Merge branch 'master' of github.com:elixir-europe/rdmkit into pr/jorgeMFS/1805

Author: bedroesb

README.md

@@ -1,4 +1,4 @@
-[![Validation of the tools and page metadata](https://github.com/elixir-europe/rdmkit/actions/workflows/tool_list_conversion.yml/badge.svg)](https://github.com/elixir-europe/rdmkit/actions/workflows/tool_list_conversion.yml) [![Jekyll site CI](https://github.com/elixir-europe/rdmkit/workflows/Jekyll%20site%20CI/badge.svg)](https://github.com/elixir-europe/rdmkit/actions?query=workflow%3A%22Jekyll+site+CI%22) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5110061.svg)](https://doi.org/10.5281/zenodo.5110061) [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
+[![Validation of the tools and page metadata](https://github.com/elixir-europe/rdmkit/actions/workflows/tool-list-validation.yml/badge.svg)](https://github.com/elixir-europe/rdmkit/actions/workflows/tool-list-validation.yml) [![Jekyll site CI](https://github.com/elixir-europe/rdmkit/workflows/Jekyll%20site%20CI/badge.svg)](https://github.com/elixir-europe/rdmkit/actions?query=workflow%3A%22Jekyll+site+CI%22) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5110061.svg)](https://doi.org/10.5281/zenodo.5110061) [![theme badge](https://img.shields.io/badge/ELIXIR%20toolkit%20theme-jekyll-blue?color=0d6efd)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
 
 <img src="https://raw.githubusercontent.com/elixir-europe/rdmkit/master/assets/img/RDMkit_logo.svg" alt="RDMkit logo" width="450"/>
 

_data/tool_and_resource_list.yml

@@ -1335,7 +1335,7 @@
   name: Minimum Information about Plant Phenotyping Experiment (MIAPPE)
   registry:
     fairsharing: nd9ce9
-    tess: MIAPPE
+    tess: Minimum Information about Plant Phenotyping Experiment
   url: https://www.miappe.org/
 - description: Cloud storage and file sharing service from Microsoft
   id: microsoft-azure
@@ -1497,11 +1497,12 @@
     fairsharing: re1278
     tess: OmicsDI
   url: https://www.omicsdi.org
-- description: OMOP is a common data model for the harmonisation for of observational health data.
+- description: OMOP is a common data model for the harmonisation of observational health data.
   id: omop-cdm
-  name: OMOP-CDM
+  name: The Observational Medical Outcomes Partnership Common Data Model (OMOP CDM)
   registry:
     tess: OMOP-CDM
+    fairsharing: qk984b
   url: https://ohdsi.github.io/CommonDataModel/
 - description: OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.
   id: onotomaton
@@ -3488,8 +3489,10 @@
     biotools: agrischemas
   url: https://github.com/Rothamsted/agri-schemas
 - description: A data model for the collection of cancer-related clinical information and genomics metadata.
-  name:  The Minimal Dataset for Cancer of the 1+Million Genomes Initiative (1+MG-MDC)
   id: 1pmg-mdc
+  name: The Minimal Dataset for Cancer of the 1+Million Genomes Initiative (1+MG-MDC)
+  registry:
+    fairsharing: 0d9069
   url: https://zenodo.org/records/10784601
 - description: The PSI-MS Controlled Vocabulary consists of a large collection of structured terms covering description and use of Mass Spectrometry instrumentation as well as Protein Identification and Quantitation software.
   id: psi-ms

pages/about/events.md

@@ -4,9 +4,10 @@ github:
     file_path: _data/events.yml
 ---
 
+Explore upcoming and past events connected to RDMkit, from webinars and workshops to conference sessions and community gatherings focused on research data management.
+
 {% include events.html event_type="upcoming_event" title=true %}
 
 
 {% include events.html event_type="past_event" title=true %}
 
-

pages/about/news.md

@@ -4,6 +4,8 @@ github:
     file_path: _data/news.yml
 ---
 
+Keep up with the latest developments around RDMkit, including new content, community highlights, collaborations, and other updates relevant to research data management in the life sciences.
+
 [<i class="fa fa-rss me-2"></i>Subscribe to the RSS feed]({{ '/feed.xml' | relative_url }}){: class="btn btn-light rounded-pill"}
 
 {% include news.html %}

pages/about/outreach.md

@@ -6,6 +6,29 @@ We are, since the beginning, actively spreading the word about RDMkit making sur
 
 ## Presentations
 
+### RDMkit at ISMB/ECCB 2025
+
+**2025-07-24**
+
+RDMkit was presented as part of the eScience Lab ISMB/ECCB 2025 presentations, with a poster titled "Research Data Management Toolkit for Life Scientists". The poster materials can be found on [Zenodo](https://zenodo.org/records/15830546).
+
+### Hands-On RDM with ELIXIR groups: Crafting short and long-term strategies
+
+**2024-06-10**
+
+These slides, presented at ELIXIR All Hands 2024, include RDMkit as part of the wider ELIXIR research data management ecosystem. The slides can be found on [F1000Research](https://f1000research.com/slides/14-27).
+
+### RDMkit: A key resource for FAIR data management
+
+**2024-06-11**
+
+RDMkit was presented as a poster at ELIXIR All Hands 2024. The poster can be found on [F1000Research](https://f1000research.com/posters/13-727).
+
+### RDMkit: The Research Data Management Toolkit for Life Sciences
+
+**2023-09-12**
+
+This presentation was given at the 1st Conference on Research Data Infrastructure (CoRDI 2023). The slides can be found on [Zenodo](https://zenodo.org/records/8354863).
 
 ### RDMkit poster at ELIXIR All Hands 2023
 
@@ -20,11 +43,35 @@ The poster can be found on [F1000Research](https://f1000research.com/posters/12-
 
 RDMkit was introduced to the [DSIG](https://www.dtls.nl/about/community/interest-groups/data-stewards-interest-group/) at one of their monthly meetings, together with introduction on IDTkit and FAIRCookBook. [Presentation slides on RDMkit (PDF)](https://drive.google.com/file/d/12aHIH0rRU6ogOOacZr3K6PrzXylYgHIo/view).
 
-### ELIXIR FAIR & Research Data Management know-how ecosystem - All hands 2022
+### Research Data Management Toolkit (RDMkit): guidelines for plant phenotyping data management and sharing
+
+**2022-09-26**
 
-**2022-06-10**
+This poster highlighted RDMkit in the context of plant phenotyping data management and sharing, and was presented at the 7th International Plant Phenotyping Symposium (IPPS2022). The poster can be found on [Zenodo](https://zenodo.org/records/7148792).
 
-RDMkit was presented at all hands. The presentation can be found on [F1000Research](https://f1000research.com/slides/11-737).
+### RDMkit - The research data management toolkit for life sciences
+
+**2022-06-08**
+
+RDMkit was presented as a poster at ELIXIR All Hands 2022. The poster can be found on [F1000Research](https://f1000research.com/posters/11-736).
+
+### The ecosystem together - walkthrough from two perspectives: a User and a Contributor
+
+**2022-06-09**
+
+This ELIXIR All Hands 2022 presentation placed RDMkit in the wider FAIR and research data management ecosystem together with FAIRsharing, the FAIR Cookbook, DSW, WorkflowHub, and TeSS. The slides can be found on [F1000Research](https://f1000research.com/slides/11-636).
+
+### RDMkit walkthrough
+
+**2022-06-07**
+
+RDMkit was presented at ELIXIR All Hands 2022 through a walkthrough of the toolkit. The slides can be found on [F1000Research](https://f1000research.com/slides/11-737).
+
+### Registries walkthrough
+
+**2022-06-09**
+
+This ELIXIR All Hands 2022 talk focused on the registries connected to the broader RDMkit ecosystem, including FAIRsharing, TeSS, bio.tools, and WorkflowHub. The slides can be found on [F1000Research](https://f1000research.com/slides/11-940).
 
 ### Q-EBRA WORKSHOP: Your next grant application - methodological approach
 
@@ -105,4 +152,3 @@ OS Fair 2021 aims to bring together and empower open science communities and ser
 ### Promotion video for RDMkit contributors
 
 <iframe class="scale" src="https://drive.google.com/file/d/1CUKAGm9Ve4WeY04T7paZgcHGpSg_9E6r/preview" width="640" height="480" allow="autoplay"></iframe>
-

pages/contribute/preview_changes.md

@@ -5,12 +5,12 @@ summary: Use your own fork to preview changes on the website.
 
 ## Introduction
 
-This guide is mainly targeted at editors who have more rights than other contributors. Other contributors who want to preview their changes on their fork can skip towards the GitHub pages section right away.
+Any contributor can preview changes from their own fork. The first part of this guide is mainly relevant for people who can edit the main repository directly and want to make sure their work happens on their fork instead. If you already work on your own fork, you can skip directly to [Preview your changes using GitHub Actions](#preview-your-changes-using-github-actions) or [Preview your changes using GitHub Codespaces](#preview-your-changes-using-github-codespaces).
 
 
 ## Make changes on your fork
 
-As an editor with editing rights, changes made by clicking on the pencil icon will be committed to a branch on the main website itself. This is not a problem in normal circumstances, but when one wants to preview changes on one's own fork, this is not wanted.
+If you have write access to the main repository, changes made by clicking on the pencil icon can be committed to a branch on the main website itself. That is often fine, but it is not what you want if you prefer to preview changes from your own fork.
 
 ### 1. Make sure you have forked the main branch
 
@@ -44,13 +44,42 @@ This step is important. Make sure to commit to a new feature branch which you na
 
 ## Preview your changes using GitHub Actions
 
-- Go to Settings > Pages and enable GitHub Actions as a source
-- Go to Environments > github-pages and remove the rule under Deployment branches if you want to deploy other branches than master via Workflow Dispatch (manually triggered action)
-- Enable GitHub Actions (and use Workflow Dispatch)
+To preview a branch on your fork, you need to trigger the repository's existing GitHub Pages workflow manually.
+
+1. Go to `Settings > Pages` in your fork and make sure the site is published from **GitHub Actions**.
+2. If you want to deploy a feature branch instead of the default branch, go to `Settings > Environments > github-pages` and remove the restriction under **Deployment branches**.
+3. Go to the `Actions` tab of your fork and open the `Jekyll site CI` workflow.
+4. Click **Run workflow**. This is the GitHub interface for the `workflow_dispatch` trigger that is already defined in the workflow file; you do not need to enable anything extra for it.
+5. Select the branch with your changes and start the workflow run.
+6. Open the completed workflow run and use the deployment link shown in the workflow graph or the `View deployment` link to open the preview site.
 
 {% include image.html file="deploy_using_gh_actions.png" alt="Got to the settings tab in your repo to enable GitHub pages" %}
 
 
+## Preview your changes using GitHub Codespaces
+
+GitHub Codespaces is another way to preview your changes without setting up Ruby or Docker on your own computer.
+
+1. Open your fork on GitHub or the and switch to the branch that contains your changes.
+2. Click `Code`, open the `Codespaces` tab, and create a new codespace for that branch.
+3. In the codespace terminal, install the site dependencies:
+
+   ```bash
+   bundle install
+   ```
+
+4. Start the local preview server from the repository root:
+
+   ```bash
+   bundle exec jekyll serve
+   ```
+
+5. Open the preview by clicking the forwarded port link for port `4000`. If it does not open automatically, go to the `PORTS` tab in the codespace and open port `4000` from there.
+6. Keep the server running while you edit files. The preview will refresh automatically after you save your changes.
+
+{% include callout.html type="note" content="GitHub Codespaces availability and included usage depend on your GitHub plan or organisation settings." %}
+
+
 ## Open a Pull Request (PR) with your changes
 
 Got to your newly created branch and click 'Contribute'. This will create a PR for the main repository.
@@ -61,6 +90,6 @@ You can always make changes after the creation of this pull request by going to
 
 {% include image.html file="files_changed_github.png" alt="Files changed tab on GitHub" %}
 
-and clicking on the 3 dots to edit the file again. Changes made this way will become visible in your preview automatically after a few minutes.
+and clicking on the 3 dots to edit the file again. After committing new changes to your branch, run the `Jekyll site CI` workflow again from the `Actions` tab to update the preview.
 
 {% include image.html file="3_dots_github.png" alt="File change options on GitHub" %}

pages/data_life_cycle/analysing.md

@@ -7,7 +7,7 @@ contributors: [Rob Hooft, Olivier Collin, Munazah Andrabi, Flora D'Anna]
 editors: [Munazah Andrabi]
 description: Introduction to data analysis.
 training:
-  - name: Training in TeSS
+  - name: Data analysis Search query in TeSS
     registry: TeSS
     url: https://tess.elixir-europe.org/search?q=%22data+analysis%22#materials
 ---

pages/data_life_cycle/collecting.md

@@ -7,7 +7,7 @@ related_pages:
 contributors: [Korbinian Bösl, Siiri Fuchs, Anastasia Chasapi, Ulrike Wittig]
 editors: [Bert Droesbeke]
 training:
-  - name: Training in TeSS
+  - name: Data collection Search query in TeSS
     registry: TeSS
     url: https://tess.elixir-europe.org/search?q=%22data+collection%22#materials
 dsw:
@@ -44,4 +44,3 @@ Independently of the tools you will use, consider the following, while collectin
 * Find suitable repository to store the data.
 * Identify suitable metadata standards.
 
-

pages/data_life_cycle/planning.md

@@ -7,7 +7,7 @@ editors: [Bert Droesbeke, Flora D'Anna]
 related_pages: 
   Your_tasks: [compliance, costs, dmp, data_security, dm_coordination, machine_actionability, creating_dataflow_diagram]
 training:
-  - name: Training in TeSS
+  - name: Data management planning Search query in TeSS
     registry: TeSS
     url: https://tess.elixir-europe.org/search?q=%22data+management+planning%22#materials
 ---

pages/data_life_cycle/preserving.md

@@ -7,7 +7,7 @@ editors: [Flora D'Anna]
 related_pages: 
   Your_tasks: [data_organisation, data_security, data_publication, metadata, storage, identifiers, licensing]
 training:
-  - name: Training in TeSS
+  - name: Data preservation Search query in TeSS
     registry: TeSS
     url: https://tess.elixir-europe.org/search?q=%22data+preserve%22#materials
 dsw: