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Update se_resources.md #1430

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merged 3 commits into from
Dec 21, 2023
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YvonneKallberg
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Review of all links and resources, and update where necessary

Review of all links and resources, and update where necessary
@YvonneKallberg
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I changed links to resources directly in the page, is this the way to do it or should it be somewhere more central in the main tool & resource page?

@Nazeeefa
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Nazeeefa commented Dec 15, 2023

@YvonneKallberg The links should also be mentioned/updated in tools and resources list which can be found in _data/tool_and_resource_list.yml.

@YvonneKallberg
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Is this true also for national resources? I'm asking since none of them are in the yml file, as far as I can see.

@Nazeeefa
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Ja, only "The European Genome-phenome Archive (EGA)" is linked to the tools and resources table. I thought national covid-portals and national EGA instances are also considered tools/resources, that's what I was thinking of in my previous comment - e.g. I see FEGA Finland and Norway in Tools and Resources list https://rdmkit.elixir-europe.org/all_tools_and_resources and Sweden's Covid portal is also mentioned there https://covid19dataportal.se/

@bedroesb
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@Nazeeefa this should not be the way of doing things. National instances are listed only on national pages, and not in the main tools and resources page. If this is the case, than this is wrong and this should be fixed.

@bedroesb
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bedroesb commented Dec 19, 2023

I migth have understood you wrong @Nazeeefa, I do not find FEGA back in https://github.com/elixir-europe/rdmkit/blob/master/_data/tool_and_resource_list.yml ?

@bedroesb
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Some information:

@bianchini88
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@bedroesb

I do not find FEGA back in https://github.com/elixir-europe/rdmkit/blob/master/_data/tool_and_resource_list.yml ?

The central EGA is indeed in the table (id: the-european-genome-phenome-archive)

The federated nodes should be on the national pages.
On the NO page we have:

  • name: Federated EGA Norway node

Which I believe is correct. A similar entry is present on the page for Finland,
so I believe there is no issue with the current "positioning" of tools.

A question: the tools on national pages do not seem to have an "id" field. Is there a reason for that?

@Nazeeefa
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Some information:

Yes that's what I mean when I wrote "I see FEGA Finland and Norway in Tools and Resources list https://rdmkit.elixir-europe.org/all_tools_and_resources"

Yep, makes sense!

@YvonneKallberg
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Does this mean that I do not have to do anything additionally to what I have done? I've updated links in the metadata header of the national page, and that is it?

@Nazeeefa
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@YvonneKallberg thank you! I think this is it, however I am wondering it might be useful to mention FEGA Sweden (https://fega.nbis.se/) in the metadata header of the page.

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I've added a metadata post for FEGA-SE now

@Nazeeefa Nazeeefa merged commit 7733324 into elixir-europe:master Dec 21, 2023
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bedroesb added a commit that referenced this pull request Mar 26, 2024
* Automatic tool/resource-list update (#1396)

* Update tool/resource_list.yaml

* Update plant_phenomics_assembly.md

* Update plant_sciences.md

---------

Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Bert Droesbeke <[email protected]>

* add editors to alumni (#1433)

* Update csc_assembly.md (#1429)

* Update csc_assembly.md

We updated our tool assembly. We would also have a new picture, but I don't know how I can upload it.

* New csc tool assembly picture

New csc tool assembly picture

* Update csc_assembly.md

changed the picture name to fi_csc_assembly_v2.svg

* Update csc_assembly.md

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

ok!

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* delete old image

* Update news.yml

Adding news about the refreshed CSC tool assembly page.

---------

Co-authored-by: Nazeeefa <[email protected]>
Co-authored-by: Federico Bianchini <[email protected]>
Co-authored-by: bedroesb <[email protected]>

* Adding a bibliography (#1434)

* Adding bibliography

* Update style_guide.md (#1435)

---------

Co-authored-by: Korbinian Bösl <[email protected]>

* Update nels_assembly.md (#1436)

Using a country keyword for a tool assembly might create undesired results when courses for other independent national resources/tools are registered into TeSS. 

With the current suggestion some results of the query get lost, but maybe the annotations on TeSS should be improved (e.g. including explicitly NeLS as a keyword or similar).

* Fairtracks assembly (#1419)

* first draft of FAIRtracks tool assembly

* adding EMBL-EBI to affiliations

* Update no_resources.md

* Update no_resources.md

* Update fairtracks_assembly.md

Added description metadata

* Update fairtracks_assembly.md

minor text improvements

* adding link to training events on TeSS

* Adding TeSS to the omnipy tool entry

* revision from Sveinung

* cross-referencing domain pages

* revision of FAIRtracks assembly

* replacing figure with new version based on feedback from the editors

* Update news.yml

news item on FAIRtracks tool assembly page

* Update news.yml

fixing wrong indentation

* adding newline

* Update news.yml

updated date of news item

---------

Co-authored-by: bedroesb <[email protected]>

* Slight clarification (#1438)

* Update fi_resources.md (#1439)

* Update fi_resources.md

Filling out "instance_of" field for FEGA Finland (instance of EGA)

* Update fi_resources.md

---------

Co-authored-by: Nazeeefa <[email protected]>

* Update se_resources.md (#1430)

* Update se_resources.md

Review of all links and resources, and update where necessary

* Update se_resources.md

* Add FEGA-SE to metadata

* Update tool/resource_list.yaml (#1440)

Co-authored-by: bedroesb <[email protected]>

* Update style_guide.md (#1442)

* Update style_guide.md

make bibliography as header

* Add suggestions

* Add full stop

---------

Co-authored-by: Bert Droesbeke <[email protected]>

* fixing display of instructions for creating a bibliography (#1446)

* fixing display of instructions for creating a bibliography

* Update pages/contribute/style_guide.md

Co-authored-by: Bert Droesbeke <[email protected]>

---------

Co-authored-by: Bert Droesbeke <[email protected]>

* Update news.yml (#1449)

added news about RIR

* Update tool/resource_list.yaml (#1451)

Co-authored-by: bedroesb <[email protected]>

* Ml domain (#1443)

* Adding md file for domain page on machine-learning

* Adding domain page for ML to the sidebar

* Changing authir name to match the one recorded in the contributors file

* Update machine_learning.md

* Update tool_and_resource_list.yml

* Update machine_learning.md

* Update references.bib

* Update machine_learning.md

* Fixing syntax for bibliography

* minor polishing of bib file

* Update machine_learning.md

* Adding missing authors based on information from the draft Google document

* Update machine_learning.md

Minor text polishing and fixed indentation for nested lists.

* Update tool_and_resource_list.yml

* Update tool_and_resource_list.yml

* updating page metadata

* adding news item about ML domain page

* minor tweaks of ML domain page

* shortening title to avoid splitting in two lines

* polishing list of tools

* Update machine_learning.md

* Update pages/your_domain/machine_learning.md

* shortening long title, splitting wall of text in smaller paragraphs, adding again list that were lost in the conversion from Google document

* polishing bib file

* Update data_management.yml

* Update news.yml

* removed duplicate entry for Schema.org

* removing license from tools and resources list

* Update machine_learning.md

---------

Co-authored-by: Stella Fragkouli <[email protected]>

* improved bibtex entries for ML domain page (#1455)

* Replaced broken links in National page of Estonia (#1452)

* Update ee_resources.md, changed broken links

* Update ee_resources.md

* Update ee_resources.md

* Update ee_resources.md

* Update ee_resources.md

minor fix

---------

Co-authored-by: Nazeeefa <[email protected]>

* Improved bibliography (#1448)

* take away and

* Update references.bib (#1454)

---------

Co-authored-by: Korbinian Bösl <[email protected]>

* Update news.yml (#1453)

Added linked PR to new item

* Update tool/resource_list.yaml (#1459)

Co-authored-by: bedroesb <[email protected]>

* Update email Bert Droesbeke

* Update email Bert Droesbeke

* Adding Daniel to past editors (#1460)

* Take Daniel out of the CODEOWNERS

* Update tool/resource_list.yaml (#1461)

Co-authored-by: bedroesb <[email protected]>

* Update tool/resource_list.yaml (#1462)

Co-authored-by: bedroesb <[email protected]>

* changing bibliography style to nature (#1456)

* changing bibliography style to nature

* custom nature bib tex style

---------

Co-authored-by: bedroesb <[email protected]>

* Adding metadata standards to the table of tools and resources (#1463)

* Update existing_data.md (#1465)

* Update no_resources.md (#1444)

* Update no_resources.md

* added VID resources

* added normen chapter on privacy in research

* Update no_resources.md

* Update tool/resource_list.yaml (#1467)

Co-authored-by: bedroesb <[email protected]>

* Adding rss feed to track RDMkit news (#1466)

* adding rss feed for news

* fix xml

* add ixon

* Rounded video

* Update tool/resource_list.yaml (#1468)

Co-authored-by: bedroesb <[email protected]>

* Update nl_resources.md (#1469)

* Update nl_resources.md

Added cBioPortal as a Dutch National Resource, requested by Lygature/EOSC4Cancer

* Update nl_resources.md

fixed the faulty URL for cBioPortal

---------

Co-authored-by: Diana Pilvar <[email protected]>

* Improve navigation by aligning the related pages with navigation tiles (#1366)

* same graphics

* fix type config

* with icons

* better theming

* fix assembly

* less css

* variables

* fix white

* gray background

* absolute path

* relative link

* variable for white

* anchor fix

* with shadow

* smaller anchor

* fix popping shadow

* no shadow

* smaller font

* add new version

* default shadow

* different sizes

* replace fix

* replace fix

* latest evrsion

* primary color buttons

* add news item

* Update _data/news.yml

Co-authored-by: Marina Popleteeva <[email protected]>

* Update news.yml

---------

Co-authored-by: Marina Popleteeva <[email protected]>

* Adding Gil Poiares-Oliveira as an editorial member (#1471)

* add @GilOliveira

* Change Gil's email to BioData.pt

---------

Co-authored-by: Gil Poiares-Oliveira <[email protected]>

* Update tool_and_resource_list.yml

Added the tools for the health data page.

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Bert Droesbeke <[email protected]>
Co-authored-by: Siiri Fuchs <[email protected]>
Co-authored-by: Nazeeefa <[email protected]>
Co-authored-by: Federico Bianchini <[email protected]>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Korbinian Bösl <[email protected]>
Co-authored-by: Sveinung Gundersen <[email protected]>
Co-authored-by: YvonneKallberg <[email protected]>
Co-authored-by: floradanna <[email protected]>
Co-authored-by: wittigue <[email protected]>
Co-authored-by: Stella Fragkouli <[email protected]>
Co-authored-by: Diana Pilvar <[email protected]>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: MijkeJetten <[email protected]>
Co-authored-by: Marina Popleteeva <[email protected]>
Co-authored-by: Gil Poiares-Oliveira <[email protected]>
smza added a commit that referenced this pull request Mar 27, 2024
* Create health_data.md

* Update health_data.md

Added content

* Update health_data.md

* Update health_data.md

Added information about TEHDAS and HealthData@EU

* Update tool_and_resource_list.yml (#1472)

* Automatic tool/resource-list update (#1396)

* Update tool/resource_list.yaml

* Update plant_phenomics_assembly.md

* Update plant_sciences.md

---------

Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Bert Droesbeke <[email protected]>

* add editors to alumni (#1433)

* Update csc_assembly.md (#1429)

* Update csc_assembly.md

We updated our tool assembly. We would also have a new picture, but I don't know how I can upload it.

* New csc tool assembly picture

New csc tool assembly picture

* Update csc_assembly.md

changed the picture name to fi_csc_assembly_v2.svg

* Update csc_assembly.md

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

ok!

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/tool_assembly/csc_assembly.md

Co-authored-by: Federico Bianchini <[email protected]>

* delete old image

* Update news.yml

Adding news about the refreshed CSC tool assembly page.

---------

Co-authored-by: Nazeeefa <[email protected]>
Co-authored-by: Federico Bianchini <[email protected]>
Co-authored-by: bedroesb <[email protected]>

* Adding a bibliography (#1434)

* Adding bibliography

* Update style_guide.md (#1435)

---------

Co-authored-by: Korbinian Bösl <[email protected]>

* Update nels_assembly.md (#1436)

Using a country keyword for a tool assembly might create undesired results when courses for other independent national resources/tools are registered into TeSS. 

With the current suggestion some results of the query get lost, but maybe the annotations on TeSS should be improved (e.g. including explicitly NeLS as a keyword or similar).

* Fairtracks assembly (#1419)

* first draft of FAIRtracks tool assembly

* adding EMBL-EBI to affiliations

* Update no_resources.md

* Update no_resources.md

* Update fairtracks_assembly.md

Added description metadata

* Update fairtracks_assembly.md

minor text improvements

* adding link to training events on TeSS

* Adding TeSS to the omnipy tool entry

* revision from Sveinung

* cross-referencing domain pages

* revision of FAIRtracks assembly

* replacing figure with new version based on feedback from the editors

* Update news.yml

news item on FAIRtracks tool assembly page

* Update news.yml

fixing wrong indentation

* adding newline

* Update news.yml

updated date of news item

---------

Co-authored-by: bedroesb <[email protected]>

* Slight clarification (#1438)

* Update fi_resources.md (#1439)

* Update fi_resources.md

Filling out "instance_of" field for FEGA Finland (instance of EGA)

* Update fi_resources.md

---------

Co-authored-by: Nazeeefa <[email protected]>

* Update se_resources.md (#1430)

* Update se_resources.md

Review of all links and resources, and update where necessary

* Update se_resources.md

* Add FEGA-SE to metadata

* Update tool/resource_list.yaml (#1440)

Co-authored-by: bedroesb <[email protected]>

* Update style_guide.md (#1442)

* Update style_guide.md

make bibliography as header

* Add suggestions

* Add full stop

---------

Co-authored-by: Bert Droesbeke <[email protected]>

* fixing display of instructions for creating a bibliography (#1446)

* fixing display of instructions for creating a bibliography

* Update pages/contribute/style_guide.md

Co-authored-by: Bert Droesbeke <[email protected]>

---------

Co-authored-by: Bert Droesbeke <[email protected]>

* Update news.yml (#1449)

added news about RIR

* Update tool/resource_list.yaml (#1451)

Co-authored-by: bedroesb <[email protected]>

* Ml domain (#1443)

* Adding md file for domain page on machine-learning

* Adding domain page for ML to the sidebar

* Changing authir name to match the one recorded in the contributors file

* Update machine_learning.md

* Update tool_and_resource_list.yml

* Update machine_learning.md

* Update references.bib

* Update machine_learning.md

* Fixing syntax for bibliography

* minor polishing of bib file

* Update machine_learning.md

* Adding missing authors based on information from the draft Google document

* Update machine_learning.md

Minor text polishing and fixed indentation for nested lists.

* Update tool_and_resource_list.yml

* Update tool_and_resource_list.yml

* updating page metadata

* adding news item about ML domain page

* minor tweaks of ML domain page

* shortening title to avoid splitting in two lines

* polishing list of tools

* Update machine_learning.md

* Update pages/your_domain/machine_learning.md

* shortening long title, splitting wall of text in smaller paragraphs, adding again list that were lost in the conversion from Google document

* polishing bib file

* Update data_management.yml

* Update news.yml

* removed duplicate entry for Schema.org

* removing license from tools and resources list

* Update machine_learning.md

---------

Co-authored-by: Stella Fragkouli <[email protected]>

* improved bibtex entries for ML domain page (#1455)

* Replaced broken links in National page of Estonia (#1452)

* Update ee_resources.md, changed broken links

* Update ee_resources.md

* Update ee_resources.md

* Update ee_resources.md

* Update ee_resources.md

minor fix

---------

Co-authored-by: Nazeeefa <[email protected]>

* Improved bibliography (#1448)

* take away and

* Update references.bib (#1454)

---------

Co-authored-by: Korbinian Bösl <[email protected]>

* Update news.yml (#1453)

Added linked PR to new item

* Update tool/resource_list.yaml (#1459)

Co-authored-by: bedroesb <[email protected]>

* Update email Bert Droesbeke

* Update email Bert Droesbeke

* Adding Daniel to past editors (#1460)

* Take Daniel out of the CODEOWNERS

* Update tool/resource_list.yaml (#1461)

Co-authored-by: bedroesb <[email protected]>

* Update tool/resource_list.yaml (#1462)

Co-authored-by: bedroesb <[email protected]>

* changing bibliography style to nature (#1456)

* changing bibliography style to nature

* custom nature bib tex style

---------

Co-authored-by: bedroesb <[email protected]>

* Adding metadata standards to the table of tools and resources (#1463)

* Update existing_data.md (#1465)

* Update no_resources.md (#1444)

* Update no_resources.md

* added VID resources

* added normen chapter on privacy in research

* Update no_resources.md

* Update tool/resource_list.yaml (#1467)

Co-authored-by: bedroesb <[email protected]>

* Adding rss feed to track RDMkit news (#1466)

* adding rss feed for news

* fix xml

* add ixon

* Rounded video

* Update tool/resource_list.yaml (#1468)

Co-authored-by: bedroesb <[email protected]>

* Update nl_resources.md (#1469)

* Update nl_resources.md

Added cBioPortal as a Dutch National Resource, requested by Lygature/EOSC4Cancer

* Update nl_resources.md

fixed the faulty URL for cBioPortal

---------

Co-authored-by: Diana Pilvar <[email protected]>

* Improve navigation by aligning the related pages with navigation tiles (#1366)

* same graphics

* fix type config

* with icons

* better theming

* fix assembly

* less css

* variables

* fix white

* gray background

* absolute path

* relative link

* variable for white

* anchor fix

* with shadow

* smaller anchor

* fix popping shadow

* no shadow

* smaller font

* add new version

* default shadow

* different sizes

* replace fix

* replace fix

* latest evrsion

* primary color buttons

* add news item

* Update _data/news.yml

Co-authored-by: Marina Popleteeva <[email protected]>

* Update news.yml

---------

Co-authored-by: Marina Popleteeva <[email protected]>

* Adding Gil Poiares-Oliveira as an editorial member (#1471)

* add @GilOliveira

* Change Gil's email to BioData.pt

---------

Co-authored-by: Gil Poiares-Oliveira <[email protected]>

* Update tool_and_resource_list.yml

Added the tools for the health data page.

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Bert Droesbeke <[email protected]>
Co-authored-by: Siiri Fuchs <[email protected]>
Co-authored-by: Nazeeefa <[email protected]>
Co-authored-by: Federico Bianchini <[email protected]>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Korbinian Bösl <[email protected]>
Co-authored-by: Sveinung Gundersen <[email protected]>
Co-authored-by: YvonneKallberg <[email protected]>
Co-authored-by: floradanna <[email protected]>
Co-authored-by: wittigue <[email protected]>
Co-authored-by: Stella Fragkouli <[email protected]>
Co-authored-by: Diana Pilvar <[email protected]>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: MijkeJetten <[email protected]>
Co-authored-by: Marina Popleteeva <[email protected]>
Co-authored-by: Gil Poiares-Oliveira <[email protected]>

* take away search exclude

* add to sidebar

* add tools

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update CONTRIBUTORS.yaml (#1473)

Added the contributors of the health data page

* Update health_data.md

fixing syntax error for tool

* add tools

* Update health_data.md

Syntax error for tool fixed

* take out duplicate contributors

* contributor fix

* bring back two palceholder contributos

* add all tools

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update health_data.md

modified  ncbo bioportal with the too id

* Update pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <[email protected]>

* Update CONTRIBUTORS.yaml

* update titles

---------

Co-authored-by: Laura Portell Silva <[email protected]>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Bert Droesbeke <[email protected]>
Co-authored-by: Siiri Fuchs <[email protected]>
Co-authored-by: Nazeeefa <[email protected]>
Co-authored-by: Federico Bianchini <[email protected]>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: Korbinian Bösl <[email protected]>
Co-authored-by: Sveinung Gundersen <[email protected]>
Co-authored-by: YvonneKallberg <[email protected]>
Co-authored-by: floradanna <[email protected]>
Co-authored-by: wittigue <[email protected]>
Co-authored-by: Stella Fragkouli <[email protected]>
Co-authored-by: Diana Pilvar <[email protected]>
Co-authored-by: bedroesb <[email protected]>
Co-authored-by: MijkeJetten <[email protected]>
Co-authored-by: Marina Popleteeva <[email protected]>
Co-authored-by: Gil Poiares-Oliveira <[email protected]>
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4 participants