Midterm course to Research Data Management for TargetRNA

Midterm update to your DMP Korbinian Bösl Data management coordinator Centre for Digital Life & ELIXIR Norway 27 November 2025 Objectives ? Questions ●How do you backup up you data? ●How can I make sure data is unaltered by storage or transfer? ●How can I document my data? ! Objectives ●Check in and update your DMP ●Identify potential gaps in your RDM strategy knowledgebase.nfdi4chem.de/knowledge_base rdmkit.elixir-europe.org Backup Backup Avoid losing data! Use (institutionally) managed storage with automatic backup (and snapshots?) OneDrive/Sharepoint @ UiB Avoid: data solely safed to laptops, stand-alone HDDs, thumb drives, … In general 3 - 2 -1 rule 3 copies 2 different media 1 off-site backup 5min to check the backup status of your data Checksums Checksum your data to detect corruption during storage or transfer MD5sum in built in every OS windows powershell: $ certutil -hashfile [filename] MD5 Mac OS/nix: $ md5sum [filename(s)|*] > checksums.md5 $ md5sum -c checksums.md5 For security critical or legally relevant: sha256 Demo + 5 min for you to checksum one of your data folders Gene: PIK3CA Sequence identifiers: Figure 6 from Zhao, S., and Zhang, B. (2015). BMC Genomics 16 licensed under Creative Commons Attribution 4.0 International License README files Study/project level README This README file was generated on [YYYY-MM-DD] by [NAME] GENERAL INFORMATION - Study/project title: - Description: <provide a short description of the study/project> - Principle Investigator: - Link to Data management plan ORGANIZATION - Folder structure: similar to folder structure example above (below) - File naming conventions (with examples) <unless your project is big and you have README files in every subfolder with this information provided there> - File formats: <Provide a list of all file formats present in this study/project> Data level README GENERAL INFORMATION - Dataset title: - Description: <provide description of the dataset origin, steps used in its generation, content and its purpose> ORGANIZATION - Folder structure: similar to folder structure example above (below) - File naming conventions: <provide explanation of the elements used, allowed values and examples> - File formats: <Provide a list of all file formats present in this dataset> [...] 15 min for you to create a README for one of your data folders RDMkit -> your task -> data documentation Minimum Information about a high-throughput Nucleotide SeQuencing Experiment (MINSEQE) Reporting standards for e.g. RNA-Seq Information regarding submission on ArrayExpress https://www.ebi.ac.uk/arrayexpress/submit/overview.html MINSEQE entry on FAIRharing: https://fairsharing.org/bsg-s000174/ https://www.fged.org/projects/minseqe/ Required for deposition of sequencing data on ArrayExpress MINSEQE Example Administrative Information: Person(s) Organisations Publications MINSEQE Type of metadata Administrative Information: Person(s) Organisations Publications Experimental Conditions/Design Protocols: ●Treatment ●Sample Collection ●Growth ●Nucleic Acid Extraction ●Library Construction ●Sequencing Protocol Administrative Information: Person(s) Organisations Publications Experimental Conditions/Design Protocols: ●Treatment ●Sample Collection ●Growth ●Nucleic Acid Extraction ●Library Construction ●Sequencing Protocol High-throughput Sequence Alignment Protocol Data Normalization Protocol Administrative Information: Person(s) Organisations Publications Experimental Conditions/Design Protocols: ●Treatment ●Sample Collection ●Growth ●Nucleic Acid Extraction ●Library Construction ●Sequencing Protocol High-throughput Sequence Alignment Protocol Data Normalization Protocol Ensembl ID RefSeq ID fastq bam HTML csv/tsv Administrative Information: Person(s) Organisations Publications Experimental Conditions/Design Protocols High-throughput Sequence Alignment Protocol Data Normalization Protocol fastq bam csv/tsv Ensembl ID RefSeq ID Taxon Administrative Information: Person(s) Organisations Publications Experimental Conditions/Design Protocols High-throughput Sequence Alignment Protocol Data Normalization Protocol fastq bam csv/tsv Ensembl ID RefSeq ID Taxon Patents in Europe Active process No prior disclosure Apply only in limited geographical scopes Fees (varying by business size and scope) Apply for max 20 years after application https://www.digitallifenorway.org/conference/2021/digital-life-2021-know-how-workshop-ipr.html Copyright in Europe Creative products: software, writing, figures, photos,... Details for software: Directive 2009/24/EC Applies by default Does not apply for facts Economic rights vs. moral rights Author lifetime + 70 years Commons:Copyright rules by territory/Norway https://lovdata.no/pro/#document/NL/lov/2018-06-15-40 https://eur-lex.europa.eu/legal-content/EN/ALL/?uri=CELEX:32009L0024 https://lovdata.no/pro/#document/NLX2/avtale/avt-1992-05-02-1-v17 Example WIPO: Genetic data Raw sequence does not have copyright Processed data might have Patenting unaffected Special consideration regarding traditional knowledge (Nagoya protocol) https://www.wipo.int/export/sites/www/tk/en/docs/ip_gr_grdataguidefin.pdf EU Database directive Defined additional (sui generis) IPR for: “collection[s] of independent works, data or other materials [that does not fall under copyright] arranged in a systematic or methodical way and individually accessible by electronic or other means” 15 years by default https://eur-lex.europa.eu/eli/dir/1996/9/oj https://lovdata.no/pro/#document/NLX2/avtale/avt-1992-05-02-1-v17 Licensing A licensor may grant a license under intellectual property laws to authorize a use (such as copying software or using a patented invention) to a licensee, sparing the licensee from a claim of infringement brought by the licensor. CC-BY-SA 3.0 License - Wikipedia Which of these is derivative work? Download some code and use one of the functions in your code Linking to libraries (static or dynamic), plug-ins, and drivers Clean room design (you never see the code) Extending code you got from somewhere Rewriting code to a different programming language CC-BY 4.0 https://coderefinery.github.io/social-coding/licensing/#exercises-licensing Which of these is derivative work? ✔Download some code and use one of the functions in your code ❌Linking to libraries (static or dynamic), plug-ins, and drivers ❌Clean room design (you never see the code) ✔Extending code you got from somewhere ✔Rewriting code to a different programming language CC-BY 4.0 https://coderefinery.github.io/social-coding/licensing/#exercises-licensing Why should I licence my research outputs? Why should I licence my research outputs? Legal security for users (Accessibility) + Funder requirement Why should I licence my research outputs? Legal security for users (Accessibility) + Funder requirement Increase of willingness to reuse outputs (Reusability) CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ CC-BY 4.0 Shaddim; original CC license symbols by https://creativecommons.org/ Creative Commons, Nathan Yergler, Alex Roberts. Licensed to the public under CC BY 3.0 Unported. Creative Commons logo used under CC Trademark Policy. Creative Commons - What is licensed? Nathan Yergler, Alex Roberts - Who is to be attributed? Licensed to the public under CC BY 3.0 Unported - Which license? CC-BY 4.0 license symbols by https://creativecommons.org/ Challenges CC-BY 4.0 license symbols by https://creativecommons.org/ Challenges Multiple Attributions for several sources (license stacking) CC-BY 4.0 license symbols by https://creativecommons.org/ Challenges Multiple Attributions for several sources (license stacking) Multiple incompatible source licenses CC-BY 4.0 license symbols by https://creativecommons.org/ Challenges Multiple Attributions for several sources (license stacking) Multiple incompatible source licenses Legal commercial definition (e.g. use by journals) CC-BY 4.0 license symbols by https://creativecommons.org/ Challenges Multiple Attributions for several sources (license stacking) Multiple incompatible source licenses Legal commercial definition (e.g. use by journals) Unintentional restrictive Databases are different to simple data (e.g. EU-copyright) Open Data Commons Icons CC-BY 4.0 https://creativecommons.org/ https://opendatacommons.org Databases are different to simple data (e.g. EU-copyright) Open Data Commons Public Domain Dedication and License (PDDL) Open Data Commons Icons CC-BY 4.0 https://creativecommons.org/ https://opendatacommons.org Databases are different to simple data (e.g. EU-copyright) Open Data Commons Public Domain Dedication and License (PDDL) Open Data Commons Attribution License (ODC-By) Open Data Commons Icons CC-BY 4.0 https://creativecommons.org/ https://opendatacommons.org Databases are different to simple data (e.g. EU-copyright) Open Data Commons Public Domain Dedication and License (PDDL) Open Data Commons Attribution License (ODC-By) Open Data Commons Open Database License (ODbL) Open Data Commons Icons CC-BY 4.0 https://creativecommons.org/ https://opendatacommons.org Open Source Software licenses MIT license Apache 2.0 GNU LGPLv3GNU GPLv3 BSD licenses Icons CC-BY 4.0 https://creativecommons.org/ GNU AGPLv3 Open Source Software licenses MIT license Apache 2.0 GNU LGPLv3 GNU AGPLv3 GNU GPLv3 BSD licenses Icons CC-BY 4.0 https://creativecommons.org/ https://opensource.org/licenses https://choosealicense.com/ Indices & Controlled vocabularies https://spdx.org/licenses/ https://opensource.org/licenses License List - maschine readable IDs Approved Licenses - also EC definition of open source license on file level # SPDX-License-Identifier: MIT MIT BSD Icon CC-BY 4.0 http://software-carpentry.org; Image unchanged from https://choosealicense.com/ LGPL MPL weak Icon CC-BY 4.0 http://software-carpentry.org; Image unchanged from https://choosealicense.com/ Icon CC-BY 4.0 http://software-carpentry.org; Image unchanged from https://choosealicense.com/ GPL AGPL strong Open Source Software licenses CC-BY 4.0 http://software-carpentry.org/ Open Source Software licenses CC-BY 4.0 http://software-carpentry.org/ Open Source Software licenses CC-BY 4.0 http://software-carpentry.org/ Does it hold in court? Yes! Free Software Foundation, Inc. v. Cisco Systems, Inc., 2009 … Busybox GPL lawsuits 2007-2009 Link to RDMkit: https://rdmkit.elixir-europe.org/ Digital Life 2021: Know-how workshop on IPR in digital biotech Data life cycle: Sharing | RDMkit Your tasks: Licensing | RDMkit EUDAT license chooser for data and software Choose a License Licenses & Standards | Open Source Initiative Next: https://coderefinery.org/ 1. As indicated here, all publicly accessible user contributions are licensed under Creative Commons Attribution-ShareAlike license. See Stackoverflow Terms of service for more detailed information. 2. “Standard” licensing rules apply. So in this case, you would need to remove the portion of code you have copied from another package before being able to release your software. 3. By default you are no authorized to use the content of a repository when there is no license. And derivative work is also not possible by default. Other risks: it may not be clear whether you can use and distribute (publish) the bugfixed code. For the repo owners it may not be clear whether they can use and distributed the bugfixed code. However, the authors may have forgotten to add a license so we suggest you to contact the authors (e.g. make an issue) and ask whether they are willing to add a license. 4. As mentionned in 3., the easiest is to fill an issue and explain the reasons why you would like to use this software (or update it). 5. Combining software with different licenses can be tricky and it is important to understand compatibilities (or lack of compatibilities) of the various licenses. GPL license is the most protective (BSD and MIT are quite permissive) so for the resulting combined software you could use a GPL license. However, re-licensing may not be necessary. 6. Derivative work would need to be shared under this viral license (e.g. AGPL or GPL), unless the components are only plugins or libraries. 7. If you keep your code for yourself, you may think you do not need a license. However, remember that in most companies/universities, your employer is “owning” your work and when you leave you may not be allowed to “distribute your code to your future self”. So the best is always to add a license! 8. The least attractive licenses for companies with proprietary software are licenses where you would need to keep an open license when creating derivative work. For instance GPL and and AGPL. The most attractive licenses are permissive licenses where they can reuse, modify and relicense with no conditions. For instance MIT, BSD and Apache License. CC-BY 4.0 https://coderefinery.github.io/social-coding/licensing/#exercises-licensing Thank you! Except where otherwise noted, this work is licensed under a Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/ elixir-norway.org digitallifenorway.org @elixirnorway @DigitaltLiv @BoslKorbinian [email protected] [email protected] k[email protected] Thank you! Except where otherwise noted, this work is licensed under a Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/ elixir-norway.org digitallifenorway.org @elixirnorway @DigitaltLiv @BoslKorbinian [email protected] [email protected] k[email protected]