Rdmkit fr by SalihaZ · Pull Request #1766 · elixir-europe/rdmkit

SalihaZ · 2026-01-08T16:59:33Z

Updating the national resources page and the the tool-resource file

bedroesb · 2026-01-10T16:01:43Z

+  name: FAIR-Checker
+  registry:
+    biotools: FAIR-Checker
+  url: https://bio.tools/fair-checker/


Do not use the bio.tools url as a url, since it is already linked as registry

bedroesb · 2026-01-10T16:04:58Z

@SalihaZ thank you for your contributions! I see currently lots of duplication between the tools added in the All tools and resources table and the french national page.

Some guide lines;

Either a tool or resource is national - or a generic tool, it can not be both at the same time. In this case I think multiple additions in the all tools and resources list in this PR can be removed.
Every general Tool or resource that gets added needs to be put in context in a non-national page using the tool snippet (see our contribute guidelines)
Tools or resources tailored towards France should be listed in the metadata of French page ( for example: Cat OPIDoR, DSW@IFB, usegalaxy-fr, ...) this looks fine!
To list the involvement of France in general tools, you can list their tool-id under: ref_to_main_resources. I see you did so, but I am suprised the existing entries get removed 🤔

bedroesb · 2026-01-10T16:06:30Z

+  name: The Committee for Open Science
+  registry:
+    fairsharing: 
+  url: https://www.ouvrirlascience.fr/the-committee-for-open-science/


this is not a tool or resource, to determine what a tool or resource is, please follow: https://rdmkit.elixir-europe.org/tool_resource_update#when-can-you-add-a-new-tool-or-resource

@bedroesb Thanks very much for the reviewing and for clarifying the guidelines. I’ll update the PR accordingly.

Part of my confusion came from existing examples such as MadBot.
MadBot is developed in France and is listed in the All tools and resources table and referenced from a non-national page (the Biodiversity domain), but it does not appear on the French national resources page. This made it less clear to me whether such tools should be treated as national or generic in RDMkit.

In order to list them on the fr page please use ref_to_main_resources, this is also why phis and faidare are listed there.

@bedroesb I have a question concerning FAIR-Checker which is a tool mentioned in the IFB tool assembly page but isn’t in tool_and_resource_list.yml nor on the French page.
Should it be added to the main YAML as a generic tool, and not listed on the French national resources page?
Tanks a lot for your help

This would make sense to add to the all tools and resources list, and refer to it from the IFB tool assembly page using the tool snippet. If activity developed by France, you can also list the id using ref_to_main_resources.

Let me know if you need help with cleaning up the all tools and resources list.

bedroesb · 2026-01-10T16:08:10Z

+  registry:
+    fairsharing: 
+  url: https://entrepot.recherche.data.gouv.fr/
+- description: EDAM is a structured ontology of key concepts used in scientific data analysis and data management, covering topics, operations, data types, identifiers, and formats. It enables consistent semantic annotation and categorisation of scientific resources and supports provenance documentation in data management.


I think https://rdmkit.elixir-europe.org/metadata_management#how-do-you-find-appropriate-vocabularies-or-ontologies is a good candidate to link to EDAM using the tool snippet. (https://rdmkit.elixir-europe.org/tool_resource_update#linking-the-tool-or-resource-in-the-text-with-the-main-yaml-file)

bedroesb · 2026-01-10T16:10:10Z

-  - phis
-  - faidare


Are you sure these can be removed?

Yes, they can be removed as they are already listed in the plant phenomics tool assembly page : https://rdmkit.elixir-europe.org/plant_phenomics_assembly

listing them like this gives acknowledgement that France is involved in the development of these resources. One does not exclude the other.

Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

bedroesb · 2026-01-15T10:04:59Z

I think something went wrong in the _data/tool_and_resource_list.yml changes since duplications are happening and the new tools that got added are not at the bottom anymore/got mixed up. a cleanup will need to happen I am afraid.

…age to the fr_resources file

bedroesb · 2026-01-19T10:58:52Z

This starts to look good! DOn't forget to mention "software-heritage" as a tool somewhere on RDMkit like you did for EDAM :)

SalihaZ · 2026-01-19T11:01:52Z

Thanks a lot for the feedback, and sorry for the earlier confusion. It was due to a commit mistake on my side and a rebase that temporarily mixed the local and remote versions of _data/tool_and_resource_list.yml.
I’m glad to hear it’s starting to look good :)
Thanks a lot for your patience.

SalihaZ · 2026-01-19T11:12:07Z

@bedroesb where do you think it would be most appropriate to mention Software Heritage in RDMkit?
I was thinking of adding it either in:
Data storage → Where should you store the data after the end of the project?
or another section you would recommend?

bedroesb · 2026-01-19T15:38:00Z

 * Estimate the volume of the (meta)data files that need to be preserved after the end of the project. Consider using a compressed file format to minimize the data volume.
 * Define the amount of time (hours, days…) that you could wait in case the data needs to be reanalysed in the future.
-* It is a good practice to publish your data in public data repositories. Usually, data publication in repositories is a requirement for scientific journals and funders. Repositories preserve your data for a long time, sometimes for free. See our [Data publication page](data_publication) for more information.
+* It is a good practice to publish your data in public data repositories. Usually, data publication in repositories is a requirement for scientific journals and funders. Repositories preserve your data for a long time, sometimes for free. To ensure long-term preservation and citation of software used in your project, you can leverage {% tool "software-heritage" %}, an archive of source code that supports reproducible science, open access, and sustainable reuse. See our [Data publication page](data_publication) for more information.


I would maybe make sa separate bullet point for it, since "See our Data publication page for more information" points to a page that does not have software-heritage described. But the content reviewers might have a different opinion, I just review from a technical/guideline standpoint :)

bedroesb · 2026-01-20T07:58:22Z

This is how it currently looks like! @Nazeeefa @floradanna @diana-pilvar @wittigue can take it from here :)

bedroesb · 2026-01-20T09:00:12Z

I see on the screenshot, that not all descriptions of the tools have a nice sentence, or start with a capital. Could you adapt them to have a self standing description?

bedroesb · 2026-01-20T09:02:40Z

and make sure that if one of the resources tailored to France is not accessible to everyone, to specify using the how_to_access field to describe which login they need, for example "You need a french institutional account."

bedroesb · 2026-01-20T09:04:23Z

+  id: edam
+  name: EDAM ontology
+  registry:
+    fairsharing: 


Suggested change

fairsharing:

fairsharing: a6r7zs

bedroesb · 2026-01-20T09:05:24Z

+  id: software-heritage
+  name: Software Heritage
+  registry:
+    fairsharing: 


Suggested change

fairsharing:

fairsharing: 6ffb92

…o_access section

bedroesb · 2026-01-20T15:17:56Z

 national_resources:
+  - name: Cat OPIDoR
+    description: Catalog of national services and tools that support research data management designed to assist researchers, data stewards, and institutions. 
+    how_to_access: Create an account


Sorry if I was not clear, I meant that if a service is only accessible with French citizenship/a French institutional account/ ... This needs to be filled in. If everyone can create an account, this field should be left empty. Sorry if I caused any confusion!

Ah ok! no problem, I'll fix that

Removed Software Heritage entry from resources list.

bedroesb · 2026-01-26T15:30:27Z

+  - madbot
+  - edam
+  - galaxy
+  - fair-checker


fair-checker is being listed a a national tool below. Either remove it here, or at it as a general tool in the tools and resources and link towards it from a non-national page.

Thanks for the review, it was an oversight. I've fixed it

bedroesb · 2026-01-30T13:48:23Z

+contributors: [Saliha Zenboudji-Beddek, Olivier Collin, Nadia Goué]
+coordinators: [Anne-Françoise Adam-Blondon, Jean-François Dufayard, Jacques Van Helden]


Would it be possible to add metadata (email, affiliation, ORCID) to the newly added coordinators/contributors? Make sure to use the exact same name: https://github.com/elixir-europe/rdmkit/blob/master/_data/CONTRIBUTORS.yaml

(and if a contributor is not already present)

@SalihaZ this is the last comment preventing this merge :) (I think!) Thank you for hanging in there. We just had a look at this PR in our editorial board meeting.

@bedroesb OK! I've just add all the contributors. Thank you so much for your help.

bedroesb · 2026-02-01T12:07:32Z

Thank you for your contributions!

SalihaZ added 2 commits January 8, 2026 17:27

update the fr_resources.md and the tool-resource file

5b78ba8

update the fr_resources.md

cb7aa3f

SalihaZ requested review from Nazeeefa, bedroesb, diana-pilvar and wittigue as code owners January 8, 2026 16:59

SalihaZ and others added 2 commits January 8, 2026 18:04

fix typo in the tool-resource file

9bb661a

Merge branch 'master' into rdmkit_fr

45ecab7

bedroesb reviewed Jan 10, 2026

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Comment thread _data/tool_and_resource_list.yml Outdated

bedroesb reviewed Jan 10, 2026

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Comment thread pages/national_resources/fr_resources.md Outdated

bedroesb reviewed Jan 10, 2026

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Comment thread pages/national_resources/fr_resources.md Outdated

bedroesb reviewed Jan 10, 2026

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Comment thread pages/national_resources/fr_resources.md Outdated

SalihaZ and others added 6 commits January 12, 2026 16:02

Update pages/national_resources/fr_resources.md

c5ec159

Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

Update pages/national_resources/fr_resources.md

c36a78f

Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

Update _data/tool_and_resource_list.yml

d6af834

Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

Update pages/national_resources/fr_resources.md

b54cf3f

Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

Fixes after review of tool resource file and fr_resources

50d20e0

Fixes after review of tool resource file and fr_resources

5d394e5

SalihaZ added 2 commits January 15, 2026 11:40

update fr_resources page

6a0e2c8

add edam to the metadata_management.md

606a675

SalihaZ requested a review from floradanna as a code owner January 15, 2026 13:12

fix tool_and_resource_list file & add phis,faidare and software-herit…

9994576

…age to the fr_resources file

add citation about software-heritage in the storage.md page

de9c879

bedroesb reviewed Jan 19, 2026

View reviewed changes

Add a bullet point about software-heritage in the storage.md page

c14f909

Add madbot to the fr national resources

d5384ef

bedroesb reviewed Jan 20, 2026

View reviewed changes

Add fairsharing code for edam and software heritages & fill the how_t…

9549a01

…o_access section

bedroesb reviewed Jan 20, 2026

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SalihaZ and others added 2 commits January 21, 2026 10:56

Fix how_to_access section & Add new collaborator

9806022

Remove Software Heritage from national resources

325deac

Removed Software Heritage entry from resources list.

bedroesb reviewed Jan 26, 2026

View reviewed changes

SalihaZ and others added 2 commits January 27, 2026 11:45

remove fair-checker from ref_to_main_resources

fa59e8c

Merge branch 'master' into rdmkit_fr

c54043d

bedroesb reviewed Jan 30, 2026

View reviewed changes

SalihaZ added 2 commits January 31, 2026 17:00

add new contributors in _data/CONTRIBUTORS.yaml

59a7235

Merge remote-tracking branch 'origin/rdmkit_fr' into rdmkit_fr

50e8cdf

bedroesb approved these changes Feb 1, 2026

View reviewed changes

bedroesb merged commit 965a520 into elixir-europe:master Feb 1, 2026
3 checks passed

		contributors: [Saliha Zenboudji-Beddek, Olivier Collin, Nadia Goué]
		coordinators: [Anne-Françoise Adam-Blondon, Jean-François Dufayard, Jacques Van Helden]

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