PGP repository: a plant phenomics and genomics data publication infrastructure

Abstract

Plant genomics and phenomics represents the most promising tools for accelerating yield gains and overcoming emerging crop productivity bottlenecks. However, accessing this wealth of plant diversity requires the characterization of this material using state-of-the-art genomic, phenomic and molecular technologies and the release of subsequent research data via a long-term stable, open-access portal. Although several international consortia and public resource centres offer services for plant research data management, valuable digital assets remains unpublished and thus inaccessible to the scientific community. Recently, the Leibniz Institute of Plant Genetics and Crop Plant Research and the German Plant Phenotyping Network have jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents.The repository is hosted at Leibniz Institute of Plant Genetics and Crop Plant Research using e!DAL as software infrastructure and a Hierarchical Storage Management System as data archival backend. A novel developed data submission tool was made available for the consortium that features a high level of automation to lower the barriers of data publication. After an internal review process, data are published as citable digital object identifiers and a core set of technical metadata is registered at DataCite. The used e!DAL-embedded Web frontend generates for each dataset a landing page and supports an interactive exploration. PGP is registered as research data repository at BioSharing.org, re3data.org and OpenAIRE as valid EU Horizon 2020 open data archive. Above features, the programmatic interface and the support of standard metadata formats, enable PGP to fulfil the FAIR data principles—findable, accessible, interoperable, reusable.Database URL: http://edal.ipk-gatersleben.de/repos/pgp/

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing

“…Read depth analyses were performed using the command “samtools depth” (Li et al., ). The SNP matrix was deposited at the Plant Genomics and Phenomics Research Data Repository (Arend et al., ) under Digital Object Identifier (https://doi.org/10.5447/ipk/2018/1). DOIs were registered with e!DAL (Arend et al., ).…”

Measures for interoperability of phenotypic data: minimum information requirements and formatting

“…All semantic and technical documentations, measured parameters, protocols and references to ontologies were manually described using ISA-Tab format. All raw files of such ISA-Tab formatted data publications are stored in the Plant Genomics and Phenomics Data Repository (PGP [51]), hosted at IPK using e!DAL as software infrastructure [52]. Recently IPK has published the first MIAPPE-compliant ISA-Tab container describing a high throughput plant phenotyping experiment including metadata, raw and processed images, extracted phenotypic features and manual validation data ([53], also stored in the PGP repository) as a data descriptor accepted at Nature’s Scientific Data journal [54].…”

Nordic research infrastructures for plant phenotyping

“…Importantly, moving plant analysis to high-throughput setting opens the way for the future of "open data" also for phenomics. Good repositories have to be developed for these large-size and multi-faceted data sets to be stored in an organized way (Arend et al 2016, Coppens et al 2017. Today, 71% of all biological datasets stay on local hard drives, where they will never be re-used and are eventually lost within 10-15 years (Stanford et al 2015).…”