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RDMkit, a Research Data Management Toolkit. Built by the Community for the Community
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https://datascience.nih.gov/news/march-data-sharing-and-reuse-seminar 11 March 2022 Starting in 2023, the US National Institutes of Health (NIH) will require institutes and researchers receiving funding to include a Data Management Plan (DMP) in their grant applications, including the making their data publicly available. Similar mandates are already in place in Europe, for example a DMP is mandatory in Horizon Europe projects involving data. Policy is one thing - practice is quite another. How do we provide the necessary information, guidance and advice for our bioscientists, researchers, data stewards and project managers? There are numerous repositories and standards. Which is best? What are the challenges at each step of the data lifecycle? How should different types of data? What tools are available? Research Data Management advice is often too general to be useful and specific information is fragmented and hard to find. ELIXIR, the pan-national European Research Infrastructure for Life Science data, aims to enable research projects to operate “FAIR data first”. ELIXIR supports researchers across their whole RDM lifecycle, navigating the complexity of a data ecosystem that bridges from local cyberinfrastructures to pan-national archives and across bio-domains. The ELIXIR RDMkit (https://rdmkit.elixir-europe.org (link is external)) is a toolkit built by the biosciences community, for the biosciences community to provide the RDM information they need. It is a framework for advice and best practice for RDM and acts as a hub of RDM information, with links to tool registries, training materials, standards, and databases, and to services that offer deeper knowledge for DMP planning and FAIR-ification practices. Launched in March 2021, over 120 contributors have provided nearly 100 pages of content and links to more than 300 tools. Content covers the data lifecycle and specialized domains in biology, national considerations and examples of “tool assemblies” developed to support RDM. It has been accessed by over 123 countries, and the top of the access list is … the United States. The RDMkit is already a recommended resource of the European Commission. The platform, editorial, and contributor methods helped build a specialized sister toolkit for infectious diseases as part of the recently launched BY-COVID project. The toolkit’s platform is the simplest we could manage - built on plain GitHub - and the whole development and contribution approach tailored to be as lightweight and sustainable as possible. In this talk, Carole and Frederik will present the RDMkit; aims and context, content, community management, how folks can contribute, and our future plans and potential prospects for trans-Atlantic cooperation. Data policy must be partnered with data practice. Our researchers need to be the best informed in order to meet these new data management and data sharing mandates.
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RDMkit, a Research Data Management Toolkit. Built by the Community for the Community
- www.elixir-europe.org/converge ELIXIR-Converge has received funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 871075. RDMkit, a Research Data Management Toolkit. Built by the Community for the Community Carole Goble, ELIXIR-UK Frederik Coppens, ELIXIR-BE NIH Data Sharing and Reuse Seminar, 11 March 2022 https://tinyurl.com/RDMkit-NIH
- Data Sharing and Reuse Nature 602, 558-559 (2022) doi: https://doi.org/10.1038/d41586-022-00402-1 European Commission, Directorate-General for Research and Innovation, Horizon Europe, open science : early knowledge and data sharing, and open collaboration, Publications Office, 2021, https://data.europa.eu/doi/10.2777/79699
- Data Sharing and Reuse https://www.go-fair.org/fair-principles/ 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.2016.18
- Where to start when writing and executing a Data Management Plan? Support is overwhelming – so many data initiatives! Support is underwhelming – much of organisation advice too generic. Bioscientists Researchers Data Stewards Investigators, Lab Managers, Project Coordinators Funders, Policy Makers
- ELIXIR Europe Federated inter-governmental organisation building a distributed European Research Infrastructure for Life Science Data Supporting FAIR data management for the diversity of life sciences across Europe 23 Nodes 250+ organisations https://elixir-europe.org
- ELIXIR Europe Beyond Europe, Connecting initiatives
- ELIXIR’s support for FAIR Data Specific communities Human Data, Structural Bioinformatics, Rare Diseases, Plant Sciences, Microbial Biotechnology ... FAIR services & resources Registries, standards, ontologies, identifiers, data management platforms, stewardship tools, templates. Trusted repositories Deposition databases and portals, scalable curation, sustainability. FAIR data techniques Workflows, reproducible processing, transparent reporting and provenance, FAIR assessment and evaluation, FAIRification methods. FAIR policy and activism FAIR principles, FAIR leadership & partnering at the global, European and national level. FAIR expertise and training Capability frameworks, skills, data managers network, training portal.
- FAIR Data Landscape enable end to end FAIR Public General Repositories Institutions Institutional Repositories My filestore, my institution’s file store, ELNs Data submission and access pipelines National Nodes Specialised and National RDM Platforms and Repositories SARS-CoV-2 Data Hubs Metadata and preparation Trusted Repositories
- How can we help researchers, data stewards and project managers navigate and contribute to this FAIR data repository landscape?
- Provides guidance on the Research Data Management support landscape https:/rdmkit.elixir-europe.org
- ELIXIR-CONVERGE distributed local support for data management A web-based toolkit for the bioscience community written by the bioscience community *https://zenodo.org/record/3474630#.YP2jIEDTXZQ Data Expert network Training and Capacity Building Competency Frameworks* Professionalising Data Stewardship Training & Training materials Data brokering pipelines From project data platforms to ELIXIR Deposition Databases Network of people in and across members states Best practice & examples The European COVID-19 Data Platform SARS-CoV-2 Data Hubs Federated European Genome- Phenome Archive SARS-CoV-2 variant surveillance data tracking services and tools
- RDM support throughout the entire life cycle of projects as outlined in DMPs Online focal point for guidance, information, best practice, examples Share Reuse Preserve Analyse Process Plan Collect https://rdmkit.elixir-europe.org Context and signpost for FAIR data resources as a Hub for a RDM Knowledge Commons Sensitive Data Toolbox
- 7719 users 52927 views 123 countries Launched March 2021 Every member state + other initiatives contributed Recommended by European Commission and national funders USA is top user! https://rdmkit.elixir-europe.org
- RDMkit https://rdmkit.elixir-europe.org
- Guidelines for common data management in life sciences
- Guidelines addressing different roles Using the Data Stewardship Competency Framework https://zenodo.org/record/448 6423#.YisPSpanxGw
- Guidelines for data management in specific domains Guidelines for Health Data under development by ELIXIR Health Data Focus Group
- Guidelines for common tasks in data management
- National guidelines and resources
- Combining tools - Real examples and showcases
- Registries, Services & Tools placed in narrative context training materials, learning paths, events tools standards, databases, policies, organised into collections
- Hookup with Specialised, Complementary Resources More Detailed Expert Guidance, Smart Linking Detailed recipes for making FAIR data FAIR Data Stewardship Guidance https://ds-wizard.org/ https://fairplus.github.io/the-fair-cookbook/
- Data Stewardship Wizard Predetermined Knowledge Models drive questionnaires to create DMPs https://rdmkit.elixir-europe.org/human_data.html https://converge.ds-wizard.org/knowledge-models/dsw:root- rdmkit:latest/preview?questionUuid=d5990471-0618-42cd-92cb- bbbfd4f61532 RDMkit provides context to the Knowledge Models in the DSW https://ds-wizard.org/ Smart Auto Linking
- FAIR Cookbook Recipes Expert recipes for FAIRifying data according to the FAIR elements RDMkit provides context to the Recipes in the FAIR Cookbook https://fairplus.github.io/the-fair-cookbook/
- A Showcase for ELIXIR’s FAIR Services Data Management Systems for user projects, supported by Nodes Public Data Repositories Standards Expert Data Stewardship decision making Expert Data FAIRification FAIR Services Sensitive Data Toolbox Registries
- Under the Hood Infrastructure designing to scale and sustain The simplest, widest used, and familiar platform, sustainable with limited resources • Freely accessible and open source . • GitHub, GitHub-pages, Markdown, Jekyll, YAML, Tags. Static pages limitation overcome with a really nifty and disciplined content tagging scheme • Auto-link with registries. Aligned with community practice • Inspired by The Turing Way Handbook. https://github.com/elixir-europe/rdmkit
- Open Contribution and Editorial Processes designing to scale and sustain, catering for different skills Google Docs Quick submit
- Open Contribution and Editorial Processes catering for different skills, designing to scale and sustain Author Editor Reviewer Proposed and Commissioned content • Guides, tools and resources, registry entries • Links with Resources (Cookbook, DSW …) Contentathons and focus groups Open authoring and review. Versioning & contributor credit. Governance.
- Contributors Credit For all contributions and for every page Roles and Processes Start-up -> maintenance contribution transitions Attribution on evolving content Light touch curation support & Templates Code of Conduct
- The RDMkit Community and Team Science mobilised using Open Research Practices Started in March 2020. Beta Launched March 2021. Entirely developed by virtual collaboration. Probably accelerated development – democratic, rapid, open.
- Start up, Co-creation and Cultivation Established ELIXIR framework of national nodes and communities Established core collaboration of folks who had been to the bar together Seed project funding Adoption of open development and open science methods • MVP, user persona, stories & scenarios, focus groups • Hackathons & contentathon • Open content Healthy Community Checklist, Anna Maglia, UMass Lowell (extended) ❑ Shared Vision ❑ Leadership ❑ Communication / Trust ❑ Democratic Processes ❑ Clear Roles ❑ Goal driven / Regular Returns ❑ Growth / Vibrancy ❑ Standards and Processes ❑ Discovery Enabling ❑ Necessary Resources
- Cultivation and Maintenance Refreshing the Community • Other Research Infrastructures and Communities • Other countries – Go USA! Refreshing the Content • Processes and roles for review and update • Mechanisms for adding new resources • Automated stale content detection • Reader feedback and correction Refreshing the People • Burn-out (Wikipedia 90:9:1 rule) • Credit & Positive Feedback
- Infrastructure & Processes as a Platform Separation of functionality & branding, content Underlying ELIXIR toolkit theme https://github.com/ELIXIR-Belgium/elixir-toolkit-theme Available on GitHub, GitHub packages & RubyGems (e.g. for Gitlab) Open Documents and data: a CC-BY license. Software available: MIT license.
- Adoption of the approach : Infectious Disease Toolkit COVID pandemic exposed lack of (cross-domain) interoperability of data & services with many developments across institutes, countries, … Infectious Diseases Toolkit to provide overview & context Link with RDMkit for data management aspects BY-COVID is funded by the European Union’s Horizon Europe research and innovation program under grant agreement number 101046203. https://by-covid.org
- The Future – Snowballing & Sustainability • Domains health, cancer, COVID, rare diseases, workflows, farm animals… • Communities biodiversity (ERGA), infectious diseases (BY-COVID), … • Tool assemblies data brokering, TREs, RDM blueprint, … • Roles project coordinator, clinical researchers … • National pages USA? Content Expansion Processes Refine for contribution, keeping data relevant and ensuring sustainability Adoption & Embedding ELIXIR Nodes, Data Expert Group, Projects, Programmes, Nations Missions Develop a “RDM Knowledge Commons” RDMkit, FAIR Cookbook, Data Stewardship Wizard, …
- Build Partnerships - USA! • Content expansion • Health Data … • Tools, registries … • Showcase USA FAIR services, know- how & capacity building • Dedicated national pages • For different areas use the platform and processes • Projects & Programmes Adoption • Sustainability partner
- End to end FAIR Data takes a village* Policy and Infrastructure not enough We need to offer Assistance before we make Assessments build capacity and skills for researchers, stewards and data providers support researchers to know, utilise, enable and demand FAIR RDM services pool the expertise of the community for the community * Borgman and Bourne, Why it takes a village to manage and share data (2021), https://arxiv.org/abs/2109.01694
- Acknowledgments All the ELIXIR-CONVERGE project All the RDMkit team & editorial board All our contributors and partners For more information https://rdmkit.elixir-europe.org ELIXIR-Converge has received funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 871075.