From 3522febe54ca00c2fe6f6f27038b76584b9b5808 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 11:29:13 +0200 Subject: [PATCH 001/112] Update references.bib --- docs/_bibliography/references.bib | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index dcf156a3..b3798d35 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -66,3 +66,17 @@ @article{miksa_2019 abstract = {Data management plans (DMPs) are documents accompanying research proposals and project outputs. DMPs are created as free-form text and describe the data and tools employed in scientific investigations. They are often seen as an administrative exercise and not as an integral part of research practice. There is now widespread recognition that the DMP can have more thematic, machine-actionable richness with added value for all stakeholders: researchers, funders, repository managers, research administrators, data librarians, and others. The research community is moving toward a shared goal of making DMPs machine-actionable to improve the experience for all involved by exchanging information across research tools and systems and embedding DMPs in existing workflows. This will enable parts of the DMP to be automatically generated and shared, thus reducing administrative burdens and improving the quality of information within a DMP. This paper presents 10 principles to put machine-actionable DMPs (maDMPs) into practice and realize their benefits. The principles contain specific actions that various stakeholders are already undertaking or should undertake in order to work together across research communities to achieve the larger aims of the principles themselves. We describe existing initiatives to highlight how much progress has already been made toward achieving the goals of maDMPs as well as a call to action for those who wish to get involved.}, number = {3}, } + +@unpublished{bobrov_2021, + author = {Bobrov, Evgeny and Adam, Lea-Sophie and Söring, Sibylle and Jäckel, Denise and Herwig, Anja and Lindstädt, Birte and Vandendorpe, Justine and Shutsko, Aliaksandra}, + title = {Workshop on Research Data}, + month = {Oct}, + year = {2021}, +} + +@unpublished{bres_2022, + author = {Bres, Ewa and Rudolf, Daniel and Lindstädt, Birte and Shutsko, Aliaksandra}, + title = {Research Data Management in Medical and Biomedical Sciences}, + month = {Feb}, + year = {2022}, +} From f431d3c13e34d78fb920cebf0e8b5dc04df3353c Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 11:32:03 +0200 Subject: [PATCH 002/112] Update 08-data-organization.md --- docs/_Research-Data-Management/08-data-organization.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 6274f634..bbd2b26c 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -18,7 +18,12 @@ For data organization, we suggest to use the 5S methodology that uses a list of * Regularly check whether rules are followed. * Implement improvements if necessary. -## File naming conventions +## File naming +File names should ideally allow to establish a connection to a certain experiment or data collection {% cite bobrov_2021 %}. Within your research group, it is recommended {% cite bobrov_2021 %} to: +1. **Choose** a file and folder naming convention. +2. **Document** your convention, for instance in Standard Operating Procedures (SOPs). +3. Make the documentation **available** to all research group members. +4. Stay **consistent**. ## File versioning From 5e03f9c1752eff27b5d914739fa0dc99cced1937 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 11:33:05 +0200 Subject: [PATCH 003/112] Update 08-data-organization.md --- docs/_Research-Data-Management/08-data-organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index bbd2b26c..984fc257 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -19,7 +19,7 @@ For data organization, we suggest to use the 5S methodology that uses a list of * Implement improvements if necessary. ## File naming -File names should ideally allow to establish a connection to a certain experiment or data collection {% cite bobrov_2021 %}. Within your research group, it is recommended {% cite bobrov_2021 %} to: +File names should ideally allow to establish a connection to a certain experiment or data collection {% cite bobrov_2021 %}. Within your research group, it is recommended {% cite bobrov_2021 bres_2022 %} to: 1. **Choose** a file and folder naming convention. 2. **Document** your convention, for instance in Standard Operating Procedures (SOPs). 3. Make the documentation **available** to all research group members. From 6e62f8ec8abac88a5b420df63d2e6e1955309df0 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 11:44:21 +0200 Subject: [PATCH 004/112] Update 08-data-organization.md --- .../_Research-Data-Management/08-data-organization.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 984fc257..09508196 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -25,6 +25,17 @@ File names should ideally allow to establish a connection to a certain experimen 3. Make the documentation **available** to all research group members. 4. Stay **consistent**. +### Recommendations for naming conventions +If you need to choose a file and folder naming convention, it is recommended {% cite assmann_2022 bobrov_2021 bres_2022 %} to include the following: +* Favor **alphabetically sortable** names (e.g. starting with the date: YYYY-MM-DD). +* Limit file names to **maximum 32 characters** (32CharactersLooksExactlyLikeThis.txt). Short names are easier to find and they need a shorter path, whereas long names can cause technical problems. Thus, select a name that is as short as possible and as long as necessary. +* Favor names that **reflect** and are **unique** to the **content** (i.e. person, project ID/part, sample ID, experiment ID, status, data, version number and/or software name). +* Use **periods** only before file extensions. +* Do not use **special characters** or **whitespaces** which can be confusing to both machines and humans. +* Use **leading zeros** when using sequential numbering: + * For a sequence of 1-10: 01-10 + * For a sequence of 1-100: 001-010-100 + ## File versioning ## Version control From 5fd907b917a36f16d838cc8cdd965361acccf198 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 11:51:35 +0200 Subject: [PATCH 005/112] Update 08-data-organization.md --- .../08-data-organization.md | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 09508196..aaff17b5 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -36,14 +36,22 @@ If you need to choose a file and folder naming convention, it is recommended {% * For a sequence of 1-10: 01-10 * For a sequence of 1-100: 001-010-100 -## File versioning +### Examples of file names +* **Good structure**: YYYY-MM-DD_JV_ProjectID_ExperimentID with IDs being linked to a table with data documentation such as metadata {% cite bobrov_2021 %}. +* **Good names** {% cite bres_2022 %}: + * 2016-01-04_ProjectA_Ex1Test1_SmithE_v1.0.xlsx + * 2000_USNM_379221_01_tiff + * USNM_379221_01.tiff +* **Bad names** {% cite bres_2022 %}: + * Test data 2016.xlsx + * Meeting notes Jan 17 + * Notes Eric.txt + * Final FINAL last version.docx -## Version control +## File versioning ## Folder structure -## Big data organization - ## Further resources ### 5S methodology From d63c3a8b454535bfd48046bbfb6555dafade2bfc Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 12:02:46 +0200 Subject: [PATCH 006/112] Update 08-data-organization.md --- .../08-data-organization.md | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index aaff17b5..fc9d9cb8 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -48,6 +48,34 @@ If you need to choose a file and folder naming convention, it is recommended {% * Notes Eric.txt * Final FINAL last version.docx +### Tools for simultaneous renaming of files + +#### Multiple OS +* [Adobe Bridge](https://www.adobe.com/products/bridge.html) +* [jExifToolGUI](https://github.com/hvdwolf/jExifToolGUI/blob/master/README.md) + +#### Linux +* [Gnome Commander](https://gcmd.github.io/) +* [GPRename](https://gprename.sourceforge.net/) + +#### Mac +* [ExifRenamer](https://www.qdev.de/?location=mac/exifrenamer) +* [NameChanger](https://mrrsoftware.com/namechanger/) +* [Renamer 6](https://renamer.com/) + +#### Unix +* mv command + +#### Windows +* [Advanced Renamer](https://www.advancedrenamer.com/) +* [Altap Salamander](https://www.altap.cz/) +* [Ant Renamer](http://www.antp.be/software/renamer) +* [Bulk Rename Utility](https://www.bulkrenameutility.co.uk/) +* [ExifToolGUI](https://exiftoolgui.informer.com/) +* [Rename-It!](https://sourceforge.net/projects/renameit/) +* [Total Commander](https://www.ghisler.com/deutsch.htm) +* [WildRename](https://www.cylog.org/utilities/wildrename.jsp) + ## File versioning ## Folder structure From 69b080b32a4447725f2e6705cffb0de56ea60db2 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 1 Jun 2023 12:05:55 +0200 Subject: [PATCH 007/112] Update 08-data-organization.md --- docs/_Research-Data-Management/08-data-organization.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index fc9d9cb8..23f85ebd 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -84,7 +84,7 @@ If you need to choose a file and folder naming convention, it is recommended {% ### 5S methodology * Lang, K., Roman, G., Jessica, R., Annett, S., Nadine, N., & Lehmann, A. (2021). The 5S Methodology in Research Data Management. Zenodo. [https://doi.org/10.5281/ZENODO.4494258](https://doi.org/10.5281/ZENODO.4494258) -* ["*5S Data: Setz dich auf deine 5 Buchstaben und organisiere deine Daten! (Coffee Lecture)*"](https://youtu.be/73XzLsLrwMk) (in German only) +* Research Data Management Thuringia (TKFDM) (2021, February 4). 5S Data: Setz dich auf deine 5 Buchstaben und organisiere deine Daten! (Coffee Lecture) [Video]. YouTube. URL [https://youtu.be/73XzLsLrwMk](https://youtu.be/73XzLsLrwMk) ### Organizing data in spreadsheets * Broman, K. W., & Woo, K. H. (2018). Data Organization in Spreadsheets. In The American Statistician (Vol. 72, Issue 1, pp. 2–10). Informa UK Limited. [https://doi.org/10.1080/00031305.2017.1375989](https://doi.org/10.1080/00031305.2017.1375989) From 25165c5a150d9e02406b890a7a09fc7357380d0c Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 5 Jun 2023 14:42:49 +0200 Subject: [PATCH 008/112] Update 08-data-organization.md --- .../08-data-organization.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 23f85ebd..3f145d36 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -78,6 +78,19 @@ If you need to choose a file and folder naming convention, it is recommended {% ## File versioning +If you decide to version your files, keep the following in mind {% cite bres_2022 %}: +* **Decide** how to version files with project partners. +* **Write down** how a version change is to be defined. +* **Document** version changes. + +Options for file versioning include {% cite bres_2022 %}: +* In **file names** +* Within **data** (e.g. header, comment field) +* In **text files** (e.g. README file) +* Within a **Version Control System** (VCS) (e.g. git, Apache Subversion) + +### Manual file versioning + ## Folder structure ## Further resources From cdd6555556dc783f846158e4ddfd0beeced4dd2e Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 5 Jun 2023 14:49:57 +0200 Subject: [PATCH 009/112] Update 08-data-organization.md --- docs/_Research-Data-Management/08-data-organization.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 3f145d36..c4110da0 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -91,6 +91,16 @@ Options for file versioning include {% cite bres_2022 %}: ### Manual file versioning +If you decide to version your files manually, it is recommended to: +* Use a version control **table**. +* Define **responsibilities** for completion of files. +* Use [semantic versioning](https://semver.org/): **MAJOR.MINOR.PATCH** {% cite bobrov_2021 bres_2022 %}. E.g.: + * Ex1Test1_SmithE_v1.0.0.xlsx + * Ex1Test1_SmithE_v1.2.5.xlsx + * Ex1Test1_SmithE_v2.1.1.xlsx +* Save **milestone versions**. +* Store **obsolete versions** separately after backup. + ## Folder structure ## Further resources From d444da4498da01dfa2730adc43b1a1e70b131d54 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 5 Jun 2023 14:56:44 +0200 Subject: [PATCH 010/112] Update 08-data-organization.md --- .../08-data-organization.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index c4110da0..9b71c3f5 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -103,6 +103,21 @@ If you decide to version your files manually, it is recommended to: ## Folder structure +### Recommendations for folder structure + +For a good folder structure, it is recommended to: +* Invest **time** planning out folder structure. +* Choose a folder structure that is {% cite bobrov_2021 bres_2022 %}: + * **Clear** (i.e. self-exaplanatory, with an intuitive navigation, also for other team members) + * **Comprehensive** + * **Efficient** + * **Hierarchical**, increasing findability +* Have maximum {% cite bres_2022 %}: + * **4 levels** + * **10 elements** per folder + +### Example of folder structure + ## Further resources ### 5S methodology From 06675378172f27e264cdb729d13888f5755542d3 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 5 Jun 2023 15:00:00 +0200 Subject: [PATCH 011/112] Update 08-data-organization.md --- .../08-data-organization.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 9b71c3f5..6c5091a3 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -117,6 +117,20 @@ For a good folder structure, it is recommended to: * **10 elements** per folder ### Example of folder structure +* Project + * Data + * Raw_data + * Processed_data + * Documentation + * Code + * Src + * Output + * Plots + * Documentation + * Protocols +* Manuscripts +* Conference_reports +* Administrative_information ## Further resources From 24637f9c846c5c38b62ddbd379093eea25262450 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 5 Jun 2023 15:16:25 +0200 Subject: [PATCH 012/112] Update 08-data-organization.md --- .../08-data-organization.md | 28 ++++++++++++++----- 1 file changed, 21 insertions(+), 7 deletions(-) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/08-data-organization.md index 6c5091a3..5c41dae1 100644 --- a/docs/_Research-Data-Management/08-data-organization.md +++ b/docs/_Research-Data-Management/08-data-organization.md @@ -133,15 +133,29 @@ For a good folder structure, it is recommended to: * Administrative_information ## Further resources +* File naming and folder hierarchy: [MIT Libraries](https://libraries.mit.edu/data-management/store/organize/) +* Naming and organizing your files and folder: [MIT Libraries Data Management Services 2020](https://www.dropbox.com/s/xx26a1onsu1qdpc/Worksheet_fileOrg.docx?dl=0) +* README: File & Folder Schema: [MIT Libraries Data Management Services 2018](https://www.dropbox.com/s/ritd1mwzyaz2dh6/Sample_README_fileOrg.docx?dl=0) ### 5S methodology -* Lang, K., Roman, G., Jessica, R., Annett, S., Nadine, N., & Lehmann, A. (2021). The 5S Methodology in Research Data Management. Zenodo. [https://doi.org/10.5281/ZENODO.4494258](https://doi.org/10.5281/ZENODO.4494258) -* Research Data Management Thuringia (TKFDM) (2021, February 4). 5S Data: Setz dich auf deine 5 Buchstaben und organisiere deine Daten! (Coffee Lecture) [Video]. YouTube. URL [https://youtu.be/73XzLsLrwMk](https://youtu.be/73XzLsLrwMk) - -### Organizing data in spreadsheets -* Broman, K. W., & Woo, K. H. (2018). Data Organization in Spreadsheets. In The American Statistician (Vol. 72, Issue 1, pp. 2–10). Informa UK Limited. [https://doi.org/10.1080/00031305.2017.1375989](https://doi.org/10.1080/00031305.2017.1375989) -* Perkel, J. M. (2022). Six tips for better spreadsheets. In Nature (Vol. 608, Issue 7921, pp. 229–230). Springer Science and Business Media LLC. [https://doi.org/10.1038/d41586-022-02076-1](https://doi.org/10.1038/d41586-022-02076-1) -* [Tidy data for librarians](https://librarycarpentry.org/lc-spreadsheets/) +* The 5S Methodology in Research Data Management: [Lang *et al.* 2021](https://doi.org/10.5281/zenodo.4494258) +* 5S Data: Setz dich auf deine 5 Buchstaben und organisiere deine Daten! (Coffee Lecture): [Research Data Management Thuringia (TKFDM)](https://youtu.be/73XzLsLrwMk) + +### File naming +* Batch file renaming tools: [Malinowski 2020](https://www.dropbox.com/s/rropbx4ewxlli09/Handout_BatchRenaming.pdf?dl=0) +* Best practices: [Malinowski 2020](https://www.dropbox.com/s/ttv3boomxlfgiz5/Handout_fileNaming.pdf?dl=0) +* Convetion worksheet: [Briney 2020](https://resolver.caltech.edu/CaltechAUTHORS:20200601-161923247) +* File naming: [ELIXIR Belgium](https://rdm.elixir-belgium.org/file_naming) +* File naming examples: [Briney *et al.* 2020](https://doi.org/10.3897/rio.6.e56508), Table 1. + +### Folder structure +* Simple Open Data template: [de Plaa 2021](https://doi.org/10.5281/zenodo.4899847) +* Template for research repositories: [Colomb *et al.* 2020](https://doi.org/10.5281/zenodo.4410128) + +### Data organization in spreadsheets +* Data Organization in Spreadsheets: [Broman & Woo 2017](https://doi.org/10.1080/00031305.2017.1375989) +* Six tips for better spreadsheets: [Perkel 2022](https://doi.org/10.1038/d41586-022-02076-1) +* Tidy data for librarians: [Library Carpentry](https://librarycarpentry.org/lc-spreadsheets/) ### Tools * [FAIR4Health Data Curation Tool](https://github.com/fair4health/data-curation-tool) From d790b429c158821d92937eb57d14fa6ce435f1ac Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:34:03 +0200 Subject: [PATCH 013/112] Update references.bib --- docs/_bibliography/references.bib | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index b3798d35..f46dfc49 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -80,3 +80,13 @@ @unpublished{bres_2022 month = {Feb}, year = {2022}, } + +@article{vandendorpe_2023, + title = {Online Training Workshop on Research Data Management in (Bio-)Medicine}, + url = {https://repository.publisso.de/resource/frl:6452660}, + DOI = {10.4126/FRL01-006452660}, + publisher = {PUBLISSO}, + author = {Vandendorpe, Justine and Lindstädt, Birte and Shutsko, Aliaksandra and Markus, Katharina}, + year = {2023}, + language = {en} +} From 97ca56245253aef96f1eca0d416d46be4269e565 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:37:07 +0200 Subject: [PATCH 014/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index a6467bea..ae6fc866 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -5,13 +5,10 @@ layout: default docs_css: markdown --- # Definition of Research Data Management (RDM) -Research Data Management (RDM) is the process that includes all methods and procedures that aim to make research data usable over the long-term. RDM usually includes the following steps: -* Planning -* Data Collection -* Data Processing & Analysis -* Data Sharing & Publishing -* Digital Preservation -* Data Discovery & Reuse +Research Data Management (RDM) is a series of measures that need to be taken during a research project in order to: +1. Obtain high-quality data (whether produced or reused) +2. Make data avaialbe and usable over the long-term +3. Make research findings reproducible beyond the research project # Research data life cycle The RDM steps can be represented as a cycle called the research data life cycle: From 701019c5ca53ed4bb55c2eb99f4be671c7b5c070 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:42:08 +0200 Subject: [PATCH 015/112] Update references.bib --- docs/_bibliography/references.bib | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index f46dfc49..fc430bd0 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -90,3 +90,16 @@ @article{vandendorpe_2023 year = {2023}, language = {en} } + +@misc{RfII_RD, + title = {Research Data}, + howpublished = {\url{https://rfii.de/en/topics/#forschungsdaten}}, + note = {Accessed: 2023-06-06} +} + +@unpublished{voigt_2022, + author = {Voight, Pia and Frericks, Sebastian and Lindstädt, Birte and Shutsko, Aliaksandra and Vandendorpe, Justine}, + title = {Workshop on Research Data}, + month = {Mar}, + year = {2022}, +} From 26850d3373914afe649f7bbe7b29742f094a9345 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:44:15 +0200 Subject: [PATCH 016/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index ae6fc866..38f7e1a8 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -4,18 +4,15 @@ category: Research-Data-Management layout: default docs_css: markdown --- -# Definition of Research Data Management (RDM) -Research Data Management (RDM) is a series of measures that need to be taken during a research project in order to: -1. Obtain high-quality data (whether produced or reused) -2. Make data avaialbe and usable over the long-term -3. Make research findings reproducible beyond the research project +## Definition of Research Data Management (RDM) +Research Data Management (RDM) is a series of measures that need to be taken during a research project in order to (1) obtain high-quality data (whether produced or reused), (2) make data avaialbe and usable over the long-term and (3) make research findings reproducible beyond the research project {% cite RfII_RDM bres_2022 voigt_2022 %}. -# Research data life cycle +## Research data life cycle The RDM steps can be represented as a cycle called the research data life cycle: ![Research data life cycle](/nfdi4microbiota-knowledge-base/assets/img/research_data_life_cycle.png) -# Benefits of RDM +## Benefits of RDM * **Researchers' own interests** * Good Scientific Practice (GSP) * Knowledge management / transfer @@ -26,10 +23,13 @@ The RDM steps can be represented as a cycle called the research data life cycle: * Publishers * Researchers' own institution -# Consequences of poor RDM +## Consequences of poor RDM Consequences of poor RDM include paper retraction (e.g. [González Amorós & de Puit](https://doi.org/10.1016/j.scijus.2015.04.005)). -# Further resources +## Further resources * A [Brief Guide - Research Data Management](https://doi.org/10.5281/zenodo.4000989) for busy people * [bio.tools](https://bio.tools/) * [Coscine - The research data management platform](https://coscine.de/) + +## References +{% bibliography --cited_in_order %} From 59935024ba82c88cfab64a27b1a519bd47158c7c Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:45:52 +0200 Subject: [PATCH 017/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index 38f7e1a8..1d018f10 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -5,7 +5,7 @@ layout: default docs_css: markdown --- ## Definition of Research Data Management (RDM) -Research Data Management (RDM) is a series of measures that need to be taken during a research project in order to (1) obtain high-quality data (whether produced or reused), (2) make data avaialbe and usable over the long-term and (3) make research findings reproducible beyond the research project {% cite RfII_RDM bres_2022 voigt_2022 %}. +Research Data Management (RDM) is a series of measures that need to be taken during a research project in order to (1) obtain high-quality data (whether produced or reused), (2) make data avaialbe and usable over the long-term and (3) make research findings reproducible beyond the research project {% cite RfII_RD bres_2022 voigt_2022 %}. ## Research data life cycle The RDM steps can be represented as a cycle called the research data life cycle: From 14c6a35f7a2cffbc4b64ec2ad404e25913b9153c Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:48:52 +0200 Subject: [PATCH 018/112] Update references.bib --- docs/_bibliography/references.bib | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index fc430bd0..8fc365b5 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -103,3 +103,9 @@ @unpublished{voigt_2022 month = {Mar}, year = {2022}, } + +@misc{NTU_LibGuides_RD_life_cycle, + title = {Research data lifecycle}, + howpublished = {\url{https://libguides.ntu.edu.sg/rdm/researchdatalifecycle}}, + note = {Accessed: 2023-06-06} +} From 11940a3208af82eb5198aa0e42645ff6e945b615 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 11:52:42 +0200 Subject: [PATCH 019/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index 1d018f10..942fb287 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -8,7 +8,7 @@ docs_css: markdown Research Data Management (RDM) is a series of measures that need to be taken during a research project in order to (1) obtain high-quality data (whether produced or reused), (2) make data avaialbe and usable over the long-term and (3) make research findings reproducible beyond the research project {% cite RfII_RD bres_2022 voigt_2022 %}. ## Research data life cycle -The RDM steps can be represented as a cycle called the research data life cycle: +The research data life cycle is a model that illustrates the steps of RDM and describes how data should ideally flow through a research project to ensure successful data curation and preservation {% cite NTU_LibGuides_RD_life_cycle bobrov_2021 %}. The research data life cycle can be illustrated as follow: ![Research data life cycle](/nfdi4microbiota-knowledge-base/assets/img/research_data_life_cycle.png) From 9a5d63541f58ff54a51199b21f849b59bde91fb5 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 12:01:20 +0200 Subject: [PATCH 020/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 23 +++++++++++++++-------- 1 file changed, 15 insertions(+), 8 deletions(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index 942fb287..3be4f9c0 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -13,15 +13,22 @@ The research data life cycle is a model that illustrates the steps of RDM and de ![Research data life cycle](/nfdi4microbiota-knowledge-base/assets/img/research_data_life_cycle.png) ## Benefits of RDM -* **Researchers' own interests** - * Good Scientific Practice (GSP) - * Knowledge management / transfer + +Benefits of RDM are numerous, some of them are liste below {% cite assmann_2022 bobrov_2021 bres_2022 voigt_2022 %}: + +* **For researchers** + * Visibility + * Reputation (ensures research quality) + * Data ownership + * Eligibility for funding + * Saves time, money and resources * Preventing data loss - * Saving yourself time in the future -* **External interests** - * Research funders - * Publishers - * Researchers' own institution + +* **Additional benefits** + * Helps keep track of the project + * Helps meet formal and legal requirements + * Enhances teamwork and collaborations + * Guaranteeing transparency, verifiability and reproducibility ## Consequences of poor RDM Consequences of poor RDM include paper retraction (e.g. [González Amorós & de Puit](https://doi.org/10.1016/j.scijus.2015.04.005)). From ce349471900b7df32307ab1c713a5e98377c9b1e Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 12:08:29 +0200 Subject: [PATCH 021/112] Update references.bib --- docs/_bibliography/references.bib | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 8fc365b5..db6b7121 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -109,3 +109,29 @@ @misc{NTU_LibGuides_RD_life_cycle howpublished = {\url{https://libguides.ntu.edu.sg/rdm/researchdatalifecycle}}, note = {Accessed: 2023-06-06} } + +@unpublished{jacob_2022, + author = {Jacob, Boris and Kroehling, Maximilian Andreas and Mertzen, Daniela and Straka, Janine and Lindstädt, Birte and Shutsko, Aliaksandra and Vandendorpe, Justine}, + title = {Workshop on Research Data}, + month = {May}, + year = {2022}, +} + +@article{engelhardt_2022, + title = {D7.4 How to be FAIR with your data. A teaching and training handbook for higher education institutions}, + url = {https://zenodo.org/record/6674301}, + DOI = {10.5281/ZENODO.6674301}, + abstractNote = {This handbook aims to support higher education institutions with the integration of FAIR-related content in their curricula and teaching. It was written and edited by a group of about 40 collaborators in a series of six book sprint events that took place between 1 and 10 June 2021. The document provides practical material, such as competence profiles, learning outcomes and lesson plans, and supporting information. It incorporates community feedback received during the public consultation which ran from 27 July to 12 September 2021. A print version as well as an Open Access PDF version (most up-to-date version) were published by Göttingen University Press in May 2022. Both are available via: https://doi.org/10.17875/gup2022-1915. A GitBook version is available at: https://fairsfair.gitbook.io/fair-teaching-handbook/ (associated GitHub repository: https://github.com/FAIRsFAIR/FAIRteachinghandbook).}, + publisher = {Zenodo}, + author = {Engelhardt, Claudia and Biernacka, Katarzyna and Coffey, Aoife and Cornet, Ronald and Danciu, Alina and Demchenko, Yuri and Downes, Stephen and Erdmann, Christopher and Garbuglia, Federica and Germer, Kerstin and Helbig, Kerstin and Hellström, Margareta and Hettne, Kristina and Hibbert, Dawn and Jetten, Mijke and Karimova, Yulia and Kryger Hansen, Karsten and Kuusniemi, Mari Elisa and Letizia, Viviana and McCutcheon, Valerie and McGillivray, Barbara and Ostrop, Jenny and Petersen, Britta and Petrus, Ana and Reichmann, Stefan and Rettberg, Najla and Reverté, Carmen and Rochlin, Nick and Saenen, Bregt and Schmidt, Birgit and Scholten, Jolien and Shanahan, Hugh and Straube, Armin and Van den Eynden, Veerle and Vandendorpe, Justine and Venkataram, Shanmugasundaram and Wiljes, Cord and Wuttke, Ulrike and Yeomans, Joanne and Zhou, Biru}, + year = {2022}, + month = {Jan}, + language = {en} + } + +@unpublished{lindstädt_2019, + author = {Lindstädt, Birte and Vandendorpe, Justine and von der Ropp, Stephan}, + title = {Reseaerch Data Management}, + month = {Dec}, + year = {2019}, +} From c5282525fa826d036b1f4110575e66d4cc17a886 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 12:09:23 +0200 Subject: [PATCH 022/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index 3be4f9c0..ab83253f 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -14,7 +14,7 @@ The research data life cycle is a model that illustrates the steps of RDM and de ## Benefits of RDM -Benefits of RDM are numerous, some of them are liste below {% cite assmann_2022 bobrov_2021 bres_2022 voigt_2022 %}: +Benefits of RDM are numerous, some of them are liste below {% cite assmann_2022 bobrov_2021 bres_2022 engelhardt_2022 jacob_2022 lindstädt_2019 voigt_2022 %}: * **For researchers** * Visibility From 0e78299090d516e935d5ae833f825e904c2b50df Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 6 Jun 2023 12:11:20 +0200 Subject: [PATCH 023/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index ab83253f..3dbad1b1 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -14,7 +14,7 @@ The research data life cycle is a model that illustrates the steps of RDM and de ## Benefits of RDM -Benefits of RDM are numerous, some of them are liste below {% cite assmann_2022 bobrov_2021 bres_2022 engelhardt_2022 jacob_2022 lindstädt_2019 voigt_2022 %}: +Benefits of RDM are numerous, some of them are listed below {% cite assmann_2022 bobrov_2021 bres_2022 engelhardt_2022 jacob_2022 lindstädt_2019 voigt_2022 %}: * **For researchers** * Visibility From 19eefdcc923f9b5326cb73090727ecb3ab33b70e Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 12 Jun 2023 13:30:24 +0200 Subject: [PATCH 024/112] Update 02-rdm.md --- docs/_Research-Data-Management/02-rdm.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_Research-Data-Management/02-rdm.md b/docs/_Research-Data-Management/02-rdm.md index 3dbad1b1..6aada043 100644 --- a/docs/_Research-Data-Management/02-rdm.md +++ b/docs/_Research-Data-Management/02-rdm.md @@ -34,9 +34,9 @@ Benefits of RDM are numerous, some of them are listed below {% cite assmann_2022 Consequences of poor RDM include paper retraction (e.g. [González Amorós & de Puit](https://doi.org/10.1016/j.scijus.2015.04.005)). ## Further resources -* A [Brief Guide - Research Data Management](https://doi.org/10.5281/zenodo.4000989) for busy people -* [bio.tools](https://bio.tools/) -* [Coscine - The research data management platform](https://coscine.de/) +* Brief Guide - Research Data Management: [Training Expert Group 2020](https://doi.org/10.5281/zenodo.4000989) +* Essential scientific and technical information about software tools, databases and services for bioinformatics and the life sciences: [bio.tools](https://bio.tools/) +* Research data management platform: [Coscine](https://coscine.de/) ## References {% bibliography --cited_in_order %} From 666d2845334b93f203b3cf3a7d094c22b531bc8d Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 12 Jun 2023 13:48:55 +0200 Subject: [PATCH 025/112] Update 03-fair.md --- docs/_Research-Data-Management/03-fair.md | 31 ++++++++++------------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/docs/_Research-Data-Management/03-fair.md b/docs/_Research-Data-Management/03-fair.md index e73ec2a5..ae816e31 100644 --- a/docs/_Research-Data-Management/03-fair.md +++ b/docs/_Research-Data-Management/03-fair.md @@ -45,27 +45,24 @@ Data interoperability is the ability of a dataset to work with other datasets or * (Meta)data are associated with detailed provenance. # Further resources - -* [Introducing the FAIR Principles for research software](https://doi.org/10.1038/s41597-022-01710-x) +* Introducing the FAIR Principles for research software: [Barker *et al.* 2022](https://doi.org/10.1038/s41597-022-01710-x) ## Learning resources - -* [FAIR Cookbook](https://faircookbook.elixir-europe.org/content/home.html) -* [FAIR in (biological) practice](https://carpentries-incubator.github.io/fair-bio-practice/index.html) -* [FAIR sharing and access](https://mantra.ed.ac.uk/fairsharingandaccess/) -* [D7.4 How to be FAIR with your data. A teaching and training handbook for higher education institutions](https://doi.org/10.5281/zenodo.6425568) +* Course on FAIR in (biological) practice: [The Carpentries Incubator](https://carpentries-incubator.github.io/fair-bio-practice/) +* How to be FAIR with your data. A teaching and training handbook for higher education institutions: [Engelhardt *et al.* 2022](https://doi.org/10.5281/zenodo.6674301) +* Unit on the benefits and challenges associated with sharing research data openly: [The University of Edinburgh](https://mantra.ed.ac.uk/fairsharingandaccess/) ## How to make data FAIR? - -* [PARTHENOS Guidelines to FAIRify data management and make data reusable](https://doi.org/10.5281/zenodo.2668479) -* [Preparing data for sharing: The FAIR Principles](https://www.slideshare.net/lshtm/preparing-data-for-sharing-the-fair-principles) -* [Top 10 FAIR Data & Software Things](https://doi.org/10.5281/zenodo.3409968) - -## How to assess the FAIRness of your dataset(s)? - -* [How FAIR are your data?](https://doi.org/10.5281/zenodo.1065991) -* Self-Assessment Tool to Improve the FAIRness of Your Dataset ([SATIFYD](https://satifyd.dans.knaw.nl/)) -* [The FAIR Data Maturity Model: An Approach to Harmonise FAIR Assessments](http://doi.org/10.5334/dsj-2020-041) +* Guidelines to FAIRify data management and make data reusable: [PARTHENOS](https://doi.org/10.5281/zenodo.2668479) +* Preparing data for sharing: [Knight 2015](https://www.slideshare.net/lshtm/preparing-data-for-sharing-the-fair-principles) +* Recipes that help you to make and keep data FAIR: [FAIR Cookbook](https://faircookbook.elixir-europe.org/content/home.html) +* Top 10 FAIR Data & Software Things: [Martinez *et al.* 2019](https://doi.org/10.5281/zenodo.3409968) + +## How to assess the FAIRness of your datasets? +* FAIR data maturity model indicators: [Bahim *et al.* 2020](https://doi.org/10.5334/dsj-2020-041), Table 1 +* FAIR evaluator service: [Fraunhofer FIT](https://gitlab.fit.fraunhofer.de/abu.ibne.bayazid/fairevaluator) +* How FAIR are your data? [Jones and Grootveld 2017](https://doi.org/10.5281/zenodo.5111307) +* Self-Assessment Tool to Improve the FAIRness of Your Dataset ([SATIFYD](https://satifyd.dans.knaw.nl/)) # References From fd81defffd2d6a23ac5a354866ec0552d4762737 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 19 Jun 2023 14:33:14 +0200 Subject: [PATCH 026/112] Update references.bib --- docs/_bibliography/references.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index db6b7121..1ef3d875 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -131,7 +131,7 @@ @article{engelhardt_2022 @unpublished{lindstädt_2019, author = {Lindstädt, Birte and Vandendorpe, Justine and von der Ropp, Stephan}, - title = {Reseaerch Data Management}, + title = {Research Data Management}, month = {Dec}, year = {2019}, } From b6b5e6bf085943de102ef7fac71eb1be53fed4ce Mon Sep 17 00:00:00 2001 From: mahdi-robbani Date: Tue, 11 Jul 2023 16:40:28 +0200 Subject: [PATCH 027/112] add Mastodon --- _includes/navbar.html | 3 +++ 1 file changed, 3 insertions(+) diff --git a/_includes/navbar.html b/_includes/navbar.html index 8ea7ae09..426ca760 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -28,6 +28,9 @@

Knowledge Base

+ + + From 6163c9bcf3cc092878158fe05cae801b6ff3da36 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 13 Jul 2023 14:04:21 +0200 Subject: [PATCH 028/112] Update 11-data-repositories.md --- docs/_Research-Data-Management/11-data-repositories.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/_Research-Data-Management/11-data-repositories.md b/docs/_Research-Data-Management/11-data-repositories.md index 534f66d5..275705ec 100644 --- a/docs/_Research-Data-Management/11-data-repositories.md +++ b/docs/_Research-Data-Management/11-data-repositories.md @@ -152,7 +152,6 @@ For more details, see this [guide](https://www.openaire.eu/zenodo-guide). * The DFG-funded registry of research data repositories ([re3data.org](https://www.re3data.org/), [search results](https://www.re3data.org/search?query=Microbiology) for "Microbiology") * The RDA-endorsed [FAIRsharing.org](https://fairsharing.org/) ([search results](https://fairsharing.org/search?fairsharingRegistry=Database&subjects=microbiology&page=1) for Databases in Microbiology) * To find Open Access repositories in the life sciences: [ELIXIR Deposition Databases for Biomolecular Data](https://elixir-europe.org/platforms/data/elixir-deposition-databases) -* To find a suitable repository in the life sciences: [PUBLISSO – Repository Finder](https://www.publisso.de/en/research-data-management/publishing/publisso-repository-finder/) * To find a suitable interdisciplinary repository: [Generalist Repository Comparison Chart](https://doi.org/10.5281/zenodo.3946720) * To find Open Access repositories: [OpenDOAR](https://v2.sherpa.ac.uk/opendoar/): Directory of Open Access Repositories From e8d715647f5107d5de7bc05e735e1cf6075ee045 Mon Sep 17 00:00:00 2001 From: Dominik Date: Thu, 13 Jul 2023 14:51:43 +0200 Subject: [PATCH 029/112] Update 01-introduction.md just stumbled across a typo --- docs/_Getting-Started/01-introduction.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/_Getting-Started/01-introduction.md b/docs/_Getting-Started/01-introduction.md index 143ae008..419df785 100644 --- a/docs/_Getting-Started/01-introduction.md +++ b/docs/_Getting-Started/01-introduction.md @@ -20,8 +20,8 @@ are collected. ## How to use this resource The available resources are shown in the left navigation. Clicking on -the link will toggle the visibility of sub-content. This resources is -puslished under the Creative Commons Attribution +the link will toggle the visibility of sub-content. This resource is +published under the Creative Commons Attribution ([CC-BY](https://creativecommons.org/licenses/by/4.0/)). ## How to find a resource From ca9e47ab8728a268900aa552392f6535c91c39dc Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 7 Aug 2023 12:46:30 +0200 Subject: [PATCH 030/112] Update 09-data-documentation.md --- docs/_Research-Data-Management/09-data-documentation.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/_Research-Data-Management/09-data-documentation.md b/docs/_Research-Data-Management/09-data-documentation.md index e56abdd3..00872e4e 100644 --- a/docs/_Research-Data-Management/09-data-documentation.md +++ b/docs/_Research-Data-Management/09-data-documentation.md @@ -10,8 +10,6 @@ empty: true # README -# Metadata standards - # Further resources # References From 030480cc86d40dff925038314792c8a41a07f4b6 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:22:32 +0200 Subject: [PATCH 031/112] Rename 01-research-data.md to 01-rd.md --- docs/_Research-Data-Management/{01-research-data.md => 01-rd.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{01-research-data.md => 01-rd.md} (100%) diff --git a/docs/_Research-Data-Management/01-research-data.md b/docs/_Research-Data-Management/01-rd.md similarity index 100% rename from docs/_Research-Data-Management/01-research-data.md rename to docs/_Research-Data-Management/01-rd.md From 1a62d2f35d63d6f30826a2b23b58d54d9cb8aa86 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:23:11 +0200 Subject: [PATCH 032/112] Update and rename 03-fair.md to 04-fair.md --- docs/_Research-Data-Management/{03-fair.md => 04-fair.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{03-fair.md => 04-fair.md} (100%) diff --git a/docs/_Research-Data-Management/03-fair.md b/docs/_Research-Data-Management/04-fair.md similarity index 100% rename from docs/_Research-Data-Management/03-fair.md rename to docs/_Research-Data-Management/04-fair.md From da2af429005f8c47170bbcee4665f2e869e67b95 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:23:45 +0200 Subject: [PATCH 033/112] Rename 04-dmp.md to 08-dmp.md --- docs/_Research-Data-Management/{04-dmp.md => 08-dmp.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{04-dmp.md => 08-dmp.md} (100%) diff --git a/docs/_Research-Data-Management/04-dmp.md b/docs/_Research-Data-Management/08-dmp.md similarity index 100% rename from docs/_Research-Data-Management/04-dmp.md rename to docs/_Research-Data-Management/08-dmp.md From d78d9ef67765bc1767d20187b1a00936722a6ef0 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:24:03 +0200 Subject: [PATCH 034/112] Rename 06-eln.md to 12-eln.md --- docs/_Research-Data-Management/{06-eln.md => 12-eln.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{06-eln.md => 12-eln.md} (100%) diff --git a/docs/_Research-Data-Management/06-eln.md b/docs/_Research-Data-Management/12-eln.md similarity index 100% rename from docs/_Research-Data-Management/06-eln.md rename to docs/_Research-Data-Management/12-eln.md From 4c23a243974530c68ec7ef33a0122f4e76692a6d Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:24:21 +0200 Subject: [PATCH 035/112] Rename 07-data-qc.md to 13-data-qc.md --- docs/_Research-Data-Management/{07-data-qc.md => 13-data-qc.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{07-data-qc.md => 13-data-qc.md} (100%) diff --git a/docs/_Research-Data-Management/07-data-qc.md b/docs/_Research-Data-Management/13-data-qc.md similarity index 100% rename from docs/_Research-Data-Management/07-data-qc.md rename to docs/_Research-Data-Management/13-data-qc.md From f4bef7e57f30824b2eec9e13b5f9e7bf761c443a Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:24:37 +0200 Subject: [PATCH 036/112] Rename 08-data-organization.md to 14-data-organization.md --- .../{08-data-organization.md => 14-data-organization.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{08-data-organization.md => 14-data-organization.md} (100%) diff --git a/docs/_Research-Data-Management/08-data-organization.md b/docs/_Research-Data-Management/14-data-organization.md similarity index 100% rename from docs/_Research-Data-Management/08-data-organization.md rename to docs/_Research-Data-Management/14-data-organization.md From e7ff2431b5097908d72490edb1259a7976c9a75c Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:24:56 +0200 Subject: [PATCH 037/112] Rename 09-data-documentation.md to 16-data-documentation.md --- .../{09-data-documentation.md => 16-data-documentation.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{09-data-documentation.md => 16-data-documentation.md} (100%) diff --git a/docs/_Research-Data-Management/09-data-documentation.md b/docs/_Research-Data-Management/16-data-documentation.md similarity index 100% rename from docs/_Research-Data-Management/09-data-documentation.md rename to docs/_Research-Data-Management/16-data-documentation.md From 6ae978019a8b9b91aaabeb788687711a93ba20d7 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:25:16 +0200 Subject: [PATCH 038/112] Rename 10-collaboration-tools.md to 20-collaboration-tools.md --- .../{10-collaboration-tools.md => 20-collaboration-tools.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{10-collaboration-tools.md => 20-collaboration-tools.md} (100%) diff --git a/docs/_Research-Data-Management/10-collaboration-tools.md b/docs/_Research-Data-Management/20-collaboration-tools.md similarity index 100% rename from docs/_Research-Data-Management/10-collaboration-tools.md rename to docs/_Research-Data-Management/20-collaboration-tools.md From 9ee7f1e5bd73401d71befeba273f06cd007fec52 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:25:34 +0200 Subject: [PATCH 039/112] Rename 11-data-repositories.md to 23-data-repositories.md --- .../{11-data-repositories.md => 23-data-repositories.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{11-data-repositories.md => 23-data-repositories.md} (100%) diff --git a/docs/_Research-Data-Management/11-data-repositories.md b/docs/_Research-Data-Management/23-data-repositories.md similarity index 100% rename from docs/_Research-Data-Management/11-data-repositories.md rename to docs/_Research-Data-Management/23-data-repositories.md From 53f76b8fb4f160c4f312a70f03cb72e2446efd20 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:25:52 +0200 Subject: [PATCH 040/112] Rename 12-digital-preservation.md to 25-digital-preservation.md --- .../{12-digital-preservation.md => 25-digital-preservation.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{12-digital-preservation.md => 25-digital-preservation.md} (100%) diff --git a/docs/_Research-Data-Management/12-digital-preservation.md b/docs/_Research-Data-Management/25-digital-preservation.md similarity index 100% rename from docs/_Research-Data-Management/12-digital-preservation.md rename to docs/_Research-Data-Management/25-digital-preservation.md From 2b1cb9c250ff7bf2a90a71e22e6822b386c60947 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:26:16 +0200 Subject: [PATCH 041/112] Rename 13-licenses.md to 26-licenses.md --- docs/_Research-Data-Management/{13-licenses.md => 26-licenses.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{13-licenses.md => 26-licenses.md} (100%) diff --git a/docs/_Research-Data-Management/13-licenses.md b/docs/_Research-Data-Management/26-licenses.md similarity index 100% rename from docs/_Research-Data-Management/13-licenses.md rename to docs/_Research-Data-Management/26-licenses.md From cab2c9038bf592d847e9490aea18d26e1573a143 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 10:30:15 +0200 Subject: [PATCH 042/112] Create 03-md.md --- docs/_Research-Data-Management/03-md.md | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 docs/_Research-Data-Management/03-md.md diff --git a/docs/_Research-Data-Management/03-md.md b/docs/_Research-Data-Management/03-md.md new file mode 100644 index 00000000..3b911b87 --- /dev/null +++ b/docs/_Research-Data-Management/03-md.md @@ -0,0 +1,21 @@ +--- +title: Metadata and Metadata Standards +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- + +# Metadata + +# Metadata standards + +# Metadata management + +# Metadata quality control + +# Further resources + +# References From a467c1422d1b83a65eebf78f9a9a3623cc178411 Mon Sep 17 00:00:00 2001 From: mahdi-robbani Date: Thu, 10 Aug 2023 10:40:07 +0200 Subject: [PATCH 043/112] fix: page hiding --- _includes/sidebar.html | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/_includes/sidebar.html b/_includes/sidebar.html index dd4ccb9c..8303598c 100644 --- a/_includes/sidebar.html +++ b/_includes/sidebar.html @@ -25,11 +25,13 @@ From c651fa0685b4148856d939a1c63cc84b16a9ae3c Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:17:44 +0200 Subject: [PATCH 044/112] Create 06-os --- docs/_Research-Data-Management/06-os | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/06-os diff --git a/docs/_Research-Data-Management/06-os b/docs/_Research-Data-Management/06-os new file mode 100644 index 00000000..476d52f8 --- /dev/null +++ b/docs/_Research-Data-Management/06-os @@ -0,0 +1,9 @@ +--- +title: Open Science +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 0ab03c6b89794955fbc9cc2c0eed7e2a383e6099 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:18:00 +0200 Subject: [PATCH 045/112] Rename 06-os to 05-os --- docs/_Research-Data-Management/{06-os => 05-os} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{06-os => 05-os} (100%) diff --git a/docs/_Research-Data-Management/06-os b/docs/_Research-Data-Management/05-os similarity index 100% rename from docs/_Research-Data-Management/06-os rename to docs/_Research-Data-Management/05-os From 926586e4da041c1a0602cc7344f967d73498d2d7 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:18:50 +0200 Subject: [PATCH 046/112] Create 06-gsp --- docs/_Research-Data-Management/06-gsp | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/06-gsp diff --git a/docs/_Research-Data-Management/06-gsp b/docs/_Research-Data-Management/06-gsp new file mode 100644 index 00000000..43dab823 --- /dev/null +++ b/docs/_Research-Data-Management/06-gsp @@ -0,0 +1,9 @@ +--- +title: Good Scientific Practice +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 3cfa1898d89b62abc3bad143be75ed85ef7df462 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:19:50 +0200 Subject: [PATCH 047/112] Create 07-policies --- docs/_Research-Data-Management/07-policies | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/07-policies diff --git a/docs/_Research-Data-Management/07-policies b/docs/_Research-Data-Management/07-policies new file mode 100644 index 00000000..bb10758b --- /dev/null +++ b/docs/_Research-Data-Management/07-policies @@ -0,0 +1,9 @@ +--- +title: Policies and Guidelines on Managing Research Data +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From a1e271a527483a77f2f20570d393e019ee5ae3c2 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:20:35 +0200 Subject: [PATCH 048/112] Create 09-preregistration --- docs/_Research-Data-Management/09-preregistration | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/09-preregistration diff --git a/docs/_Research-Data-Management/09-preregistration b/docs/_Research-Data-Management/09-preregistration new file mode 100644 index 00000000..2ed0a12e --- /dev/null +++ b/docs/_Research-Data-Management/09-preregistration @@ -0,0 +1,9 @@ +--- +title: Preregistration +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From ad72aa1bd0b01f737e2a958431ea01c06a1ed658 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:21:11 +0200 Subject: [PATCH 049/112] Create 10-data-creation --- docs/_Research-Data-Management/10-data-creation | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/10-data-creation diff --git a/docs/_Research-Data-Management/10-data-creation b/docs/_Research-Data-Management/10-data-creation new file mode 100644 index 00000000..ccbd0898 --- /dev/null +++ b/docs/_Research-Data-Management/10-data-creation @@ -0,0 +1,9 @@ +--- +title: Data Creation +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 8c9acf2bc41ce367c2d308dcbf54c54c14cb97af Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:21:40 +0200 Subject: [PATCH 050/112] Create 11-informed-consent --- docs/_Research-Data-Management/11-informed-consent | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/11-informed-consent diff --git a/docs/_Research-Data-Management/11-informed-consent b/docs/_Research-Data-Management/11-informed-consent new file mode 100644 index 00000000..b4162ac8 --- /dev/null +++ b/docs/_Research-Data-Management/11-informed-consent @@ -0,0 +1,9 @@ +--- +title: Informed Consent +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 88f50ee4487bdb50c4e9b2b5fdbab9c24764bf6b Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:21:55 +0200 Subject: [PATCH 051/112] Rename 05-os to 05-os.md --- docs/_Research-Data-Management/{05-os => 05-os.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{05-os => 05-os.md} (100%) diff --git a/docs/_Research-Data-Management/05-os b/docs/_Research-Data-Management/05-os.md similarity index 100% rename from docs/_Research-Data-Management/05-os rename to docs/_Research-Data-Management/05-os.md From fd820b8bccefd0e363416316cc2543069a7698f6 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:22:08 +0200 Subject: [PATCH 052/112] Rename 06-gsp to 06-gsp.md --- docs/_Research-Data-Management/{06-gsp => 06-gsp.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{06-gsp => 06-gsp.md} (100%) diff --git a/docs/_Research-Data-Management/06-gsp b/docs/_Research-Data-Management/06-gsp.md similarity index 100% rename from docs/_Research-Data-Management/06-gsp rename to docs/_Research-Data-Management/06-gsp.md From 1adb5d29f035ea3175c8bd1c0249556ba4727d71 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:22:22 +0200 Subject: [PATCH 053/112] Rename 07-policies to 07-policies.md --- docs/_Research-Data-Management/{07-policies => 07-policies.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{07-policies => 07-policies.md} (100%) diff --git a/docs/_Research-Data-Management/07-policies b/docs/_Research-Data-Management/07-policies.md similarity index 100% rename from docs/_Research-Data-Management/07-policies rename to docs/_Research-Data-Management/07-policies.md From 58c68935e0b930a41a773b12e8dd9051ac957904 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:22:36 +0200 Subject: [PATCH 054/112] Rename 09-preregistration to 09-preregistration.md --- .../{09-preregistration => 09-preregistration.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{09-preregistration => 09-preregistration.md} (100%) diff --git a/docs/_Research-Data-Management/09-preregistration b/docs/_Research-Data-Management/09-preregistration.md similarity index 100% rename from docs/_Research-Data-Management/09-preregistration rename to docs/_Research-Data-Management/09-preregistration.md From 0276e74bdf8c63c8eb17ce489cf3e77838b85818 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:22:48 +0200 Subject: [PATCH 055/112] Rename 10-data-creation to 10-data-creation.md --- .../{10-data-creation => 10-data-creation.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{10-data-creation => 10-data-creation.md} (100%) diff --git a/docs/_Research-Data-Management/10-data-creation b/docs/_Research-Data-Management/10-data-creation.md similarity index 100% rename from docs/_Research-Data-Management/10-data-creation rename to docs/_Research-Data-Management/10-data-creation.md From 70abe5b591cc5b891100e18e6dc321b8192c437a Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:22:59 +0200 Subject: [PATCH 056/112] Rename 11-informed-consent to 11-informed-consent.md --- .../{11-informed-consent => 11-informed-consent.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{11-informed-consent => 11-informed-consent.md} (100%) diff --git a/docs/_Research-Data-Management/11-informed-consent b/docs/_Research-Data-Management/11-informed-consent.md similarity index 100% rename from docs/_Research-Data-Management/11-informed-consent rename to docs/_Research-Data-Management/11-informed-consent.md From da2a6186c629885d5d5209a8b08a9c419e872f9d Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:23:50 +0200 Subject: [PATCH 057/112] Create 15-file-formats.md --- docs/_Research-Data-Management/15-file-formats.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/15-file-formats.md diff --git a/docs/_Research-Data-Management/15-file-formats.md b/docs/_Research-Data-Management/15-file-formats.md new file mode 100644 index 00000000..3321d678 --- /dev/null +++ b/docs/_Research-Data-Management/15-file-formats.md @@ -0,0 +1,9 @@ +--- +title: File Formats +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 28a7c4aa9d004cb8f32ef6ba5818976060d55ea1 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:24:33 +0200 Subject: [PATCH 058/112] Create 17-data-standardisation.md --- .../_Research-Data-Management/17-data-standardisation.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/17-data-standardisation.md diff --git a/docs/_Research-Data-Management/17-data-standardisation.md b/docs/_Research-Data-Management/17-data-standardisation.md new file mode 100644 index 00000000..9cff2966 --- /dev/null +++ b/docs/_Research-Data-Management/17-data-standardisation.md @@ -0,0 +1,9 @@ +--- +title: Data Standardisation +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 12e2cdb24386a2e8970cb9d93c7b24bc3e649380 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:25:17 +0200 Subject: [PATCH 059/112] Create 18-data-security.md --- docs/_Research-Data-Management/18-data-security.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/18-data-security.md diff --git a/docs/_Research-Data-Management/18-data-security.md b/docs/_Research-Data-Management/18-data-security.md new file mode 100644 index 00000000..9670d53e --- /dev/null +++ b/docs/_Research-Data-Management/18-data-security.md @@ -0,0 +1,9 @@ +--- +title: Access Control and Data Security +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From a130b442b7deb763dbb567dbe136218652df0166 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:25:38 +0200 Subject: [PATCH 060/112] Rename 20-collaboration-tools.md to 19-collaboration-tools.md --- .../{20-collaboration-tools.md => 19-collaboration-tools.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{20-collaboration-tools.md => 19-collaboration-tools.md} (100%) diff --git a/docs/_Research-Data-Management/20-collaboration-tools.md b/docs/_Research-Data-Management/19-collaboration-tools.md similarity index 100% rename from docs/_Research-Data-Management/20-collaboration-tools.md rename to docs/_Research-Data-Management/19-collaboration-tools.md From 4537a2f6768ab786f5228e925acc9c0a58fc8aa9 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:29:59 +0200 Subject: [PATCH 061/112] Create 20-pids.md --- docs/_Research-Data-Management/20-pids.md | 35 +++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 docs/_Research-Data-Management/20-pids.md diff --git a/docs/_Research-Data-Management/20-pids.md b/docs/_Research-Data-Management/20-pids.md new file mode 100644 index 00000000..96cb62a3 --- /dev/null +++ b/docs/_Research-Data-Management/20-pids.md @@ -0,0 +1,35 @@ +--- +title: Persistent Identifiers (PIDs) +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- + +# Definition + +# Examples of PIDs + +# Benefits of assigning PIDs + +# Disambiguation + +# Syntax + +# Use cases + +# Link to the FAIR data principles + +# Using PIDs to access resources + +# Receiving a PID for research outputs + +# Collaborations + +# Provenance and versioning + +# PID graph + +# Further resources From fde9c398f7dc5fad84d4ed76e8d407f07fe3a3e3 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:30:47 +0200 Subject: [PATCH 062/112] Create 22-data-publishing.md --- docs/_Research-Data-Management/22-data-publishing.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/22-data-publishing.md diff --git a/docs/_Research-Data-Management/22-data-publishing.md b/docs/_Research-Data-Management/22-data-publishing.md new file mode 100644 index 00000000..273e807f --- /dev/null +++ b/docs/_Research-Data-Management/22-data-publishing.md @@ -0,0 +1,9 @@ +--- +title: Data Publishing +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 96720446b7ab5c6b1aa96ef58bdad61bf61794c4 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:31:08 +0200 Subject: [PATCH 063/112] Rename 22-data-publishing.md to 21-data-publishing.md --- .../{22-data-publishing.md => 21-data-publishing.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{22-data-publishing.md => 21-data-publishing.md} (100%) diff --git a/docs/_Research-Data-Management/22-data-publishing.md b/docs/_Research-Data-Management/21-data-publishing.md similarity index 100% rename from docs/_Research-Data-Management/22-data-publishing.md rename to docs/_Research-Data-Management/21-data-publishing.md From e3a740e24cc92ab8af5f959c44b06a02c76190d1 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:31:20 +0200 Subject: [PATCH 064/112] Rename 23-data-repositories.md to 22-data-repositories.md --- .../{23-data-repositories.md => 22-data-repositories.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{23-data-repositories.md => 22-data-repositories.md} (100%) diff --git a/docs/_Research-Data-Management/23-data-repositories.md b/docs/_Research-Data-Management/22-data-repositories.md similarity index 100% rename from docs/_Research-Data-Management/23-data-repositories.md rename to docs/_Research-Data-Management/22-data-repositories.md From d81dad50f218d9c274ae2a26188941451ae06723 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:31:48 +0200 Subject: [PATCH 065/112] Create 23-data-storage.md --- docs/_Research-Data-Management/23-data-storage.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/23-data-storage.md diff --git a/docs/_Research-Data-Management/23-data-storage.md b/docs/_Research-Data-Management/23-data-storage.md new file mode 100644 index 00000000..27b1c196 --- /dev/null +++ b/docs/_Research-Data-Management/23-data-storage.md @@ -0,0 +1,9 @@ +--- +title: Data Storage +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 8b6c698c9a2e6410ae39b801026f3505a2f34a48 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:32:09 +0200 Subject: [PATCH 066/112] Rename 25-digital-preservation.md to 24-digital-preservation.md --- .../{25-digital-preservation.md => 24-digital-preservation.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{25-digital-preservation.md => 24-digital-preservation.md} (100%) diff --git a/docs/_Research-Data-Management/25-digital-preservation.md b/docs/_Research-Data-Management/24-digital-preservation.md similarity index 100% rename from docs/_Research-Data-Management/25-digital-preservation.md rename to docs/_Research-Data-Management/24-digital-preservation.md From f32068c561093f7612bbf5090033a9c2d5ccd275 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:32:31 +0200 Subject: [PATCH 067/112] Rename 26-licenses.md to 25-licenses.md --- docs/_Research-Data-Management/{26-licenses.md => 25-licenses.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename docs/_Research-Data-Management/{26-licenses.md => 25-licenses.md} (100%) diff --git a/docs/_Research-Data-Management/26-licenses.md b/docs/_Research-Data-Management/25-licenses.md similarity index 100% rename from docs/_Research-Data-Management/26-licenses.md rename to docs/_Research-Data-Management/25-licenses.md From 9fbf9f0178714736b0acc4f1bc23ed6461f067d9 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:36:08 +0200 Subject: [PATCH 068/112] Create 26-data-reuse.md --- .../26-data-reuse.md | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 docs/_Research-Data-Management/26-data-reuse.md diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md new file mode 100644 index 00000000..641e5400 --- /dev/null +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -0,0 +1,35 @@ +--- +title: Data Discovery and Reuse +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- + +# Benefits and drawbacks + +# Primary *vs.* secondary data + +# Relevant licenses and terms of use + +# Criteria that "trustworthy" data should meet + +# Data provenance + +# Data discovery + +## Services to search for data + +## Strategies to search for data + +# Data citation + +## Importance of data citation + +## Common standards for data citation + +## Code citation + +# Further resources From 7653dc4d0d1308e903cbd03337f240c0f1130ce3 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:36:47 +0200 Subject: [PATCH 069/112] Create 27-privacy-issues.md --- docs/_Research-Data-Management/27-privacy-issues.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/27-privacy-issues.md diff --git a/docs/_Research-Data-Management/27-privacy-issues.md b/docs/_Research-Data-Management/27-privacy-issues.md new file mode 100644 index 00000000..e1a12eb2 --- /dev/null +++ b/docs/_Research-Data-Management/27-privacy-issues.md @@ -0,0 +1,9 @@ +--- +title: Privacy Issues +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From f30a785092436de3cf341b72f84cd577971279ca Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 10 Aug 2023 11:37:24 +0200 Subject: [PATCH 070/112] Create 28-rdm-in-industry.md --- docs/_Research-Data-Management/28-rdm-in-industry.md | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 docs/_Research-Data-Management/28-rdm-in-industry.md diff --git a/docs/_Research-Data-Management/28-rdm-in-industry.md b/docs/_Research-Data-Management/28-rdm-in-industry.md new file mode 100644 index 00000000..b1d70919 --- /dev/null +++ b/docs/_Research-Data-Management/28-rdm-in-industry.md @@ -0,0 +1,9 @@ +--- +title: Research Data Management (RDM) in Industry +category: Research-Data-Management +layout: default +docs_css: markdown +redirect_from: /Research-Data-Management +empty: true +hide: true +--- From 109c2cbdc6a16fb65f1dce055502072390e6caa5 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 17 Aug 2023 13:48:48 +0200 Subject: [PATCH 071/112] Update references.bib --- docs/_bibliography/references.bib | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 1ef3d875..86c5f8b5 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -135,3 +135,23 @@ @unpublished{lindstädt_2019 month = {Dec}, year = {2019}, } + +@unpublished{rehwald_2022, + author = {Rehwald, Stephanie and Leimer, Sophie and Lindstädt, Birte and Shutsko, Aliaksandra and Vandendorpe, Justine}, + title = {Workshop on Research Data Management in Medical and Biomedical Sciences}, + month = {Jun}, + year = {2022}, +} + +@unpublished{pauls_2023, + author = {Pauls, Christian and Feeken, Corinna and Steen, Enno-Edzard and Lindstädt, Birte and Vandendorpe, Justine and Markus, Katharina}, + title = {Workshop on Research Data Management}, + month = {Jun}, + year = {2023}, +} + +@misc{FSD, + title = {Why are research data managed and reused?}, + howpublished = {\url{https://www.fsd.tuni.fi/en/services/data-management-guidelines/why-are-research-data-managed-and-reused/}}, + note = {Accessed: 2023-08-17} +} From f8ff0cbd36aef2c88b456832a125085d4a932612 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 17 Aug 2023 14:01:16 +0200 Subject: [PATCH 072/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 641e5400..a272b956 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -8,7 +8,12 @@ empty: true hide: true --- -# Benefits and drawbacks +# Benefits + +Making data reusable benefits researchers who publish their data, researchers who reuse data, and society. +Researchers who publish their data see an increase in their scientific reputation, citations and collaborations {% cite rehwald_2022 pauls_2023 %}. Furthermore, researchers who publish their data not only comply with the [FAIR Data Principles](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/04-fair), but also increase transparency and thus trust in research {% cite engelhardt_2022 rehwald_2022 pauls_2023 %}. Finally, by sharing their resources and perspectives, researchers who publish their data accelerate scientific discovery and improve future research {% cite engelhardt_2022 rehwald_2022 %}. +Researchers can recycle unique data by performing secondary analyses to answer new research questions and/or with new methods {% cite rehwald_2022 pauls_2023 %}. Reusing data in this way saves resources such as time, energy and money {% cite engelhardt_2022 FSD rehwald_2022 pauls_2023 %}. Data reuse also increases collaboration and, over time, enables the comparison of different samples {% cite rehwald_2022 pauls_2023 %}. +Making data reusable can also benefit society. It reduces unnecessary experimentation {% cite rehwald_2022 %}, avoids duplication of data collection and minimises collection from hard-to-reach, vulnerable or over-researched populations {% cite FSD rehwald_2022 %}. It also enables replication and thus promotes reproducibility. Finally, it benefits teaching and improves the link between academia and industry {% cite rehwald_2022 %}. # Primary *vs.* secondary data From dad6ca7dedc07fbf2235fbcc7d0467defca5657b Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 17 Aug 2023 14:24:29 +0200 Subject: [PATCH 073/112] Update references.bib --- docs/_bibliography/references.bib | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 86c5f8b5..a1b4c065 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -155,3 +155,19 @@ @misc{FSD howpublished = {\url{https://www.fsd.tuni.fi/en/services/data-management-guidelines/why-are-research-data-managed-and-reused/}}, note = {Accessed: 2023-08-17} } + +@incollection{IOM_2015, + author = "Committee on Strategies for Responsible Sharing of Clinical Trial Data; Board on Health Sciences Policy; Institute of Medicine", + title = "Guiding Principles for Sharing Clinical Trial Data", + booktitle = "Sharing Clinical Trial Data", + publisher = "National Academies Press (US)", + address = "Washington (DC)", + year = 2015, + chapter = 2, +} + +@misc{pavone_2020, + title = {Data Reuse Stories. Some concrete cases involving several institutions and consortia in Europe}, + howpublished = {\url{https://www.openaire.eu/blogs/data-reuse-stories-some-concrete-cases-involving-several-institutions-and-consortia-in-europe}}, + note = {Accessed: 2020-11-30} +} From 6fe67cf50a498cc4666938e261d9318b8ef19b96 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 17 Aug 2023 14:30:46 +0200 Subject: [PATCH 074/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index a272b956..6b1ecf67 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -11,8 +11,8 @@ hide: true # Benefits Making data reusable benefits researchers who publish their data, researchers who reuse data, and society. -Researchers who publish their data see an increase in their scientific reputation, citations and collaborations {% cite rehwald_2022 pauls_2023 %}. Furthermore, researchers who publish their data not only comply with the [FAIR Data Principles](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/04-fair), but also increase transparency and thus trust in research {% cite engelhardt_2022 rehwald_2022 pauls_2023 %}. Finally, by sharing their resources and perspectives, researchers who publish their data accelerate scientific discovery and improve future research {% cite engelhardt_2022 rehwald_2022 %}. -Researchers can recycle unique data by performing secondary analyses to answer new research questions and/or with new methods {% cite rehwald_2022 pauls_2023 %}. Reusing data in this way saves resources such as time, energy and money {% cite engelhardt_2022 FSD rehwald_2022 pauls_2023 %}. Data reuse also increases collaboration and, over time, enables the comparison of different samples {% cite rehwald_2022 pauls_2023 %}. +Researchers who publish their data see an increase in their scientific reputation, citations and collaborations {% cite rehwald_2022 pauls_2023 %}. In addition, researchers who publish their data not only comply with the [FAIR Data Principles](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/04-fair), but also avoid bias in the body of evidence {% cite IOM_2015 %}, increase transparency and thus trust in research {% cite engelhardt_2022 rehwald_2022 pauls_2023 %}. Finally, by sharing their resources and perspectives, researchers who publish their data enable other researchers to build on their work, accelerating scientific discovery {% cite engelhardt_2022 IOM_2015 rehwald_2022 %}. +Researchers can recycle unique data by performing secondary analyses to answer new research questions and/or with new methods {% cite rehwald_2022 pauls_2023 %}. Reusing data in this way saves resources such as time, energy and money {% cite engelhardt_2022 FSD rehwald_2022 pauls_2023 %}. Data reuse also increases collaboration and, over time, enables the comparison of different samples {% cite rehwald_2022 pauls_2023 %}. Indeed, data reuse is essential for interdisciplinary experiments and cross-cutting research approaches {% cite pavone_2020 %}. Making data reusable can also benefit society. It reduces unnecessary experimentation {% cite rehwald_2022 %}, avoids duplication of data collection and minimises collection from hard-to-reach, vulnerable or over-researched populations {% cite FSD rehwald_2022 %}. It also enables replication and thus promotes reproducibility. Finally, it benefits teaching and improves the link between academia and industry {% cite rehwald_2022 %}. # Primary *vs.* secondary data From ae0ce8c61fc119493185517d4326a4fecf14541f Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 13:54:31 +0200 Subject: [PATCH 075/112] Update references.bib --- docs/_bibliography/references.bib | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index a1b4c065..ffdb96cf 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -171,3 +171,18 @@ @misc{pavone_2020 howpublished = {\url{https://www.openaire.eu/blogs/data-reuse-stories-some-concrete-cases-involving-several-institutions-and-consortia-in-europe}}, note = {Accessed: 2020-11-30} } + +@article{wood-charlson_2022, + doi = {10.1371/journal.pcbi.1010476}, + author = {Wood-Charlson, Elisha M. AND Crockett, Zachary AND Erdmann, Chris AND Arkin, Adam P. AND Robinson, Carly B.}, + journal = {PLOS Computational Biology}, + publisher = {Public Library of Science}, + title = {Ten simple rules for getting and giving credit for data}, + year = {2022}, + month = {09}, + volume = {18}, + url = {https://doi.org/10.1371/journal.pcbi.1010476}, + pages = {1-11}, + abstract = {null}, + number = {9} +} From 068d3331774d24469ec2cc2ce6995c8efcdef2bb Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 13:59:48 +0200 Subject: [PATCH 076/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 6b1ecf67..468954cf 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -5,7 +5,6 @@ layout: default docs_css: markdown redirect_from: /Research-Data-Management empty: true -hide: true --- # Benefits @@ -37,4 +36,18 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ## Code citation +# How-tos + +## How to make your data reusable? +* Properly document your data with metadata {% cite pavone_2020 %}. +* Use common metadata standards and terminologies {% cite pavone_2020 %}. +* Standardise your data. +* Share your raw data with an open licence. + +## How to maximise already existing data? +See {% cite wood-charlson_2022 %}. + # Further resources + +# References +{% bibliography --cited_in_order %} From c9559a37323257c49d51c466856e7b76801d998d Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:01:43 +0200 Subject: [PATCH 077/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 468954cf..6ecfb13d 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -4,14 +4,16 @@ category: Research-Data-Management layout: default docs_css: markdown redirect_from: /Research-Data-Management -empty: true --- # Benefits Making data reusable benefits researchers who publish their data, researchers who reuse data, and society. + Researchers who publish their data see an increase in their scientific reputation, citations and collaborations {% cite rehwald_2022 pauls_2023 %}. In addition, researchers who publish their data not only comply with the [FAIR Data Principles](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/04-fair), but also avoid bias in the body of evidence {% cite IOM_2015 %}, increase transparency and thus trust in research {% cite engelhardt_2022 rehwald_2022 pauls_2023 %}. Finally, by sharing their resources and perspectives, researchers who publish their data enable other researchers to build on their work, accelerating scientific discovery {% cite engelhardt_2022 IOM_2015 rehwald_2022 %}. + Researchers can recycle unique data by performing secondary analyses to answer new research questions and/or with new methods {% cite rehwald_2022 pauls_2023 %}. Reusing data in this way saves resources such as time, energy and money {% cite engelhardt_2022 FSD rehwald_2022 pauls_2023 %}. Data reuse also increases collaboration and, over time, enables the comparison of different samples {% cite rehwald_2022 pauls_2023 %}. Indeed, data reuse is essential for interdisciplinary experiments and cross-cutting research approaches {% cite pavone_2020 %}. + Making data reusable can also benefit society. It reduces unnecessary experimentation {% cite rehwald_2022 %}, avoids duplication of data collection and minimises collection from hard-to-reach, vulnerable or over-researched populations {% cite FSD rehwald_2022 %}. It also enables replication and thus promotes reproducibility. Finally, it benefits teaching and improves the link between academia and industry {% cite rehwald_2022 %}. # Primary *vs.* secondary data @@ -45,7 +47,7 @@ Making data reusable can also benefit society. It reduces unnecessary experiment * Share your raw data with an open licence. ## How to maximise already existing data? -See {% cite wood-charlson_2022 %}. +See Wood-Charlson *et al.* 2022 {% cite wood-charlson_2022 %}. # Further resources From abda3aa7161341b86ca835f7976c37df42b3d9c4 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:02:32 +0200 Subject: [PATCH 078/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 6ecfb13d..bf4b7d7e 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -16,8 +16,6 @@ Researchers can recycle unique data by performing secondary analyses to answer n Making data reusable can also benefit society. It reduces unnecessary experimentation {% cite rehwald_2022 %}, avoids duplication of data collection and minimises collection from hard-to-reach, vulnerable or over-researched populations {% cite FSD rehwald_2022 %}. It also enables replication and thus promotes reproducibility. Finally, it benefits teaching and improves the link between academia and industry {% cite rehwald_2022 %}. -# Primary *vs.* secondary data - # Relevant licenses and terms of use # Criteria that "trustworthy" data should meet From a9e170606a4c606bc63e10532c7551d6e7a21596 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:03:12 +0200 Subject: [PATCH 079/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index bf4b7d7e..39ceafca 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -47,7 +47,5 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ## How to maximise already existing data? See Wood-Charlson *et al.* 2022 {% cite wood-charlson_2022 %}. -# Further resources - # References {% bibliography --cited_in_order %} From 9239397b1de0ebdfdb619125755aeaade4f49371 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:11:28 +0200 Subject: [PATCH 080/112] Update references.bib --- docs/_bibliography/references.bib | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index ffdb96cf..6730aa4b 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -186,3 +186,9 @@ @article{wood-charlson_2022 abstract = {null}, number = {9} } + +@misc{escience_center_2021, + title = {Code citation was made possible by research software engineers in Germany and the Netherlands}, + howpublished = {\url{https://www.esciencecenter.nl/news/code-citation-was-made-possible-by-research-software-engineers-in-germany-and-the-netherlands/}}, + note = {Accessed: 2023-08-23} +} From ceb8bf38899e3da048b2eec155e0661415c8383b Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:15:26 +0200 Subject: [PATCH 081/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 39ceafca..277cea6a 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -35,6 +35,7 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ## Common standards for data citation ## Code citation +Code citation allows for greater recognition of research software. Some major platforms and tools offer code citation: GitHub, GitLab, JabRef, Zenodo and Zotero {% cite escience_center_2021 %}. # How-tos From 9d86e5ce6fde7e157af7cb819249dc8783fa2f54 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:19:11 +0200 Subject: [PATCH 082/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 277cea6a..cc5c49f1 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -35,7 +35,7 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ## Common standards for data citation ## Code citation -Code citation allows for greater recognition of research software. Some major platforms and tools offer code citation: GitHub, GitLab, JabRef, Zenodo and Zotero {% cite escience_center_2021 %}. +Code citation allows for greater recognition of research software. Some major platforms and tools offer code citation: GitHub, GitLab, JabRef, Zenodo and Zotero {% cite escience_center_2021 %}. # How-tos From c5142787018d837661ad0e83a62dbf5c3e151fc7 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:27:44 +0200 Subject: [PATCH 083/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index cc5c49f1..6a5b831d 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -33,6 +33,9 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ## Importance of data citation ## Common standards for data citation +* **FORCE 11**: Author(s), Year, Data set title, Data repository or archive, Version, Global persistent identifier (preferably as link) +* **DataCite 2019**: Creator (PublicationYear): Title. Version. Publisher. (resourceTypeGeneral). Identifier +* **[DOI Citation Formatter](https://citation.crosscite.org/)** ## Code citation Code citation allows for greater recognition of research software. Some major platforms and tools offer code citation: GitHub, GitLab, JabRef, Zenodo and Zotero {% cite escience_center_2021 %}. From 63a9529c50e8577e7741f986ffb1048e62a5e1a5 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:36:37 +0200 Subject: [PATCH 084/112] Update references.bib --- docs/_bibliography/references.bib | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 6730aa4b..376b9d34 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -192,3 +192,15 @@ @misc{escience_center_2021 howpublished = {\url{https://www.esciencecenter.nl/news/code-citation-was-made-possible-by-research-software-engineers-in-germany-and-the-netherlands/}}, note = {Accessed: 2023-08-23} } + +@misc{escience_center_2021, + title = {Code citation was made possible by research software engineers in Germany and the Netherlands}, + howpublished = {\url{https://www.esciencecenter.nl/news/code-citation-was-made-possible-by-research-software-engineers-in-germany-and-the-netherlands/}}, + note = {Accessed: 2023-08-23} +} + +@misc{ball_2015, + title = {How to Cite Datasets and Link to Publications}, + howpublished = {\url{https://www.dcc.ac.uk/guidance/how-guides/cite-datasets}}, + note = {Accessed: 2023-08-23} +} From 196b28ca12b5bbc926adefdbb5350810917ec17f Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:40:35 +0200 Subject: [PATCH 085/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 6a5b831d..b9111d9c 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -33,9 +33,19 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ## Importance of data citation ## Common standards for data citation -* **FORCE 11**: Author(s), Year, Data set title, Data repository or archive, Version, Global persistent identifier (preferably as link) + +### Interdisciplinary * **DataCite 2019**: Creator (PublicationYear): Title. Version. Publisher. (resourceTypeGeneral). Identifier +* **FORCE 11**: Author(s), Year, Data set title, Data repository or archive, Version, Global persistent identifier (preferably as link) +* **[BibGuru](https://app.bibguru.com/p/3420f069-22ea-42f6-ba23-4bc6b8ae37e4)** * **[DOI Citation Formatter](https://citation.crosscite.org/)** +* **How to Cite Datasets and Link to Publications** {% cite ball_2015 %} + +### For nucleic acid sequences and functional genomics +* [How do I cite my ArrayExpress data sets in my publication?](https://www.ebi.ac.uk/biostudies/arrayexpress/help#cite) +* [How to Cite Data in ENA](https://www.ebi.ac.uk/ena/browser/about/citing-ena) +* [Citing and linking to the GEO database](https://www.ncbi.nlm.nih.gov/geo/info/linking.html) +* [How do I cite NCBI services and databases?](https://support.nlm.nih.gov/knowledgebase/article/KA-03391/en-us) ## Code citation Code citation allows for greater recognition of research software. Some major platforms and tools offer code citation: GitHub, GitLab, JabRef, Zenodo and Zotero {% cite escience_center_2021 %}. From ad379ad8bfa96289989082eef880471ab9f4be54 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:47:17 +0200 Subject: [PATCH 086/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index b9111d9c..6dfbdecf 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -17,6 +17,7 @@ Researchers can recycle unique data by performing secondary analyses to answer n Making data reusable can also benefit society. It reduces unnecessary experimentation {% cite rehwald_2022 %}, avoids duplication of data collection and minimises collection from hard-to-reach, vulnerable or over-researched populations {% cite FSD rehwald_2022 %}. It also enables replication and thus promotes reproducibility. Finally, it benefits teaching and improves the link between academia and industry {% cite rehwald_2022 %}. # Relevant licenses and terms of use +See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/25-licenses). # Criteria that "trustworthy" data should meet @@ -37,9 +38,9 @@ Making data reusable can also benefit society. It reduces unnecessary experiment ### Interdisciplinary * **DataCite 2019**: Creator (PublicationYear): Title. Version. Publisher. (resourceTypeGeneral). Identifier * **FORCE 11**: Author(s), Year, Data set title, Data repository or archive, Version, Global persistent identifier (preferably as link) -* **[BibGuru](https://app.bibguru.com/p/3420f069-22ea-42f6-ba23-4bc6b8ae37e4)** -* **[DOI Citation Formatter](https://citation.crosscite.org/)** -* **How to Cite Datasets and Link to Publications** {% cite ball_2015 %} +* [BibGuru](https://app.bibguru.com/p/3420f069-22ea-42f6-ba23-4bc6b8ae37e4) +* [DOI Citation Formatter](https://citation.crosscite.org/) +* How to Cite Datasets and Link to Publications {% cite ball_2015 %} ### For nucleic acid sequences and functional genomics * [How do I cite my ArrayExpress data sets in my publication?](https://www.ebi.ac.uk/biostudies/arrayexpress/help#cite) From d8d01194026fbc730a9eb67d0302299331717e91 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:57:20 +0200 Subject: [PATCH 087/112] Update 26-data-reuse.md --- .../26-data-reuse.md | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 6dfbdecf..808c0255 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -27,6 +27,41 @@ See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/ ## Services to search for data +### Registries of data repositories +* Registry of Research Data Repositories ([re3data.org](https://www.re3data.org/)) +* [OpenAIRE Explore](https://explore.openaire.eu/) +* [OpenDOAR](https://v2.sherpa.ac.uk/opendoar/) +* [FAIRsharing.org](https://fairsharing.org/) +* [Master Data Repository List](https://clarivate.com/webofsciencegroup/master-data-repository-list/) + +### Search engines +* [Mendeley Data](https://data.mendeley.com/) +* **Google** + * Keywork + "dataset" + * [Dataset Search](https://datasetsearch.research.google.com/) +* **Library search engines** + * Bielefeld Academic Search Engine ([BASE](https://www.base-search.net/)) + * [LIVIVO – The Search Portal for Life Sciences](https://www.livivo.de/app) +* **Discipline-specific search engines** + * Bacterial and Viral Bioinformatics Resource Center ([BV-BRC](https://www.bv-brc.org/)) + * [NFDI4Chem Search](https://search.nfdi4chem.de/) + * [Study Hub NFDI4Health COVID-19](https://csh.nfdi4health.de/) + * [TerrestrialMetagenomeDB](https://webapp.ufz.de/tmdb/) + + +### (Meta)data aggregators +* [B2FIND](https://b2find.eudat.eu/) +* [data.europa.eu](https://data.europa.eu/en) +* [DataCite Commons](https://commons.datacite.org/) +* [gesisDataSearch](https://datasearch.gesis.org/start) + +### Data catalogues + +### Services where data can be published +* **Interdisciplinary and [discipline-specific](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/22-data-repositories) repositories +* **Data reports** +* **Data journals** (see e.g. [here](https://www.forschungsdaten.org/index.php/Data_Journals)) + ## Strategies to search for data # Data citation From b993254a3d1360a7c17c3bc2f4599ba261da841e Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 23 Aug 2023 14:58:42 +0200 Subject: [PATCH 088/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 808c0255..3547fd02 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -58,7 +58,7 @@ See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/ ### Data catalogues ### Services where data can be published -* **Interdisciplinary and [discipline-specific](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/22-data-repositories) repositories +* **Interdisciplinary and [discipline-specific](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/22-data-repositories) repositories** * **Data reports** * **Data journals** (see e.g. [here](https://www.forschungsdaten.org/index.php/Data_Journals)) From 284792f84bc2bfd37a3cfc58dcbb14d2d3154276 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 10:04:55 +0200 Subject: [PATCH 089/112] Update references.bib --- docs/_bibliography/references.bib | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 376b9d34..f491f5e6 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -204,3 +204,13 @@ @misc{ball_2015 howpublished = {\url{https://www.dcc.ac.uk/guidance/how-guides/cite-datasets}}, note = {Accessed: 2023-08-23} } + +@article{sielemann_2020, + doi = {10.7717/peerj.9954}, + author = {Sielemann, Katharina AND Hafner​, Alenka AND Pucker, Boas}, + journal = {PeerJ}, + title = {The reuse of public datasets in the life sciences: potential risks and rewards}, + year = {2020}, + month = {09}, + url = {https://doi.org/10.7717/peerj.9954} +} From 308dbd394f2780ff0daa26102afa5364ad36fe44 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 10:06:26 +0200 Subject: [PATCH 090/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 3547fd02..9cdda657 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -6,7 +6,7 @@ docs_css: markdown redirect_from: /Research-Data-Management --- -# Benefits +# Benefits & Drawbacks Making data reusable benefits researchers who publish their data, researchers who reuse data, and society. @@ -16,6 +16,12 @@ Researchers can recycle unique data by performing secondary analyses to answer n Making data reusable can also benefit society. It reduces unnecessary experimentation {% cite rehwald_2022 %}, avoids duplication of data collection and minimises collection from hard-to-reach, vulnerable or over-researched populations {% cite FSD rehwald_2022 %}. It also enables replication and thus promotes reproducibility. Finally, it benefits teaching and improves the link between academia and industry {% cite rehwald_2022 %}. +As suggested by Sielemann *et al.* 2020 {% cite sielemann_2020 %}, there are also challenges, limitations and risks associated with data reuse. + +For researchers who publish their data, preparing datasets for reuse is time-consuming. + +For researchers reusing data, there are risks such as unknown quality and denormalisation (i.e. "the same data is stored multiple times in the same database under different names/identifiers"). There is also the challenge of comparing and integrating datasets from different sources {% cite sielemann_2020 %}. + # Relevant licenses and terms of use See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/25-licenses). From c58d4870d3e14f5051e1fcc7b0883ce738150042 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 10:34:45 +0200 Subject: [PATCH 091/112] Update 26-data-reuse.md --- .../26-data-reuse.md | 35 +++++++++++++++++-- 1 file changed, 32 insertions(+), 3 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 9cdda657..0dab6eb2 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -1,5 +1,5 @@ --- -title: Data Discovery and Reuse +title: Data Reuse category: Research-Data-Management layout: default docs_css: markdown @@ -25,7 +25,36 @@ For researchers reusing data, there are risks such as unknown quality and denorm # Relevant licenses and terms of use See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/25-licenses). -# Criteria that "trustworthy" data should meet +# Criteria for selection trustworthy datasets + +Below is a list of criteria for selecting trustworthy datasets {% cite bres_2022 sielemann_2020 %}. As in Sielemann *et al.* 2020 {% cite sielemann_2020 %}, for each possible criterion, several questions to consider are listed. + +* **Integrity of the source** + * Is the source/submitter associated with data fabrication/plagiarism? + * Is the way missing values handled documented? + +* **Biases** + * How was the data generated? + * Is the data generation clearly and precisely documented? + +* **Missing metainformation (sparsity)** + * Do you have all relevant information? + * Is the information understandable and consistent? + +* **Integration of datasets from different sources** + * Is the data comparable? + * Are the methods used for data generation and analysis well documented and comparable? + +* **Quality issues** + * Is the quality high enough to reach your goals? + * Are there any scores/hints available to check the quality of the dataset? + +* **Copyright/Legal issues** + * Are there any restrictions for reuse and publication of the data, especially due to the [Nagoya protocol](https://www.cbd.int/abs/)? + +* **Further documentation** + * Is the research purpose/(hypo-)thesis well documented? + * Is it documented whether the data are raw or processed? # Data provenance @@ -81,7 +110,7 @@ See [Licenses](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/ * **FORCE 11**: Author(s), Year, Data set title, Data repository or archive, Version, Global persistent identifier (preferably as link) * [BibGuru](https://app.bibguru.com/p/3420f069-22ea-42f6-ba23-4bc6b8ae37e4) * [DOI Citation Formatter](https://citation.crosscite.org/) -* How to Cite Datasets and Link to Publications {% cite ball_2015 %} +* [How to Cite Datasets and Link to Publications](https://www.dcc.ac.uk/guidance/how-guides/cite-datasets) ### For nucleic acid sequences and functional genomics * [How do I cite my ArrayExpress data sets in my publication?](https://www.ebi.ac.uk/biostudies/arrayexpress/help#cite) From 1e0086c40c02d0dab428e5de7cd0a5abcd5dc682 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 13:31:44 +0200 Subject: [PATCH 092/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 0dab6eb2..5809d0c8 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -6,7 +6,7 @@ docs_css: markdown redirect_from: /Research-Data-Management --- -# Benefits & Drawbacks +# Benefits and drawbacks Making data reusable benefits researchers who publish their data, researchers who reuse data, and society. From fd5dfee84cd15eb17e59d85e6f83b74a5623982f Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 13:40:30 +0200 Subject: [PATCH 093/112] Update references.bib --- docs/_bibliography/references.bib | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index f491f5e6..cfac9722 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -214,3 +214,9 @@ @article{sielemann_2020 month = {09}, url = {https://doi.org/10.7717/peerj.9954} } + +@misc{cessda_2017, + title = {CESSDA Data Management Expert Guide}, + howpublished = {\url{https://dmeg.cessda.eu/}}, + note = {Accessed: 2023-08-24} +} From 9e6f8a5535224cbadc8369d663a8412057e3e253 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 13:43:23 +0200 Subject: [PATCH 094/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 5809d0c8..78c426c0 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -99,6 +99,18 @@ Below is a list of criteria for selecting trustworthy datasets {% cite bres_2022 ## Strategies to search for data +The Consortium of European Social Science Data Archives (CESSDA) {% cite cessda_2017 %} has produced a list of steps in data discovery. The main ones are outlined below, and you can look at their [website](https://dmeg.cessda.eu/) for the sub-steps. +1. Develop a clear picture of the research data you need +2. Locate appropriate data resources +3. Set up a search query and search the data resource +4. Select data candidates +5. Evaluate data quality + +CESSDA also suggests three steps to adjust your search strategy {% cite cessda_2017 %}: +Use appropriate words in appropriate fields +Broaden your scope +Narrow your scope + # Data citation ## Importance of data citation From 52b591e37620553ec65c265e85fa41536bad1892 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 13:44:49 +0200 Subject: [PATCH 095/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 78c426c0..1d7ab9d7 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -107,9 +107,9 @@ The Consortium of European Social Science Data Archives (CESSDA) {% cite cessda_ 5. Evaluate data quality CESSDA also suggests three steps to adjust your search strategy {% cite cessda_2017 %}: -Use appropriate words in appropriate fields -Broaden your scope -Narrow your scope +1. Use appropriate words in appropriate fields +2. Broaden your scope +3. Narrow your scope # Data citation From af17c7b138ffc793bdbd3daa321d64961a0e56d8 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 13:56:06 +0200 Subject: [PATCH 096/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 1d7ab9d7..e602039f 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -56,8 +56,6 @@ Below is a list of criteria for selecting trustworthy datasets {% cite bres_2022 * Is the research purpose/(hypo-)thesis well documented? * Is it documented whether the data are raw or processed? -# Data provenance - # Data discovery ## Services to search for data From 64d56eedc4cd3c51ea21e6671ac10d9732c9d4ba Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 14:01:55 +0200 Subject: [PATCH 097/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index e602039f..48aba9a1 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -88,8 +88,6 @@ Below is a list of criteria for selecting trustworthy datasets {% cite bres_2022 * [DataCite Commons](https://commons.datacite.org/) * [gesisDataSearch](https://datasearch.gesis.org/start) -### Data catalogues - ### Services where data can be published * **Interdisciplinary and [discipline-specific](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/22-data-repositories) repositories** * **Data reports** From 05fbdb9339d08c39ba5162ad7607cc524dbd2086 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Thu, 24 Aug 2023 14:03:44 +0200 Subject: [PATCH 098/112] Update 26-data-reuse.md --- docs/_Research-Data-Management/26-data-reuse.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/_Research-Data-Management/26-data-reuse.md b/docs/_Research-Data-Management/26-data-reuse.md index 48aba9a1..0b8dc122 100644 --- a/docs/_Research-Data-Management/26-data-reuse.md +++ b/docs/_Research-Data-Management/26-data-reuse.md @@ -109,8 +109,6 @@ CESSDA also suggests three steps to adjust your search strategy {% cite cessda_2 # Data citation -## Importance of data citation - ## Common standards for data citation ### Interdisciplinary From 1e21a3071dfaf31be4c66495955fde83b00f70a0 Mon Sep 17 00:00:00 2001 From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com> Date: Thu, 24 Aug 2023 15:01:58 +0200 Subject: [PATCH 099/112] Update README.md with contributing.md and contributors.md see issue 77 https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/issues/77 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ea19d96f..b7552289 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ This knowledge base is a collection of documents and references important to the ## Contributing to the Knowledge Base -If you want to contribtute to the Knowledge base, please see the [CONTRIBUTING.md](CONTRIBUTING.md) file, and be sure to add yourself to the [CONTRIBUTORS.md](CONTRIBUTORS.md) file. +If you want to contribtute to the Knowledge base, please see the [02-contributing.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/02-contributing.md) file, and be sure to add yourself to the [03-contributors.md](https://github.com/NFDI4Microbiota/nfdi4microbiota-knowledge-base/blob/main/docs/_Getting-Started/03-contributors.md) file. ## License From 2cdbd29b75708b9490fd2285a7effdb37d26261c Mon Sep 17 00:00:00 2001 From: KK-NFDI <115994792+KK-NFDI@users.noreply.github.com> Date: Tue, 29 Aug 2023 12:44:14 +0200 Subject: [PATCH 100/112] Update 02-workflows.md to work with new location of 04-fair.md The file 03-fair.md has been moved/renamed. This link is now adjusted to the new version. --- docs/_Reproducible-Data-Analysis/02-workflows.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Reproducible-Data-Analysis/02-workflows.md b/docs/_Reproducible-Data-Analysis/02-workflows.md index 86c6d6a4..bf7e2bac 100644 --- a/docs/_Reproducible-Data-Analysis/02-workflows.md +++ b/docs/_Reproducible-Data-Analysis/02-workflows.md @@ -12,7 +12,7 @@ This page should give an overview of suggested standards for workflows. Not all ## FAIR Principles for Data management -In NFDI4Microbiota, we aim to follow the FAIR principles for data management (see [here](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/RDM/03-fair) for more details). +In NFDI4Microbiota, we aim to follow the FAIR principles for data management (see [here](https://nfdi4microbiota.github.io/nfdi4microbiota-knowledge-base/Research-Data-Management/04-fair) for more details). In essence, data should be Findable, Accessible, Interoperable, and Reusable. For workflows this means, data and/or results in the form of processed data should (if possible): From 4661d657be13251e716abdd642fc151b3cdcc89b Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 10:07:23 +0200 Subject: [PATCH 101/112] Update references.bib --- docs/_bibliography/references.bib | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index cfac9722..9b59ae05 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -220,3 +220,31 @@ @misc{cessda_2017 howpublished = {\url{https://dmeg.cessda.eu/}}, note = {Accessed: 2023-08-24} } + +@misc{kwok_2018, + title = {How to pick an electronic laboratory notebook}, + volume = {560}, + url = {http://dx.doi.org/10.1038/d41586-018-05895-3}, + DOI = {10.1038/d41586-018-05895-3}, + number = {7717}, + journal = {Nature}, + publisher = {Springer Science and Business Media LLC}, + author = {Kwok, Roberta}, + year = {2018}, + month = {Aug}, + pages = {269–270}, + language={en} +} + +@misc{lma_rdmwg, + title = {Longwood Medical Area Research Data Management Working Group}, + howpublished = {\url{https://datamanagement.hms.harvard.edu/collect-analyze/electronic-lab-notebooks}}, + note = {Accessed: 2023-09-01} +} + +@unpublished{vieten_2023, + author = {Vieten, Anne and Lindstädt, Birte and Vandendorpe, Justine}, + title = {Introduction to Research Data Management}, + month = {May}, + year = {2023}, +} From 8a814b8a3b602c10fd47708cc00365441d59d3b9 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 10:11:43 +0200 Subject: [PATCH 102/112] Update references.bib --- docs/_bibliography/references.bib | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 9b59ae05..2c560fbf 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -242,6 +242,12 @@ @misc{lma_rdmwg note = {Accessed: 2023-09-01} } +@unpublished{vandendorpe_2023, + author = {Vandendorpe, Justine and Adams, Beatrix and Sutsko, Aliaksandra and Lindstädt, Birte}, + title = {Ten Quick Tips for Implementing Electronic Laboratory Notebooks (ELNs)}, + year = {2023}, +} + @unpublished{vieten_2023, author = {Vieten, Anne and Lindstädt, Birte and Vandendorpe, Justine}, title = {Introduction to Research Data Management}, From ed0e7bf47b9bac7ae588637ad526c4877578e23d Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 10:12:56 +0200 Subject: [PATCH 103/112] Update 12-eln.md --- docs/_Research-Data-Management/12-eln.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md index f2a0352d..848ea78c 100644 --- a/docs/_Research-Data-Management/12-eln.md +++ b/docs/_Research-Data-Management/12-eln.md @@ -4,8 +4,8 @@ category: Research-Data-Management layout: default docs_css: markdown --- -# Introduction -Electronic Lab Notebooks (ELNs) are software meant to document experiments and research data. They act as a replacement for paper lab notebooks in the context of the digital transformation. ELNs include features such as protocol templates, collaboration tools, support for electronic signatures and the ability to manage the lab inventory. +# Definition +An Electronic Lab Notebook (ELN) is a software meant for documenting experiments, resulting research data and processes. In its most basic form, an ELN replicates an interface similar to a page in a physical lab notebook. More advanced forms often offer features such as protocol templates, collaboration tools, support for electronic signatures and the ability to manage the lab inventory. Ultimately, ELNs will replace physical lab notebooks as part of the digital transformation {% cite kwok_2018 lindstädt_2019 lma_rdmwg vandendorpe_2023 vieten_2023 %}. # Further resources * [ELN Finder - Demo](https://eln-finder.ulb.tu-darmstadt.de/home) - Tool to help researchers searching and selecting a suitable ELN thanks to more than 40 filter criteria. @@ -14,3 +14,6 @@ Electronic Lab Notebooks (ELNs) are software meant to document experiments and r * Free consultation sessions to get advice on the selection and introduction of an ELN (). * [Video tutorial series](https://www.youtube.com/playlist?list=PLJYlS0FDTMq17tvYMeuI2Ct5XtykRFy0K) (only in German). * Working groups on ELNs (e.g. in [North Rhine-Westphalia](https://www.fdm.nrw/index.php/fdm-nrw/elb/), Germany). + +# References +{% bibliography --cited_in_order %} From 52a695b24b4169eb51408d5edffec81ebc4615b5 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 10:14:48 +0200 Subject: [PATCH 104/112] Update references.bib --- docs/_bibliography/references.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 2c560fbf..4e47a786 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -242,7 +242,7 @@ @misc{lma_rdmwg note = {Accessed: 2023-09-01} } -@unpublished{vandendorpe_2023, +@unpublished{vandendorpe_nd, author = {Vandendorpe, Justine and Adams, Beatrix and Sutsko, Aliaksandra and Lindstädt, Birte}, title = {Ten Quick Tips for Implementing Electronic Laboratory Notebooks (ELNs)}, year = {2023}, From b5f03c39e1f058e54797c82f8ae98f64352f3264 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 10:15:05 +0200 Subject: [PATCH 105/112] Update 12-eln.md --- docs/_Research-Data-Management/12-eln.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md index 848ea78c..e578e594 100644 --- a/docs/_Research-Data-Management/12-eln.md +++ b/docs/_Research-Data-Management/12-eln.md @@ -5,7 +5,7 @@ layout: default docs_css: markdown --- # Definition -An Electronic Lab Notebook (ELN) is a software meant for documenting experiments, resulting research data and processes. In its most basic form, an ELN replicates an interface similar to a page in a physical lab notebook. More advanced forms often offer features such as protocol templates, collaboration tools, support for electronic signatures and the ability to manage the lab inventory. Ultimately, ELNs will replace physical lab notebooks as part of the digital transformation {% cite kwok_2018 lindstädt_2019 lma_rdmwg vandendorpe_2023 vieten_2023 %}. +An Electronic Lab Notebook (ELN) is a software meant for documenting experiments, resulting research data and processes. In its most basic form, an ELN replicates an interface similar to a page in a physical lab notebook. More advanced forms often offer features such as protocol templates, collaboration tools, support for electronic signatures and the ability to manage the lab inventory. Ultimately, ELNs will replace physical lab notebooks as part of the digital transformation {% cite kwok_2018 lindstädt_2019 lma_rdmwg vandendorpe_nd vieten_2023 %}. # Further resources * [ELN Finder - Demo](https://eln-finder.ulb.tu-darmstadt.de/home) - Tool to help researchers searching and selecting a suitable ELN thanks to more than 40 filter criteria. From 94492afcbafa14c980a393f2033eda1d0d63ecf6 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 10:16:45 +0200 Subject: [PATCH 106/112] Update references.bib --- docs/_bibliography/references.bib | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 4e47a786..f17cf85b 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -245,7 +245,6 @@ @misc{lma_rdmwg @unpublished{vandendorpe_nd, author = {Vandendorpe, Justine and Adams, Beatrix and Sutsko, Aliaksandra and Lindstädt, Birte}, title = {Ten Quick Tips for Implementing Electronic Laboratory Notebooks (ELNs)}, - year = {2023}, } @unpublished{vieten_2023, From d7a13942fde733ab4e0ae6441ee775db35a1d398 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 14:28:53 +0200 Subject: [PATCH 107/112] Update references.bib --- docs/_bibliography/references.bib | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index f17cf85b..2ed985d0 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -253,3 +253,22 @@ @unpublished{vieten_2023 month = {May}, year = {2023}, } + +@book{bezjak_2018, + title = {Open Science Training Handbook}, + url = {https://zenodo.org/record/1212496}, + DOI = {10.5281/ZENODO.1212496}, + abstractNote = {For a readable version of the book, please visit https://book.fosteropenscience.eu A group of fourteen authors came together in February 2018 at the TIB (German National Library of Science and Technology) in Hannover to create an open, living handbook on Open Science training. High-quality trainings are fundamental when aiming at a cultural change towards the implementation of Open Science principles. Teaching resources provide great support for Open Science instructors and trainers. The Open Science training handbook will be a key resource and a first step towards developing Open Access and Open Science curricula and andragogies. Supporting and connecting an emerging Open Science community that wishes to pass on their knowledge as multipliers, the handbook will enrich training activities and unlock the community’s full potential. In this first release of the Open Science Training Handbook, some initial feedback from the community is already included.}, + publisher = {Zenodo}, + author = {Bezjak, Sonja and Clyburne-Sherin, April and Conzett, Philipp and Fernandes, Pedro and Görögh, Edit and Helbig, Kerstin and Kramer, Bianca and Labastida, Ignasi and Niemeyer, Kyle and Psomopoulos, Fotis and Ross-Hellauer, Tony and Schneider, René and Tennant, Jon and Verbakel, Ellen and Brinken, Helene and Heller, Lambert}, + year = {2018}, + month = {Apr}, + language = {en} +} + +@unpublished{n4m_wc_elns_2023, + author = {Vandendorpe, Justine and Wilbrandt, Jeanne and Grünwald, Katharina and Magel, Maja}, + title = {NFDI4Microbiota World Café on Electronic Lab Notebooks (ELNs)}, + month = {February}, + year = {2023}, +} From d8dc0cf4f644e46d991ce79416e533c6e333d853 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Fri, 1 Sep 2023 14:29:28 +0200 Subject: [PATCH 108/112] Update 12-eln.md --- docs/_Research-Data-Management/12-eln.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md index e578e594..dd29064e 100644 --- a/docs/_Research-Data-Management/12-eln.md +++ b/docs/_Research-Data-Management/12-eln.md @@ -4,9 +4,16 @@ category: Research-Data-Management layout: default docs_css: markdown --- -# Definition +# Definition of Electronic Lab Notebooks (ELNs) An Electronic Lab Notebook (ELN) is a software meant for documenting experiments, resulting research data and processes. In its most basic form, an ELN replicates an interface similar to a page in a physical lab notebook. More advanced forms often offer features such as protocol templates, collaboration tools, support for electronic signatures and the ability to manage the lab inventory. Ultimately, ELNs will replace physical lab notebooks as part of the digital transformation {% cite kwok_2018 lindstädt_2019 lma_rdmwg vandendorpe_nd vieten_2023 %}. +# Uses of lab notebooks + +## Physical lab notebooks +As well as documenting your experiments, resulting research data and processes, a physical lab notebook is also intended to communicate your work (e.g. why experiments were initiated?). It also serves as a legal document to prove patents and defend your data against accusations of misconduct. Finally, it is your scientific legacy in the laboratory {% n4m_wc_elns_2023 %}. + +## Additional uses of ELNs + # Further resources * [ELN Finder - Demo](https://eln-finder.ulb.tu-darmstadt.de/home) - Tool to help researchers searching and selecting a suitable ELN thanks to more than 40 filter criteria. * ELN Filter - Selection of ELNs that are suitable for the life sciences and that can be filtered out according to criteria ([English](https://www.publisso.de/fileadmin/user_upload/PUBLISSO/PUBLISSO_ELN-Filter_2021-06_english.xlsx), [German](https://www.publisso.de/fileadmin/user_upload/PUBLISSO/PUBLISSO_ELN-Filter_2020-12-01.xlsx)). From 7856da7bcbff60e99edf413e00530a007f6d6694 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Mon, 4 Sep 2023 09:09:10 +0200 Subject: [PATCH 109/112] Update 12-eln.md --- docs/_Research-Data-Management/12-eln.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md index dd29064e..d5fc1d55 100644 --- a/docs/_Research-Data-Management/12-eln.md +++ b/docs/_Research-Data-Management/12-eln.md @@ -10,7 +10,7 @@ An Electronic Lab Notebook (ELN) is a software meant for documenting experiments # Uses of lab notebooks ## Physical lab notebooks -As well as documenting your experiments, resulting research data and processes, a physical lab notebook is also intended to communicate your work (e.g. why experiments were initiated?). It also serves as a legal document to prove patents and defend your data against accusations of misconduct. Finally, it is your scientific legacy in the laboratory {% n4m_wc_elns_2023 %}. +As well as documenting your experiments, resulting research data and processes, a physical lab notebook is also intended to communicate your work (e.g. why experiments were initiated?). It also serves as a legal document to prove patents and defend your data against accusations of misconduct. Finally, it is your scientific legacy in the laboratory {% cite n4m_wc_elns_2023 %}. ## Additional uses of ELNs From 231bc769e7dead8c0ec9633b42fe89a63676d566 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 5 Sep 2023 15:28:54 +0200 Subject: [PATCH 110/112] Update 12-eln.md --- docs/_Research-Data-Management/12-eln.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md index d5fc1d55..e411a2ae 100644 --- a/docs/_Research-Data-Management/12-eln.md +++ b/docs/_Research-Data-Management/12-eln.md @@ -13,6 +13,7 @@ An Electronic Lab Notebook (ELN) is a software meant for documenting experiments As well as documenting your experiments, resulting research data and processes, a physical lab notebook is also intended to communicate your work (e.g. why experiments were initiated?). It also serves as a legal document to prove patents and defend your data against accusations of misconduct. Finally, it is your scientific legacy in the laboratory {% cite n4m_wc_elns_2023 %}. ## Additional uses of ELNs +ELNs offer features and functions that can pave the way for significant time savings and knowledge transfer in daily laboratory work. For example, ELNs support the annotation of raw data (e.g. with tags or metadata {% cite rathmann_2021 vandendorpe_nd %} without having to switch between different media formats. Annotating data makes it searchable, discoverable, traceable and reusable {% cite vandendorpe_nd %}. ELNs also bring data and their description closer together through embedded multimedia files (e.g. videos of experimental setups), links to shared resources (e.g. chemical databases or analysis software), links to other experiments, and direct links to (raw) data sets and analysis workflows {% cite rehwald_2022 %}. ELNs also allow for the versioning of experiment descriptions {% cite rehwald_2022 %} and the structuring and visualisation of workflows and processes {% cite rathmann_2021 %}. ELNs also have the ability to manage inventories of samples, reagents and other supplies, and track equipment and equipment maintenance schedules {% cite lma_rdmwg %}. ELNs also provide for collaboration {% cite lma_rdmwg %} through a common medium {% cite rehwald_2022 %}. Last but not least, ELNs provide for auditing {% cite lma_rdmwg %}, security and safety. Indeed, ELNs are fireproof, waterproof and cannot be lost, misplaced or stolen. ELNs can also be automatically backed up. They allow timestamping (RFC 3161 using DFN-PKI) and finalisation to prevent further changes {% cite rehwald_2022 %}. They also support electronic signatures {% cite cozatl_2021 %} and require access management {% cite rehwald_2022 %}. # Further resources * [ELN Finder - Demo](https://eln-finder.ulb.tu-darmstadt.de/home) - Tool to help researchers searching and selecting a suitable ELN thanks to more than 40 filter criteria. From c49f313242e7f97c11c4f5ef8687910fd05e7904 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Tue, 5 Sep 2023 15:35:52 +0200 Subject: [PATCH 111/112] Update references.bib --- docs/_bibliography/references.bib | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/docs/_bibliography/references.bib b/docs/_bibliography/references.bib index 2ed985d0..4793f3ab 100644 --- a/docs/_bibliography/references.bib +++ b/docs/_bibliography/references.bib @@ -272,3 +272,17 @@ @unpublished{n4m_wc_elns_2023 month = {February}, year = {2023}, } + +@unpublished{rathmann_2021, + author = {Rathmann, Torsten and Kastrup, Daniela and Weiß, Bastian and Lindstädt, Birte and Shutsko, Aliaksandra and Vandendorpe, Justine}, + title = {Workshop on Research Data Management}, + month = {October}, + year = {2021}, +} + +@unpublished{cozatl_2021, + author = {Cozat, Roberto and Grenzebach, Gerrit and Lindstädt, Birte and Shutsko, Aliaksandra and Vandendorpe, Justine}, + title = {Workshop on Research Data Management}, + month = {November}, + year = {2021}, +} From 666837e40c231718ffcf45467300d571d4d4bf91 Mon Sep 17 00:00:00 2001 From: Justine Vandendorpe Date: Wed, 6 Sep 2023 09:51:12 +0200 Subject: [PATCH 112/112] Update 12-eln.md --- docs/_Research-Data-Management/12-eln.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/_Research-Data-Management/12-eln.md b/docs/_Research-Data-Management/12-eln.md index e411a2ae..5d50ad2c 100644 --- a/docs/_Research-Data-Management/12-eln.md +++ b/docs/_Research-Data-Management/12-eln.md @@ -13,7 +13,10 @@ An Electronic Lab Notebook (ELN) is a software meant for documenting experiments As well as documenting your experiments, resulting research data and processes, a physical lab notebook is also intended to communicate your work (e.g. why experiments were initiated?). It also serves as a legal document to prove patents and defend your data against accusations of misconduct. Finally, it is your scientific legacy in the laboratory {% cite n4m_wc_elns_2023 %}. ## Additional uses of ELNs -ELNs offer features and functions that can pave the way for significant time savings and knowledge transfer in daily laboratory work. For example, ELNs support the annotation of raw data (e.g. with tags or metadata {% cite rathmann_2021 vandendorpe_nd %} without having to switch between different media formats. Annotating data makes it searchable, discoverable, traceable and reusable {% cite vandendorpe_nd %}. ELNs also bring data and their description closer together through embedded multimedia files (e.g. videos of experimental setups), links to shared resources (e.g. chemical databases or analysis software), links to other experiments, and direct links to (raw) data sets and analysis workflows {% cite rehwald_2022 %}. ELNs also allow for the versioning of experiment descriptions {% cite rehwald_2022 %} and the structuring and visualisation of workflows and processes {% cite rathmann_2021 %}. ELNs also have the ability to manage inventories of samples, reagents and other supplies, and track equipment and equipment maintenance schedules {% cite lma_rdmwg %}. ELNs also provide for collaboration {% cite lma_rdmwg %} through a common medium {% cite rehwald_2022 %}. Last but not least, ELNs provide for auditing {% cite lma_rdmwg %}, security and safety. Indeed, ELNs are fireproof, waterproof and cannot be lost, misplaced or stolen. ELNs can also be automatically backed up. They allow timestamping (RFC 3161 using DFN-PKI) and finalisation to prevent further changes {% cite rehwald_2022 %}. They also support electronic signatures {% cite cozatl_2021 %} and require access management {% cite rehwald_2022 %}. +ELNs offer features and functions that can pave the way for significant time savings and knowledge transfer in daily laboratory work. For example, ELNs support the annotation of raw data (e.g. with tags or metadata {% cite rathmann_2021 vandendorpe_nd %} without having to switch between different media formats. Annotating data makes it searchable, discoverable, traceable and reusable {% cite vandendorpe_nd %}. ELNs also bring data and their description closer together through embedded multimedia files (e.g. videos of experimental setups), links to shared resources (e.g. chemical databases or analysis software), links to other experiments, and direct links to (raw) data sets and analysis workflows {% cite rehwald_2022 %}. ELNs also allow for the versioning of experiment descriptions {% cite rehwald_2022 %} and the structuring and visualisation of workflows and processes {% cite rathmann_2021 %}. ELNs also have the ability to manage inventories of samples, reagents and other supplies, and track equipment and equipment maintenance schedules {% cite lma_rdmwg %}. ELNs also provide for collaboration {% cite lma_rdmwg %} through a common medium {% cite rehwald_2022 %}. Last but not least, ELNs provide for auditing {% cite lma_rdmwg %}, security and safety. Indeed, ELNs are fireproof, waterproof and cannot be lost, misplaced or stolen. ELNs can also be automatically backed up. They allow timestamping (RFC 3161 using DFN-PKI) and finalisation to prevent further changes {% cite rehwald_2022 %}. They also support electronic signatures {% cite cozatl_2021 %} and require access management {% cite rehwald_2022 %}. + +## What ELNs should not be used for +ELNs are not data publishing platforms and are not suitable for storing large files. Large files require special technology for secure storage (e.g. Object Store, Nextcloud), but can still be linked in the ELN {% cite rehwald_2022 %}. # Further resources * [ELN Finder - Demo](https://eln-finder.ulb.tu-darmstadt.de/home) - Tool to help researchers searching and selecting a suitable ELN thanks to more than 40 filter criteria.