Foundations of Research Data Management (RDM) for Beginners

© envato Foundations of RDM for Beginners Justine Vandendorpe and Sophie Boße 04 November 2025 Online Seite Icebreaker Seite 3Source: ZB MED 2023; icon from Kücklich 2020 Meet & Greet ►Name ►Affiliation ►Level of expertise ►Expectations about this workshop 2025-11-04 Seite Introduction of the Trainers Seite 5Source: ZB MED 2024 Justine Vandendorpe ►Background in Organism Biology & Ecology and Computational Evolutionary Biology ►Member of the Data Science & Services team of ZB MED ►Coordinating the ZB MED RDM training team ►Data steward within NFDI4Microbiota ►Project member of RDMTraining4NFDI 2025-11-04 Seite 6 Sophie Boße 2025-11-04 ►Background in Food & Nutritional Science ►Member of the Research Data Management team of ZB MED ►Training coordinator in FAIRagro Seite Introduction of Our Affiliations Seite 8 Source: modified from Vandendorpe 2021 by ZB MED 2022 ZB MED –Information Centre for Life Sciences ►INFORMATION: fostering Open Access and Open Data. ►KNOWLEDGE: conducting applied research to improve ZB MED’s services, and providing research support in the Life Sciences. ►LIFE: German National Library of Medicine, Health, Environment, Nutrition and Agriculture 2025-11-04 Seite 9Source: ZB MED 2024 NFDI4Microbiota 2025-11-042025-11-04 Seite 16Source: ZB MED 2023; icon from Kücklich 2020 Conversation Among RDM Professionals A conversation between multiple RDM experts and the participants, rather than a presentation of concepts in an authoritative way. 2025-11-04 Seite Research Data Seite 18Source: modified from Biernacka et al. 2020 by Vandendorpe 2025 Ideas Out Loud What is research data? Share your answer out loud or in the chat if you wish (5 minutes). 2025-11-04 Seite Research Data ►Object ►Scientific research activities ►Original research results Seite 20 Classification of Research Data ►Primary / raw data –Observational –Experimental –Simulation ►Secondary data –Derived –Compiled Source: modified from Pomerantz 2015, Darby n.d. and Goldman and Martin 2023 by Vandendorpe 2025 Photo by The New York Public Library on Unsplash 2025-11-04 Seite 21 Classification of Research Data ►Processed data ►Analysed data ►Finaled / published / reference data ►Information about the means Source: modified from Goldman and Martin 2023 and Darby n.d. by Vandendorpe 2025 Photo by Walkator on Unsplash 2025-11-04 Seite 22 Classification of Research Data Source: Gerlich et al. 2023 2025-11-04 Seite 23 Source: modified from NC State University Library. (n.d.), Steen et al. 2022, Voigt et al. 2022 and DFG 2015 by Vandendorpe 2025 General Data Types ►Data files ►Documents ►Measurement data, lab and observation data ►Lab and field notebooks ►Questionnaires, transcripts ►Survey data ►Images, audio and video tapes ►Spectra Photo by Nathan Dumlao on Unsplash 2025-11-04 Seite 24 Data Types What type of research data does your community handle? Share your answer out loud or in the chat if you wish (4 minutes). Source: modified from Biernacka et al. 2020 by Vandendorpe 2025; photos from Unsplash 2025-11-04 Seite Seite 32Source: modified from Vandendorpe and Lindstädt 2023 by Vandendorpe 2025 Discipline-Specificity of Research Data Management E.g. with personal health data: ►Informed consent ►Access monitoring / restriction ►Sending algorithms to data Photo by National Cancer Institute on Unsplash 2025-11-04 Seite 33 Discipline-Specificity of Research Data Management What makes research data management unique in your field? Share your answer out loud or in the chat if you wish (5 minutes). Source: modified from Biernacka et al. 2020 by Vandendorpe 2025 2025-11-04 Seite 34Source: modified from Bres et al. 2022 and Jacob et al. 2022 by Vandendorpe 2025 Benefits of Research Data Management for Researchers ►Enhancing visibility, reputation, data ownership ►Meeting formal requirements from third parties Photo by Brooke Lark on Unsplash 2025-11-04 Seite 35 Source: modified from the NFDI4Microbiota Knowledge Base and Pauls et al. 2023 by Vandendorpe 2025 Further Benefits of Robust Data Management Practices ►Making data accessible, reusable and verifiable ►Ensuring integrity ►Maximising the impact, reproducibility, transparency and rigours of analyses and findings ►Enhancing collaboration and knowledge sharing ►Preserving the scientific record ►Advancing scientific knowledge 2025-11-04 Seite 36Source: modified from Bartlett 2021 and Joelving 2023 by Vandendorpe 2025 Consequences of Poor Research Data Practices ►Retractions of papers ►Correction and re-submission for review Screenshot from The University of Chicago Press 2025-11-04 Seite 37 Flip and Turn Arrange the steps of the research data life cycle in the correct order on a physical or digital sheet of paper (6 minutes): ►Analyse ►Collect ►Plan ►Preserve ►Process ►Reuse ►Share Source: modified from Biernacka et al. 2020 by Vandendorpe 2025 2025-11-04 Seite 38Source: RDMkit Flip and Turn (solution) 2025-11-04 Seite 39Source: Mau 2019 Research Data Life Cycle 2025-11-04 Seite 40Source: modified from Science Europe and Sheikh et al. 2023 by Vandendorpe 2025 Issues and Challenges in Research Data Management For researchers: ►Different organisational requirements ►Lack of connectivity between tools Photo by x ) on Unsplash 2025-11-04 Seite 41Source: modified from Yamaji 2024 and Cox et al. 2017 by Vandendorpe 2025 Developments and Initiatives in Research Data Management ►Libraries –Advocacy – Policy development – Advisory and consultancy services ►KU Leuven: dashboard to review datasets ►German National Research Data Infrastructure (NFDI) Photo by redcharlie on Unsplash 2025-11-04 Seite 48Source: Vandendorpe 2025 Main Components of a DMP ►Administrative project-specific information ►Roles, responsibilities and obligations Screenshot from Smirnov 2024 2025-11-04 Seite 49Source: Vandendorpe 2025 Main Components of a DMP ►Administrative project-specific information ►Roles, responsibilities and obligations ►Budget, costs and resources Screenshot from Smirnov 2024 2025-11-04 Seite 50Source: Vandendorpe 2025 Main Components of a DMP ►Administrative project-specific information ►Roles, responsibilities and obligations ►Budget, costs and resources ►Description of the data to be collected and shared Screenshot from Smirnov 2024 2025-11-04 Seite 51Source: Vandendorpe 2025 Main Components of a DMP ►Administrative project-specific information ►Roles, responsibilities and obligations ►Budget, costs and resources ►Description of the data to be collected and shared ►Data documentation Screenshot from Smirnov 2024 2025-11-04 Seite 52Source: Vandendorpe 2025 Main Components of a DMP ►Administrative project-specific information ►Roles, responsibilities and obligations ►Budget, costs and resources ►Description of the data to be collected and shared ►Data documentation ►Data access and publishing Screenshot from Smirnov 2024 2025-11-04 Seite 53Source: Vandendorpe 2025 Main Components of a DMP ►Administrative project-specific information ►Roles, responsibilities and obligations ►Budget, costs and resources ►Description of the data to be collected and shared ►Data documentation ►Data access and publishing ►Further points Screenshot from Smirnov 2024 2025-11-04 Seite 54Source: modified from Wallace et al. 2022 by Vandendorpe 2025 Ideas Out Loud Aside from it being a requirement, there are many benefits to researchers of writing a DMP. What benefits do you think there are? Share your answer out loud or in the chat if you wish (5 minutes). 2025-11-04 Seite 55Source: Vandendorpe 2025; icon from Kücklich 2020 Benefits of Writing a DMP ►Save time and nerves for yourself and others – Roles, responsibilities and efforts – IT staff and data protection officer – Data quality – Processing steps – Access rights and security – Gaps and vulnerabilities 2025-11-04 Seite 56Source: Vandendorpe 2025; icon from Kücklich 2020 Benefits of Writing a DMP ►Save time and nerves for yourself and others ►Harmonising the common handling of data – Overview and control – Standards and common vocabulary – Data storage – Data organisation 2025-11-04 Seite 57Source: Vandendorpe 2025; icon from Kücklich 2020 Benefits of Writing a DMP ►Save time and nerves for yourself and others ►Harmonising the common handling of data ►Enable verification and control 2025-11-04 Seite Collect Figure by RDMkit Seite 65Source: Vandendorpe 2025 Use an Electronic Lab Notebook (ELN) for Data Collection To document the data generated through controlled experiments and laboratory analysis. Figure from Schröder et al. 2022 2025-11-04 Seite 66Source: Vandendorpe 2025 Use an Electronic Lab Notebook (ELN) for Data Collection To document the data generated through controlled experiments and laboratory analysis. ►Features: annotation of raw data, versioning of experiment description, real-time collaboration Figure from Schröder et al. 2022 2025-11-04 Seite 67Source: Vandendorpe 2025 Use an Electronic Lab Notebook (ELN) for Data Collection To document the data generated through controlled experiments and laboratory analysis. ►Features: annotation of raw data, versioning of experiment description, real-time collaboration ►Benefits: increasing efficiency in daily tasks, ensuring reproducibility, contributing to good research practice Figure from Schröder et al. 2022 2025-11-04 Seite 68Source: Vandendorpe 2025 Use an Electronic Lab Notebook (ELN) for Data Collection To document the data generated through controlled experiments and laboratory analysis. ►Features: annotation of raw data, versioning of experiment description, real-time collaboration ►Benefits: increasing efficiency in daily tasks, ensuring reproducibility, contributing to good research practice ►Examples: eLabFTW, openBIS, SciNote Figure from Schröder et al. 2022 2025-11-04 Seite 69Source: Vandendorpe 2025 Use Protocols for Data Collection ►Standardization Screenshot from Schulz 2023 2025-11-04 Seite 70Source: Vandendorpe 2025 Use Protocols for Data Collection ►Standardization ►Protocol repositories (e.g. protocols.io) Screenshot from Schulz 2023 2025-11-04 Seite 71Source: Vandendorpe 2025 Use Protocols for Data Collection ►Standardization ►Protocol repositories (e.g. protocols.io) ►Protocols in microbiology: –Fecal sample collection: International Human Microbiome Standards (IHMS) –DNA extraction and sequencing from environmental samples: Earth Microbiome Project (EMP) Screenshot from Schulz 2023 2025-11-04 Seite 72 Source: modified from Lindstädt et al. 2019, RfII 2021, Bres et al. 2022, KU Leuven 2022 and Voigt et al. 2022 by Vandendorpe 2025 Document Your Data With Metadata Metadata = data about data. ►Standardised ►Formal ►Human-readable ►Machine-readable Figure from Jaindeepali 2025-11-04 Seite 73Source: Vandendorpe 2025 Validate and Check Your Data ►Definition: “process of ensuring data has undergone data cleansing to confirm it has data quality, that is, that it is both correct and useful” [Wikipedia 2025]. 2025-11-04 Seite Seite Process & Analyse Figure by RDMkit Seite 82Source: modified from Wallace et al. 2022 by Vandendorpe 2025 Ideas Out Loud Which table layout is best for analysis? Share your answer out loud or in the chat if you wish (2 minutes). 2025-11-04 Seite 83 Create Analysis-Friendly Data ►Make each column a variable ○Store units as metadata ►Make each row an observation ►Document each step processing your data in a README file Comic from xkcd 2025-11-04Source: modified from Training Expert Group 2020 and Wallace et al. 2022 by Vandendorpe 2025 Seite Preserve Figure by RDMkit Seite 85 Multiple Choice Question Which of the following do you believe are good ways and bad ways of backing up your data? Put a ✓or a ✕ next to the answer(s) (5 minutes). ►Commercial cloud service ►In-house cloud service (operates similarly to a commercial cloud service but with servers and infrastructure maintained by your organization) ►USB pen-drive ►External hard-drive ►My laptop ►My workstation’s hard-disk ►Network drive Source: modified from Wallace et al. 2022 by Vandendorpe 2025, Screenshot: Zoom 2025-11-04 Seite 86 Multiple Choice Question (Solution) Which of the following do you believe are good ways and bad ways of backing up your data? Put a + sign next to the correct answer(s) in the pad. ►Commercial cloud service: it depends. ►In-house cloud service (operates similarly to a commercial cloud service but with servers and infrastructure maintained by your organization): usually a good way. ►USB pen-drive: definitely not. ►External hard-drive: definitely not. ►My laptop: good as a temporary storage solution for active data. ►My workstation’s hard-disk: good as a temporary storage solution for active data. ►Network drive: usually a good way. Source: modified from Wallace et al. 2022 by Vandendorpe 2025 2025-11-04 Seite 87Source: modified by Vandendorpe 2024 Follow the 3-2-1 Rule When Backing Up Your Data 23 1 Different media types Copy off site / in the cloud Copies 2025-11-04 Seite Other Best Practices ►IT group or library ►Large data sets ►Versioning ► Checksums ► Newer technologies Seite 89Source: Vandendorpe 2025 Ideas Out Loud If you had to store something for 100 years, how would you do it? Share your answer out loud or in the chat if you wish (5 minutes). 2025-11-04 Seite Reuse Figure by RDMkit Seite 97Source: modified from Pavone 2020 by ZB MED 2022; image from van de Sandt et al. 2019 Make Your Data Reusable ►Documentation ►Metadata standards and terminologies ►Standardisation ►Open license 2025-11-04 Seite Summary Photo by Aaron Burden on Unsplash Seite 99 Ideas Out Loud Which of the above recommendations would be the most helpful for your discipline? Which could your community try to implement first? Share your answer out loud or in the chat if you wish (5 minutes). Source: modified from Wallace et al. 2022 by Vandendorpe 2025 2025-11-04 Seite Feedback Seite 101 Evaluation & Feedback ►Short feedback in the pad ►Evaluation on 2ask: https://www.2ask-survey.com/c/ PWY144JSQS17W/?_init=true 2025-10-28 Seite Closing Seite 103 Next Live Session: Practical Data Protection in Research ►Date and time: 2025-11-06 09:00 - 12:00 ►Location: https://us02web.zoom.us/j/83165166230?pwd=enCPBxjQ1kdBtW1rp3j2wETbfnDTpi.1 ►Trainer(s): Neelam Vishen (Base4NFDI) ►Overview: – GDPR principles – Practical tools – Common scenarios – Simple strategies 2025-10-29 Seite 104 Self-Learning Modules ►Date: 2025-11-03 - 2025-11-21 ►Guide: https://liascript.github.io/course/?https://raw.githubusercontent.com/MUebachs/RDMTraining4NFDI_Hybrid-Event-Res earch_Data_Management_for-NFDI_Consortia/refs/heads/main/README.md#1 ►Overview – Foundations of RDM for Trainers – Open Science – Python for Advanced – Git for Beginners – Train-The-Trainer Workshop on Data Management Plans (DMPs) – Sharing Data & Metadata 2025-10-29 Seite 105 Contact us Justine Vandendorpe Data Steward ZB MED – Information Centre for Life Sciences Gleueler Straße 60 50931 Köln [email protected] 2025-11-04 This work is licensed under the Creative Commons Attribution 4.0 International License (unless stated otherwise within the sources cited in this work).