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: Genome Reference Consortium
            summary: Genome Reference Consortium
          example-1:
            value: GRCh38
            summary: GRCh38
          example-2:
            value: C57BL/6J
            summary: C57BL/6J
      - name: filters.is_metagenome_derived
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter'
        examples:
          example-0:
            value: metagenome_derived_exclude
            summary: Exclude metagenome derived assemblies
          example-1:
            value: metagenome_derived_only
            summary: Return only metagenome derived assemblies
      - name: filters.is_type_material
        description: 'If true, include only type materials'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of type materials
          example-1:
            value: true
            summary: Only return genomes that are classified as type materials
      - name: filters.is_ictv_exemplar
        description: 'If true, include only ICTV Exemplars'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of type ICTV exemplar
          example-1:
            value: true
            summary: Only return genomes that are classified as ICTV exemplar
      - name: filters.exclude_multi_isolate
        description: 'If true, exclude large multi-isolate projects'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of large multi-isolate projects
          example-1:
            value: true
            summary: Exclude genomes that are classified as large multi-isolate projects
      - name: tax_exact_match
        description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: table_fields
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - assminfo-accession
              - assminfo-name
            summary: Genome Accession and Name
          example-1:
            value: assminfo-accession
            summary: Just accession
      - name: returned_content
        description: 'Return either assembly accessions, or complete assembly reports'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType'
      - name: page_size
        description: 'The maximum number of genome assembly reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: page_token
        description: 'A page token is returned from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
  /genome/bioproject/{bioprojects}/dataset_report:
    get:
      summary: Get dataset reports by bioproject
      description: 'Get dataset reports by bioprojects.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: bioprojects
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: PRJNA489243
            summary: Vertebrate Genomes Project
          example-1:
            value: PRJNA31257
            summary: Human Genome Project
      - name: filters.reference_only
        description: 'If true, only return reference and representative (GCF_ and GCA_) genome assemblies.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to reference & representative genomes
          example-1:
            value: false
            summary: Include reference and non-reference genomes
      - name: filters.assembly_source
        description: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
          default: all
        examples:
          example-0:
            value: refseq
            summary: Limit to RefSeq genomes
          example-1:
            value: genbank
            summary: Limit to GenBank genomes
          example-2:
            value: all
            summary: All genomes
      - name: filters.has_annotation
        description: 'Return only annotated genome assemblies'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: true
            summary: Limit to annotated assemblies
          example-1:
            value: false
            summary: Return all assemblies
      - name: filters.exclude_paired_reports
        description: 'For paired (GCA/GCF) records, only return the primary record'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all assemblies
          example-1:
            value: true
            summary: Only return single record for GCA/GCF pairs
      - name: filters.exclude_atypical
        description: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones that are atypical
          example-1:
            value: true
            summary: Only return genomes that have not been classified as atypical
      - name: filters.assembly_version
        description: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
          default: current
        examples:
          example-0:
            value: current
            summary: Only return current assemblies
          example-1:
            value: all_assemblies
            summary: Return all assemblies, including suppressed and replaced
      - name: filters.assembly_level
        description: 'Only return genome assemblies that have one of the specified assembly levels. By default, do not filter.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAssemblyLevel'
        examples:
          example-0:
            value:
              - chromosome
              - complete_genome
            summary: Chromosome and complete genome
          example-1:
            value:
              - scaffold
              - chromosome
              - complete_genome
            summary: Scaffold and higher
      - name: filters.first_release_date
        description: 'Only return genome assemblies that were released on or after the specified date By default, do not filter.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 01/10/2015
            summary: Jan 10, 2015
      - name: filters.last_release_date
        description: 'Only return genome assemblies that were released on or before to the specified date By default, do not filter.'
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 01/10/2021
            summary: Jan 10, 2021
      - name: filters.search_text
        description: 'Only return results whose fields contain the specified search terms in their taxon, infraspecific, assembly name or submitter fields By default, do not filter'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: Genome Reference Consortium
            summary: Genome Reference Consortium
          example-1:
            value: GRCh38
            summary: GRCh38
          example-2:
            value: C57BL/6J
            summary: C57BL/6J
      - name: filters.is_metagenome_derived
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter'
        examples:
          example-0:
            value: metagenome_derived_exclude
            summary: Exclude metagenome derived assemblies
          example-1:
            value: metagenome_derived_only
            summary: Return only metagenome derived assemblies
      - name: filters.is_type_material
        description: 'If true, include only type materials'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of type materials
          example-1:
            value: true
            summary: Only return genomes that are classified as type materials
      - name: filters.is_ictv_exemplar
        description: 'If true, include only ICTV Exemplars'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of type ICTV exemplar
          example-1:
            value: true
            summary: Only return genomes that are classified as ICTV exemplar
      - name: filters.exclude_multi_isolate
        description: 'If true, exclude large multi-isolate projects'
        in: query
        required: false
        schema:
          type: boolean
          default: false
        examples:
          example-0:
            value: false
            summary: Return all selected genomes, including ones of large multi-isolate projects
          example-1:
            value: true
            summary: Exclude genomes that are classified as large multi-isolate projects
      - name: tax_exact_match
        description: 'If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: table_fields
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - assminfo-accession
              - assminfo-name
            summary: Genome Accession and Name
          example-1:
            value: assminfo-accession
            summary: Just accession
      - name: returned_content
        description: 'Return either assembly accessions, or complete assembly reports'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType'
      - name: page_size
        description: 'The maximum number of genome assembly reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.'
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: page_token
        description: 'A page token is returned from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: sort.field
        in: query
        required: false
        schema:
          type: string
      - name: sort.direction
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2SortDirection'
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
  /genome/dataset_report:
    post:
      summary: Get dataset reports by accessions
      description: 'Get a dataset report by accession.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2AssemblyDatasetReportsRequest'
  /genome/accession/{accession}/revision_history:
    get:
      summary: Get revision history for assembly by accession
      description: 'Get revision history for assembly by accession'
      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
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: GCF_000001405.40
            summary: Human
  /genome/revision_history:
    post:
      summary: Get revision history for assembly by accession
      description: ''
      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'
  /genome/accession/{accession}/sequence_reports:
    get:
      summary: Get sequence reports by accessions
      description: 'Get a sequence report by 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:
        - 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
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: GCF_000001635.27
            summary: Mouse
          example-1:
            value: GCF_000001405.40
            summary: Human
      - name: chromosomes
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - 1
              - 2
              - 3
              - X
              - Y
              - MT
            summary: Selected chromosomes #1
          example-1:
            value:
              - X
              - Y
            summary: Human sex chromosomes
      - name: role_filters
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - assembled-molecule
              - unlocalized-scaffold
              - unplaced-scaffold
            summary: All types of sequence
          example-1:
            value: assembled-molecule
            summary: Only assembled molecules
      - name: table_fields
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - accession
              - chr-name
            summary: Genome Accession and Chromosome Name
          example-1:
            value: ucsc-style-name
            summary: UCSC Name
      - name: count_assembly_unplaced
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: page_size
        description: 'The maximum number of genome 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
          default: 20
      - name: page_token
        description: 'A page token is returned from an `GetSequenceReports` call with more than `page_size` results. Use this token, along with the previous `AssemblyMetadataRequest` 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 sequence reports by accessions
      description: 'Get a sequence report by accession.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
  /genome/accession/{accessions}/links:
    get:
      summary: Get assembly links by accessions
      description: 'Get links to available assembly resources by accessions.'
      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: 'NCBI genome assembly accessions, limited to 1000'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - GCF_000001405.40
              - GCF_000001635.27
            summary: Human and Mouse
          example-1:
            value: GCF_000001405.40
            summary: Human
  /genome/links:
    post:
      summary: Get assembly links by accessions
      description: 'Get links to available assembly resources by accessions.'
      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'
            example:
              accessions:
                accessions:
                - GCF_000001405.40
  /genome/taxon/{species_taxon}/checkm_histogram:
    get:
      summary: Get CheckM histogram by species taxon
      description: 'Get CheckM histogram by species taxon. CheckM histograms are only available for certain bacterial species.'
      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
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: 202956
            summary: Acinetobacter towneri
  /genome/checkm_histogram:
    post:
      summary: Get CheckM histogram by species taxon
      description: 'Get CheckM histogram by species taxon. CheckM histograms are only available for certain bacterial species.'
      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'
  /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: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: SAMEA103927779
            summary: BioSample Identifier
  /genome/accession/{accessions}/download:
    get:
      summary: Get a genome dataset by accession
      description: 'Download a genome dataset including fasta sequence, annotation and a detailed data report by 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: 'NCBI genome assembly accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - GCF_000001405.40
              - GCF_000001635.27
            summary: Human and Mouse
          example-1:
            value: GCF_000001405.40
            summary: Human
      - name: chromosomes
        description: 'The default setting is all chromosome. Specify individual chromosome by string (1,2,MT or chr1,chr2.chrMT). Unplaced sequences are treated like their own chromosome (''Un''). The filter only applies to fasta sequence.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - 1
              - 2
              - 3
              - X
              - Y
              - MT
            summary: Selected chromosomes #1
          example-1:
            value:
              - X
              - Y
            summary: Human sex chromosomes
      - name: include_annotation_type
        description: 'Select additional types of annotation to include in the data package.  If unset, no annotation is provided.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2AnnotationForAssemblyType'
        examples:
          example-0:
            value:
              - GENOME_FASTA
              - PROT_FASTA
              - RNA_FASTA
            summary: Genomic, Transcript & Protein Sequence
          example-1:
            value:
              - GENOME_GFF
              - GENOME_GBFF
              - GENOME_GTF
              - PROT_FASTA
              - RNA_FASTA
              - CDS_FASTA, SEQUENCE_REPORT
            summary: All
      - name: hydrated
        description: 'Set to DATA_REPORT_ONLY, to only retrieve data-reports.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2AssemblyDatasetRequestResolution'
      - name: _exp_debug_values
        description: 'Supports debugging, e.g. by controlling data download speeds'
        in: query
        required: false
        schema:
          type: string
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /genome/download:
    post:
      summary: Get a genome dataset by post
      description: 'The ''GET'' version of download is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions).  The POST operation is provided to allow users to supply a larger number of accessions in a single request.'
      tags:
        - Genome
      operationId: 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'
            example:
              accessions:
              - GCF_000001405.40
      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 dataset by gene ID
      description: 'Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by gene ID.'
      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: 'NCBI gene ids'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: IL21 GeneID
          example-1:
            value:
              - 59067
              - 50615
            summary: IL21 & IL21R GeneIDs
      - name: include_annotation_type
        description: 'Select additional types of annotation to include in the data package.  If unset, no annotation is provided.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
      - name: fasta_filter
        description: 'Limit the FASTA sequences in the datasets package to these transcript and protein accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: aux_report
        description: 'list additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
        examples:
          example-0:
            value: PRODUCT_REPORT
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
          example-1:
            value: gene-id
            summary: Just GeneID
      - name: table_report_type
        description: 'Specify the report from which the table fields will be taken'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /gene/download:
    post:
      summary: Get a gene dataset by POST
      description: 'Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by POST.'
      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'
            example:
              gene_ids:
              - 59067
              - 50615
      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 dataset by RefSeq protein accession
      description: 'Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote 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: 'WP prokaryote protein accession'
        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: 'Select additional types of annotation to include in the data package.  If unset, no annotation is provided.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
        examples:
          example-0:
            value: FASTA_GENE
            summary: Gene range FASTA
          example-1:
            value:
              - FASTA_RNA
              - FASTA_PROTEIN
            summary: Transcript & protein sequence FASTA
          example-2:
            value:
              - FASTA_GENE
              - FASTA_RNA
              - FASTA_PROTEIN
            summary: All annotation
      - name: gene_flank_config.length
        in: query
        required: false
        schema:
          type: integer
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree'
        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 dataset by RefSeq protein accession by POST
      description: 'Get a prokaryote gene dataset including gene and protein fasta sequence, annotation and metadata by prokaryote protein accession by POST.'
      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'
            example:
              accessions:
              - WP_000000001.1
              - WP_000000002.1
      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 an annotation report dataset by accession
      description: 'Download an annotation report including fasta sequence and a detailed annotation report by genomic 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
        in: path
        required: true
        schema:
          type: string
      - name: annotation_ids
        description: 'Limit the reports by internal, unstable annotation ids.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: symbols
        description: 'Filter parameters'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: locations
        description: 'Locations with a chromosome or accession and optional start-stop range: chromosome|accession[:start-end]'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: gene_types
        description: 'granular gene_types'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: search_text
        in: query
        required: false
        schema:
          type: array
          items:
            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_annotation_type
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GenomeAnnotationRequestAnnotationType'
      - 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_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - 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: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: 'A page token is returned from a `GetFeatures` call with more than `page_size` results. Use this token, along with the previous `FeatureRequest` 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: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /genome/annotation_report/download:
    post:
      summary: Get an annotation report dataset by accession
      description: 'Download an annotation report including fasta sequence and a detailed annotation report by genomic 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'
      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 tax ID
      description: 'Download a taxonomy report and names data package.'
      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
              - 10090
            summary: NCBI Taxonomy Identifier
      - name: aux_reports
        description: 'list additional reports to include with download. TAXONOMY_REPORT is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyDatasetRequestTaxonomyReportType'
        examples:
          example-0:
            value:
              - NAMES_REPORT
              - TAXONOMY_SUMMARY
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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 tax_id
      description: 'Download a taxonomy report and names data package.'
      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'
            example:
              tax_ids:
              - 9606
              - 10090
      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 genome accessions
      description: 'The ''GET'' version of check is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions).  The POST operation is provided to allow users to supply a larger number of accessions in a single request.'
      tags:
        - Genome
      operationId: 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: 'NCBI genome assembly accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - GCF_000001405.40
              - GCF_000001635.27
            summary: Human and Mouse
          example-1:
            value: GCF_000001405.40
            summary: Human
      - name: _exp_debug_values
        description: 'Supports debugging, e.g. by controlling data download speeds'
        in: query
        required: false
        schema:
          type: string
  /genome/check:
    post:
      summary: Check the validity of many genome accessions in a single request
      description: 'The ''GET'' version of check is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions).  The POST operation is provided to allow users to supply a larger number of accessions in a single request.'
      tags:
        - Genome
      operationId: 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'
            example:
              accessions:
              - GCF_000001405.40
  /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:
      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: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return either gene-ids, or entire gene metadata'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
      - name: gene_ids
        description: 'NCBI gene ids'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: IL21 GeneID
          example-1:
            value:
              - 59067
              - 50615
            summary: IL21 & IL21R GeneIDs
      - 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:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
          example-1:
            value: gene-id
            summary: Just GeneID
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - 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 from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
  /gene/accession/{accessions}:
    get:
      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: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return either gene-ids, or entire gene metadata'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
      - name: accessions
        description: 'RNA or Protein accessions.'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - NM_021803.4
              - NM_181078.3
            summary: RefSeq transcripts
          example-1:
            value:
              - NP_068575.1
              - NP_851564.1
            summary: RefSeq proteins
      - 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:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
          example-1:
            value: gene-id
            summary: Just GeneID
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - 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 from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
  /gene/symbol/{symbols}/taxon/{taxon}:
    get:
      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: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return either gene-ids, or entire gene metadata'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
      - name: symbols
        description: 'Gene symbol'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: GNAS
            summary: GNAS
      - name: taxon
        description: 'Taxon for provided gene symbol'
        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'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
          example-1:
            value: gene-id
            summary: Just GeneID
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - 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 from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
  /gene/taxon/{taxon}:
    get:
      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: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: returned_content
        description: 'Return either gene-ids, or entire gene metadata'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetReportsRequestContentType'
      - name: taxon
        description: 'NCBI Taxonomy ID or name (common or scientific) that the genes are annotated at  end oneof }'
        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'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
          example-1:
            value: gene-id
            summary: Just GeneID
      - name: include_tabular_header
        description: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - 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 from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: query
        description: 'text search within gene symbol, aliases, name, and protein name'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: A2M immunoglobulin
            summary: 
      - name: types
        description: 'Gene types to filter'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
        examples:
          example-0:
            value: PROTEIN_CODING
            summary: Only protein coding genes
  /gene:
    post:
      summary: Get gene metadata as JSON
      description: 'Get a gene summary. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GeneDatasetReportsRequest'
            example:
              gene_ids:
              - 59067
              - 50615
  /gene/id/{gene_ids}/download_summary:
    get:
      summary: Get gene download summary by GeneID
      description: 'Get a download summary by GeneID in a JSON output 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: 'NCBI gene ids'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: IL21 GeneID
          example-1:
            value:
              - 59067
              - 50615
            summary: IL21 & IL21R GeneIDs
      - name: include_annotation_type
        description: 'Select additional types of annotation to include in the data package.  If unset, no annotation is provided.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2Fasta'
      - name: returned_content
        description: 'Return either gene-ids, or entire gene metadata'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetRequestContentType'
      - name: fasta_filter
        description: 'Limit the FASTA sequences in the datasets package to these transcript and protein accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: aux_report
        description: 'list additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
        examples:
          example-0:
            value: PRODUCT_REPORT
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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:
              - gene-id
              - gene-type
              - description
            summary: GeneID, type and description
          example-1:
            value: gene-id
            summary: Just GeneID
      - name: table_report_type
        description: 'Specify the report from which the table fields will be taken'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2GeneDatasetRequestGeneDatasetReportType'
  /gene/download_summary:
    post:
      summary: Get gene download summary
      description: 'Get gene download summary in a JSON output 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'
            example:
              gene_ids:
              - 59067
              - 50615
  /gene/taxon/{taxon}/counts:
    get:
      summary: Get gene counts by taxonomic identifier
      description: 'Get gene counts for a specified NCBI Taxonomy ID or name (common or scientific) 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 Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
  /gene/taxon/counts:
    post:
      summary: Get gene counts by taxonomic identifier
      description: 'Get gene counts for a specified NCBI Taxonomy ID or name (common or scientific) 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'
  /gene/id/{gene_id}/orthologs:
    get:
      summary: Get gene orthologs by gene ID
      description: 'Get a gene summary for an ortholog set by gene ID in a JSON output 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
        in: path
        required: true
        schema:
          type: integer
        examples:
          example-0:
            value: 2778
            summary: GNAS
          example-1:
            value: 2
            summary: A2M
      - name: returned_content
        description: 'Return either gene-ids, or entire gene metadata'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrthologRequestContentType'
      - name: taxon_filter
        description: 'Filter genes by taxa'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value:
              - 9606
              - 10090
            summary: NCBI Taxonomy Identifier
          example-1:
            value:
              - human
              - house mouse
            summary: Common Name
          example-2:
            value:
              - homo sapiens
              - mus musculus
            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 from an `OrthologRequest` call with more than `page_size` results. Use this token, along with the previous `OrthologRequest` 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 gene orthologs by gene ID
      description: 'Get a gene summary for an ortholog set by gene ID in a JSON output format by POST'
      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'
  /gene/id/{gene_ids}/links:
    get:
      summary: Get gene links by gene ID
      description: 'Get links to available gene resources by gene ID.'
      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: 'NCBI gene ids, limited to 1000 ids'
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 59067
            summary: IL21 GeneID
          example-1:
            value:
              - 59067
              - 50615
            summary: IL21 & IL21R GeneIDs
  /gene/links:
    post:
      summary: Get gene links by gene ID
      description: 'Get links to available gene resources by gene ID.'
      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'
            example:
              gene_ids:
              - 59067
              - 50615
  /gene/taxon/{taxon}/annotation/{annotation_name}/chromosome_summary:
    get:
      summary: Get summary of chromosomes for a particular taxon's annotation
      description: 'Get summary of chromosomes for a particular taxon''s annotation.'
      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
        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: annotation_name
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: Annotation Release 109.20211119
            summary: Human annotation release
  /genome/accession/{accession}/annotation_report:
    get:
      summary: Get genome annotation reports by genome accession
      description: 'Get genome annotation reports by genome accession.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accession
        in: path
        required: true
        schema:
          type: string
      - name: annotation_ids
        description: 'Limit the reports by internal, unstable annotation ids.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: symbols
        description: 'Filter parameters'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: locations
        description: 'Locations with a chromosome or accession and optional start-stop range: chromosome|accession[:start-end]'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: gene_types
        description: 'granular gene_types'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: search_text
        in: query
        required: false
        schema:
          type: array
          items:
            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: 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_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - 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: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: 'A page token is returned from a `GetFeatures` call with more than `page_size` results. Use this token, along with the previous `FeatureRequest` 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 accession
      description: 'Get genome annotation reports by genome accession.  By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2GenomeAnnotationRequest'
  /genome/accession/{accession}/id/{annotation_ids}/annotation_summary:
    get:
      summary: Get genome annotation report summary information
      description: 'Get genome annotation report summary information by genome accession. The return facets can be used in subsequent queries.'
      tags:
        - Genome
      operationId: annotation_report_facets
      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
        in: path
        required: true
        schema:
          type: string
      - name: annotation_ids
        description: 'Limit the reports by internal, unstable annotation ids.'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
      - 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
      description: 'Get genome annotation report summary information by genome accession. The return facets can be used in subsequent queries.'
      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'
  /genome/accession/{accession}/annotation_report/download_summary:
    get:
      summary: Preview feature dataset download
      description: 'Get a download feature summary by accession in a JSON output 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
        in: path
        required: true
        schema:
          type: string
      - name: annotation_ids
        description: 'Limit the reports by internal, unstable annotation ids.'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: symbols
        description: 'Filter parameters'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: locations
        description: 'Locations with a chromosome or accession and optional start-stop range: chromosome|accession[:start-end]'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: gene_types
        description: 'granular gene_types'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - name: search_text
        in: query
        required: false
        schema:
          type: array
          items:
            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_annotation_type
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2GenomeAnnotationRequestAnnotationType'
      - name: table_fields
        description: 'Specify which fields to include in the tabular report'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
      - 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: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
  /genome/annotation_report/download_summary:
    post:
      summary: Preview feature download by POST
      description: 'The ''GET'' version of feature download summary is limited by the size of the GET URL (2KB).  The POST operation is provided to allow users to supply a larger number of annotation_ids in a single request.'
      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'
  /taxonomy/taxon/{taxons}:
    get:
      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
              - 10090
            summary: NCBI Taxonomy Identifier
          example-1:
            value:
              - human
              - mouse
            summary: Common Name
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific Name
      - name: returned_content
        description: 'Return either tax-ids alone, or entire taxononmy-metadata records'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
      - 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: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: 'A page token is returned from `GetTaxonomyDataReportFor` and `GetTaxonomyNamesDataReportFor` calls with more than `page_size` results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: table_format
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
      - name: children
        description: 'Flag for tax explosion.'
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: 'Only include taxons of the provided ranks. If empty, return all ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy:
    post:
      summary: Use taxonomic identifiers to get taxonomic metadata by post
      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_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'
            example:
              taxons:
              - 9606
              - mouse
  /taxonomy/taxon/{taxons}/dataset_report:
    get:
      summary: Use taxonomic identifiers to get taxonomic data report
      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_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'
            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
              - 10090
            summary: NCBI Taxonomy Identifier
          example-1:
            value:
              - human
              - mouse
            summary: Common Name
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific Name
      - name: returned_content
        description: 'Return either tax-ids alone, or entire taxononmy-metadata records'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
      - 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: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: 'A page token is returned from `GetTaxonomyDataReportFor` and `GetTaxonomyNamesDataReportFor` calls with more than `page_size` results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: table_format
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
      - name: children
        description: 'Flag for tax explosion.'
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: 'Only include taxons of the provided ranks. If empty, return all ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy/dataset_report:
    post:
      summary: Use taxonomic identifiers to get taxonomic names data report by post
      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_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'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            example:
              taxons:
              - 9606
              - mouse
  /taxonomy/taxon/{taxons}/name_report:
    get:
      summary: Use taxonomic identifiers to get taxonomic names data report
      description: 'Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about associated taxonomic names.'
      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
              - 10090
            summary: NCBI Taxonomy Identifier
          example-1:
            value:
              - human
              - mouse
            summary: Common Name
          example-2:
            value:
              - Homo sapiens
              - Mus musculus
            summary: Scientific Name
      - name: returned_content
        description: 'Return either tax-ids alone, or entire taxononmy-metadata records'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
      - 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: 'Whether this request for tabular data should include the header row'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: 'A page token is returned from `GetTaxonomyDataReportFor` and `GetTaxonomyNamesDataReportFor` calls with more than `page_size` results. When `page_token` is empty, all results have been retrieved.'
        in: query
        required: false
        schema:
          type: string
      - name: table_format
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
      - name: children
        description: 'Flag for tax explosion.'
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: 'Only include taxons of the provided ranks. If empty, return all ranks.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy/name_report:
    post:
      summary: Use taxonomic identifiers to get taxonomic names data report by post
      description: 'Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about associated taxonomic names.'
      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'
            example:
              taxons:
              - 9606
              - mouse
  /taxonomy/taxon/{tax_id}/related_ids:
    get:
      summary: Use taxonomic identifier to get related taxonomic identifiers, such as children
      description: 'Using a single NCBI Taxonomy ID at any rank, get a list of related taxonomic IDs 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 Identifier
      - name: include_lineage
        description: 'If true, return reports for all taxonomy nodes in the lineages of the requested tax_id'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: include_subtree
        description: 'If true, return reports for all taxonomy nodes that are children of the requested tax_ids'
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: ranks
        description: 'Only include taxons of the provided ranks. If empty, return all 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 from a `GetRelatedTaxids` call with more than `page_size` results. Use this token, along with the previous `TaxonomyRelatedIdRequest` 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: Use taxonomic identifier to get related taxonomic identifiers, such as children
      description: 'Using a single NCBI Taxonomy ID at any rank, get a list of related taxonomic IDs 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'
            example:
              tax_id: 9606
  /taxonomy/taxon/{taxons}/filtered_subtree:
    get:
      summary: Use taxonomic identifiers to get a filtered taxonomic subtree
      description: 'Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks 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
              - 10090
            summary: NCBI Taxonomy Identifier
          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: 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'
  /taxonomy/filtered_subtree:
    post:
      summary: Use taxonomic identifiers to get a filtered taxonomic subtree by post
      description: 'Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get a filtered taxonomic subtree that includes the full parent lineage and all immediate children from the selected taxonomic ranks 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'
  /taxonomy/taxon_suggest/{taxon_query}:
    get:
      summary: Get a list of taxonomy names and IDs given a partial taxonomic name
      description: 'This endpoint retrieves a list of taxonomy names and IDs given a possibly partial taxonomic name of any rank.'
      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: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: hum
            summary: hum
      - name: tax_rank_filter
        description: 'Set the scope of searched tax ranks when filtering by gene or genome.  Not used for ''all'''
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxRankFilter'
          default: species
      - name: taxon_resource_filter
        description: 'Limit results to those with gene or genome counts (no filter by default)'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxonResourceFilter'
          default: TAXON_RESOURCE_FILTER_ALL
      - name: exact_match
        description: 'If true, only return results that exactly match the provided name or tax-id'
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /taxonomy/taxon_suggest:
    post:
      summary: Get a list of taxonomy names and IDs given a partial taxonomic name
      description: 'This endpoint retrieves a list of taxonomy names and IDs given a possibly partial taxonomic name of any rank, by post.'
      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'
  /taxonomy/taxon/{taxon}/links:
    get:
      summary: Retrieve external links associated with a taxonomic identifier.
      description: 'Using an NCBI Taxonomy ID at any rank, get the external links associated with the taxon.'
      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 Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
  /taxonomy/links:
    post:
      summary: Retrieve external links associated with a taxonomic identifier.
      description: 'Using an NCBI Taxonomy ID at any rank, get the external links associated with the taxon.'
      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'
            example:
              taxon:
              - 9606
  /taxonomy/taxon/{taxon}/image:
    get:
      summary: Retrieve image associated with a taxonomic identifier
      description: 'Using an NCBI Taxonomy ID or a name (common or scientific) at any rank, get the image associated with the taxon.'
      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 Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
      - name: image_size
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2ImageSize'
  /taxonomy/image:
    post:
      summary: Retrieve image associated with a taxonomic identifier by post
      description: 'Using an NCBI Taxonomy ID or a name (common or scientific) at any rank, get the image associated with the taxon.'
      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'
            example:
              taxon:
              - 9606
  /taxonomy/taxon/{taxon}/image/metadata:
    get:
      summary: Retrieve image metadata associated with a taxonomic identifier
      description: 'Using an NCBI Taxonomy ID or a name (common or scientific) at any rank, get the image metadata associated with the taxon.'
      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 Identifier
          example-1:
            value: human
            summary: Common Name
          example-2:
            value: Homo sapiens
            summary: Scientific Name
  /taxonomy/image/metadata:
    post:
      summary: Retrieve image metadata associated with a taxonomic identifier by post
      description: 'Using an NCBI Taxonomy ID or a name (common or scientific) at any rank, get the image metadata associated with the taxon.'
      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'
            example:
              taxon:
              - 9606
  /virus/taxon/{taxon}/genome:
    get:
      summary: Get summary data for Coronaviridae genomes by taxon
      description: 'Get summary data and download by command line instructions for Coronaviridae genomes by taxon.'
      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: 'genome sequence accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_045512.2
            summary: SARS-COV-2 isolate Wuhan-Hu-1, 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: 2697049
            summary: SARS-COV-2
          example-1:
            value: 11118
            summary: Coronaviridae
          example-2:
            value: 1335626
            summary: MERS
      - 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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 download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'list additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
  /virus/genome:
    post:
      summary: Get summary data for Coronaviridae genomes by post
      description: 'Get summary data and download by command line instructions for Coronaviridae genomes by taxon.'
      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'
  /virus/taxon/sars2/protein/{proteins}:
    get:
      summary: Summary of SARS-CoV-2 protein and CDS datasets by protein name
      description: 'Download a summary of available SARS-CoV-2 protein datasets'
      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: 'Which proteins to retrieve in the data package'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: spike protein
            summary: Spike Protein
          example-1:
            value:
              - spike protein
              - envelope protein
              - RdRp
            summary: SARS-CoV-2 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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 download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'List additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
  /virus/taxon/sars2/protein:
    post:
      summary: Summary of SARS-CoV-2 protein and CDS datasets by protein name
      description: 'Download a summary of available SARS-CoV-2 protein datasets'
      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'
  /virus/taxon/{taxon}/genome/table:
    get:
      summary: Get viral genomic metadata in a tabular format.
      description: 'Get viral genomic metadata in tabular format for Coronaviridae 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: 'genome sequence accessions'
        in: query
        required: false
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_045512.2
            summary: SARS-COV-2 isolate Wuhan-Hu-1, 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: 2697049
            summary: SARS-COV-2
          example-1:
            value: 11118
            summary: Coronaviridae
          example-2:
            value: 1335626
            summary: MERS
      - 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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:
              - nucleotide_accession
              - nucleotide_length
              - nuc_completeness
            summary: Assembly Fields
      - name: include_sequence
        description: 'specify which sequence files to include in the download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'list additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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.
      description: 'Get protein metadata in tabular format for SARS-CoV-2 genomes.'
      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: 'Which proteins to retrieve in the data package'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: spike protein
            summary: Spike Protein
          example-1:
            value:
              - spike protein
              - envelope protein
              - RdRp
            summary: SARS-CoV-2 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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:
              - nucleotide_accession
              - nucleotide_length
              - nuc_completeness
            summary: Assembly Fields
      - name: include_sequence
        description: 'Specify which sequence files to include in the download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'List additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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/{taxon}/dataset_report:
    get:
      summary: Get virus metadata by taxon
      description: 'Get virus metadata by taxon. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            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: 2697049
            summary: SARS-COV-2
          example-1:
            value: 11118
            summary: Coronaviridae
          example-2:
            value: 1335626
            summary: MERS
      - 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: Both GenBank & RefSeq 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: All genomes
      - name: filter.released_since
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: filter.host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: filter.pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: filter.geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'only include complete genomes.'
        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 either virus genome accessions, or complete virus metadata'
        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 from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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 virus metadata by accession
      description: 'Get virus metadata by accesion. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        description: 'genome sequence accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_045512.2,NC_038294.1
            summary: SARS-COV-2 isolate Wuhan-Hu-1 and Middle East respiratory syndrome-related coronavirus, complete genomes
      - 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: Both GenBank & RefSeq 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: All genomes
      - name: filter.released_since
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: filter.host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: filter.pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: filter.geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'only include complete genomes.'
        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 either virus genome accessions, or complete virus metadata'
        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 from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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 virus metadata by POST
      description: 'Get virus metadata. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2VirusDataReportRequest'
            example:
              taxon: 2697049
              refseq_only: true
  /virus/taxon/{taxon}/annotation_report:
    get:
      summary: Get virus annotation report by taxon
      description: 'Get virus annotation report by taxon. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            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: 2697049
            summary: SARS-COV-2
          example-1:
            value: 11118
            summary: Coronaviridae
          example-2:
            value: 1335626
            summary: MERS
      - 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: Both GenBank & RefSeq genomes
      - name: filter.released_since
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: filter.host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: filter.pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: filter.geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'only include complete genomes.'
        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:
            type: string
        examples:
          example-0:
            value:
              - accession
              - isolate-name
            summary: Virus Annotation 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 from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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 virus annotation report by accession
      description: 'Get virus annotation report by accesion. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: accessions
        description: 'genome sequence accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_045512.2,NC_038294.1
            summary: SARS-COV-2 isolate Wuhan-Hu-1 and Middle East respiratory syndrome-related coronavirus, complete genomes
      - 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: Both GenBank & RefSeq genomes
      - name: filter.released_since
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: filter.updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: filter.host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: filter.pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: filter.geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: filter.complete_only
        description: 'only include complete genomes.'
        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:
            type: string
        examples:
          example-0:
            value:
              - accession
              - isolate-name
            summary: Virus Annotation 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 from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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 virus annotation report by POST
      description: 'Get virus annotation report. By default, in paged JSON format, but also available as tabular (accept: x-tabular) or json-lines (accept: x-jsonlines)'
      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'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2VirusAnnotationReportRequest'
            example:
              taxon: 2697049
              refseq_only: true
  /virus/accession/{accessions}/check:
    get:
      summary: Check available viruses by accession
      description: 'Check available viruses'
      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_045512.2,NC_038294.1
            summary: SARS-COV-2 isolate Wuhan-Hu-1 and Middle East respiratory syndrome-related coronavirus, complete genomes
  /virus/check:
    post:
      summary: Check available viruses by accession
      description: 'Check available viruses'
      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'
  /virus/taxon/{taxon}/genome/download:
    get:
      summary: Download a coronavirus genome dataset by taxon
      description: 'Download a coronavirus genome dataset 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: 2697049
            summary: SARS-COV-2
          example-1:
            value: 11118
            summary: Coronaviridae
          example-2:
            value: 1335626
            summary: MERS
      - 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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 download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'list additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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: Download a coronavirus genome dataset by accession
      description: 'Download a coronavirus genome dataset by 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: 'genome sequence accessions'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: NC_045512.2
            summary: SARS-COV-2 isolate Wuhan-Hu-1, complete genome
      - 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: pangolin_classification
        description: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        in: query
        required: false
        schema:
          type: string
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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 download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - GENOME
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'list additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
      - 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 coronavirus genome dataset by post
      description: 'The ''GET'' version of download is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions).  The POST operation is provided to allow users to supply a larger number of accessions in a single request.'
      tags:
        - 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'
      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: Download SARS-CoV-2 protein and CDS datasets by protein name
      description: 'Download SARS-CoV-2 protein datasets'
      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: 'Which proteins to retrieve in the data package'
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: spike protein
            summary: Spike Protein
          example-1:
            value:
              - spike protein
              - envelope protein
              - RdRp
            summary: SARS-CoV-2 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
        description: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2020-08-01
            summary: August 1, 2020
      - name: updated_since
        in: query
        required: false
        schema:
          type: string
          format: date-time
        examples:
          example-0:
            value: 2021-07-18
            summary: July 18, 2021
      - name: host
        description: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: human
            summary: human
      - name: geo_location
        description: 'Assemblies from this location (country and state, or continent)'
        in: query
        required: false
        schema:
          type: string
        examples:
          example-0:
            value: USA
            summary: USA
          example-1:
            value: TX
            summary: Texas
      - name: complete_only
        description: 'only include complete genomes.'
        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 download'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2ViralSequenceType'
        examples:
          example-0:
            value:
              - CDS
              - PROTEIN
            summary: Select viral sequences to include
      - name: aux_report
        description: 'List additional reports to include with download. Data report is included by default.'
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2VirusDatasetReportType'
        examples:
          example-0:
            value: ANNOTATION
            summary: Select additional report types to include with download. The base data report will always be included.
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /virus/taxon/sars2/protein/download:
    post:
      summary: Download SARS-CoV-2 protein and CDS datasets by protein name by POST request
      description: 'Download SARS-CoV-2 protein datasets POST request'
      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'
      parameters:
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
components:
  securitySchemes:
    ApiKeyAuth:
      type: apiKey
      in: query
      name: api_key
    ApiKeyAuthHeader:
      type: apiKey
      in: header
      name: api-key
  schemas:
    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
    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, only return reference and representative (GCF_ and GCA_) genome assemblies.'
        assembly_source:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblySource'
          title: 'Return only RefSeq (GCF_) or GenBank (GCA_) genome assemblies'
        has_annotation:
          type: boolean
          title: 'Return only annotated genome assemblies'
        exclude_paired_reports:
          type: boolean
          title: 'For paired (GCA/GCF) records, only return the primary record'
        exclude_atypical:
          type: boolean
          title: 'If true, exclude atypical genomes, i.e. genomes that have assembly issues or are otherwise atypical'
        assembly_version:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterAssemblyVersion'
          title: 'Return all assemblies, including replaced and suppressed, or only current assemblies'
        assembly_level:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAssemblyLevel'
        first_release_date:
          type: string
          format: date-time
          title: 'Only return genome assemblies that were released on or after the specified date By default, do not filter.'
        last_release_date:
          type: string
          format: date-time
          title: 'Only return genome assemblies that were released on or before to the specified date By default, do not filter.'
        search_text:
          type: array
          items:
            type: string
        is_metagenome_derived:
          $ref: '#/components/schemas/v2AssemblyDatasetDescriptorsFilterMetagenomeDerivedFilter'
        is_type_material:
          type: boolean
          title: 'If true, include only type materials'
        is_ictv_exemplar:
          type: boolean
          title: 'If true, include only ICTV Exemplars'
        exclude_multi_isolate:
          type: boolean
          title: 'If true, exclude large multi-isolate projects'
    v2AssemblyDatasetReportsRequest:
      type: object
      properties:
        taxons:
          type: array
          items:
            type: string
        bioprojects:
          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 with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.'
        chromosomes:
          type: array
          items:
            type: string
        table_fields:
          type: array
          items:
            type: string
        returned_content:
          $ref: '#/components/schemas/v2AssemblyDatasetReportsRequestContentType'
          title: 'Return either assembly accessions, or complete assembly reports'
        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 from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        sort:
          type: array
          items:
            $ref: '#/components/schemas/v2SortField'
        include_tabular_header:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
          title: 'Whether this request for tabular data should include the header row'
        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: 'Set to DATA_REPORT_ONLY, to only retrieve data-reports.'
        include_tsv:
          type: boolean
          title: 'Set to true to include a TSV representation of the data-report.'
        _exp_debug_values:
          type: string
          title: 'Supports debugging, e.g. by controlling data download speeds'
    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
    v2AssemblyRevisionHistory:
      type: object
      properties:
        assembly_revisions:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsAssemblyRevision'
        total_count:
          type: integer
    v2AssemblyRevisionHistoryRequest:
      type: object
      properties:
        accession:
          type: string
    v2AssemblySequenceReportsRequest:
      type: object
      properties:
        accession:
          type: string
        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
        page_size:
          type: integer
          title: 'The maximum number of genome 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 `GetSequenceReports` call with more than `page_size` results. Use this token, along with the previous `AssemblyMetadataRequest` 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
    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
    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
        annotation_name:
          type: string
    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 either gene-ids, or entire gene metadata'
        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  end oneof }'
        table_fields:
          type: array
          items:
            type: string
        table_format:
          type: string
          title: 'Optional pre-defined template for processing a tabular data request'
        include_tabular_header:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
          title: 'Whether this request for tabular data should include the header row'
        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 from an `AssemblyDatasetReportsRequest` call with more than `page_size` results. Use this token, along with the previous `AssemblyDatasetReportsRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.'
        query:
          type: string
          title: 'text search within gene symbol, aliases, name, and protein name'
        types:
          type: array
          items:
            $ref: '#/components/schemas/v2GeneType'
    v2GeneDatasetReportsRequestSymbolsForTaxon:
      type: object
      properties:
        symbols:
          type: array
          items:
            type: string
        taxon:
          type: string
          title: 'Taxon for 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 either gene-ids, or entire gene metadata'
        fasta_filter:
          type: array
          items:
            type: string
        aux_report:
          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'
    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
    v2GenomeAnnotationRequest:
      type: object
      properties:
        accession:
          type: string
        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: 'Whether this request for tabular data should include the header row'
        page_token:
          type: string
          title: 'A page token is returned from a `GetFeatures` call with more than `page_size` results. Use this token, along with the previous `FeatureRequest` 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
    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.'
    v2MethodPayloadRequest:
      type: object
      properties:
        method:
          type: string
          title: 'These are a special form of base64 + special encoding to be suitable for a URI.'
        payload:
          type: string
    v2MicroBiggeDatasetRequest:
      type: object
      properties:
        opaque_solr_query:
          type: string
        files:
          type: array
          items:
            $ref: '#/components/schemas/v2MicroBiggeDatasetRequestFileType'
        element_flank_config:
          $ref: '#/components/schemas/v2MicroBiggeDatasetRequestElementFlankConfig'
    v2MicroBiggeDatasetRequestElementFlankConfig:
      type: object
      properties:
        length:
          type: integer
    v2OrganismQueryRequest:
      type: object
      properties:
        organism_query:
          type: string
        taxon_query:
          type: string
          title: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank'
        tax_rank_filter:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxRankFilter'
          title: 'Set the scope of searched tax ranks when filtering by gene or genome.  Not used for ''all'''
        taxon_resource_filter:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxonResourceFilter'
          title: 'Limit results to those with gene or genome counts (no filter by default)'
        exact_match:
          type: boolean
          title: 'If true, only return results that exactly match the provided name or tax-id'
    v2OrthologRequest:
      type: object
      properties:
        gene_id:
          type: integer
        returned_content:
          $ref: '#/components/schemas/v2OrthologRequestContentType'
          title: 'Return either gene-ids, or entire gene metadata'
        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 from an `OrthologRequest` call with more than `page_size` results. Use this token, along with the previous `OrthologRequest` 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: 'NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank When specified, return data from this taxon and its subtree'
    v2ProkaryoteGeneRequestGeneFlankConfig:
      type: object
      properties:
        length:
          type: integer
    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
          title: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        geo_location:
          type: string
          title: 'Assemblies from this location (country and state, or continent)'
        complete_only:
          type: boolean
          title: 'only include complete genomes.'
        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)'
    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)'
    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.'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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'
        rank_limits:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
    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'
    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
    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 either tax-ids alone, or entire taxononmy-metadata records'
        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: 'Whether this request for tabular data should include the header row'
        page_token:
          type: string
          title: 'A page token is returned from `GetTaxonomyDataReportFor` and `GetTaxonomyNamesDataReportFor` calls with more than `page_size` results. When `page_token` is empty, all results have been retrieved.'
        table_format:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
        children:
          type: boolean
          title: 'Flag for tax explosion.'
        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)'
        _indexed_names:
          type: array
          items:
            type: string
    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, return reports for all taxonomy nodes in the lineages of the requested tax_id'
        include_subtree:
          type: boolean
          title: 'If true, return reports for all taxonomy nodes that are children of the requested tax_ids'
        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 from a `GetRelatedTaxids` call with more than `page_size` results. Use this token, along with the previous `TaxonomyRelatedIdRequest` 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'
        refseq_only:
          type: boolean
          title: 'If true, limit results to RefSeq genomes.'
        released_since:
          type: string
          format: date-time
          title: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        pangolin_classification:
          type: string
          title: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        geo_location:
          type: string
          title: 'Assemblies from this location (country and state, or continent)'
        complete_only:
          type: boolean
          title: 'only include complete genomes.'
    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 from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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 either virus genome accessions, or complete virus metadata'
        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 from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` 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'
        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
          title: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        pangolin_classification:
          type: string
          title: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        geo_location:
          type: string
          title: 'Assemblies from this location (country and state, or continent)'
        complete_only:
          type: boolean
          title: 'only include complete genomes.'
    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'
        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
          title: 'If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as ''2020-04-01T00:00:00.000Z'''
        updated_since:
          type: string
          format: date-time
        host:
          type: string
          title: 'If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default'
        pangolin_classification:
          type: string
          title: 'If set, limit results to genomes classified to this lineage by the PangoLearn tool.'
        geo_location:
          type: string
          title: 'Assemblies from this location (country and state, or continent)'
        complete_only:
          type: boolean
          title: 'only include complete genomes.'
        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
        organism_name:
          type: string
        category:
          $ref: '#/components/schemas/v2reportsANITypeCategory'
        ani:
          type: number
          format: float
        assembly_coverage:
          type: number
          format: float
          title: 'AKA qcoverage'
        type_assembly_coverage:
          type: number
          format: float
          title: 'AKA scoverage'
    v2reportsAnnotation:
      type: object
      properties:
        assembly_accession:
          type: string
        assembly_name:
          type: string
        annotation_name:
          type: string
        annotation_release_date:
          type: string
        genomic_locations:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGenomicLocation'
    v2reportsAnnotationInfo:
      type: object
      properties:
        name:
          type: string
        provider:
          type: string
        release_date:
          type: string
        report_url:
          type: string
        stats:
          $ref: '#/components/schemas/v2reportsFeatureCounts'
        busco:
          $ref: '#/components/schemas/v2reportsBuscoStat'
        method:
          type: string
        pipeline:
          type: string
        software_version:
          type: string
        status:
          type: string
        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'
        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'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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_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 is either reference or representative genome and indicates the RefSeq project classification'
        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'
        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
    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'
        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
    v2reportsAverageNucleotideIdentity:
      type: object
      properties:
        taxonomy_check_status:
          $ref: '#/components/schemas/v2reportsAverageNucleotideIdentityTaxonomyCheckStatus'
        match_status:
          $ref: '#/components/schemas/v2reportsAverageNucleotideIdentityMatchStatus'
        submitted_organism:
          type: string
          title: 'Column 5 of ANI Report'
        submitted_species:
          type: string
          title: 'Column 6 of ANI Report'
        category:
          $ref: '#/components/schemas/v2reportsANITypeCategory'
        submitted_ani_match:
          $ref: '#/components/schemas/v2reportsANIMatch'
        best_ani_match:
          $ref: '#/components/schemas/v2reportsANIMatch'
        comment:
          type: string
    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.'
    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'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _report_format:
          type: string
          title: 'bool _first_page = 502;'
    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'
    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
    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'
    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'
        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'
    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.'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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'
        rna_type:
          $ref: '#/components/schemas/v2reportsRnaType'
        orientation:
          $ref: '#/components/schemas/v2reportsOrientation'
        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
        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
        protein_count:
          type: integer
        transcript_type_counts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTranscriptTypeCount'
        gene_groups:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsGeneGroup'
    v2reportsGeneGroup:
      type: object
      properties:
        id:
          type: string
        method:
          type: string
    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'
    v2reportsGenomeAnnotation:
      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'
        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: 'WIP - SEQUI-5271 - TODO fix breaking changes'
        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.'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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'
    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: 'Male or female'
        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'
    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.'
    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:
        definition:
          type: string
          title: 'e.g. Homo sapiens mitochondrion, complete genome'
        description:
          $ref: '#/components/schemas/v2reportsOrganelleType'
        genbank_info:
          $ref: '#/components/schemas/v2reportsSequenceInformation'
        refseq_info:
          $ref: '#/components/schemas/v2reportsSequenceInformation'
        organism:
          $ref: '#/components/schemas/v2reportsOrganism'
          title: 'Taxon from which the virus sample was isolated'
        bioprojects:
          type: array
          items:
            type: string
        gene_counts:
          $ref: '#/components/schemas/v2reportsOrganelleGeneCounts'
        length:
          type: integer
          title: 'Genome length'
        topology:
          $ref: '#/components/schemas/v2reportsOrganelleTopology'
    v2reportsOrganelleDataReports:
      type: object
      properties:
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        organelles:
          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: 'Additional details about sequence differences between the GenBank and RefSeq assemblies'
    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'
        rna_type:
          $ref: '#/components/schemas/v2reportsRnaType'
        transcripts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTranscript'
        transcript_count:
          type: integer
        protein_count:
          type: integer
        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'
    v2reportsRange:
      type: object
      properties:
        begin:
          type: string
          format: uint64
        end:
          type: string
          format: uint64
        orientation:
          $ref: '#/components/schemas/v2reportsOrientation'
        order:
          type: integer
        ribosomal_slippage:
          type: integer
          title: 'When ribosomal slippage is desired, fill out slippage amount between this and previous range.'
    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'
    v2reportsSequenceInfo:
      type: object
      properties:
        assembly_accession:
          type: string
          title: 'The GenColl 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: 'The NCBI Assembly accession of the associated assembly unit. Assembly units can include the primary assembly and non-nuclear assembly units'
        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'
        submitter_institution:
          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 (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.'
        _report_type:
          type: string
          title: 'this'
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
          title: 'The template name'
    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 (ignoring the page_size parameter).'
        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.'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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
    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)'
    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'
    v2reportsTranscriptTypeCount:
      type: object
      properties:
        type:
          $ref: '#/components/schemas/v2reportsTranscriptTranscriptType'
        count:
          type: integer
    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.'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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'
        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'
        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'
    v2reportsVirusAssemblyCollectionLocation:
      type: object
      properties:
        geographic_location:
          type: string
          title: 'Country of virus specimen collection'
        geographic_region:
          type: string
          title: 'Region of virus specimen collection'
    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.'
        _report_type:
          type: string
        _report_fields:
          type: array
          items:
            type: string
        _first_page:
          type: boolean
        _report_format:
          type: string
    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
        master_wgs_url:
          type: string
        wgs_contigs_url:
          type: string
    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
    
    v2AnnotationForAssemblyType:
      type: string
      enum:
        - GENOME_GFF
        - GENOME_GBFF
        - RNA_FASTA
        - PROT_FASTA
        - GENOME_GTF
        - CDS_FASTA
        - GENOME_FASTA
        - SEQUENCE_REPORT
      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
    
    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:
        - GDV_LINK
        - FTP_LINK
        - ASSEMBLY_PUBMED
        - BLAST_LINK
      default: DEFAULT
      title: 'Types of assembly links that may be returned'
    
    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
    
    v2GeneDatasetReportsRequestContentType:
      type: string
      enum:
        - COMPLETE
        - IDS_ONLY
        - PRODUCT
        - COUNTS_ONLY
      default: COMPLETE
      title: 'Specify a specific group of values to be returned, currently either all fields or gene-ids only'
    
    v2GeneDatasetRequestContentType:
      type: string
      enum:
        - COMPLETE
        - IDS_ONLY
      default: COMPLETE
    
    v2GeneDatasetRequestGeneDatasetReportType:
      type: string
      enum:
        - DATASET_REPORT
        - PRODUCT_REPORT
      default: DATASET_REPORT
    
    v2GeneLinksReplyGeneLinkType:
      type: string
      enum:
        - GENE_LINK
        - GDV_LINK
        - ORTHOLOG_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:
        - 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:
        - FILE_TYPE_UNSPECIFIED
        - element_fasta
        - element_flank_fasta
        - contig_fasta
        - protein_fasta
      default: FILE_TYPE_UNSPECIFIED
    
    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
      default: TAXON_RESOURCE_FILTER_ALL
    
    v2OrthologRequestContentType:
      type: string
      enum:
        - COMPLETE
        - IDS_ONLY
      default: COMPLETE
    
    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
      default: UNSPECIFIED
    
    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
        - BIOSAMPLE
      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
        - syntype
        - 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
      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
      default: COUNT_TYPE_UNSPECIFIED
    
    v2reportsErrorAssemblyErrorCode:
      type: string
      enum:
        - UNKNOWN_ASSEMBLY_ERROR_CODE
        - INVALID_BIOPROJECT_IDS
        - NO_ASSEMBLIES_FOR_BIOPROJECTS
        - INVALID_TAXON
        - MISSING_SEARCH_FIELD
      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
    
    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
    
    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
      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
        - 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
      default: NO_RANK
      title: 'Rank level'
    
    v2reportsRnaType:
      type: string
      enum:
        - rna_UNKNOWN
        - premsg
        - tmRna
      default: rna_UNKNOWN
    
    v2reportsSourceDatabase:
      type: string
      enum:
        - SOURCE_DATABASE_UNSPECIFIED
        - SOURCE_DATABASE_GENBANK
        - SOURCE_DATABASE_REFSEQ
      default: SOURCE_DATABASE_UNSPECIFIED
    
    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
    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'