bulk commit

UtrechtUniversity · Feb 16, 2023 · b52450f · b52450f
1 parent cb9f16e
commit b52450f
Show file tree

Hide file tree

Showing 37 changed files with 214 additions and 40 deletions.
diff --git a/docs/archiving.md b/docs/archiving.md
@@ -0,0 +1,4 @@
+# Data Archiving
+
+archiving/preservation
+file formats
diff --git a/docs/rdm-in-practice/codebooks.md → docs/codebooks.md b/docs/rdm-in-practice/codebooks.md → docs/codebooks.md
diff --git a/docs/rdm-in-practice/data-storage.md → docs/data-cleaning.md b/docs/rdm-in-practice/data-storage.md → docs/data-cleaning.md
diff --git a/docs/rdm-in-practice/data-collection.md → docs/data-collection.md b/docs/rdm-in-practice/data-collection.md → docs/data-collection.md
diff --git a/docs/data-management-planning.md b/docs/data-management-planning.md
@@ -0,0 +1,66 @@
+# Data Management Plans
+
+## What Is A Data Management Plan?
+
+A Data Management Plan (DMP) is a formal document that describes your data and outlines all aspects of managing your data - both during and after your project.
+
+Moreover, it is a _living_ document that can you can revise and update as needed.
+
+![](images/data-management-plan.jpg)
+
+<figcaption><a href="https://the-turing-way.netlify.app/">The Turing Way</a> project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: <a href="https://doi.org/10.5281/zenodo.3332807">10.5281/zenodo.3332807</a>.</figcaption>
+
+## Why Should You Write A DMP?
+
+Writing a DMP provides an opportunity to reflect on your data, particularly how you organize and manage it. It nudges you to think about how to make your RDM more _concrete_ and _actionable_. This creates efficiency and more value for your data.
+
+## When Should You Write A DMP?
+
+Working on a DMP at the start of your project will ensure that you are better informed of best practices in RDM and prepared to implement them. That being said, you can also write a DMP can during the project or when it's completed.
+
+## DMPonline & DMP Templates
+
+DMPonline is a tool that helps you create and maintain DMPs. With DMPonline, you can:
+
+- register and sign in with your institutional credentials,
+- write and collaborate on (multiple) DMPs,
+- share DMPs or switch their visibility between private and public,
+- request feedback from RDM Support,
+- download DMPs in various formats.
+
+DMPonline offers DMP templates from various institutions and funders, including:
+
+- Utrecht University
+- UMC Utrecht
+- [NWO](https://dmponline.dcc.ac.uk/template_export/1753695087.pdf)
+- [ZonMw](https://dmponline.dcc.ac.uk/template_export/1461074155.pdf)
+- [ERC](https://dmponline.dcc.ac.uk/template_export/2088403152.pdf)
+- [Horizon 2020](https://dmponline.dcc.ac.uk/template_export/1612436782.pdf)
+- [Horizon Europe](https://dmponline.dcc.ac.uk/template_export/5992485.pdf)
+
+These templates also contain example answers and guidance.
+
+![](images/uu-dmp-template.JPG)
+
+## Tips
+
+!!! note "Tips"
+
+    - Contact your DoY data manager! They can (co)write your DMP and/or review it.
+    - If the DoY data manager is unavailable, you can still request feedback from RDM Support.
+
+## Resources
+
+- [Create your DMP online](https://www.uu.nl/en/research/research-data-management/tools-services/tool-to-create-your-dmp-online)
+- [Data management planning](https://www.uu.nl/en/research/research-data-management/guides/data-management-planning)
+- [Learn to write your DMP (online training)](https://www.uu.nl/en/research/research-data-management/training-workshops/online-training-learn-to-write-your-dmp) 
+
+## References
+
+1. [https://www.uu.nl/en/research/research-data-management/guides/data-management-planning](https://www.uu.nl/en/research/research-data-management/guides/data-management-planning)
+
+2. [https://www.kuleuven.be/rdm/en/faq/faq-dmp](https://www.kuleuven.be/rdm/en/faq/faq-dmp)
+
+3. [https://rdm.uva.nl/en/planning/data-management-plan/data-management-plan.html](https://rdm.uva.nl/en/planning/data-management-plan/data-management-plan.html)
+
+4. [https://www.uu.nl/en/research/research-data-management/tools-services/tool-to-create-your-dmp-online.html](https://www.uu.nl/en/research/research-data-management/tools-services/tool-to-create-your-dmp-online.html)
diff --git a/docs/rdm-in-practice/data-pipelining.md → docs/data-pipelining.md b/docs/rdm-in-practice/data-pipelining.md → docs/data-pipelining.md
diff --git a/docs/rdm-in-practice/data-sharing.md → docs/data-sharing.md b/docs/rdm-in-practice/data-sharing.md → docs/data-sharing.md
diff --git a/docs/rdm-in-practice/documentation.md → docs/documentation.md b/docs/rdm-in-practice/documentation.md → docs/documentation.md
diff --git a/...in-practice/fair-assessment-checklists.md → docs/fair-assessment-checklists.md b/...in-practice/fair-assessment-checklists.md → docs/fair-assessment-checklists.md
diff --git a/docs/file-formats.md b/docs/file-formats.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/folder-structures.md b/docs/folder-structures.md
@@ -0,0 +1,24 @@
+# Folder Structures
+
+## #what
+
+## #why
+
+## #when
+
+## Project-Level Folder Structure
+
+00_README
+01_administration: finances, meeting notes, access rights, agreements, contracts, communications, reports
+02_documentation: grant/study proposals, fetc application, data management plan, reference library, codebooks, journals
+04_protocols: from recruitment to data storage to data subjects rights - sops, protocols, tools, instruments
+05_materials: questionnaires, interview schemes
+06_data: raw, preprocessed, processed, postprocessed
+07_scripts
+08_dissemination: preregistrations, preprints, publications + presentations, posters, reports, articles, website
+
+## Publication-Level Folder Structure
+
+good enough project template / worcs / research compendium
+
+## References
diff --git a/docs/images/Tickets for Star Wars Celebration Europe 2023 from ReedPOP.pdf b/docs/images/Tickets for Star Wars Celebration Europe 2023 from ReedPOP.pdf
diff --git a/docs/images/data-management-plan.jpg b/docs/images/data-management-plan.jpg
diff --git a/docs/images/uu-dmp-template.JPG b/docs/images/uu-dmp-template.JPG
diff --git a/docs/images/xkcd-file-naming.png b/docs/images/xkcd-file-naming.png
diff --git a/docs/index.md b/docs/index.md
@@ -1,5 +1,5 @@
 # Welcome!
 
-![The FAIR Principles](https://the-turing-way.netlify.app/_images/fair-principles.svg "The Turing Way project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: 10.5281/zenodo.3332807.")
+![The FAIR Principles](https://the-turing-way.netlify.app/_images/fair-principles.svg)
 
 <figcaption><a href="https://the-turing-way.netlify.app/">The Turing Way</a> project illustration by Scriberia. Used under a CC-BY 4.0 licence. DOI: <a href="https://doi.org/10.5281/zenodo.3332807">10.5281/zenodo.3332807</a>.</figcaption>
diff --git a/docs/licenses.md b/docs/licenses.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/rdm-in-practice/metadata.md → docs/metadata.md b/docs/rdm-in-practice/metadata.md → docs/metadata.md
diff --git a/docs/naming-conventions.md b/docs/naming-conventions.md
@@ -0,0 +1,86 @@
+# Naming Conventions
+
+## What Is A Naming Convention?
+
+A naming convention is a set of rules for naming things. You can apply it to things like folders, files, and variables.
+
+## Why Should I Apply A Naming Convention?
+
+Names that are informative and useful for machines and humans are a step toward efficient data management and reproducible research. The more consistent and meaningful the name, the easier it will be to locate and identify things, understand what they contain, and (re)use them.
+
+## When Should I Apply A Naming Convention?
+
+Aim to select and implement a naming convention at the beginning of a project. If you want to retroactively apply a naming convention, there are several tools for bulk renaming.
+
+The entire research team should agree on and adopt a naming convention. Document the choice of naming convention in the DMP, so others can refer to and grasp it quickly.
+
+![](images/xkcd-file-naming.png)
+
+<figcaption><a href="https://xkcd.com/1459/">Documents - xkcd</a>. Used under a CC BY-NC 2.5 license. </figcaption>
+
+## Popular Naming Conventions
+
+Instead of developing a naming convention from scratch, you can start with one that is already being used in programming and software development communities:
+
+| Naming Covention | Example           | Description |
+| ---------------- | ----------------- | ----------- |
+| original name    | `an awesome name` | N/A
+| snake_case       | `an_awesome_name` | All words are lowercase and separated by an underscore ( `_` ) |
+| kebab-case       | `an-awesome-name` | All words are lowercase and separated by a hyphen ( `-` ) |
+| PascalCase       | `AnAwesomeName`   | All words are capitalized. Spaces are not used. |
+| camelCase        | `anAwesomeName`   | The first word is lowercase, the remaining words are capitalized. Spaces are not used. |
+
+## Human-Readable Names
+
+You can tailor naming conventions like `snake_case` and `PascalCase` to suit your project and workflow. Determine what information is relevant (or not) to create meaningful names and how you can string this information together. Don't forget to document this in your DMP!
+
+!!! note "Elements for Human-Readable Names"
+
+    Names should be =<25 characters long and can include:
+
+    - Date of creation/update (`YYYY-MM-DD` or `YYYYMMDD`)
+    - Description of content, like type of data
+    - Initials of creator/reviewer
+    - Project number or acronym
+    - Location/coordinates
+    - Version number (like `v2` or v2.2`)
+
+## Machine-Readable Names
+
+When names are machine-readable, they can be efficiently processed by computers and software. This makes it easier to search for files and run operations that involve programming like extracting information from file names or working with regular expressions.  
+
+!!! note "Avoid"
+
+    - Spaces
+    - Special characters like `$`, `@`, `%`, `#`, `&`, `*`, `!`, `/`, `\`
+    - Punction characters like `,`, `:`, `;`, `?`, `'`, `"`
+    - Accented characters
+
+## A Note on Numbering, Dates, Versioning
+
+- Append numbers to the beginning of a name to enable sorting according to a logical structure. Use multiple digits like `01` or `001`.
+
+- Dates should follow the ISO 8601 standard which is either `YYYY-MM-DD` or `YYYYMMDD`. Append dates to the beginning of names to enable sorting in chronological order.
+
+- Specify versions using ordinal numbers (1,2,3) for major revisions and decimals for minor changes (1.1, 1.2, 2.1, 2.2). Alternatively, you can specify versions with multiple digits like v01 and v02.
+
+## Renaming files
+
+The following tools enable renaming in bulk:
+
+- [Bulk Rename Utility](https://www.bulkrenameutility.co.uk/) (Windows, free)
+- [Renamer](https://renamer.com/) (MacOS, paid)
+- [NameChanger](https://mrrsoftware.com/namechanger/), (MacOS, free)
+- [GPRename](https://gprename.sourceforge.net/) (Linux, free)
+
+## References
+
+1. [https://en.wikipedia.org/wiki/Naming_convention](https://en.wikipedia.org/wiki/Naming_convention)
+2. [https://help.osf.io/article/146-file-naming](https://help.osf.io/article/146-file-naming)
+3. [https://rdm.elixir-belgium.org/file_naming.html](https://rdm.elixir-belgium.org/file_naming.html)
+4. [https://khalilstemmler.com/blogs/camel-case-snake-case-pascal-case/](https://khalilstemmler.com/blogs/camel-case-snake-case-pascal-case/)
+5. [https://dev.to/chaseadamsio/most-common-programming-case-types-30h9](https://dev.to/chaseadamsio/most-common-programming-case-types-30h9)
+6. [https://rdmkit.elixir-europe.org/data_organisation](https://rdmkit.elixir-europe.org/data_organisation)
+[http://dataabinitio.com/?p=987](http://dataabinitio.com/?p=987)
+7. [https://dmeg.cessda.eu/Data-Management-Expert-Guide/2.-Organise-Document/File-naming-and-folder-structure](https://dmeg.cessda.eu/Data-Management-Expert-Guide/2.-Organise-Document/File-naming-and-folder-structure)
+8. [https://annakrystalli.me/rrresearchACCE20/filenaming-view.html](https://annakrystalli.me/rrresearchACCE20/filenaming-view.html)
diff --git a/docs/outreach.md b/docs/outreach.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/preprints.md b/docs/preprints.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/preregistration.md b/docs/preregistration.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/rdm-in-practice/data-publication.md → docs/publishing.md b/docs/rdm-in-practice/data-publication.md → docs/publishing.md
diff --git a/docs/rdm-in-practice/.DS_Store b/docs/rdm-in-practice/.DS_Store
diff --git a/docs/rdm-in-practice/data-archiving.md b/docs/rdm-in-practice/data-archiving.md
diff --git a/docs/rdm-in-practice/data-management-planning.md b/docs/rdm-in-practice/data-management-planning.md
diff --git a/docs/rdm-in-practice/file-and-folder-naming.md b/docs/rdm-in-practice/file-and-folder-naming.md
diff --git a/docs/rdm-in-practice/folder-structure.md b/docs/rdm-in-practice/folder-structure.md
diff --git a/docs/reference-management.md b/docs/reference-management.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/reproducibility.md b/docs/reproducibility.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/storage-and-backup.md b/docs/storage-and-backup.md
@@ -0,0 +1 @@
+# Data Storage 
diff --git a/docs/the-fair-principles/.DS_Store b/docs/the-fair-principles/.DS_Store
diff --git a/docs/the-fair-principles/accessibility.md b/docs/the-fair-principles/accessibility.md
diff --git a/docs/the-fair-principles/findability.md b/docs/the-fair-principles/findability.md
diff --git a/docs/the-fair-principles/interoperability.md b/docs/the-fair-principles/interoperability.md
diff --git a/docs/the-fair-principles/reusability.md b/docs/the-fair-principles/reusability.md
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -25,30 +25,34 @@ plugins:
 markdown_extensions:
   - attr_list
   - md_in_html
+  - admonition
+  - pymdownx.details
+  - pymdownx.superfences
 
 repo_url: https://github.com/nehamoopen/doy-data-guide
 repo_name: nehamoopen/doy-data-guide
 
 nav:
-  - Welcome!: index.md
-  - Jargon:
-      - The FAIR Principles:
-          - Findability: the-fair-principles/findability.md
-          - Accessibility: the-fair-principles/accessibility.md
-          - Interoperability: the-fair-principles/interoperability.md
-          - Reusability: the-fair-principles/reusability.md
-  - RDM in Practice:
-    - rdm-in-practice/data-management-planning.md
-    - rdm-in-practice/fair-assessment-checklists.md
-    - rdm-in-practice/folder-structure.md
-    - rdm-in-practice/file-and-folder-naming.md
-    - rdm-in-practice/data-collection.md
-    - rdm-in-practice/data-pipelining.md
-    - rdm-in-practice/metadata.md
-    - rdm-in-practice/codebooks.md
-    - rdm-in-practice/documentation.md
-    - rdm-in-practice/data-storage.md
-    - rdm-in-practice/data-archiving.md
-    - rdm-in-practice/data-publication.md
-    - rdm-in-practice/data-sharing.md
+  - index.md
+  - data-management-planning.md
+  - naming-conventions.md
+  - folder-structures.md
+  - storage-and-backup.md
+  - data-collection.md
+  - data-pipelining.md
+  - data-cleaning.md
+  - preregistration.md
+  - reproducibility.md
+  - reference-management.md
+  - codebooks.md
+  - metadata.md
+  - documentation.md
+  - archiving.md
+  - publishing.md
+  - preprints.md
+  - licenses.md
+  - file-formats.md
+  - data-sharing.md
+  - outreach.md
+  - fair-assessment-checklists.md