README.md

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

README

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

Badges

Package details

Description

This R-package provides a suite of tools to help format and standardize metadata and environmental data of 'omics datasets. The aim is to help improve data interoperability and re-use in biodiversity 'omics fields, such as metabarcoding (e.g. eDNA, amplicon sequencing of microbes) and metagenomics (e.g. shotgun meta genome sequencing).

Improving the re-use of data

There are functions to retrieve metadata from sequences stored at the INSDC databases, together with the sequences themselves. Metadata can be downloaded into the R-environment or passed-on into files. Sequences are downloaded as fastq.tar.gz files, and are written to a folder, as the volume of data would likely be to big for an everyday computer. As such, this package offers the users tools to help them integrate online open access data and metadata into their analyses.

Improving data interoperability

There are also tools that guide users into standardizing metadata (assuming the sequences are already standardized following the FASTA or FASTQ format). User-provided data can be standardized with MIxS or DwC in a supervised way, and can be readied for upload and archiving on one of the INSDC databases. The formatted and standardized metadata has the advantage of passing the INSDC quality control much quicker and easier than formatting data by hand using the INSDC templates. Finally, there are several tools for common manipulations in ecological molecular data, such as easy conversion between wide and long formats.

Installation instructions

• install with devtools

install.packages("devtools") library(devtools)

when the GitHub repo was downloaded to the local machine (with path_to_package the quoted path to the local location of the package source files):

devtools::install(path_to_package)

install directly from GitHub at https://github.com/biodiversity-aq/OmicsMetaData

devtools::install_github("https://github.com/biodiversity-aq/OmicsMetaData")

Additional setup requirements

• Some functions require a personal API key to access the INSDC databases. Such an API key can be obtained from NCBI by first registering an NCBI account at https://account.ncbi.nlm.nih.gov/signup/?back_url=, then go to the “Settings” page of your NCBI account, and go to the “API Key Management” area. Click the “Create an API Key” button, and copy the resulting key.

Resources

The OmicsMetaData R-package can be used to access sequence data and any associated metadata on INSDC, or the Lifewatch taxonomic backbone at marinespecies.org. Below these and other resources that can be consulted are described in detail.

International Nucleotide Sequence Database Consortium (INSDC)

This package connects to the API of INSDC (via NCBI) to download sequence data and associated metadata from the world's leading nucleotide sequence databases. INSDC is a consortium of European, American and Japanese interconnected databases that house all sorts of nucleotide sequence data. More information on the API client of NCBI can be found here: https://www.ncbi.nlm.nih.gov/home/develop/api/

World Registry of Marine Species (WoRMS) and the worrms R-package

This packages also contains function that wrap and integrates several worrms package (Chamberlain, 2020; Horton et al. 2021) functions to obtain taxonomy information from the WoRMS database in a better structured way. The WoRMS (World Registry of Marine Species) is a LifeWatch database that houses the (near) complete taxonomic backbone of Marine and Antarctic (marine and terrestrial) species. In the database, each taxonomic unit, whether it is a species, genus or phylum, is identified by a unique ID (aphID) that is unchainable, even when taxonomic names are updated and changed. The aphID helps to identify synonym names and older names that are no longer in use. As such, each taxon is unambiguously identifiable, now and in the future as well. Extensive documentation can be found at this link: http://www.marinespecies.org/about.php.

Minimum on Any (x) Sequence (MIxS)

This package used the Minimum on Any (x) Sequence (MIxS) standard, developed by the Genomics Standards Consortium (GSC) (Yilmaz et al. 2011). This is a data standard for nucleotide sequence data and it's metadata. More information can be found here: https://gensc.org/mixs/. Development of the latest version can be found here: https://github.com/GenomicsStandardsConsortium/mixs

DarwinCore

This package also uses the DarwinCore data standard (Darwin Core Task Group, 2009). DarwinCore is a data standard for biodiversity occurrence data, and is developed and maintained by TDWG. More information can be found here: https://dwc.tdwg.org

References

Yilmaz, P., Gilbert, J., Knight, R. et al. The genomic standards consortium: bringing standards to life for microbial ecology. ISME J 5, 1565–1567 (2011). https://doi.org/10.1038/ismej.2011.39

Darwin Core Task Group. 2009. Darwin Core. Biodiversity Information Standards (TDWG) http://www.tdwg.org/standards/450

Chamberlain, S. (2020). worrms: World Register of Marine Species (WoRMS) Client. R package version 0.4.2. https://CRAN.R-project.org/package=worrms

Horton, T., Kroh, A., et al. (2021). World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. doi:10.14284/170

Brief demonstration usage

library(OmicsMetaData) OmicsMetaData.help()

dataset <- get.BioProject.metadata.INSDC("PRJNA305344") dataset.MIxS <- dataQC.MIxS(dataset)

Citation information

Please cite as: Sweetlove M. 2021, OmicsMetaData: an R package to download, format and standardize genomic meta- and environmental data.

Code of conduct

Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

lisence

This package is distributed under a GNU General Public License v3 (GLP-3.0) https://www.gnu.org/licenses/gpl-3.0.en.html

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