Love your Data! FAIR and Open Science in Action [Workshop]

Jeanne Wilbrandt Love your Data! 2025-10-22 1st Open Access Day University of South Bohemia, České Budějovice FAIR AND OPEN SCIENCE IN ACTION Jeanne Wilbrandt — [email protected] 2 WHO AM I? • Trained biologist („Entomological phylogenomics“, genomics, transcriptomics, zoology) • PhD in 2019 •Data Steward at Leibniz FLI since 2020 • Consultation on RDM • Help with Data Management Plans (DMPs) • Talks, workshops, training Jeanne What I do Jeanne Wilbrandt — [email protected] 3 TODAY’S OBJECTIVES i Know Data Management Basics i Importance of Documentation i Starting points to take action Jeanne Wilbrandt — [email protected] How confident do you feel with the topics of today? CHECK 1 (OF 2) 4 ‣Please follow the QR-code: https://www.menti.com Code: 4142 4573 5 min Jeanne Wilbrandt — [email protected] 5 WHY TALK ABOUT IT? Jeanne Wilbrandt — [email protected] 1. HISTORICAL PERSPECTIVE 6 https://c8.alamy.com/comp/B36213/medieval-scribe-writingat-a-desk-surrounded-by-open-manuscripts-hand-B36213.jpg Increasing digitization and data density call for adjustments in information handling Value Big Data Volume Variety Veracity Velocity Variability Jeanne Wilbrandt — [email protected] 25 Minimize risk of data loss https://www.theatlantic.com/national/archive/2013/12/scientific-data-lostforever/356422/ 1. HISTORICAL PERSPECTIVE 7 Increasing digitization and data density call for adjustments in information handling https://www.theatlantic.com/national/archive/2013/12/scientificdata-lost-forever/356422/ (2013) Value Big Data Volume Variety Veracity Velocity Variability Jeanne Wilbrandt — [email protected] 2. INDIVIDUAL PERSPECTIVE 8 Benefits • Save time and resources • Improve data safety (less loss) • Publication-ready data • Where is my precious file? • Is this the latest version? • How did I generate this file? • What is this abbreviation? Panic & Confusion Increase research efficiency. Increase Efficiency Decrease potential for ScaryTales Jeanne Wilbrandt — [email protected] 3. CAREER PERSPECTIVE 9 Knowledge Transfer Left-behind data can be used by the next person https://doi.org/10.1016/j.isci.2023.107166 (2023) Jeanne Wilbrandt — [email protected] WHAT IS RESEARCH DATA? 16 + Research Data? Metadata? Jeanne Wilbrandt — [email protected] WHAT IS RESEARCH DATA? WHO generated the data? HOW was it generated and processed? WHAT is the content of the data? WHY was the data generated? WHEN was the data generated? WHERE was the data generated? What are the RELATIONS? 17 Research Data All digital data that are used or produced in the research process or are its result •Raw and processed data •Simulation data •Observational data •Code, algorithms, scripts •Audio-visual data •Training data for LLMs •… Metadata Data on data: Provenance, genesis, background information Sole Communication Jeanne Wilbrandt — [email protected] MANAGEMENT & LIFE CYCLE 18 Productive phase •Identify existing data •Data organization •Data quality •Documentation •File formats •Safety and access Postproduction •Data publication •Repositories •Licenses •Metadata •Legal Aspects •Archiving Project preparation Planning of all further steps incl. financial, legal, ethical, statistical, RDM aspects RDM describes the entirety of all handling measures of research data along its life cycle: Jeanne Wilbrandt — [email protected] RESEARCH DATA MANAGEMENT 19 "Research data management (RDM) [has] the common goal of making the data ‣accessible, ‣reusable and ‣verifiable in the long term and independent of particular people." forschungsdaten.info FAIR Jeanne Wilbrandt — [email protected] FAIR (META)DATA PRINCIPLES 20 ➡As FAIR as possible for machines and humans FINDABLE ACCESSIBLE INTEROPERABLE REUSABLE F A + + = Wilkinson et al. (2016). https://doi.org/10.1038/sdata.2016.18 “I can find the digital object” “I can download the digital object” Password ******** “I can open the digital object” “I can use the digital object” Jeanne Wilbrandt — [email protected] FAIR (META)DATA PRINCIPLES 21 + F A + = •Open Science != Open Access •As open as possible, as closed as necessary •Not a standard, but guiding principles •Spectrum “Fitness for use”, dep. on question FINDABLE ACCESSIBLE INTEROPERABLE REUSABLE Jeanne Wilbrandt — [email protected] Talk to each other! 22 Please discuss with your neighbor ‣What is Open Science? •If unsure, speculate ‣How could science be made more open? 3 min Jeanne Wilbrandt — [email protected] OPEN SCIENCE 23 UNESCO Recommendation on Open Science (2021) https://doi.org/10.54677/MNMH8546 UNESCO FactSheet: Understanding Open Science (2022) https://doi.org/10.54677/UTCD9302 OS aims to • make multilingual scientific knowledge openly available, accessible and reusable for everyone • increase scientific collaborations and sharing of information for the benefits of science and society Jeanne Wilbrandt — [email protected] BEAR DATA — GOOD DATA? 24 How do you want data to be when you reuse? ‣Please follow the QR-code: 5 min https://www.menti.com Code: 4142 4573 Jeanne Wilbrandt — [email protected] HOW DO WE GET THERE? 25 RDM Practices & Tools Guiding FAIR Principles Reusable Data Jeanne Wilbrandt — [email protected] PHASE I — “WRITE” 32 ‣Build a vehicle ‣Write the assembly instruction (document what you do) 0 5 10 15 min Start! Stop! 15 min Jeanne Wilbrandt — [email protected] INTERM. STEPS — “PUBLISH” 33 1. Take a picture (Jeanne too) 2. Disassemble the vehicle 3. Pass on the instructions 5 min Jeanne Wilbrandt — [email protected] PHASE II — “REUSE” 34 ‣Build according to new instructions Start! Stop! 0 5 10 min 10 min Jeanne Wilbrandt — [email protected] EXPERIMENT OBSERVATIONS 35 How did it go? •How detailed do you have to describe? Depends on: •Complexity (how many pieces) •Basic assumptions •What knowledge can be assumed? •Table of content 5 min Jeanne Wilbrandt — [email protected] STARTERS FOR DOCUMENTATION 36 Consider: ‣Record early and fully! ‣Capture metadata during data generation ‣Choose appropriate documentation methods ‣Use standardised terms and IDs How to record? ‣General guide https://dmeg.cessda.eu/Data-Management-Expert-Guide/2.- Organise-Document/Documentation-and-metadata ‣READMEs https://doi.org/10.5281/zenodo.10648864 ‣Data Dictionaries https://help.osf.io/article/217-how-to-make-a-datadictionary ‣Wet lab https://oir.nih.gov/system/files/media/file/2021-08/presentationscientific_recordkeeping-april2014.pdf ‣Computational https://jupyter.org/, https://quarto.org/ Jeanne Wilbrandt — [email protected] 37 DATA PUBLICATION Jeanne Wilbrandt — [email protected] •Appendix (Supplement) of an article WHERE IS DATA PUBLISHED? 38 Data as „afterthought“ to scientific Narrative, Unclear License, sometimes behind Paywall https://doi.org/10.1073/pnas.1817794116 e.g.: Jeanne Wilbrandt — [email protected] •Appendix (Supplement) of an article •Repository (generic ➲ specific) WHERE IS DATA PUBLISHED? 39 e.g.: https://zenodo.org https:// www.ncbi.nlm.nih.gov/geo/ https://www.uniprot.org/ Data as linkable object for publications Finding Repos: https://www.re3data.org/ Jeanne Wilbrandt — [email protected] https://www.nature.com/sdata/ https://bmcresnotes.biomedcentral.com e.g.: •Appendix (Supplement) of an article •Repository (generic ➲ specific) •Data Journal WHERE IS DATA PUBLISHED? 40 Data As stand-alone Publication https://doi.org/10.1038/s41597-020-0490-y https://www.sciencedirect.com/journal/softwarex Jeanne Wilbrandt — [email protected] STARTERS FOR PUBLICATION 41 •FAIR Cookbook https://faircookbook.elixir-europe.org/content/home.html •RDMkit: Data Publication https://rdmkit.elixir-europe.org/data_publication •CESSDA RDM Guide https://dmeg.cessda.eu/Data-Management-Expert-Guide •Five things about open and reproducible science … https://osf.io/dztvq/ •Open Science Best Practices for Data Science and AI - NFDI4DS https://nfdi4ds.github.io/ds-best-practices/ •How to write a good Data in Brief article https://researcheracademy.elsevier.com/uploads/2017-11/Quick_guide_Data_in_brief.pdf Consider: ‣What would you like to see? ‣Start early ‣Publish FAIR data (stand-alone) Jeanne Wilbrandt — [email protected] CLICK HERE TO ENTER TEXT 48 ≈ INSIDE 02_PROJECTS Demerdash, Dockhorn & Wilbrandt (in rev.) ‣6 zipped folders ‣Quickly reuse standard structure Jeanne Wilbrandt — [email protected] 49 WHEN PROJECTS END… Jeanne Wilbrandt — [email protected] … WHAT IS LEFT BEHIND? 50 https://doi.org/10.1016/j.isci.2023.107166 (2023) Nice unpublished data package, but… • which project(s) did it belong to? • where is it stored? • who has access rights? • which freezer box holds the samples? • where is the documentation? Knowledge Transfer File? Jeanne Wilbrandt — [email protected] 51 KTF TEMPLATE https://doi.org/10.5281/zenodo.17341188 Jeanne Wilbrandt — [email protected] 52 WHEN A PROJECT STARTS … Jeanne Wilbrandt — [email protected] … REMEMBER RDM IS HELPFUL 53 Documentation Conventions and Standards Labelling File organization Metadata Backups RDM Benefits hand-over and publication! Easier when planned! Consider: ‣Find documentation habits ‣You will forget things ‣Ask peers & data stewards Jeanne Wilbrandt — [email protected] 54 OUTRO Document! Document! Document! And a cookie! Jeanne Wilbrandt — [email protected] How confident do you feel now with the topics of today? CHECK 2 (OF 2) 55 ‣Please follow the QR-code: https://www.menti.com Code: 4142 4573 Jeanne Wilbrandt — [email protected] Take Home Messages 56 Pen & Paper ‣What was new for you? ‣What do you want to remember? ‣What do you want to apply to your work as a first step? ‣What do you want to find out more about? 5 min If not stated otherwise, CC-BY 4.0 International License Love your Data! No data is perfect — Love is a journey Jeanne Wilbrandt 57 THANK YOU FOR YOUR ATTENTION! Feedback Survey