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IT-Concept DPPN

DPPN Techno Data Management across locations

Plant phenotyping platforms, as provided by the German Plant Phenotyping Network (DPPN), produce huge amounts of heterogeneous data. Their scientific potential can only fully exploited if the datasets are FAIR. Thus, the DPPN Techno module develop infrastructures for experiment documentation and data publication as well as methods for linking heterogeneous phenomic and genomic data for knowledge discovery.

The IPK Gatersleben developed a FAIR-aware infrastructure called e!DAL (electronic Data Archive Library), which assigns citable digital object identifiers to datasets and registers their metadata at DataCite. The high level of automation lowers the barriers of data submission for scientists, and a journal-like review process ensures the quality of released data. The Plant Genomics and Phenomics Research Data Repository (PGP) is the first instance based on this infrastructure and was released in 2016. It is hosted by the IPK Gatersleben and was successfully registered as research data repository at FAIRsharing.orgre3data.org and OpenAIRE. Furthermore, the ScientificData and GigaScience Journal accepted PGP as institutional data repository. PGP already provides access to a large dataset from IPK's LemnaTec high-throughput plant phenotyping platform with a MIAPPE-compliant ISA-Tab metadata representation (Arend et al., 2016, Chen et al, 2018).

With the integration of the ELIXIR Authentication and Authorization Infrastructure (AAI) e!DAL is now able to support multiple institutional and third-party login provider. Doing so, in June 2018 a second e!DAL based infrastructure was established at the Jülich Plant Phenotyping Center (JPPC) and is hosted by Forschungszentrum Jülich.


Bild des DPPN DataInterfacesFigure 1: Overview of DPPN IT-Concept across locations

The core of sustainable experiment annotation is the description of samples with respect to all experimental factors and source characteristics as well as protocols and parameters for plant growth and specific assays. The international ISA-Tab standard provides table formats for general-purpose data documentation. We are involved in the development of recommendations for minimal information about plant phenotyping experiments (MIAPPE), which is registered on FAIRsharing.org and is together with the implementation in a specific ISA-Tab configuration for plant phenotyping data published(Ćwiek-Kupczyńska et al. 2016) . The corresponding checklists are applied in the local data management systems of the DPPN sites to support sustainable experiment documentation. At IPK Gatersleben, a PhenoLIMS module based on the commercial LIMSOPHY lab information management system was developed for that purpose, Helmholtz Zentrum München sets up an openBIS framework and Forschungszentrum Jülich employs a custom-built integrative information system. All sites use the ISA-Tab standard to export datasets for publication and exchange.

 

To further improve interoperability of datasets within and beyond DPPN, we suggest controlled vocabularies integrating existing public ontologies and universal identifiers to extend the current ISA-Tab configuration and homogeneously describe crucial metadata of plant phenotyping experiments. This will enable targeted searches for relevant datasets via keywords in DataCite or a structured metadata registry. Compatible annotations of datasets from different research sites, measurement domains and omics levels open up new chances of data-driven hypothesis generation. In studies with Arabidopsis and Poplar we demonstrate how integration of heterogeneous data from phenotypic observations to gene expression contributed findings that suggest potential mechanisms of abiotic stress responses, which in part are supported by reviewing multiple annotated previous datasets in context.

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Grant-Number: 031A053A/B/C

 


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