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The de.NBI/ELIXIR Service "PGP" for Phenomics Data Publication


by Daniel Arend

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Short Abstract

Many of the published high-throughput phenotyping studies used imaging based methods to derive plant traits in a quantitative, non-invasive, and reproducible manner. However, most of these studies do not give access to raw and result image datasets in the context of experimental metadata. According to the FAIR data management principles, the availability of and sustainable access to imaging datasets is one of the key criteria in the scientific value chain. Supported by the IPK Gatersleben, we herewith announce as pilot the free use of the “Plant Genomics and Phenomics” (PGP) (Arend et al., Database, 2016) data repository as a service for IPPN and EMPHASIS partners to publish comprehensive data sets derived from imaging-based, high-throughput phenotyping experiments. The PGP scalable infrastructure enables the sharing and publishing (imaging) of datasets in the range of up to several gigabytes and fulfills the data publication policies of relevant scientific and data journals as well as funding agencies. PGP enables the assignment of permanently citable DOIs for supplemental datasets or standalone data publications. Examples of PGP-published phenotyping experiments are datasets from high-throughput plant phenotyping platforms at IPK (http://dx.doi.org/10.5447/IPK/2016/7) and FZJ-Jülich (http://dx.doi.org/10.5447/IPK/2017/10).

Further information is available at https://edal-pgp.ipk-gatersleben.de. In order to provide a quick-start tutorial, we offer a webinar about how to use the PGP repository for data publication.

 

Bio

Daniel Arend – Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

I studied bioinformatics at the Martin-Luther University Halle-Wittenberg, Germany with the focus on genomic sequence analysis and database management systems. Since I finished my diploma thesis 2012 in cooperation with the IPK Gatersleben, I started working as research assistant in the "Bioinformatics and Information Technology" research group in frame of the German Plant Phenotyping Network (DPPN).

I am interested in the field of bioinformatics and research data management in life sciences and concentrating on standards and infrastructures for data sharing and publication. I contributed to the MIAPPE standard for plant phenotyping data and I am the main developer of the e!DAL infrastructure which is the basis for the PGP repository hosted at the IPK Gatersleben.