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and public resource centres offer services for plant research data management, valuable digital assets remains unpublished and thus inaccessible to the scientific community.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

Figure 1.

Data publication cycle. This cycle illustrates the scientific value chain for research data publication. The documentation of experimental metadata and result data represent the basis for scientific journal publications. These are the main outcomes of scientific work, representing scientific successes as the most important way of communication of research results in the community. A parallel public sharing of experimental data increase the scientific value by enabling tests for reproducibility and providing valuable resources for further downstream analysis. In turn, new findings that are reported in published datasets increase its scientific impact and boost the author’s scholarly credit. Data citation indexes are increasingly accepted as measurement for scientific success which in turn represents the most important prerequisite for project proposals and the acquisition of funding for new projects.

Figure 2.

Report page PGP repository. Screenshot of the report page embedded in the PGP Repository for each experiment. The report provides information on the current data stock, access frequencies and the number of downloads for the respective DOI. All datasets are linked and access statistics are mapped on a world map.

Figure 3.

DataCite metadata search interface. This screenshot shows the web interface of DataCite, where a number of filter functionalities are implemented and additional options can be defined using the advanced search functionalities.

Figure 4.

DataCite OAI-interface. This snapshot illustrates the result of an OAI request to DataCite.

Figure 5.

The data publication process. This flowchart illustrates the several steps of the described data publication and approval workflow.

Figure 6.

Data publication tool. This screenshot shows the user interface of the submission tool used for data review and publication.

Figure 7.

Email notification system. These screenshots show example emails that are generated for communication of the requesting user and the reviewers during the approval process. (A) DOI request notification to reviewer. (B) Accept notification to requesting user. (C) Notification with finally assigned DOI.

Figure 8.

Schema of DOI assignment. This schema used to generate a unique DOI for a new dataset.