HeFDI Data Talk Abstract: Together with other disciplines, plant research increasingly relies on effective research data management services and infrastructures that facilitate the acquisition, archival, exchange, and processing of research data sets to enable the exchange of interdisciplinary expertise. Focused on its core mission to minimize the additional work of research data management, DataPLANT wants to support plant researchers in practice, providing technical services and infrastructure and personal support. A central element for achieving this goal is the Annotated Research Context (ARC), which acts as single entry point and will define the structure of a future data publication. ARCs are FAIR Digital Objects covering the entire research cycle, from the experiment to the computational aspects to the actual data and metadata, as well as the resulting data publications using existing repositories. Several tools and services are already available to ensure working with ARCs is done without friction in a collaborative research environment. Accordingly, DataPLANT represents the central point of contact for plant researchers to set up appropriate research data management. About the HeFDI Data Talks: The HeFDI Data Talks are a bi-weekly open information and discussion event focused on data management in the context of science, in which relevant NFDI consortia as well as research data management services present themselves. The series discusses current topics and presents numerous –including local and regional –tools and services. The HeFDI Data Talks are an offer of the HeFDI Initiative (Landesinitiative HeFDI), which is funded by Hesse’s Ministry for Science and Arts (HMWK). DOI link: https://doi.org/10.5281/zenodo.7254512; License information: Creative Commons Attribution 4.0 International (CC BY 4.0) Date Topic Presenter(s) 23. September 2022 DataPLANT - Provider of Tools and Services to structure the Data Jungle Dr. Kathryn Dumschott (IBG4 at the Forschungszentrum Jülich) gefördert durch
Data PLANT Provider of Tools and Services to Structure the Data Jungle Kathryn Dumschott
[email protected] 23 September 2022
Classical journal publication •Scientists acquire data to discover knowledge which is shared in scientific journal publications knowledge data selected data 3
Data: a primary product in science •Data itself has value for science: •It can be reused to gain further knowledge •New techniques or theories may require it to be re-examined knowledge data information 4
Becoming FAIR will drive science knowledge notes digital information •Increasing the level of annotation at the source, tracking provenance using community standards •Maximize data discoverability and reuse
•National Research Data Management Infrastructure (NFDI) •Provide tools to structure research data according to FAIR principles •Effectively manage your own research data •Annotate with metadata as early as possible
ARC Annotated Research Context
Your entire investigation in a single unified bag =C A G A G A G A G G GAGGT A G G T G GGTGA C A G A G G T G A m/z experimental data computation annotation https://github.com/nfdi4plants/ARC-specification Annotated Research Context (ARC)
Domain-relevant community standards repositories EBI: MetaboLights checklists controlled vocabularies standards analyses & workflows Galaxy 9 New responsibilities for researchers to handle more than 600 content ‘standards’
Annotation principle 16 AB C D Sample Data Parameter [instrument model] ´TripleTOF4600 ’ ´TripleTOF4600 ’ ´TripleTOF4600 ’ ´TripleTOF4600 ’ ´TripleTOF4600 ’ •Low friction metadata annotation •Familiar spreadsheet, row and column based environment
AB C D Sink Source Parameter [´parent term’] ´child term’ ´child term’ ´child term’ ´child term’ ´child term’ Swate –Metadata annotation tool 17 Excel + Swate Plug-In isa new parameter Excel + Swate Plug-In https://github.com/nfdi4plants/Swat e
source characteristic new parameter datafile / sample factor 18
Templates and checklists AB C D Sink Source Parameter [´parent term’] ´child term’ ´child term’ ´child term’ ´child term’ ´child term’ = Checklists and requirements can be displayed as templates 19
Swate Ontology DB (MySQL/MariaDB) external ontologies GitHUB Nfdi4plants ontology Swobup Service Excel + swate GitHUB metadata templates Behind the scenes of Swate 20
Controlled vocabularies Metadata need to “speak“ the same language = dictionaries ontologies TripleTOF4600 instrument model Q Exactive mass spectrometer is_a 21
Bridging the ontology gap Swate Ontology DB (MySQL/MariaDB) external ontologies GitHUB Nfdi4plants ontology Swobup Service Excel + swate DataPLANT helps in connecting user wishes and requirements with the international community and standardization efforts. DataPLANT will act as a broker Any participation is welcome if you want 22
Realization of lab-specific metadata templates measurements processing analysis m/z = C A G A G A G A G G GAGGT A G G T G GGTGA C A G A G G T G A C A G A G A G A G G GAGGT A G G T G GGTGA C A G A G G T G A Sink Source P1 P2 P3 …Pn Sink Source P1 P2 P3 …Pn 23
Prebuilt templates for endpoint repositories https://github.com/nfdi4plants/SWATE_templates/tree/main/templates 24
ARCs: Share yours and work together •ARCs are the basis of the collaborative research platform •ARCs can be seamlessly shared between researchers 25
ARCs are easy to distribute GEO / ENA Pride / etc. MetaboLights Move your data to the appropriate endpoint repositories required by the scientific journals or core facilities … RO-Crate 32
Swate Ontology DB (MySQL/MariaDB) external ontologies GitHUB Nfdi4plants ontology Swobup Service Excel + swate GitHUB metadata templates ARCcommander DataPLANT metadata tool chain converter repositories EBI: MetaboLights 33 https://github.com/nfdi4plants/arcCommander
Support for your research tooling personal •Tools to facilitate creation and management of ARCs •Personal assistance 34 Technical-digital assistance Data stewards
DataPLANT service •Tools to facilitate creation and management of ARCs •Communication and realization of FAIR best practices •Data management plan generator creates a data management plan in a few simple steps https://dmpg.nfdi4plants.org/ 35
DataPLANT service 36 Helpdesk https://helpdesk.nfdi4plants.org/ E-Mail [email protected] Website https://www.nfdi4plants.org/
Acknowledgements & the whole team at DataPLANT
Thank you for your attention
