Combined Cancer data page changes by bedroesb · Pull Request #1809 · elixir-europe/rdmkit

bedroesb · 2026-03-12T11:33:28Z

No description provided.

* Update cancer_data.md main text edits to insert the Minimal set for cancer * Update pages/your_domain/cancer_data.md thanks for suggestion Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> * Update pages/your_domain/cancer_data.md Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com> --------- Co-authored-by: Federico Bianchini <72258479+bianchini88@users.noreply.github.com>

Added reference to The Minimal Dataset for Cancer of the 1+ Million Genomes in the reference file

Addition of my records in the contributors file

* Update cancer_data.md Change in Introduction to include the concept of data model for cancer and standard formats * Update Riba et al. citation --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

bedroesb · 2026-03-12T15:33:46Z

@MichelaRiba I have combined all your changes in this PR. Could you double check if they are the way you want them to be? @bianchini88 I guess we still have to add a reference in the text itself?

MichelaRiba · 2026-03-12T15:48:17Z

Hi, Thanks. I have gone through cancer data-dev branch and think this is fine. Sorry for mixing up. Don’t know if since the FAIRsharing record has changed status into approved, we are supposed to update this GitHub when a DOi and amendments there have been done. Michela

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On 12 Mar 2026, at 16:34, Bert Droesbeke ***@***.***> wrote: bedroesb left a comment (elixir-europe/rdmkit#1809) <#1809 (comment)> @MichelaRiba <https://github.com/MichelaRiba> I have combined all your changes in this PR. Could you double check if they are the way you want them to be? @bianchini88 <https://github.com/bianchini88> I guess we still have to add a reference in the text itself? — Reply to this email directly, view it on GitHub <#1809 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7SX6YZU57U4EYEDC4OIDVT4QLKHFAVCNFSM6AAAAACWPR34R2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DANBXG4ZTIOBVHE>. You are receiving this because you were mentioned.

bedroesb · 2026-03-16T07:48:28Z

@MichelaRiba No problem! @bianchini88 do you know more about this fairsharing record?

bianchini88 · 2026-03-16T08:21:55Z

Hi @bedroesb and @MichelaRiba.

do you know more about this fairsharing record?

The record is approved and awaiting a DOI (https://fairsharing.org/7812). If we merge this (quite likely) before the entry gets a DOI, I will open an issue and edit the page when the time comes; no need for @MichelaRiba to come back to fix it.

@MichelaRiba, for clarity, Bert did merge your PRs, but now this PR is from a branch of this repository and not from your fork. I could not perform this operation on your fork, as I do not have collaborator privileges there.

I will proceed with the review on this PR as time allows. I remember the citation of the bibliography entry was not actually present.

MichelaRiba · 2026-03-16T10:51:28Z

Hi, concerning the refrence I have updated in the last days as mentioned and I can see that it is recorded in the following branch. https://github.com/elixir-europe/rdmkit/blob/cancerdata-dev/_bibliography/references.bib Do you think it is still problematic, please tell me. I have exported from Mendeley this time Thanks a lot Michela

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On 16 Mar 2026, at 09:22, Federico Bianchini ***@***.***> wrote: bianchini88 left a comment (elixir-europe/rdmkit#1809) <#1809 (comment)> Hi @bedroesb <https://github.com/bedroesb> and @MichelaRiba <https://github.com/MichelaRiba>. do you know more about this fairsharing record? The record is approved and awaiting a DOI (https://fairsharing.org/7812). If we merge this (quite likely) before the entry gets a DOI, I will open an issue and edit the page when the time comes; no need for @MichelaRiba <https://github.com/MichelaRiba> to come back to fix it. @MichelaRiba <https://github.com/MichelaRiba>, for clarity, Bert did merge your PRs, but now this PR is from a branch of this repository and not from your fork. I could not perform this operation on your fork, as I do not have collaborator privileges there. I will proceed with the review on this PR as time allows. I remember the citation of the bibliography entry was not actually present. — Reply to this email directly, view it on GitHub <#1809 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7SX6Y6L2ARDOIQXNKOY6734Q62TTAVCNFSM6AAAAACWPR34R2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DANRVHEYDAMRVHE>. You are receiving this because you were mentioned.

bianchini88 · 2026-03-16T11:28:13Z

@MichelaRiba, I will deploy locally as part of the review and verify if the entry looks ok.

I was mostly referring above to the lack of a bibliography section on the page and to the missing citation tag (see https://rdmkit.elixir-europe.org/style_guide#bibliography), but I will add these myself as part of the review.

MichelaRiba · 2026-03-16T11:30:45Z

Hi Federico, thanks a lot Michela

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On 16 Mar 2026, at 12:28, Federico Bianchini ***@***.***> wrote: bianchini88 left a comment (elixir-europe/rdmkit#1809) <#1809 (comment)> @MichelaRiba <https://github.com/MichelaRiba>, I will deploy locally as part of the review and verify if the entry looks ok. I was mostly referring above to the lack of a bibliography section on the page and to the missing citation tag (see https://rdmkit.elixir-europe.org/style_guide#bibliography), but I will add these myself as part of the review. — Reply to this email directly, view it on GitHub <#1809 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7SX6Y2BDJOHK6JXE3CCORD4Q7QOJAVCNFSM6AAAAACWPR34R2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DANRWHE4DKMRUGI>. You are receiving this because you were mentioned.

Fixed conflict

fixing conflicts

_data/tool_and_resource_list.yml

pages/your_domain/cancer_data.md

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

Grammar and style improvements

bianchini88 · 2026-03-17T14:48:51Z

@MichelaRiba Approved by me. Let's give the other editors time to comment before merging.

MichelaRiba · 2026-03-17T17:10:36Z

Grazie mille Michela

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On 17 Mar 2026, at 15:49, Federico Bianchini ***@***.***> wrote: bianchini88 left a comment (elixir-europe/rdmkit#1809) <#1809 (comment)> @MichelaRiba <https://github.com/MichelaRiba> Approved by me. Let's give the other editors time to comment before merging. — Reply to this email directly, view it on GitHub <#1809 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7SX6Y6EIRK4E2SMZ7CPWYL4RFQWZAVCNFSM6AAAAACWPR34R2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DANZVGU2DQNZXGY>. You are receiving this because you were mentioned.

pages/your_domain/cancer_data.md

Co-authored-by: Gil Poiares-Oliveira <gil.oliveira@tecnico.ulisboa.pt>

MichelaRiba and others added 3 commits March 12, 2026 12:26

Update references.bib (#1802)

17750e8

Added reference to The Minimal Dataset for Cancer of the 1+ Million Genomes in the reference file

Update CONTRIBUTORS.yaml (#1801)

6b71075

Addition of my records in the contributors file

bedroesb requested review from GilOliveira, bianchini88 and floradanna as code owners March 12, 2026 11:33

Additional cancer data changes (#1804)

32e4968

* Update cancer_data.md Change in Introduction to include the concept of data model for cancer and standard formats * Update Riba et al. citation --------- Co-authored-by: Bert Droesbeke <44875756+bedroesb@users.noreply.github.com>

bianchini88 added 3 commits March 16, 2026 12:48

Adding M Riba as a page author

7c3d8c1

Adding bibliography section and citation

1cf5770

Adding the data model using the tool syntax

5bb964a

bianchini88 requested a review from wittigue as a code owner March 17, 2026 13:27

bianchini88 added 3 commits March 17, 2026 14:29

Merge branch 'master' into cancerdata-dev

5cf21f9

Update cancer_data.md

03eb7b9

Fixed conflict

Update tool_and_resource_list.yml

2ff2a14

fixing conflicts