NCBI Datasets API

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  • Author: NCBI
  • Tags OpenAPI , OpenAPI-Generator , NCBI Datasets API
  • Requires: Python >=3.9
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Project description

ncbi-datasets-pyclient

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.

This Python package is automatically generated by the OpenAPI Generator project:

  • API version: v2
  • Package version: v18.18.0
  • Generator version: 7.20.0
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.9+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/misialq/ncbi-datasets-pyclient.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/misialq/ncbi-datasets-pyclient.git)

Then import the package:

import ncbi.datasets.openapi

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import ncbi.datasets.openapi

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

import ncbi.datasets.openapi
from ncbi.datasets.openapi.rest import ApiException
from pprint import pprint

# Defining the host is optional and defaults to https://api.ncbi.nlm.nih.gov/datasets/v2
# See configuration.py for a list of all supported configuration parameters.
configuration = ncbi.datasets.openapi.Configuration(
    host = "https://api.ncbi.nlm.nih.gov/datasets/v2"
)

# The client must configure the authentication and authorization parameters
# in accordance with the API server security policy.
# Examples for each auth method are provided below, use the example that
# satisfies your auth use case.

# Configure API key authorization: ApiKeyAuthHeader
configuration.api_key['ApiKeyAuthHeader'] = os.environ["API_KEY"]

# Uncomment below to setup prefix (e.g. Bearer) for API key, if needed
# configuration.api_key_prefix['ApiKeyAuthHeader'] = 'Bearer'


# Enter a context with an instance of the API client
with ncbi.datasets.openapi.ApiClient(configuration) as api_client:
    # Create an instance of the API class
    api_instance = ncbi.datasets.openapi.BioSampleApi(api_client)
    accessions = ['SAMN15960293'] # List[str] | 

    try:
        # Get BioSample dataset reports by accession(s)
        api_response = api_instance.bio_sample_dataset_report(accessions)
        print("The response of BioSampleApi->bio_sample_dataset_report:\n")
        pprint(api_response)
    except ApiException as e:
        print("Exception when calling BioSampleApi->bio_sample_dataset_report: %s\n" % e)

Documentation for API Endpoints

All URIs are relative to https://api.ncbi.nlm.nih.gov/datasets/v2

Class Method HTTP request Description
BioSampleApi bio_sample_dataset_report GET /biosample/accession/{accessions}/biosample_report Get BioSample dataset reports by accession(s)
GeneApi download_gene_package GET /gene/id/{gene_ids}/download Get a gene data package by GeneID
GeneApi download_gene_package_post POST /gene/download Get a gene data package
GeneApi gene_chromosome_summary GET /gene/taxon/{taxon}/annotation/{annotation_name}/chromosome_summary Get gene counts per chromosome by taxon and annotation name
GeneApi gene_counts_for_taxon GET /gene/taxon/{taxon}/counts Get gene counts by taxon
GeneApi gene_counts_for_taxon_by_post POST /gene/taxon/counts Get gene counts by taxon
GeneApi gene_dataset_report POST /gene/dataset_report Get a gene data report
GeneApi gene_dataset_report_by_accession GET /gene/accession/{accessions}/dataset_report Get a gene data report by RefSeq nucleotide or protein accession
GeneApi gene_dataset_report_by_tax_and_symbol GET /gene/symbol/{symbols}/taxon/{taxon}/dataset_report Get a gene data report by symbol and taxon
GeneApi gene_dataset_reports_by_id GET /gene/id/{gene_ids}/dataset_report Get a gene data report by GeneID
GeneApi gene_dataset_reports_by_locus_tag GET /gene/locus_tag/{locus_tags}/dataset_report Get a gene data report by locus tag
GeneApi gene_dataset_reports_by_taxon GET /gene/taxon/{taxon}/dataset_report Get a gene data report by taxon
GeneApi gene_download_summary_by_id GET /gene/id/{gene_ids}/download_summary Get a download summary of a gene data package by GeneID
GeneApi gene_download_summary_by_post POST /gene/download_summary Get a download summary of a gene data package
GeneApi gene_links_by_id GET /gene/id/{gene_ids}/links Get gene links by GeneID
GeneApi gene_links_by_id_by_post POST /gene/links Get gene links by GeneID
GeneApi gene_metadata_by_accession GET /gene/accession/{accessions} Get gene metadata by RefSeq Accession (deprecated)
GeneApi gene_metadata_by_post POST /gene Get gene metadata as JSON (deprecated)
GeneApi gene_metadata_by_tax_and_symbol GET /gene/symbol/{symbols}/taxon/{taxon} Get gene metadata by gene symbol (deprecated)
GeneApi gene_orthologs_by_id GET /gene/id/{gene_id}/orthologs Get a gene data report for a gene ortholog set by GeneID
GeneApi gene_orthologs_by_post POST /gene/orthologs Get a gene data report for a gene ortholog set by GeneID
GeneApi gene_product_report POST /gene/product_report Get a gene product report
GeneApi gene_product_report_by_accession GET /gene/accession/{accessions}/product_report Get a gene product report by RefSeq nucleotide or protein accession
GeneApi gene_product_report_by_tax_and_symbol GET /gene/symbol/{symbols}/taxon/{taxon}/product_report Get a gene product report by symbol and taxon
GeneApi gene_product_reports_by_id GET /gene/id/{gene_ids}/product_report Get a gene product report by GeneID
GeneApi gene_product_reports_by_locus_tags GET /gene/locus_tag/{locus_tags}/product_report Get a gene product report by locus tag
GeneApi gene_product_reports_by_taxon GET /gene/taxon/{taxon}/product_report Get a gene product report by taxon
GeneApi gene_reports_by_id GET /gene/id/{gene_ids} Get gene reports by GeneID (deprecated)
GeneApi gene_reports_by_taxon GET /gene/taxon/{taxon} Get gene reports by taxonomic identifier (deprecated)
GenomeApi annotation_report_facets_by_accession GET /genome/accession/{accession}/annotation_summary Get genome annotation report summary information by genome assembly accession
GenomeApi annotation_report_facets_by_post POST /genome/annotation_summary Get genome annotation report summary information by genome assembly accession
GenomeApi assembly_accessions_for_sequence_accession GET /genome/sequence_accession/{accession}/sequence_assemblies Get a genome assembly accession for a nucleotide sequence accession
GenomeApi assembly_accessions_for_sequence_accession_by_post POST /genome/sequence_assemblies Get a genome assembly accession for a nucleotide sequence accession
GenomeApi assembly_revision_history_by_get GET /genome/accession/{accession}/revision_history Get a revision history for a genome assembly by genome assembly accession
GenomeApi assembly_revision_history_by_post POST /genome/revision_history Get a revision history for a genome assembly by genome assembly accession
GenomeApi check_assembly_availability GET /genome/accession/{accessions}/check Check the validity of a genome assembly accession
GenomeApi check_assembly_availability_post POST /genome/check Check the validity of a genome assembly accession
GenomeApi checkm_histogram_by_taxon GET /genome/taxon/{species_taxon}/checkm_histogram Get CheckM histogram data by species taxon
GenomeApi checkm_histogram_by_taxon_by_post POST /genome/checkm_histogram Get CheckM histogram data by species taxon
GenomeApi download_assembly_package GET /genome/accession/{accessions}/download Get a genome data package by genome assembly accession
GenomeApi download_assembly_package_post POST /genome/download Get a genome data package by genome assembly accession
GenomeApi download_genome_annotation_package GET /genome/accession/{accession}/annotation_report/download Get a genome annotation data package by genome assembly accession
GenomeApi download_genome_annotation_package_by_post POST /genome/annotation_report/download Get a genome annotation data package by genome assembly accession
GenomeApi genome_annotation_download_summary GET /genome/accession/{accession}/annotation_report/download_summary Get a download summary (preview) of a genome annotation data package by genome assembly accession
GenomeApi genome_annotation_download_summary_by_post POST /genome/annotation_report/download_summary Get a download summary (preview) of a genome annotation data package by genome assembly accession
GenomeApi genome_annotation_report GET /genome/accession/{accession}/annotation_report Get genome annotation reports by genome assembly accession
GenomeApi genome_annotation_report_by_post POST /genome/annotation_report Get genome annotation reports by genome assembly accession
GenomeApi genome_dataset_report GET /genome/accession/{accessions}/dataset_report Get a genome assembly report by genome assembly accession
GenomeApi genome_dataset_report_by_post POST /genome/dataset_report Get a genome assembly report
GenomeApi genome_dataset_reports_by_assembly_name GET /genome/assembly_name/{assembly_names}/dataset_report Get genome assembly reports by assembly name
GenomeApi genome_dataset_reports_by_bioproject GET /genome/bioproject/{bioprojects}/dataset_report Get genome assembly reports by BioProject accession
GenomeApi genome_dataset_reports_by_biosample_id GET /genome/biosample/{biosample_ids}/dataset_report Get genome assembly reports by BioSample accession
GenomeApi genome_dataset_reports_by_taxon GET /genome/taxon/{taxons}/dataset_report Get a genome assembly report by taxon
GenomeApi genome_dataset_reports_by_wgs GET /genome/wgs/{wgs_accessions}/dataset_report Get a genome assembly data report by WGS accession
GenomeApi genome_download_summary GET /genome/accession/{accessions}/download_summary Get a download summary (preview) of a genome data package by genome assembly accession
GenomeApi genome_download_summary_by_post POST /genome/download_summary Get a download summary (preview) of a genome data package by genome assembly accession
GenomeApi genome_links_by_accession GET /genome/accession/{accessions}/links Get assembly links by genome assembly accession
GenomeApi genome_links_by_accession_by_post POST /genome/links Get assembly links by genome assembly accession
GenomeApi genome_sequence_report GET /genome/accession/{accession}/sequence_reports Get a genome sequence report by genome assembly accession
GenomeApi genome_sequence_report_by_post POST /genome/sequence_reports Get a genome sequence report by genome assembly accession
OrganelleApi download_organelle_package GET /organelle/accession/{accessions}/download Get an organelle data package by nucleotide accession
OrganelleApi download_organelle_package_by_post POST /organelle/download Get an organelle data package
OrganelleApi organelle_datareport_by_accession GET /organelle/accessions/{accessions}/dataset_report Get an organelle data report by nucleotide accession
OrganelleApi organelle_datareport_by_post POST /organelle/dataset_report Get an organelle data report
OrganelleApi organelle_datareport_by_taxon GET /organelle/taxon/{taxons}/dataset_report Get an organelle data report by taxon
ProkaryoteApi download_prokaryote_gene_package GET /protein/accession/{accessions}/download Get a prokaryote gene data package by RefSeq protein accession
ProkaryoteApi download_prokaryote_gene_package_post POST /protein/accession/download Get a prokaryote gene data package by RefSeq protein accession
TaxonomyApi download_taxonomy_package GET /taxonomy/taxon/{tax_ids}/download Get a taxonomy data package by Taxonomy ID
TaxonomyApi download_taxonomy_package_by_post POST /taxonomy/download Get a taxonomy data package by Taxonomy ID
TaxonomyApi tax_name_query GET /taxonomy/taxon_suggest/{taxon_query} Get a list of taxonomy names and IDs by partial taxonomic name
TaxonomyApi tax_name_query_by_post POST /taxonomy/taxon_suggest Get a list of taxonomy names and IDs by partial taxonomic name
TaxonomyApi taxonomy_data_report GET /taxonomy/taxon/{taxons}/dataset_report Get a taxonomy data report by taxon
TaxonomyApi taxonomy_data_report_post POST /taxonomy/dataset_report Get a taxonomy data report by taxon
TaxonomyApi taxonomy_filtered_subtree GET /taxonomy/taxon/{taxons}/filtered_subtree Get a filtered taxonomic subtree by taxon
TaxonomyApi taxonomy_filtered_subtree_post POST /taxonomy/filtered_subtree Get a filtered taxonomic subtree by taxon
TaxonomyApi taxonomy_image GET /taxonomy/taxon/{taxon}/image Get a taxonomy image by taxon
TaxonomyApi taxonomy_image_metadata GET /taxonomy/taxon/{taxon}/image/metadata Get taxonomy image metadata by Taxonomy ID
TaxonomyApi taxonomy_image_metadata_post POST /taxonomy/image/metadata Get taxonomy image metadata by Taxonomy ID
TaxonomyApi taxonomy_image_post POST /taxonomy/image Get a taxonomy image by taxon
TaxonomyApi taxonomy_links GET /taxonomy/taxon/{taxon}/links Get external links by Taxonomy ID
TaxonomyApi taxonomy_links_by_post POST /taxonomy/links Get external links by Taxonomy ID
TaxonomyApi taxonomy_metadata GET /taxonomy/taxon/{taxons} Use taxonomic identifiers to get taxonomic metadata (deprecated)
TaxonomyApi taxonomy_metadata_post POST /taxonomy Get taxonomy metadata by taxon (deprecated)
TaxonomyApi taxonomy_names GET /taxonomy/taxon/{taxons}/name_report Get a taxonomy names report by taxon
TaxonomyApi taxonomy_names_post POST /taxonomy/name_report Get a taxonomy names report by taxon
TaxonomyApi taxonomy_related_ids GET /taxonomy/taxon/{tax_id}/related_ids Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
TaxonomyApi taxonomy_related_ids_post POST /taxonomy/related_ids Get child nodes, and optionally parent nodes, for a given taxon by Taxonomy ID
VersionApi version GET /version Retrieve service version
VirusApi sars2_protein_download GET /virus/taxon/sars2/protein/{proteins}/download Get a SARS-CoV-2 protein data package by protein name
VirusApi sars2_protein_download_post POST /virus/taxon/sars2/protein/download Get a SARS-CoV-2 protein data package
VirusApi sars2_protein_summary GET /virus/taxon/sars2/protein/{proteins} Get a download summary of a SARS-CoV-2 protein data package by protein name
VirusApi sars2_protein_summary_by_post POST /virus/taxon/sars2/protein Get a download summary of a SARS-CoV-2 protein data package by protein name
VirusApi sars2_protein_table GET /virus/taxon/sars2/protein/{proteins}/table Get SARS-CoV-2 protein metadata in a tabular format by protein name
VirusApi virus_accession_availability GET /virus/accession/{accessions}/check Check the validity of a virus genome nucleotide accession
VirusApi virus_accession_availability_post POST /virus/check Check the validity of a virus genome nucleotide accession
VirusApi virus_annotation_reports_by_acessions GET /virus/accession/{accessions}/annotation_report Get a virus annotation report by nucleotide accession
VirusApi virus_annotation_reports_by_post POST /virus/annotation_report Get a virus annotation report
VirusApi virus_annotation_reports_by_taxon GET /virus/taxon/{taxon}/annotation_report Get a virus annotation report by taxon
VirusApi virus_genome_download GET /virus/taxon/{taxon}/genome/download Get a virus genome data package by taxon
VirusApi virus_genome_download_accession GET /virus/accession/{accessions}/genome/download Get a virus genome data package by nucleotide accession
VirusApi virus_genome_download_post POST /virus/genome/download Get a virus genome data package
VirusApi virus_genome_summary GET /virus/taxon/{taxon}/genome Get a download summary of a virus genome data package by taxon
VirusApi virus_genome_summary_by_post POST /virus/genome Get a download summary of a virus genome data package
VirusApi virus_genome_table GET /virus/taxon/{taxon}/genome/table Get virus genome metadata in a tabular format (deprecated)
VirusApi virus_reports_by_acessions GET /virus/accession/{accessions}/dataset_report Get a virus data report by nucleotide accession
VirusApi virus_reports_by_post POST /virus Get a virus data report
VirusApi virus_reports_by_taxon GET /virus/taxon/{taxon}/dataset_report Get a virus data report by taxon

Documentation For Models

Documentation For Authorization

Authentication schemes defined for the API:

ApiKeyAuth

  • Type: API key
  • API key parameter name: api_key
  • Location: URL query string

ApiKeyAuthHeader

  • Type: API key
  • API key parameter name: api-key
  • Location: HTTP header

Author

Project details

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Meta
  • Author: NCBI
  • Tags OpenAPI , OpenAPI-Generator , NCBI Datasets API
  • Requires: Python >=3.9

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