PGP repository: a plant phenomics and genomics data publication infrastructure.

Daniel Arend,Uwe Scholz,Astrid Junker,Matthias Lange,Danuta Schüler,Juliane Wylie

doi:10.1093/database/baw033

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and public resource centres offer services for plant research data management, valuable digital assets remains unpublished and thus inaccessible to the scientific community.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/

Highlights

The technical progress in plant genomics and phenomics enables a new quality in studying plant development and underlying mechanisms and processes [1, 2]
We introduce the Plant Phenomics and Genomics Data Publication Infrastructure (PGP) repository that implements all components of a sustainable data publication culture cycle [18] (Figure 1)
The PGP repository provides access to plant phenomics and genomics research data, which is hitherto not supported by any existing international repository

Summary

Introduction

The technical progress in plant genomics and phenomics enables a new quality in studying plant development and underlying mechanisms and processes [1, 2]. DataCite provides a free service to assign digital object identifiers (DOIs) [17] as globally proven standard for persistent identifiers, enabling the registration of a minimal commonly accepted set of technical metadata for a scientific dataset. Since DOIs have already represent an accepted data citation standard (e.g. by publishers, journals and public databases), these identifiers are the preferred way for citation of datasets.

Results

Conclusion