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IPK Gatersleben joins DataPLANT as participating institution

Thu Sep 05 2024

Following its community centered strategy, DataPLANT took in a new participant broadening its base and now including a non-university research institution in the field of plant biology. The research goals of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) are directed towards an efficient and sustainable supply of food, energy and raw materials and thus towards meeting global challenges. At the IPK, the conservation, research and utilisation of the genetic diversity of crop plants in the Federal Ex situ Gene Bank are combined with innovative research approaches in the fields of molecular genetics, genome research, molecular plant biology, systems biology, bioinformatics and modelling.

Uwe Scholz is the representative and PI joining DataPLANT. He is head of the Bioinformatics and Information Technology group and coordinates the Biodiversity Informatics research at IPK. He focuses on management of crop data and on the development of reusable interactive data visualization and analysis tools. The main data domains are plant phenotypic and genotypic data. His group is contributing to the development standards like MIAPPE (Minimum Information about a Plant Phenotyping Experiment) and to the specification of programmatic interface like BrAPI (Breeding API). He is leading the German Crop BioGreenformatics Network (GCBN), Center of the German Network for Bioinformatics Infrastructure (de.NBI) and is a member of the ELIXIR Plant Science and Biodiversity communities. Within de.NBI he is leading the working group “Services and Service Monitoring”. Besides DataPLANT, he is also co-speaker of the NFDI4Biodiversity consortium and fosters our cross-community activities.

As a member of DataPLANT, the IPK will contribute by undertaking the following activities:

  • The ISA Wizard tool with MIAPPE profile was and is being developed by IPK in collaboration with DataPLANT during the Biohackathon Germany in 2022, 2023 and now also in 2024 (see: https://doi.org/10.37044/osf.io/ekhdw). This tool allows the step-by-step and user-friendly generation of ISA JSON according to the MIAPPE standard. The ongoing tool development will be geard to transfer it to active use in the community.
  • The ARCtrl library developed by DataPLANT offers serialization as an Annotated Research Context (ARC) and a connection to the DataHUB via the Gitlab API. IPK has developed MIRA, a tool that enables the automated instantiation of a BrAPI phenotyping server on an ARC RO-Crate. The ARC data can then be accessed programmatically. This work will be incorporated by the IPK in a use case in NFDI4Biodiversity. This demonstrates how results from DataPLANT are used in other NFDI consortia and is an important step towards OneNFDI.
  • Scorpion is a KPI dashboard that is being developed on the basis of preliminary work from de.NBI as part of the NFDI4Biodiversity project. It enables the collection, storage and visualization of KPI measurements for the evaluation of service quality. As the developer of Scorpion, IPK will adapt this tool for the DataPLANT application and prepare it for use.

Find out more about the IPK here