get.BioProject.metadata.INSDC: Fetch BioProject metadata

In biodiversity-aq/OmicsMetaData: OmicsMetaData: an R-package for interoperable and re-usable biodiversity 'omics (meta)data

Description

downloads a minimal set of sample metadata of all samples ("Runs") within a BioProject (argument BioPrjct) from the International Nucleotide Sequence Database Consortium (INSDC) databases.

Usage

get.BioProject.metadata.INSDC(BioPrjct, just.names=FALSE)

Arguments

BioPrjct	A chracter string. A single Bioproject ID, e.g. "PRJNA369175"
just.names	Boolean. If TRUE, only the INSDC sample names are returned, else all data are returned. default FALSE

Details

BioProjects combine all biological nucleotide sequence data related to a single initiative, originating from a single organization. With each sample ("Run") within a BioProject, there is additional data associated that is crucial to the correct interpretation of the nucleotide sequence data, but is not automatically downloaded along with it. The get.BioProject.metadata.INSDC function will fetch the most basic metadata of a BioProject from the INSDC repositories to complete the nucleotide sequence dataset, using E-utils API function of NCBI. These basic metadata typically include Run number, relsease date, load date, spots, bases, av_MB and download path. Note that the data returned by get.BioProject.metadata.INSDC does not include all the metadata associated with a BioProject. Other information, like coordinates, sampling dates or environmental measurements may also be available, but require the user to register at NCBI and request a personal API-key (this is required by NCBI to acces their data since 2017). The complete set of additional data can be downloaded using the get.sample.attributes.INSDC function, given a user-specified API-key. see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Value

if get.BioProject.metadata.INSDC(just.names=FALSE) (default) a data.frame with n rows an m columns is returned, n being the number of samples in the BioProject, and m being the number of variables found. If get.BioProject.metadata.INSDC(just.names=TRUE), a character vector of length n is returned with the sample numbers ("Run numbers", SRR numbers)

Author(s)

Maxime Sweetlove CC-0 2019

References

Sayers, E. (2009) The E-utilities In-Depth: Parameters, Syntax and More, https://www.ncbi.nlm.nih.gov/books/NBK25499/

See Also

get.sample.attributes.INSDC

Other downloading data functions: download.sequences.INSDC(), get.sample.attributes.INSDC()

Examples

get.BioProject.metadata.INSDC(BioPrjct="PRJNA303951", just.names=FALSE)

biodiversity-aq/OmicsMetaData documentation built on Dec. 19, 2021, 9:44 a.m.