The ELIXIR FAIR Knowledge Ecosystem for practical know-how: RDMkit and FAIRCookbook
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Presented at the FAIR Data in Practice Symposium, 16 may 2023 at BioITWorld Boston. https://www.bio-itworldexpo.com/fair-data. The ELIXIR European research Infrastructure for life science data is an inter-governmental organizations coordinating, integrating and sustaining FAIR data and software resources across its 23 nations. To help advise users, data stewards, project managers and service providers, ELIXIR has developed complementary community-driven, open knowledge resources for guiding FAIR Research Data Management (RDMkit) and providing FAIRification recipes (FAIRCookbook). 150+ people have contributed content so far, including representatives of the pharmaceutical industry.
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The ELIXIR FAIR Knowledge Ecosystem for practical know-how: RDMkit and FAIRCookbook
- 1. www.elixir-europe.org www.elixir-europe.org The ELIXIR FAIR Knowledge Ecosystem for Practical Know-How: RDMkit and FAIRCookbook Carole Goble, University of Manchester, UK ELIXIR UK Head of Node Philippe Rocca-Serra, University of Oxford, UK https://www.bio-itworldexpo.com/fair-data
- 2. ELIXIR: The European Research Infrastructure for Life Science Data 23 Nodes 220+ Orgs Towards a federated digital infrastructure for Life Science Data, coordinating national capabilities Data & software FAIR and open as possible Transnational access and analysis Sensitive data Gateway to Communities of Practice, European and Global initiatives, Standards Bodies Coordinate joint funding actions and participations Hub https://elixir-europe.org
- 3. FAIR is at the heart Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.1 Barker, M., Chue Hong, N.P., Katz, D.S. et al. Introducing the FAIR Principles for research software. Sci Data 9, 622 (2022). https://doi.org/10.1038/s41597-022-01710-x Data Software Digital Objects
- 4. Bioscience communities FAIR RDM know-how Systems Biology Single Cell omics Biodiversity Microbiome Cancer Health Data Machine Learning Bio Curation Infectious Disease RDM Cross-cutting & general Specialised & community specific
- 5. FAIR Research Data and Software is at the heart An ecosystem of FAIR services, platforms and resources Activities and methodologies for FAIR awareness, review, assistance and implementation Registries Trusted Repositories RDMTools FAIR Services RDM Platforms Methodologies Training Stewardship Analysis Metadata Platform
- 6. FAIR Research Data and Software Collaborators
- 7. Practical know-how Knowledge sharing & dissemination Smart navigating the registries and repositories landscape Relevant to bio-scientists and related trades General and specialist Bioscientists Researchers Data Stewards Research Software Engineers Investigators, Lab Managers, Project Coordinators Funders, Policy Makers, Budget holders, Managers
- 8. FAIR Knowledge Ecosystem RDMTools Registries Repositories Training RDM Platforms Data Stewardship & RSE networks https://rdmkit.elixir-europe.org Guidance for RDM services Recipes for FAIR data https://faircookbook.elixir-europe.org/ https://ds-wizard.org/
- 9. Guidance on the Research Data Management support landscape A web-based toolkit for the bioscience community written by the bioscience community https:/rdmkit.elixir-europe.org
- 11. Interconnected pages, indexed registry entries, links to tools
- 12. Specialised data management Written by expert networks
- 13. A collection of recipes by the bioscience community that cover the specific operation steps of FAIR data management. Pre-print: https://doi.org/10.5281/zenodo.7156792 (in press at Nature’s Scientific Data) Ingredients An idea of tools/skills needed Step by step process Guidelines, process, description Practical elements, code snippets #Python3 #zooma-annotator-script.py file def get_annotations(propertyTy pe, propertyValues, filters = ""): " Examples Conclusions What should I read next? Anatomy of a recipe Different levels of granularity https://faircookbook.elixir-europe.org
- 14. Includes guidance on data FAIRification pipelines and insights into the impact on FAIR maturity of your datasets https://w3id.org/faircookbook/FCB079 https://fairplus.github.io/Data-Maturity How far am I in my FAIR journey Is my dataset FAIR? How to make it FAIR?
- 15. http://bit.ly/FAIRplusNewProcess My lab has datasets - what do I need to do to make them FAIR? https://w3id.org/faircookbook/FCB079
- 17. Linking together - what identifiers for data should I be using?
- 18. FAIR knowledge is in demand USA is top 143+ countries Both recommended by EC programmes and multiple national funders
- 19. Crowd contributed Full author credit Clear contribution processes Encourage networks to contribute
- 20. Simple Sustainable Platforms, Community owned & Open Governance Editorial Boards (NIH ODSS representation) Open meetings Hackathons & Refreshes Simple platform • Git (RDMkit) • Jupyter Book (FAIRCookbook) Open licenses for content and platform • CC-BY-4.0 license.
- 21. Alliance https://rdmkit.elixir-europe.org/rdmkit_alliance Advise on how to adopt, use, reuse, attribute and contribute to the components, content and practices Forum to manage sustainability and governance Enable all stakeholders to engage.
- 22. Summary: FAIR Knowledge Ecosystem for Practical Know-How So much FAIR know-how and so many services and resources. Essential to have toolkits and cookbooks to navigate and for context, understanding and tactics. Living resources with content, governance and management by the community for the community. Open. You are welcome to use and join.
- 23. Funding Acknowledgements Grant agreement ID: 802750 https://fairplus-project.eu/ Grant agreement ID: 871075 https://elixir-europe.org/ https://rdmkit.elixir-europe.org https://faircookbook.elixir-europe.org/