Create health_data.md #1432

smza · 2023-12-15T14:07:53Z

Transferring the content for Health data page from a google doc

Added content

bedroesb · 2023-12-18T08:28:09Z

Maybe related to: #753

lauportell · 2023-12-19T15:01:28Z

I just reviewed the document and it looks great. My only comment is that it would be good to mention the specific aspects of the use of EHR data for secondary use, which involves using this data for purposes beyond the initial clinical care, like research. For example, how this data should be adapted for it or if there's need of processing (anonymisation?). It would be good to add information about the HealthData@EU project, for example? This would contribute to a general understanding of the management and ethical use of health data in research studies. What do you think?

If you agree, I can give it a try to add this information.

smza · 2023-12-21T11:22:03Z

I just reviewed the document and it looks great. My only comment is that it would be good to mention the specific aspects of the use of EHR data for secondary use, which involves using this data for purposes beyond the initial clinical care, like research. For example, how this data should be adapted for it or if there's need of processing (anonymisation?). It would be good to add information about the HealthData@EU project, for example? This would contribute to a general understanding of the management and ethical use of health data in research studies. What do you think?

If you agree, I can give it a try to add this information.

Hi @lauportell , thanks for your valuable comment. To add this information I think to is best to discuss this with the authors of the page mainly Tim Beck (from Health Data Focus group). I'll write an email and copy you in since I don't have Tim's gitid.

Added information about TEHDAS and HealthData@EU

lauportell · 2024-01-19T15:33:08Z

Hi all!
I have added the information about TEHDAS and HealthData@EU in the page. Let me know if you think it fits there. I agree with Tim's comment about leaving the anonymisation piece for the sensitive data page as it is already mentioned there.
Thank you all for the good work!

lauportell · 2024-01-23T15:37:01Z

I just approved again the PR ( didn't know I could do it as I did some changes :) )
Small things to be done before merging:

Add contributors to the contributors yaml
Add tools to the tools table and change to the new way of visualizing tools
Add page to the sidebar
Add news item
@smza will you do it?

smza · 2024-01-24T12:33:30Z

I just approved again the PR ( didn't know I could do it as I did some changes :) ) Small things to be done before merging:

Add contributors to the contributors yaml

Add tools to the tools table and change to the new way of visualizing tools

Add page to the sidebar

Add news item
@smza will you do it?

Hi @lauportell thanks for your contributions. I'm waiting from the group for information/description for the tools before adding them to yaml. Once I get that then I'll add the tools to the yaml file.

Cheers
Munazah

pages/your_domain/health_data.md

bedroesb · 2024-02-20T09:58:37Z

@smza do you have a look a the review from @bianchini88 ?

smza · 2024-02-20T11:18:53Z

@smza do you have a look a the review from @bianchini88 ?
not yet

@bedroesb I'm waiting for review of some new content that was added by Laura from the team. The team also have to provide the Tools descriptions. probably end of feb

bedroesb · 2024-02-20T14:43:41Z

@smza I know, but Federico's comments are small typos that just need to be committed :) (Commit suggestion button)

@GilOliveira

* Automatic tool/resource-list update (#1396) * Update tool/resource_list.yaml * Update plant_phenomics_assembly.md * Update plant_sciences.md --------- Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * 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 <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/csc_assembly.md ok! Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/tool_assembly/csc_assembly.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * delete old image * Update news.yml Adding news about the refreshed CSC tool assembly page. --------- Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: bedroesb <bedro@psb.vib-ugent.be> * Adding a bibliography (#1434) * Adding bibliography * Update style_guide.md (#1435) --------- Co-authored-by: Korbinian Bösl <korbinian.bosl@uib.no> * 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 <bedro@psb.vib-ugent.be> * 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 <fatima.nazeefa@gmail.com> * 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 <bedroesb@users.noreply.github.com> * Update style_guide.md (#1442) * Update style_guide.md make bibliography as header * Add suggestions * Add full stop --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * 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 <44875756+bedroesb@users.noreply.github.com> --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> * Update news.yml (#1449) added news about RIR * Update tool/resource_list.yaml (#1451) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * 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 <79847870+sfragkoul@users.noreply.github.com> * 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 <fatima.nazeefa@gmail.com> * Improved bibliography (#1448) * take away and * Update references.bib (#1454) --------- Co-authored-by: Korbinian Bösl <korbinian.bosl@uib.no> * Update news.yml (#1453) Added linked PR to new item * Update tool/resource_list.yaml (#1459) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * 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 <bedroesb@users.noreply.github.com> * Update tool/resource_list.yaml (#1462) Co-authored-by: bedroesb <bedroesb@users.noreply.github.com> * changing bibliography style to nature (#1456) * changing bibliography style to nature * custom nature bib tex style --------- Co-authored-by: bedroesb <bert.droesbeke@vib.be> * 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 <bedroesb@users.noreply.github.com> * 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 <bedroesb@users.noreply.github.com> * 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 <125961725+diana-pilvar@users.noreply.github.com> * 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 <108409595+marikapop@users.noreply.github.com> * Update news.yml --------- Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> * Adding Gil Poiares-Oliveira as an editorial member (#1471) * add @GilOliveira * Change Gil's email to BioData.pt --------- Co-authored-by: Gil Poiares-Oliveira <gpo@biodata.pt> * 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 <bedroesb@users.noreply.github.com> Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com> Co-authored-by: Siiri Fuchs <71016867+siirif@users.noreply.github.com> Co-authored-by: Nazeeefa <fatima.nazeefa@gmail.com> Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> Co-authored-by: bedroesb <bedro@psb.vib-ugent.be> Co-authored-by: Korbinian Bösl <korbinian.bosl@uib.no> Co-authored-by: Sveinung Gundersen <sveinugu@ifi.uio.no> Co-authored-by: YvonneKallberg <35992574+YvonneKallberg@users.noreply.github.com> Co-authored-by: floradanna <51486716+floradanna@users.noreply.github.com> Co-authored-by: wittigue <ulrike.wittig@h-its.org> Co-authored-by: Stella Fragkouli <79847870+sfragkoul@users.noreply.github.com> Co-authored-by: Diana Pilvar <125961725+diana-pilvar@users.noreply.github.com> Co-authored-by: bedroesb <bert.droesbeke@vib.be> Co-authored-by: MijkeJetten <69034034+MijkeJetten@users.noreply.github.com> Co-authored-by: Marina Popleteeva <108409595+marikapop@users.noreply.github.com> Co-authored-by: Gil Poiares-Oliveira <gpo@biodata.pt>

Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com>

smza

Accepted all changes

Added the contributors of the health data page

fixing syntax error for tool

Syntax error for tool fixed

…mza-patch-1

bedroesb · 2024-03-27T10:16:59Z

_data/CONTRIBUTORS.yaml

+Arshiya Merchant:
+    email: arshiya.merchant@elixir-europe.org
+    affiliation: ELIXIR 
+Carlos Luís Parra Calderón:


@smza still to be filled in or you can take them out :)

This is all the information I have for the contributors for now. Should I take their email out?

bedroesb · 2024-03-27T10:27:54Z

Question to all: did we tackle #753 ?

bianchini88 · 2024-03-27T10:25:11Z

_data/CONTRIBUTORS.yaml

+    email: tim.beck@nottingham.ac.uk
+    orcid: 0000-0002-0292-7972
+    affiliation: University of Nottingham
+Marcus Buchwald:


Most new contributors do not have ORCID.

Yes thats the way it's going to be for now. They don't have time to chase the authors and the page is needed live asap!

pages/your_domain/health_data.md

Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com>

modified ncbo bioportal with the too id

Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com>

smza

Review done! All suggestions have been resolved.

smza · 2024-03-27T10:54:45Z

_data/CONTRIBUTORS.yaml

+    email: tim.beck@nottingham.ac.uk
+    orcid: 0000-0002-0292-7972
+    affiliation: University of Nottingham
+Marcus Buchwald:


Yes thats the way it's going to be for now. They don't have time to chase the authors and the page is needed live asap!

…mza-patch-1

Create health_data.md

5b06fe3

smza requested review from DanFaria, pinarpink, bianchini88 and lauportell as code owners December 15, 2023 14:07

smza self-assigned this Dec 15, 2023

smza marked this pull request as draft December 15, 2023 14:09

smza marked this pull request as ready for review December 15, 2023 14:11

smza added 2 commits December 15, 2023 15:11

Update health_data.md

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Added content

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bedroesb linked an issue Dec 15, 2023 that may be closed by this pull request

Request for a new Domain page for Health data #1431

Closed

Update health_data.md

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Added information about TEHDAS and HealthData@EU

lauportell approved these changes Jan 23, 2024

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smza commented Mar 26, 2024

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smza and others added 9 commits March 27, 2024 10:51

Update CONTRIBUTORS.yaml (#1473)

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Added the contributors of the health data page

Update health_data.md

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fixing syntax error for tool

add tools

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Update health_data.md

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Syntax error for tool fixed

Merge branch 'smza-patch-1' of github.com:elixir-europe/rdmkit into s…

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…mza-patch-1

Merge branch 'smza-patch-1' of github.com:elixir-europe/rdmkit into s…

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…mza-patch-1

take out duplicate contributors

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contributor fix

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bring back two palceholder contributos

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bedroesb reviewed Mar 27, 2024

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bianchini88 approved these changes Mar 27, 2024

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add all tools

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smza commented Mar 27, 2024

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…mza-patch-1

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Create health_data.md #1432

Create health_data.md #1432

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Create health_data.md #1432

Create health_data.md #1432

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