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

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

    '
servers:
- url: https://api.ncbi.nlm.nih.gov/datasets/v2
security:
- ApiKeyAuthHeader: []
tags:
- name: Taxonomy
  description: '#### Options to download taxonomy data.

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

    '
paths:
  /taxonomy/taxon/{tax_ids}/download:
    get:
      summary: Get a taxonomy data package by Taxonomy ID
      description: Download a taxonomy data package, including taxonomy and names reports, as a compressed zip archive.
      tags:
      - Taxonomy
      operationId: download_taxonomy_package
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/zip:
              schema:
                format: binary
                type: string
                description: Zip compressed stream
      parameters:
      - name: tax_ids
        in: path
        required: true
        schema:
          type: array
          items:
            type: integer
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
            - 9606
            - 10090
            summary: NCBI Taxonomy IDs for human and mouse
      - name: aux_reports
        description: Specify additional report files to include in the data package. The taxonomy report is always included, and its inclusion is not affected by this parameter.
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyDatasetRequestTaxonomyReportType'
        examples:
          example-0:
            value:
            - NAMES_REPORT
            - TAXONOMY_SUMMARY
            summary: Add the names report (JSON Lines format) and taxonomy summary (TSV) files.
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /taxonomy/download:
    post:
      summary: Get a taxonomy data package by Taxonomy ID
      description: Download a taxonomy data package, including taxonomy and names reports, as a compressed zip archive.
      tags:
      - Taxonomy
      operationId: download_taxonomy_package_by_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/zip:
              schema:
                format: binary
                type: string
                description: Zip compressed stream
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyDatasetRequest'
            examples:
              Multiple TaxID examples:
                description: Taxonomy report, names report, and taxonomy summary table for human and mouse
                value:
                  tax_ids:
                  - 9606
                  - 10090
                  aux_reports:
                  - NAMES_REPORT
                  - TAXONOMY_SUMMARY
      parameters:
      - name: filename
        description: Output file name.
        in: query
        required: false
        schema:
          type: string
          default: ncbi_dataset.zip
  /taxonomy/taxon/{taxons}:
    get:
      deprecated: true
      summary: Use taxonomic identifiers to get taxonomic metadata
      description: Using NCBI Taxonomy IDs or names (common or scientific) at any rank, get metadata about a taxonomic node including taxonomic identifiers, lineage information, child nodes, and gene and genome counts in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_metadata
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyMetadataResponse'
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
            - human
            - house mouse
            summary: Common names
          example-2:
            value:
            - Homo sapiens
            - Mus musculus
            summary: Scientific names
      - name: returned_content
        description: Return complete taxonomy reports, Taxonomy IDs only, or reports without assembly and gene counts (metadata).
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
        examples:
          example-0:
            value: TAXIDS
            summary: Return Taxonomy IDs only
          example-1:
            value: METADATA
            summary: Return abbreviated taxonomy report without genome assembly and gene counts
      - name: page_size
        description: The maximum number of taxons to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: include_tabular_header
        description: Specify when to include the table header when requesting a tabular report.
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
        in: query
        required: false
        schema:
          type: string
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
        examples:
          example-0:
            value: SUMMARY
            summary: This template specifies a basic set of fields available from the taxonomy report
      - name: children
        description: If true, return results for child taxa.
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: Limit results to taxa of the specified ranks.
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy:
    post:
      deprecated: true
      summary: Get taxonomy metadata by taxon
      description: Get taxonomy metadata by taxon in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_metadata_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyMetadataResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            examples:
              Multiple TaxID and common name examples:
                description: NCBI Taxonomy ID for human and common name for Mus musculus
                value:
                  taxons:
                  - '9606'
                  - house mouse
  /taxonomy/taxon/{taxons}/dataset_report:
    get:
      summary: Get a taxonomy data report by taxon
      description: 'Get a taxonomy data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.'
      tags:
      - Taxonomy
      operationId: taxonomy_data_report
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
            - human
            - house mouse
            summary: Common names
          example-2:
            value:
            - Homo sapiens
            - Mus musculus
            summary: Scientific names
      - name: returned_content
        description: Return complete taxonomy reports, Taxonomy IDs only, or reports without assembly and gene counts (metadata).
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
        examples:
          example-0:
            value: TAXIDS
            summary: Return Taxonomy IDs only
          example-1:
            value: METADATA
            summary: Return abbreviated taxonomy report without genome assembly and gene counts
      - name: page_size
        description: The maximum number of taxons to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: include_tabular_header
        description: Specify when to include the table header when requesting a tabular report.
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
      - name: page_token
        description: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
        in: query
        required: false
        schema:
          type: string
      - name: table_format
        description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
        examples:
          example-0:
            value: SUMMARY
            summary: This template specifies a basic set of fields available from the taxonomy report
      - name: children
        description: If true, return results for child taxa.
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: Limit results to taxa of the specified ranks.
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy/dataset_report:
    post:
      summary: Get a taxonomy data report by taxon
      description: 'Get a taxonomy data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.'
      tags:
      - Taxonomy
      operationId: taxonomy_data_report_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyDataReportPage'
            application/x-ndjson:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyDataReportPage'
            text/tab-separated-values:
              schema:
                type: string
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            examples:
              Multiple TaxID and common name examples:
                description: NCBI Taxonomy ID for human and common name for Mus musculus
                value:
                  taxons:
                  - '9606'
                  - house mouse
  /taxonomy/taxon/{taxons}/name_report:
    get:
      summary: Get a taxonomy names report by taxon
      description: Get a taxonomy names report, including common names and other synonyms, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_names
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyNamesDataReportPage'
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
            - human
            - house mouse
            summary: Common names
          example-2:
            value:
            - Homo sapiens
            - Mus musculus
            summary: Scientific names
      - name: page_size
        description: The maximum number of taxons to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: page_token
        description: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
        in: query
        required: false
        schema:
          type: string
      - name: children
        description: If true, return results for child taxa.
        in: query
        required: false
        schema:
          type: boolean
      - name: ranks
        description: Limit results to taxa of the specified ranks.
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
  /taxonomy/name_report:
    post:
      summary: Get a taxonomy names report by taxon
      description: Get a taxonomy names report, including common names and other synonyms, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_names_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2reportsTaxonomyNamesDataReportPage'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyMetadataRequest'
            examples:
              Multiple TaxID and common name examples:
                description: NCBI Taxonomy ID for human and common name for Mus musculus
                value:
                  taxons:
                  - '9606'
                  - house mouse
  /taxonomy/taxon/{tax_id}/related_ids:
    get:
      summary: Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
      description: Get child nodes, and optionally parent nodes, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_related_ids
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyTaxIdsPage'
      parameters:
      - name: tax_id
        in: path
        required: true
        schema:
          type: integer
        examples:
          example-0:
            value: 9606
            summary: NCBI Taxonomy ID for human
      - name: include_lineage
        description: If true, include parent nodes
        in: query
        required: false
        schema:
          type: boolean
          default: false
      - name: ranks
        description: Limit to taxonomic nodes from the given ranks.
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
      - name: page_size
        description: The maximum number of taxids to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
        in: query
        required: false
        schema:
          type: integer
          default: 20
      - name: page_token
        description: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
        in: query
        required: false
        schema:
          type: string
  /taxonomy/related_ids:
    post:
      summary: Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
      description: Get child nodes, and optionally parent nodes, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_related_ids_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyTaxIdsPage'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyRelatedIdRequest'
            examples:
              Single TaxID example:
                description: Child and parent nodes for human
                value:
                  tax_id: 9606
                  include_lineage: true
  /taxonomy/taxon/{taxons}/filtered_subtree:
    get:
      summary: Get a filtered taxonomic subtree by taxon
      description: Get a filtered taxonomic subtree, including parent and child nodes, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_filtered_subtree
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponse'
      parameters:
      - name: taxons
        in: path
        required: true
        schema:
          type: array
          items:
            type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
          example-1:
            value:
            - human
            - mouse
            summary: Common Name
          example-2:
            value:
            - Homo sapiens
            - Mus musculus
            summary: Scientific Name
      - name: specified_limit
        description: Limit to specified species
        in: query
        required: false
        schema:
          type: boolean
      - name: exclude_extinct
        description: Limit to species that are not extinct
        in: query
        required: false
        schema:
          type: boolean
      - name: levels
        description: Number of taxonomic levels to return with a valid range of 1-5. Values above 5 will return 5 levels and if level is 0 or not specified, 1 level will be returned.
        in: query
        required: false
        schema:
          type: integer
      - name: rank_limits
        description: Limit to the provided ranks.  If empty, accept any rank.
        in: query
        required: false
        schema:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
      - name: include_incertae_sedis
        description: Include nodes with ranks not in 'rank_limits' if their names meet criteria for incertae sedis (of unknown origin).
        in: query
        required: false
        schema:
          type: boolean
  /taxonomy/filtered_subtree:
    post:
      summary: Get a filtered taxonomic subtree by taxon
      description: Get a filtered taxonomic subtree, including parent and child nodes, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_filtered_subtree_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeRequest'
            examples:
              Multiple TaxID example:
                description: NCBI Taxonomy IDs for human and mouse
                value:
                  taxons:
                  - '9606'
                  - '10090'
  /taxonomy/taxon_suggest/{taxon_query}:
    get:
      summary: Get a list of taxonomy names and IDs by partial taxonomic name
      description: Get a list of taxonomy names and IDs in JSON format.
      tags:
      - Taxonomy
      operationId: tax_name_query
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2SciNameAndIds'
      parameters:
      - name: taxon_query
        description: Taxonomy ID or name (common or scientific) at any taxonomic rank
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: hum
            summary: Partial taxonomic name for human
      - name: tax_rank_filter
        description: Optionally return results for taxonomic ranks above species using `higher_taxon`
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxRankFilter'
          default: species
      - name: taxon_resource_filter
        description: Limit to taxonomy nodes with gene, genome or organelle data
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxonResourceFilter'
          default: TAXON_RESOURCE_FILTER_ALL
        examples:
          example-0:
            value: TAXON_RESOURCE_FILTER_GENOME
            summary: Limit to nodes with genome data
          example-1:
            value: TAXON_RESOURCE_FILTER_GENE
            summary: Limit to nodes with gene data
      - name: exact_match
        description: If true, only return results that exactly match the provided taxonomic name
        in: query
        required: false
        schema:
          type: boolean
          default: false
  /taxonomy/taxon_suggest:
    post:
      summary: Get a list of taxonomy names and IDs by partial taxonomic name
      description: Get a list of taxonomy names and IDs in JSON format.
      tags:
      - Taxonomy
      operationId: tax_name_query_by_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2SciNameAndIds'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2OrganismQueryRequest'
            examples:
              Incomplete taxon name example:
                description: Partial taxonomic name for human
                value:
                  taxon_query: hum
  /taxonomy/taxon/{taxon}/links:
    get:
      summary: Get external links by Taxonomy ID
      description: Get external links associated with a given taxon in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_links
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyLinksResponse'
      parameters:
      - name: taxon
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
  /taxonomy/links:
    post:
      summary: Get external links by Taxonomy ID
      description: Get external links associated with a given taxon in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_links_by_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyLinksResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyLinksRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: '9606'
  /taxonomy/taxon/{taxon}/image:
    get:
      summary: Get a taxonomy image by taxon
      description: 'Get an image associated with the specified taxon. By default, in JPEG format, but also available in PNG (accept: image/png), TIFF (accept: accept: image/tiff), and SVG+XML (accept: image/svg+xml) formats.'
      tags:
      - Taxonomy
      operationId: taxonomy_image
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            image/jpeg:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/png:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/gif:
              schema:
                $ref: '#/components/schemas/v2HttpBody'
            image/tiff:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/svg+xml:
              schema:
                format: binary
                type: string
                description: SVG Image stream
      parameters:
      - name: taxon
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
      - name: image_size
        in: query
        required: false
        schema:
          $ref: '#/components/schemas/v2ImageSize'
  /taxonomy/image:
    post:
      summary: Get a taxonomy image by taxon
      description: 'Get an image associated with the specified taxon. By default, in JPEG format, but also available in PNG (accept: image/png), TIFF (accept: accept: image/tiff), and SVG+XML (accept: image/svg+xml) formats.'
      tags:
      - Taxonomy
      operationId: taxonomy_image_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            image/jpeg:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/png:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/tiff:
              schema:
                format: binary
                type: string
                description: Image stream (jpeg/png/tiff)
            image/svg+xml:
              schema:
                format: binary
                type: string
                description: SVG Image stream
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyImageRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: '9606'
  /taxonomy/taxon/{taxon}/image/metadata:
    get:
      summary: Get taxonomy image metadata by Taxonomy ID
      description: Get taxonomy image metadata, including the image URL and license information, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_image_metadata
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyImageMetadataResponse'
      parameters:
      - name: taxon
        in: path
        required: true
        schema:
          type: string
        examples:
          example-0:
            value: '9606'
            summary: NCBI Taxonomy ID for human
  /taxonomy/image/metadata:
    post:
      summary: Get taxonomy image metadata by Taxonomy ID
      description: Get taxonomy image metadata, including the image URL and license information, in JSON format.
      tags:
      - Taxonomy
      operationId: taxonomy_image_metadata_post
      responses:
        default:
          description: An unexpected error response.
          content:
            text/plain:
              schema:
                $ref: '#/components/schemas/rpcStatus'
        '200':
          description: A successful response
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/v2TaxonomyImageMetadataResponse'
      requestBody:
        required: true
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/v2TaxonomyImageMetadataRequest'
            examples:
              Single TaxID example:
                description: NCBI Taxonomy ID for human
                value:
                  taxon: '9606'
components:
  schemas:
    v2OrganismQueryRequest:
      type: object
      properties:
        organism_query:
          type: string
        taxon_query:
          type: string
          title: Taxonomy ID or name (common or scientific) at any taxonomic rank
        tax_rank_filter:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxRankFilter'
          title: Optionally return results for taxonomic ranks above species using `higher_taxon`
        taxon_resource_filter:
          $ref: '#/components/schemas/v2OrganismQueryRequestTaxonResourceFilter'
          title: Limit to taxonomy nodes with gene, genome or organelle data
        exact_match:
          type: boolean
          title: If true, only return results that exactly match the provided taxonomic name
    v2TaxonomyFilteredSubtreeResponseEdgeChildStatus:
      type: string
      enum:
      - UNSPECIFIED
      - HAS_MORE_CHILDREN
      - NO_VISIBLE_CHILDREN
      - ONLY_UNSPECIFIED_CHILDREN
      default: UNSPECIFIED
      title: HAS_MORE_CHILDREN means there are children of a valid rank that are not unspecified NO_VISIBLE_CHILDREN means there are no children at all, not even unspecified children ONLY_UNSPECIFIED_CHILDREN Means that there are children, but those children are all unspecified (e.g. environmental samples)
    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
    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)
    v2reportsClassification:
      type: object
      properties:
        superkingdom:
          $ref: '#/components/schemas/v2reportsTaxData'
        kingdom:
          $ref: '#/components/schemas/v2reportsTaxData'
        phylum:
          $ref: '#/components/schemas/v2reportsTaxData'
        class:
          $ref: '#/components/schemas/v2reportsTaxData'
        order:
          $ref: '#/components/schemas/v2reportsTaxData'
        family:
          $ref: '#/components/schemas/v2reportsTaxData'
        genus:
          $ref: '#/components/schemas/v2reportsTaxData'
        species:
          $ref: '#/components/schemas/v2reportsTaxData'
        domain:
          $ref: '#/components/schemas/v2reportsTaxData'
          title: 'NOTE: These are out of order'
        realm:
          $ref: '#/components/schemas/v2reportsTaxData'
        acellular_root:
          $ref: '#/components/schemas/v2reportsTaxData'
    v2reportsTaxData:
      type: object
      properties:
        name:
          type: string
          title: Taxonomic name
        id:
          type: integer
          title: NCBI Taxonomy identifier
    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)
    v2OrganismQueryRequestTaxRankFilter:
      type: string
      enum:
      - species
      - higher_taxon
      default: species
    v2reportsTaxonomyNamesDescriptorCitation:
      type: object
      properties:
        full_citation:
          type: string
        short_citation:
          type: string
        pmid:
          type: string
          format: uint64
    v2reportsErrorGeneErrorCode:
      type: string
      enum:
      - UNKNOWN_GENE_ERROR_CODE
      - INCOMPLETE_LOOKUP_SYMBOL
      - INVALID_TAXON_GENE_ARGUMENT
      default: UNKNOWN_GENE_ERROR_CODE
    v2reportsTaxonomyDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyReportMatch'
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        total_count:
          type: integer
          title: The total count of available taxons - deprecated because it not supported for multiple-page results.
        next_page_token:
          type: string
          title: A token that can be sent as `page_token` to retrieve the next page. If this field is omitted, there are no subsequent pages.
    v2TaxonomyDatasetRequestTaxonomyReportType:
      type: string
      enum:
      - TAXONOMY_SUMMARY
      - NAMES_REPORT
      default: TAXONOMY_SUMMARY
    v2TaxonomyImageMetadataResponse:
      type: object
      properties:
        tax_id:
          type: string
        src:
          type: string
        license:
          type: string
        attribution:
          type: string
        source:
          type: string
        image_sizes:
          type: array
          items:
            $ref: '#/components/schemas/v2ImageSize'
        format:
          type: string
        license_url:
          type: string
    v2TaxonomyRelatedIdRequest:
      type: object
      properties:
        tax_id:
          type: integer
        include_lineage:
          type: boolean
          title: If true, include parent nodes
        include_subtree:
          type: boolean
          title: This field is deprecated because all requests include the subtree, so it has no effect
        ranks:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
        page_size:
          type: integer
          title: The maximum number of taxids to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
        page_token:
          type: string
          title: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
    v2TaxonomyFilteredSubtreeResponseEdgesEntry:
      description: A map.
      properties:
        default:
          $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdge'
      additionalProperties:
        $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdge'
    v2TaxonomyDatasetRequest:
      type: object
      properties:
        tax_ids:
          type: array
          items:
            type: integer
        aux_reports:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyDatasetRequestTaxonomyReportType'
    v2TaxonomyImageMetadataRequest:
      type: object
      properties:
        taxon:
          type: string
    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'
    v2reportsTaxonomyNode:
      type: object
      properties:
        tax_id:
          type: integer
          title: NCBI Taxonomy identifier
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
          title: The taxonomic rank of the taxonomic node.
        current_scientific_name:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: The currently accepted name chosen out of all synonyms for the taxonomic node.
        basionym:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: The originally described name, no longer in use. Attached to the type material and species description.
        curator_common_name:
          type: string
          title: The canonical common name.
        group_name:
          type: string
          title: A common name describing large, well-known taxa.
        has_type_material:
          type: boolean
          title: A boolean that indicates whether or not type material is available for the species.
        classification:
          $ref: '#/components/schemas/v2reportsClassification'
          title: A subset of parent nodes including well-established ranks.
        parents:
          type: array
          items:
            type: integer
        children:
          type: array
          items:
            type: integer
        counts:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyNodeCountByType'
        genomic_moltype:
          type: string
          title: Genomic molecule type (dsDNA, ssDNA, ssDNA(-), ssRNA)
        current_scientific_name_is_formal:
          type: boolean
          title: Specify if the current scientific name is considered 'formal' or not.
        secondary_tax_ids:
          type: array
          items:
            type: integer
        extinct:
          type: boolean
          title: True if organism is extinct
    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'
    v2reportsTaxonomyNodeCountByType:
      type: object
      properties:
        type:
          $ref: '#/components/schemas/v2reportsCountType'
        count:
          type: integer
    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.
    v2ImageSize:
      type: string
      enum:
      - UNSPECIFIED
      - SMALL
      - MEDIUM
      default: UNSPECIFIED
    v2reportsErrorAssemblyErrorCode:
      type: string
      enum:
      - UNKNOWN_ASSEMBLY_ERROR_CODE
      - INVALID_BIOPROJECT_IDS
      - NO_ASSEMBLIES_FOR_BIOPROJECTS
      - INVALID_TAXON
      - MISSING_SEARCH_FIELD
      - INVALID_BIOSAMPLE_IDS
      - NO_ASSEMBLIES_FOR_BIOSAMPLE_IDS
      - NO_ASSEMBLIES_FOR_ASSEMBLY_NAMES
      - INVALID_WGS_ACCESSIONS
      - NO_ASSEMBLIES_FOR_WGS_ACCESSIONS
      default: UNKNOWN_ASSEMBLY_ERROR_CODE
    v2TaxonomyLinksResponseGenericLink:
      type: object
      properties:
        link_name:
          type: string
        link_url:
          type: string
    v2reportsTaxonomyNamesDataReportPage:
      type: object
      properties:
        reports:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyNamesReportMatch'
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        total_count:
          type: integer
          title: The total count of available taxons - deprecated because it not supported for multiple-page results.
        next_page_token:
          type: string
          title: A page token.  A token that can be used in a future request as `page_token` to retrieve the next page. If this field is emtpy then there are no subsequent pages available.
    v2TaxonomyMetadataRequest:
      type: object
      properties:
        taxons:
          type: array
          items:
            type: string
        returned_content:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestContentType'
          title: Return complete taxonomy reports, Taxonomy IDs only, or reports without assembly and gene counts (metadata).
        page_size:
          type: integer
          title: The maximum number of taxons to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
        include_tabular_header:
          $ref: '#/components/schemas/v2IncludeTabularHeader'
          title: Specify when to include the table header when requesting a tabular report.
        page_token:
          type: string
          title: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
        table_format:
          $ref: '#/components/schemas/v2TaxonomyMetadataRequestTableFormat'
          title: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
        children:
          type: boolean
          title: If true, return results for child taxa.
        ranks:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
    v2reportsErrorVirusErrorCode:
      type: string
      enum:
      - UNKNOWN_VIRUS_ERROR_CODE
      default: UNKNOWN_VIRUS_ERROR_CODE
    v2TaxonomyMetadataRequestContentType:
      type: string
      enum:
      - COMPLETE
      - TAXIDS
      - METADATA
      default: COMPLETE
    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
    v2reportsErrorTaxonomyErrorCode:
      type: string
      enum:
      - UNKNOWN_TAXONOMY_ERROR_CODE
      - INVALID_TAXONOMY_TAXON
      default: UNKNOWN_TAXONOMY_ERROR_CODE
    rpcStatus:
      type: object
      properties:
        code:
          type: integer
          format: int32
        message:
          type: string
        details:
          type: array
          items:
            $ref: '#/components/schemas/protobufAny'
    v2OrganismQueryRequestTaxonResourceFilter:
      type: string
      enum:
      - TAXON_RESOURCE_FILTER_ALL
      - TAXON_RESOURCE_FILTER_GENOME
      - TAXON_RESOURCE_FILTER_GENE
      - TAXON_RESOURCE_FILTER_ORGANELLE
      default: TAXON_RESOURCE_FILTER_ALL
    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
    v2reportsError:
      type: object
      properties:
        assembly_error_code:
          $ref: '#/components/schemas/v2reportsErrorAssemblyErrorCode'
        gene_error_code:
          $ref: '#/components/schemas/v2reportsErrorGeneErrorCode'
        organelle_error_code:
          $ref: '#/components/schemas/v2reportsErrorOrganelleErrorCode'
        virus_error_code:
          $ref: '#/components/schemas/v2reportsErrorVirusErrorCode'
        taxonomy_error_code:
          $ref: '#/components/schemas/v2reportsErrorTaxonomyErrorCode'
        reason:
          type: string
        message:
          type: string
        invalid_identifiers:
          type: array
          items:
            type: string
    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'
    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'
    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'
    v2TaxonomyImageRequest:
      type: object
      properties:
        taxon:
          type: string
        image_size:
          $ref: '#/components/schemas/v2ImageSize'
    v2TaxonomyFilteredSubtreeResponseEdge:
      type: object
      properties:
        visible_children:
          type: array
          items:
            type: integer
        children_status:
          $ref: '#/components/schemas/v2TaxonomyFilteredSubtreeResponseEdgeChildStatus'
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
        scientific_name:
          type: string
        curator_common_name:
          type: string
        assembly_count:
          type: integer
    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.
    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)
    v2TaxonomyMetadataResponse:
      type: object
      properties:
        messages:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsMessage'
        taxonomy_nodes:
          type: array
          items:
            $ref: '#/components/schemas/v2TaxonomyMatch'
    v2reportsRankType:
      type: string
      enum:
      - NO_RANK
      - SUPERKINGDOM
      - DOMAIN
      - REALM
      - KINGDOM
      - SUBKINGDOM
      - SUPERPHYLUM
      - SUBPHYLUM
      - PHYLUM
      - CLADE
      - SUPERCLASS
      - CLASS
      - SUBCLASS
      - INFRACLASS
      - COHORT
      - SUBCOHORT
      - SUPERORDER
      - ORDER
      - SUBORDER
      - INFRAORDER
      - PARVORDER
      - SUPERFAMILY
      - FAMILY
      - SUBFAMILY
      - GENUS
      - SUBGENUS
      - SPECIES_GROUP
      - SPECIES_SUBGROUP
      - SPECIES
      - SUBSPECIES
      - TRIBE
      - SUBTRIBE
      - FORMA
      - VARIETAS
      - STRAIN
      - SECTION
      - SUBSECTION
      - PATHOGROUP
      - SUBVARIETY
      - GENOTYPE
      - SEROTYPE
      - ISOLATE
      - MORPH
      - SERIES
      - FORMA_SPECIALIS
      - SEROGROUP
      - BIOTYPE
      - ACELLULAR_ROOT
      - CELLULAR_ROOT
      default: NO_RANK
      title: Rank level
    v2TaxonomyMetadataRequestTableFormat:
      type: string
      enum:
      - SUMMARY
      default: SUMMARY
      title: Optional pre-defined template for processing a tabular data request
    v2SciNameAndIds:
      type: object
      properties:
        sci_name_and_ids:
          type: array
          items:
            $ref: '#/components/schemas/v2SciNameAndIdsSciNameAndId'
    v2reportsMessage:
      type: object
      properties:
        error:
          $ref: '#/components/schemas/v2reportsError'
        warning:
          $ref: '#/components/schemas/v2reportsWarning'
    v2reportsTaxonomyNamesDescriptor:
      type: object
      properties:
        tax_id:
          type: string
          format: uint64
          title: NCBI Taxonomy identifier
        rank:
          $ref: '#/components/schemas/v2reportsRankType'
          title: The taxonomic rank of the taxonomic node.
        current_scientific_name:
          $ref: '#/components/schemas/v2reportsNameAndAuthority'
          title: The currently accepted name chosen out of all synonyms for the taxonomic node.
        group_name:
          type: string
          title: Group name for the species.
        curator_common_name:
          type: string
          title: The canonical common name.
        other_common_names:
          type: array
          items:
            type: string
        general_notes:
          type: array
          items:
            type: string
        links_from_type:
          type: string
          title: TBD
        citations:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsTaxonomyNamesDescriptorCitation'
        current_scientific_name_is_formal:
          type: boolean
          title: Specify if the current scientific name is considered 'formal' or not.
    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
    v2TaxonomyNodeCountByType:
      type: object
      properties:
        type:
          $ref: '#/components/schemas/v2reportsCountType'
        count:
          type: integer
    v2reportsErrorOrganelleErrorCode:
      type: string
      enum:
      - UNKNOWN_ORGANELLE_ERROR_CODE
      - INVALID_ORGANELLE_TAXON
      - NO_ORGANELLES_FOR_ACCESSION
      default: UNKNOWN_ORGANELLE_ERROR_CODE
    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.
    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.
    v2reportsCollectionType:
      type: string
      enum:
      - no_collection_type
      - collection_culture_collection
      - specimen_voucher
      default: no_collection_type
    v2TaxonomyFilteredSubtreeRequest:
      type: object
      properties:
        taxons:
          type: array
          items:
            type: string
        specified_limit:
          type: boolean
          title: Limit to specified species
        exclude_extinct:
          type: boolean
          title: Limit to species that are not extinct
        levels:
          type: integer
          title: Number of taxonomic levels to return with a valid range of 1-5. Values above 5 will return 5 levels and if level is 0 or not specified, 1 level will be returned.
        rank_limits:
          type: array
          items:
            $ref: '#/components/schemas/v2reportsRankType'
        include_incertae_sedis:
          type: boolean
          title: Include nodes with ranks not in 'rank_limits' if their names meet criteria for incertae sedis (of unknown origin).
    v2reportsCountType:
      type: string
      enum:
      - COUNT_TYPE_UNSPECIFIED
      - COUNT_TYPE_ASSEMBLY
      - COUNT_TYPE_GENE
      - COUNT_TYPE_tRNA
      - COUNT_TYPE_rRNA
      - COUNT_TYPE_snRNA
      - COUNT_TYPE_scRNA
      - COUNT_TYPE_snoRNA
      - COUNT_TYPE_PROTEIN_CODING
      - COUNT_TYPE_PSEUDO
      - COUNT_TYPE_TRANSPOSON
      - COUNT_TYPE_miscRNA
      - COUNT_TYPE_ncRNA
      - COUNT_TYPE_BIOLOGICAL_REGION
      - COUNT_TYPE_OTHER
      - COUNT_TYPE_ORGANELLE
      default: COUNT_TYPE_UNSPECIFIED
    v2reportsNameAndAuthorityPublication:
      type: object
      properties:
        name:
          type: string
          title: Name of the publication (article, book, etc.).
        citation:
          type: string
          title: Citation to the publication.
        pmid:
          type: string
          format: uint64
    v2TaxonomyLinksRequest:
      type: object
      properties:
        taxon:
          type: string
    protobufAny:
      type: object
      properties:
        type_url:
          type: string
        value:
          type: string
          format: byte
    v2reportsWarningReplacedId:
      type: object
      properties:
        requested:
          type: string
        returned:
          type: string
  securitySchemes:
    ApiKeyAuth:
      type: apiKey
      in: query
      name: api_key
    ApiKeyAuthHeader:
      type: apiKey
      in: header
      name: api-key
externalDocs:
  description: Interactively explore genome assembly datasets
  url: https://www.ncbi.nlm.nih.gov/datasets/genomes/