Merge branch 'master' into bianchini88-human_pathogen_genomics

CODEOWNERS

@@ -6,8 +6,8 @@
 
 # Contribute
 /pages/contribute       @floradanna @bedroesb
-/pages/contribute/copyright.md       @martin-nc
-/pages/contribute/style_guide.md       @martin-nc
+/pages/contribute/copyright.md
+/pages/contribute/style_guide.md
 CONTRIBUTING.md       @floradanna
 
 # Different Sections
@@ -20,14 +20,14 @@ CONTRIBUTING.md       @floradanna
 
 #About
 /pages/about/about.md       @frederikcoppens @CaroleGoble
-/pages/about/accessibility.md       @martin-nc
-/pages/about/privacy.md       @martin-nc
+/pages/about/accessibility.md
+/pages/about/privacy.md
 CODE_OF_CONDUCT.md       @frederikcoppens @CaroleGoble
 
 
 #Theme
-/assets       @martin-nc @bedroesb
-/_sass       @martin-nc @bedroesb
+/assets @bedroesb
+/_sass @bedroesb
 
 # Sidebar
 /_data/sidebars/*      @bedroesb

_data/CONTRIBUTORS.yaml

@@ -28,7 +28,7 @@ Daniel Faria:
 Pinar Alper:
     git: pinarpink
     orcid: 0000-0002-2224-0780
-    affiliation: LCSB / ELIXIR-LU
+    affiliation: ELIXIR-LU
 Carole Goble:
     git: CaroleGoble
     role: lead
@@ -201,7 +201,6 @@ Alexander Botzki:
 Martin Cook:
     git: martin-nc
     email: [email protected]
-    role: editor
     affiliation: ELIXIR Hub
 Victoria Dominguez D. Angel:
     git: vdda
@@ -496,8 +495,8 @@ Teresa D'Altri:
 Marina Popleteeva:
     git: marikapop
     orcid: 0000-0002-8409-6147
-    email: marina.popleteeva@uni.lu
-    affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg
+    email: marina.popleteeva@lih.lu
+    affiliation: Luxembourg Institute of Health
     role: editor
 Vilem Ded:
     git: vildead
@@ -638,4 +637,12 @@ Magda Chegkazi:
     affiliation: ELIXIR 
 Arshiya Merchant:
     email: [email protected]
-    affiliation: ELIXIR 
+    affiliation: ELIXIR
+Xènia Pérez Sitjà:
+    affiliation: Earlham Institute / ELIXIR-UK
+    git: sitjart
+Aina Jené Cortada:
+    git: ainajene
+    email: [email protected]
+    orcid: 0000-0001-7721-7097
+    affiliation: European Genome-phenome Archive (EGA) / CRG

_data/news.yml

@@ -182,3 +182,11 @@
   date: 2024-06-10
   linked_pr: 1489
   description: We are gradually improving the icons that are in use on the RDMkit by applying our own style. You can discover them throughout the whole website!
+- name: "Improved contribute pages"
+  date: 2024-10-07
+  linked_pr: 1437
+  description: Our [contribute section](how_to_contribute) got an overhaul, with clear ways in how to contribute and improved documentation. 
+- name: "New page: Data discoverability"
+  date: 2024-10-10
+  linked_pr: 1517
+  description: A "your task" page about how to make your data more discoverable was added. [Discover the page here](data_discoverability).

_data/sidebars/contribute.yml

@@ -5,7 +5,7 @@ subitems:
     subitems:
       - title: GitHub way
         url: /github_way
-      - title: Google doc way
+      - title: Google Docs way
         url: /google_doc_way
       - title: Git way (advanced)
         url: /working_with_git

_data/sidebars/data_management.yml

@@ -74,6 +74,8 @@ subitems:
         url: /data_analysis
       - title: Data brokering
         url: /data_brokering
+      - title: Data discoverability
+        url: /data_discoverability
       - title: Data management coordination
         url: /dm_coordination
       - title: Data management plan

_data/tool_and_resource_list.yml

@@ -26,6 +26,7 @@
   id: bioimage
   name: BioImage Model Zoo
   registry:
+    fairsharing: 77fc63
     tess: BioImage Model Zoo
   url: https://bioimage.io/#/
 - description: Data, Optimisation, Model and Evaluation in Machine Learning (DOME-ML) is a set of community guidelines, recommendations and checklists for supervised ML validation in biology.
@@ -560,6 +561,7 @@
   name: CTD
   registry:
     biotools: ctd
+    tess: CTD
   url: http://ctdbase.org/
 - description: Command line tool and library for transferring data with URLs
   id: curl
@@ -1319,9 +1321,9 @@
   id: microsoft-onedrive
   name: Microsoft OneDrive
   url: https://www.microsoft.com/en-us/microsoft-365/onedrive/online-cloud-storage
-- description: Minimum Information about a (Meta)Genome Sequence
+- description: a conceptual structure for extending the core INSDC information to describe genomic and metagenomic sequences.
   id: migs-mims
-  name: MIGS/MIMS
+  name: Minimum Information about a (Meta)Genome Sequence (MIxS - MIGS/MIMS)
   registry:
     fairsharing: va1hck
   url: https://www.gensc.org/pages/projects/mixs-gsc-project.html
@@ -1331,12 +1333,11 @@
   registry:
     biotools: mineprot
   url: https://github.com/huiwenke/MineProt
-- description: Minimum Information about any (x) Sequence
+- description: An overarching framework of standard metadata that includes sequence-type and technology-specific checklists.
   id: mixs
-  name: MIxS
+  name: Minimum Information about any (x) Sequence (MIxS)
   registry:
     fairsharing: 9aa0zp
-    tess: MIxS
   url: https://genomicsstandardsconsortium.github.io/mixs/
 - description: Provides a set of open-source, cross-platform software libraries and tools that facilitate proteomics data analysis.
   id: msconvert
@@ -1409,6 +1410,8 @@
 - description: Online database hosting a vast amount of biotechnological information including nucleic acids, proteins, genomes and publications. Also boasts integrated tools for analysis.
   id: national-center-for-biotechnology-information
   name: National Center for Biotechnology Information (NCBI)
+  registry:
+    tess: National Center for Biotechnology Information (NCBI)
   url: https://www.ncbi.nlm.nih.gov
 - description: The National Biomonitoring Program (NBP) is a public resource that offers an assessment of nutritional status and the exposure of the U.S. population to environmental chemicals and toxic substances.
   id: nbp
@@ -1594,6 +1597,7 @@
   name: Pharos
   registry:
     biotools: pharos
+    fairsharing: 52d6ae
   url: https://pharosproject.net/
 - description: The open-source Phenotyping Hybrid Information System (PHIS) manages and collects data from plants phenotyping and high throughput phenotyping experiments on a day to day basis.
   id: phis
@@ -2303,6 +2307,7 @@
   id: integrated-database-of-small-molecules
   name: Integrated Database of Small Molecules (IDSM)
   registry:
+    biotools: idsm
     fairsharing: nn9r0d
   url: https://idsm.elixir-czech.cz/
 - description: The OME Model is a specification for storing data on biological imaging.
@@ -2660,6 +2665,20 @@
   id: better-bibtex
   name: Better BibTeX (BBT)
   url: https://retorque.re/zotero-better-bibtex/
+- description: Beacon for OMOP (B4OMOP) software allows for the integration of a Beacon onto any OMOP Common Data Model (CDM) database.
+  id: b4omop
+  name: Beacon for OMOP (B4OMOP)
+  url: https://gitlab.bsc.es/impact-data/impd-beacon_omopcdm
+- description: Developed through the Global Alliance for Genomics and Health (GA4GH) Discovery workstream with support from ELIXIR, Beacon is a data discovery protocol defining an open standard for discovering genomic and phenoclinic data in research and clinical applications.
+  id: beacon-v2
+  name: Beacon v2
+  registry:
+    tess: Beacon v2
+  url: https://docs.genomebeacons.org/implementations-options/
+- description: An open-source out-of-the-box toolkit to initiate a Beacon v2. B2RI includes tools for loading metadata, such as phenotypic data and genomic variants into a MongoDB database, and features a Beacon query engine (REST API).
+  id: beacon-ri
+  name: Beacon v2 Reference Implementation (B2RI)
+  url: https://github.com/EGA-archive/beacon2-ri-tools-v2
 - description: GA4GH frames policy and builds standards to meet the real-world needs of the global genomics and health community.
   id: ga4gh
   name: Global Alliance for Genomics and Health (GA4GH)

_sass/_custom_classes.scss

@@ -94,20 +94,7 @@
 
 /* -----Homepage----- */
 
-.landingpage {
-    .h-icon-8 {
-        height: 8em;
-    }
-    .h-icon-6 {
-        height: 6em;
-    }
-    .h-icon-5 {
-        height: 5em;
-    }
-    .h-icon-4 {
-        height: 4em;
-    }
-
+.landingpage, .ways-to-contribute  {
     .card {
         &:hover {
             box-shadow: $box-shadow;
@@ -136,6 +123,21 @@
     }
 }
 
+// Icon sizing
+
+.h-icon-8 {
+    height: 8em;
+}
+.h-icon-6 {
+    height: 6em;
+}
+.h-icon-5 {
+    height: 5em;
+}
+.h-icon-4 {
+    height: 4em;
+}
+
 // Search box
 
 section#search-section {

pages/about/contributors.md

@@ -1,8 +1,9 @@
 ---
 title: Contributors
 custom_editme: _data/CONTRIBUTORS.yaml
+toc: false
 ---
 
 This project would not be possible without the many amazing community contributors. RDMkit is an open community project, and you are welcome to [join us](how_to_contribute)!
 
-{% include contributor-tiles-all.html %}
+{% include contributor-tiles-all.html col=6 %}

pages/about/editorial_board.md

@@ -4,7 +4,7 @@ title: Editorial board
 
 ## Meet the editorial board members
 
-{% include contributor-carousel-selection.html custom="Bert Droesbeke, Carole Goble, Flora D'Anna, Frederik Coppens, Munazah Andrabi, Ulrike Wittig, Laura Portell Silva, Martin Cook, Korbinian Bösl, Federico Bianchini, Nazeefa Fatima, Ishwar Chandramouliswaran, Diana Pilvar, Marina Popleteeva, Gil Poiares-Oliveira" %}
+{% include contributor-carousel-selection.html custom="Bert Droesbeke, Carole Goble, Flora D'Anna, Frederik Coppens, Munazah Andrabi, Ulrike Wittig, Laura Portell Silva, Korbinian Bösl, Federico Bianchini, Nazeefa Fatima, Ishwar Chandramouliswaran, Diana Pilvar, Marina Popleteeva, Gil Poiares-Oliveira" %}
 
 ## Join as editorial board member
 
@@ -54,4 +54,4 @@ Please, send your application to [email protected].
 
 In this section we would like to thank contributions of our past editorial members.
 
-{% include contributor-tiles-all.html custom="Mijke Jetten, Niclas Jareborg, Pinar Alper, Rob Hooft, Daniel Faria" %}
+{% include contributor-tiles-all.html custom="Mijke Jetten, Niclas Jareborg, Pinar Alper, Rob Hooft, Daniel Faria, Martin Cook" %}

pages/contribute/copyright.md

@@ -18,16 +18,16 @@ Please do not copy the text and tweak the wording slightly. If you are not givin
 
 ## Images
 
-**It is your responsibility to make sure you have permission to use the images you put on the website.**
+**It is your responsibility to ensure you have permission to use the images you put on the website.**
 
-The great majority of images on the web are copyrighted. This includes images on social media, even if they have been reposted or shared. Please make sure you have permission to use them before including them on the website, ideally in writing. If you are not sure whether you can use them, assume that you do not have permission, and contact the copyright owner. 
+The great majority of images on the web are copyrighted. This includes images on social media, even if they have been reposted or shared. Please ensure you have permission to use them before including them on the website, ideally in writing. If you are not sure whether you can use them, assume that you do not have permission and contact the copyright owner. 
 
 If you are using an image with a [Creative Commons license](https://creativecommons.org/licenses/), remember you still need to attribute the creator in accordance with the license.
 
-If you are using a stock image you have bought, or a royalty-free image, check the image license to make sure that you can use it on the RDMkit website. If you are using images provided by your institute or organisation, please also check that you can use them on this site.
+If you are using a stock image you have bought or a royalty-free image, check the image license to make sure that you can use it on the RDMkit website. If you use images provided by your institute or organisation, please also check that you can use them on this site.
 
-You are welcome to create the images yourself, but please follow the [site style guide](style_guide), and bear in mind the image may be modified to better suite the style of the site. The content of the site is published under the [Creative Commons 4 license](https://creativecommons.org/licenses/by/4.0/).
+You are welcome to create the images yourself, but please follow the [site style guide](style_guide) and bear in mind the image may be modified to better suit the style of the site. The content of the site is published under the [Creative Commons 4 license](https://creativecommons.org/licenses/by/4.0/).
 
-If you think an image would be helpful to explain your content but you cannot find the right one, then [create a new issue](https://github.com/elixir-europe/rdmkit/issues) to suggest a new image.
+If you think an image would be helpful to explain your content, but you cannot find the right one, then [create a new issue](https://github.com/elixir-europe/rdmkit/issues) to suggest a new image.
 
 

pages/contribute/editorial_board_guide.md

@@ -166,7 +166,7 @@ If the markdown page is named example_1.md, you can link towards it using:
 
 ## Adding extra info to the contributors
 
-Do you want that the GitHub picture of a contributor is shown next to their name? Or maybe you want that the name is clickable and links towards the GitHub page of that person? To enable this please add the name and the necessary metadata to the [CONTRIBUTORS.yaml](https://github.com/elixir-europe/rdmkit/blob/master/_data/CONTRIBUTORS.yaml) file in the *_data* directory like this:
+It is strongly recommended to let the contributors fill in their ORCID and email address. This can be added together with the name, affiliation and GitHub ID to the [CONTRIBUTORS.yaml](https://github.com/elixir-europe/rdmkit/blob/master/_data/CONTRIBUTORS.yaml) file in the *_data* directory like this:
 
 ```yaml
 Bert Droesbeke:
@@ -176,7 +176,7 @@ Bert Droesbeke:
     role: editor
     affiliation: VIB Data Core / ELIXIR-BE
 ```
-{% include callout.html type="important" content="Make sure that the name in the yaml file is identically the same as the one used in the metadata of the page." %}
+{% include callout.html type="important" content="Make sure that the name of the contributor in the yaml file is identical as the one used in the metadata of the page." %}
 
 
 ## Adding an institution, infrastructure, project or funder

pages/contribute/editors_checklist.md

@@ -4,7 +4,7 @@ summary: Checklist for editors before approving and merging a pull request (PR).
 ---
 
 ## Before approving and merging a pull request (PR), the editors must check that
-1. The page layout in preview looks correct.
+1. The page layout in the preview looks correct.
 2. The new page is linked in the appropriate [sidebar](https://github.com/elixir-europe/rdmkit/tree/master/_data/sidebars) menu, in the same branch of the PR.
 3. The contributors' names are listed in the [CONTRIBUTORS file](https://github.com/elixir-europe/rdmkit/blob/master/_data/CONTRIBUTORS.yaml), in the same branch of the PR. Advice to have at least one  contributor per page having its contact information in this  [CONTRIBUTORS file](https://github.com/elixir-europe/rdmkit/blob/master/_data/CONTRIBUTORS.yaml).
 4. All relevant metadata fields in a specific page are correctly filled in (see the [page metadata](page_metadata) and the [Editorial board guide](editorial_board_guide)). Some critical ones are listed below.
@@ -19,9 +19,9 @@ summary: Checklist for editors before approving and merging a pull request (PR).
    * `resources`
 5. Make sure that listed tools or resources are tagged in the text with the [correct snippet](tool_resource_update) + that its metadata is described in the [tool_and_resource_list.yml](https://github.com/elixir-europe/rdmkit/blob/master/_data/tool_and_resource_list.yml) file. 
 6. Check if relevant recipes on FAIR Cookbook can be linked to the RDMkit page that is being added/changed ([Linking from RDMkit to FAIR Cookbook](editorial_board_guide#linking-from-rdmkit-to-fair-cookbook)).
-7. The content is conform to RDMkit scope, [style](style_guide) and templates.
+7. The content conforms to RDMkit's scope, [style](style_guide) and templates.
 8. There are no [copyright](copyright) issues related to the content of the page.
 9. The contributors implemented the requested changes.
 10. When a new page is added, a news item is added to the [news.yml file](https://github.com/elixir-europe/rdmkit/blob/master/_data/news.yml), in the same branch of the PR.
-11. The contributors are thanked for their effort and informed about the publication of their content.
-12. The PR is linked to related issues and can be merged in main branch with no conflicts.
+11. The contributors are acknowledged for their efforts and informed about the publication of their content.
+12. The PR is linked to related issues and can be merged into the main branch with no conflicts.