#### Options to download RefSeq organelle genome data, including the associated sequence and metadata. These organelle services allow you to get RefSeq organelle genome metadata as a data report or download gene, transcript and protein sequence, and metadata, as an organelle data package, for RefSeq organelle genomes.
openapi: 3.0.3
info:
title: ClinicalTrials.gov REST BioSample Organelle API
description: This API is made available to provide users meta data, statistics, and the most recent version of the clinical trials available on ClinicalTrials.gov.
version: 2.0.5
servers:
- url: https://clinicaltrials.gov/api/v2
description: This server
tags:
- name: Organelle
description: '#### Options to download RefSeq organelle genome data, including the associated sequence and metadata.
These organelle services allow you to get RefSeq organelle genome metadata as a data report or download gene, transcript and protein sequence, and metadata, as an organelle data package, for RefSeq organelle genomes.
'
paths:
/organelle/accession/{accessions}/download:
get:
summary: Get an organelle data package by nucleotide accession
description: Download an organelle data package including sequence, annotation, and detailed data reports as a compressed zip archive.
tags:
- Organelle
operationId: download_organelle_package
responses:
default:
description: An unexpected error response.
content:
text/plain:
schema:
$ref: '#/components/schemas/rpcStatus'
'200':
description: A successful response
content:
application/zip:
schema:
format: binary
type: string
description: Zip compressed stream
parameters:
- name: accessions
description: NCBI organelle assembly accessions
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: NC_001643.1
summary: Chimpanzee mitochondrial genome
example-1:
value:
- NC_001643.1
- NC_002082.1
summary: Chimpanzee and common Gibbon mitochondrial genomes
- name: include_annotation_type
description: Specify which sequence files to include in the data package.
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2AnnotationForOrganelleType'
- name: filename
description: Output file name.
in: query
required: false
schema:
type: string
default: ncbi_dataset.zip
/organelle/download:
post:
summary: Get an organelle data package
description: Download an organelle data package including sequence, annotation, and detailed data reports as a compressed zip archive.
tags:
- Organelle
operationId: download_organelle_package_by_post
responses:
default:
description: An unexpected error response.
content:
text/plain:
schema:
$ref: '#/components/schemas/rpcStatus'
'200':
description: A successful response
content:
application/zip:
schema:
format: binary
type: string
description: Zip compressed stream
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/v2OrganelleDownloadRequest'
examples:
Single organelle accession example:
description: Organelle accession (just one)
value:
accessions:
- NC_001643.1
parameters:
- name: filename
description: Output file name.
in: query
required: false
schema:
type: string
default: ncbi_dataset.zip
/organelle/accessions/{accessions}/dataset_report:
get:
summary: Get an organelle data report by nucleotide accession
description: Get an organelle data report in JSON format.
tags:
- Organelle
operationId: organelle_datareport_by_accession
responses:
default:
description: An unexpected error response.
content:
text/plain:
schema:
$ref: '#/components/schemas/rpcStatus'
'200':
description: A successful response
content:
application/json:
schema:
$ref: '#/components/schemas/v2reportsOrganelleDataReports'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsOrganelleDataReports'
text/tab-separated-values:
schema:
type: string
parameters:
- name: accessions
description: One or more organelle nucleotide accessions
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: NC_001643.1
summary: Chimpanzee mitochondrial genome
example-1:
value:
- NC_001643.1
- NC_002082.1
summary: Chimpanzee and common gibbon mitochondrial genomes
- name: organelle_types
description: Limit results to the specified organelle types.
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2reportsOrganelleType'
- name: first_release_date
description: Limit results to organelle genomes released on or after the specified date.
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: '2015-01-10'
summary: Jan 10, 2015, in ISO 8601 YYYY-MM-DD format
- name: last_release_date
description: Limit results to organelle genomes released on or before the specified date.
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: '2021-01-10'
summary: Jan 10, 2021, in ISO 8601 YYYY-MM-DD format
- name: sort.field
in: query
required: false
schema:
type: string
- name: sort.direction
in: query
required: false
schema:
$ref: '#/components/schemas/v2SortDirection'
- name: returned_content
description: Return complete organelle reports or nucleotide accessions only.
in: query
required: false
schema:
$ref: '#/components/schemas/v2OrganelleMetadataRequestContentType'
examples:
example-0:
value: ASSM_ACC
summary: Return nucleotide accessions only
- name: table_format
description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
in: query
required: false
schema:
$ref: '#/components/schemas/v2OrganelleMetadataRequestOrganelleTableFormat'
examples:
example-0:
value: SUMMARY
summary: This template specifies a basic set of fields available from the organelle report
- name: include_tabular_header
description: Specify when to include the table header when requesting a tabular report.
in: query
required: false
schema:
$ref: '#/components/schemas/v2IncludeTabularHeader'
/organelle/taxon/{taxons}/dataset_report:
get:
summary: Get an organelle data report by taxon
description: Get an organelle data report in JSON format.
tags:
- Organelle
operationId: organelle_datareport_by_taxon
responses:
default:
description: An unexpected error response.
content:
text/plain:
schema:
$ref: '#/components/schemas/rpcStatus'
'200':
description: A successful response
content:
application/json:
schema:
$ref: '#/components/schemas/v2reportsOrganelleDataReports'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsOrganelleDataReports'
text/tab-separated-values:
schema:
type: string
parameters:
- name: taxons
description: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank
in: path
required: true
schema:
type: array
items:
type: string
examples:
example-0:
value: '9443'
summary: Primate organelle genomes
example-1:
value:
- '9606'
- '10090'
summary: Human and mouse organelle genomes
- name: organelle_types
description: Limit results to the specified organelle types.
in: query
required: false
schema:
type: array
items:
$ref: '#/components/schemas/v2reportsOrganelleType'
- name: first_release_date
description: Limit results to organelle genomes released on or after the specified date.
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: '2015-01-10'
summary: Jan 10, 2015, in ISO 8601 YYYY-MM-DD format
- name: last_release_date
description: Limit results to organelle genomes released on or before the specified date.
in: query
required: false
schema:
type: string
format: date-time
examples:
example-0:
value: '2021-01-10'
summary: Jan 10, 2021, in ISO 8601 YYYY-MM-DD format
- name: tax_exact_match
description: If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.
in: query
required: false
schema:
type: boolean
default: false
- name: sort.field
in: query
required: false
schema:
type: string
- name: sort.direction
in: query
required: false
schema:
$ref: '#/components/schemas/v2SortDirection'
- name: returned_content
description: Return complete organelle reports or nucleotide accessions only.
in: query
required: false
schema:
$ref: '#/components/schemas/v2OrganelleMetadataRequestContentType'
examples:
example-0:
value: ASSM_ACC
summary: Return nucleotide accessions only
- name: page_size
description: The maximum number of organelle assemblies to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
in: query
required: false
schema:
type: integer
- name: page_token
description: A page token is returned from an `OrganelleMetadata` call with more than `page_size` results. Use this token, along with the previous `OrganelleMetadata` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
in: query
required: false
schema:
type: string
- name: table_format
description: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
in: query
required: false
schema:
$ref: '#/components/schemas/v2OrganelleMetadataRequestOrganelleTableFormat'
examples:
example-0:
value: SUMMARY
summary: This template specifies a basic set of fields available from the organelle report
- name: include_tabular_header
description: Specify when to include the table header when requesting a tabular report.
in: query
required: false
schema:
$ref: '#/components/schemas/v2IncludeTabularHeader'
/organelle/dataset_report:
post:
summary: Get an organelle data report
description: Get an organelle data report in JSON format.
tags:
- Organelle
operationId: organelle_datareport_by_post
responses:
default:
description: An unexpected error response.
content:
text/plain:
schema:
$ref: '#/components/schemas/rpcStatus'
'200':
description: A successful response
content:
application/json:
schema:
$ref: '#/components/schemas/v2reportsOrganelleDataReports'
application/x-ndjson:
schema:
$ref: '#/components/schemas/v2reportsOrganelleDataReports'
text/tab-separated-values:
schema:
type: string
requestBody:
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/v2OrganelleMetadataRequest'
examples:
Single TaxID example:
description: Primate organelle genomes
value:
taxons:
- '9443'
components:
schemas:
v2OrganelleMetadataRequest:
type: object
properties:
taxons:
type: array
items:
type: string
accessions:
type: array
items:
type: string
organelle_types:
type: array
items:
$ref: '#/components/schemas/v2reportsOrganelleType'
first_release_date:
type: string
format: date-time
title: Limit results to organelle genomes released on or after the specified date.
last_release_date:
type: string
format: date-time
title: Limit results to organelle genomes released on or before the specified date.
tax_exact_match:
type: boolean
title: If true, only return assemblies with the given NCBI Taxonomy ID, or name. Otherwise, assemblies from taxonomy subtree are included, too.
sort:
type: array
items:
$ref: '#/components/schemas/v2OrganelleSort'
returned_content:
$ref: '#/components/schemas/v2OrganelleMetadataRequestContentType'
title: Return complete organelle reports or nucleotide accessions only.
page_size:
type: integer
title: The maximum number of organelle assemblies to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
page_token:
type: string
title: A page token is returned from an `OrganelleMetadata` call with more than `page_size` results. Use this token, along with the previous `OrganelleMetadata` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
table_format:
$ref: '#/components/schemas/v2OrganelleMetadataRequestOrganelleTableFormat'
title: 'Specify a predefined set of fields for the tabular report using built-in templates. Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.'
include_tabular_header:
$ref: '#/components/schemas/v2IncludeTabularHeader'
title: Specify when to include the table header when requesting a tabular report.
v2reportsOrganelleDataReports:
type: object
properties:
messages:
type: array
items:
$ref: '#/components/schemas/v2reportsMessage'
reports:
type: array
items:
$ref: '#/components/schemas/v2reportsOrganelle'
total_count:
type: integer
title: The total count of available datasets (ignoring the cutoff parameter). Only provided for the first page of results (when `page_token` is empty in the request).
next_page_token:
type: string
title: A token that can be sent as `page_token` to retrieve the next page. If this field is omitted, there are no subsequent pages.
v2reportsErrorOrganelleErrorCode:
type: string
enum:
- UNKNOWN_ORGANELLE_ERROR_CODE
- INVALID_ORGANELLE_TAXON
- NO_ORGANELLES_FOR_ACCESSION
default: UNKNOWN_ORGANELLE_ERROR_CODE
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
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
v2reportsOrganelle:
type: object
properties:
description:
$ref: '#/components/schemas/v2reportsOrganelleType'
genbank:
$ref: '#/components/schemas/v2reportsSequenceInformation'
refseq:
$ref: '#/components/schemas/v2reportsSequenceInformation'
organism:
$ref: '#/components/schemas/v2reportsOrganism'
title: Taxon for the organelle
bioprojects:
type: array
items:
$ref: '#/components/schemas/v2reportsBioProject'
biosample:
$ref: '#/components/schemas/v2reportsOrganelleBiosample'
title: The associated BioSample.
gene_counts:
$ref: '#/components/schemas/v2reportsOrganelleGeneCounts'
length:
type: integer
title: Genome length
topology:
$ref: '#/components/schemas/v2reportsOrganelleTopology'
gene_count:
type: integer
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
v2reportsOrganelleType:
type: string
enum:
- ORGANELLE_TYPE_UNKNOWN
- Mitochondrion
- Chloroplast
- Plastid
- Kinetoplast
- Apicoplast
- Chromatophore
- Cyanelle
default: ORGANELLE_TYPE_UNKNOWN
v2reportsOrganelleTopology:
type: string
enum:
- TOPOLOGY_UNKNOWN
- Circular
- Linear
- Tandem
default: TOPOLOGY_UNKNOWN
v2reportsOrganelleBiosample:
type: object
properties:
accession:
type: string
title: BioSample Accession identifier
v2reportsInfraspecificNames:
type: object
properties:
breed:
type: string
title: A homogenous group of animals within a domesticated species
cultivar:
type: string
title: A variety of plant within a species produced and maintained by cultivation
ecotype:
type: string
title: A population or subspecies occupying a distinct habitat
isolate:
type: string
title: The individual isolate from which the sequences in the genome assembly were derived
sex:
type: string
title: Physical sex of sampled organism
strain:
type: string
title: A genetic variant, subtype or culture within a species
v2OrganelleMetadataRequestContentType:
type: string
enum:
- COMPLETE
- ASSM_ACC
default: COMPLETE
v2reportsWarningReplacedId:
type: object
properties:
requested:
type: string
returned:
type: string
v2reportsErrorVirusErrorCode:
type: string
enum:
- UNKNOWN_VIRUS_ERROR_CODE
default: UNKNOWN_VIRUS_ERROR_CODE
v2SortDirection:
type: string
enum:
- SORT_DIRECTION_UNSPECIFIED
- SORT_DIRECTION_ASCENDING
- SORT_DIRECTION_DESCENDING
default: SORT_DIRECTION_UNSPECIFIED
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
v2AnnotationForOrganelleType:
type: string
enum:
- DEFAULT
- GENOME_FASTA
- CDS_FASTA
- PROTEIN_FASTA
default: DEFAULT
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
v2OrganelleSort:
type: object
properties:
field:
type: string
direction:
$ref: '#/components/schemas/v2SortDirection'
v2reportsErrorTaxonomyErrorCode:
type: string
enum:
- UNKNOWN_TAXONOMY_ERROR_CODE
- INVALID_TAXONOMY_TAXON
default: UNKNOWN_TAXONOMY_ERROR_CODE
v2reportsLineageOrganism:
type: object
properties:
tax_id:
type: integer
title: NCBI Taxonomy identifier
name:
type: string
title: Scientific name
protobufAny:
type: object
properties:
type_url:
type: string
value:
type: string
format: byte
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
v2reportsMessage:
type: object
properties:
error:
$ref: '#/components/schemas/v2reportsError'
warning:
$ref: '#/components/schemas/v2reportsWarning'
v2reportsErrorGeneErrorCode:
type: string
enum:
- UNKNOWN_GENE_ERROR_CODE
- INCOMPLETE_LOOKUP_SYMBOL
- INVALID_TAXON_GENE_ARGUMENT
default: UNKNOWN_GENE_ERROR_CODE
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'
v2OrganelleDownloadRequest:
type: object
properties:
accessions:
type: array
items:
type: string
exclude_sequence:
type: boolean
title: If true, exclude the genome sequence from the data package.
include_annotation_type:
type: array
items:
$ref: '#/components/schemas/v2AnnotationForOrganelleType'
rpcStatus:
type: object
properties:
code:
type: integer
format: int32
message:
type: string
details:
type: array
items:
$ref: '#/components/schemas/protobufAny'
v2OrganelleMetadataRequestOrganelleTableFormat:
type: string
enum:
- ORGANELLE_TABLE_FORMAT_NO_TABLE
- SUMMARY
default: ORGANELLE_TABLE_FORMAT_NO_TABLE
v2reportsWarningGeneWarningCode:
type: string
enum:
- UNKNOWN_GENE_WARNING_CODE
- ACCESSION_VERSION_MISMATCH
- REPLACED_GENE_ID
- DISCONTINUED_GENE_ID
- UNRECOGNIZED_GENE_ID
- UNRECOGNIZED_GENE_SYMBOL
- UNRECOGNIZED_ACCESSION
- UNRECOGNIZED_TAX_TOKEN
- NO_GENE_ANNOTATION_FOUND
- ABOVE_SPECIES_TAXON
default: UNKNOWN_GENE_WARNING_CODE
v2reportsWarning:
type: object
properties:
gene_warning_code:
$ref: '#/components/schemas/v2reportsWarningGeneWarningCode'
reason:
type: string
message:
type: string
replaced_id:
$ref: '#/components/schemas/v2reportsWarningReplacedId'
unrecognized_identifier:
type: string
externalDocs:
description: Introduction on clinicaltrials.gov
url: https://clinicaltrials.gov/data-about-studies/learn-about-api