Skip to content

Update human biomolecular data sources page - #155

Merged
hedi-ee merged 16 commits into
mainfrom
update-hbd-data-sources
Sep 19, 2023
Merged

Update human biomolecular data sources page#155
hedi-ee merged 16 commits into
mainfrom
update-hbd-data-sources

Conversation

@lauportell

Copy link
Copy Markdown
Contributor

Closes #141

@lauportell
lauportell requested a review from a team as a code owner March 15, 2023 10:07
@lauportell

Copy link
Copy Markdown
Contributor Author

@M-casado to review

@lauportell lauportell changed the title Update data sources page Update human biomolecular data sources page Mar 15, 2023
@lauportell lauportell self-assigned this Mar 15, 2023
@lauportell

Copy link
Copy Markdown
Contributor Author

Yesterday we had a meeting to see if we merge the data sources pages for human biomolecular and human clinical health data ant for the moment we will leave them separate and reference them when necessary, as the information they contain right now is different.
We still need to decide where we are going to place the FAIRness page that @M-casado is preparing for human clinical health data as that one will be useful for biomolecular data as well.

@lauportell
lauportell requested a review from IrisVanDam May 5, 2023 08:42
@bedroesb

bedroesb commented May 5, 2023

Copy link
Copy Markdown
Member

Writing a FAIRness page, which is not one of the pages we decided to have in IDTk, was a risky thing I think :) This needs more discussing imo!

@M-casado

Copy link
Copy Markdown
Contributor

Hi @bedroesb, The FAIRness content was reviewed and, albeit a few details, is mostly done.
The issue I created for its addition is #163, but I don't mind whether it becomes a page on its own or rather an addition to an already existing page.

As soon as it is discussed, we can continue with this conversation 👍

@M-casado M-casado left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Reviewed the document from GitHub. Besides the smaller comments, I have two overall comments:

  • We definitely need to merge the two pages (#165), given how everything I read rang a bell with regards to the Human clinical data sources page.
  • Wherever it may end at, I would add a mention to the FAIRness page (#163) whenever speaking about discoverability, access, etc. within this page.

Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md Outdated
Comment thread human-biomolecular-data/data-sources.md Outdated
Comment thread human-biomolecular-data/data-sources.md Outdated
Comment thread human-biomolecular-data/data-sources.md Outdated
solcos added a commit to solcos/infectious-diseases-toolkit that referenced this pull request Jun 28, 2023
Edit of the changes suggested elixir-europe#155
@solcos solcos mentioned this pull request Jun 28, 2023
lauportell pushed a commit that referenced this pull request Jun 29, 2023
Edit of the changes suggested #155
solcos and others added 5 commits June 29, 2023 14:58
Add of Data Deposition part
Put links to data deposition
Update links in data deposition
Removal of Beacon training UI link
@lauportell

Copy link
Copy Markdown
Contributor Author

Hi @IrisVanDam :)
Same for this one.. can you do a final review so we can merge this page?
Thank you!

@IrisVanDam IrisVanDam left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The page is really nice and structured clearly. Thanks for all the work on this!
My main concern does not relate to this page specifically, but rather that we might need to discuss (again) exactly what we are aiming to do with the data sources pages. From my understanding the aim was to give the user information on where to find these types of data and how to access them (~secondary use of the data). However, this page seems to be more focused on what to do with your own data as a researcher. I think both approaches are fine, but for the IDTk that we should choose one approach for all pages as to ensure consistency. What do you think?

Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md Outdated
Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md Outdated
@lauportell

Copy link
Copy Markdown
Contributor Author

Hi @IrisVanDam :)
Arnau did some other changes to resolve your comments - let us know if anything else has to be done.

@IrisVanDam IrisVanDam left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I've focused on the new changes made to the page and these look wonderful. I've added a few suggestions, but nothing major :).

Comment thread human-biomolecular-data/data-sources.md
Comment thread human-biomolecular-data/data-sources.md
new way of adding tools
lauportell and others added 4 commits September 19, 2023 10:27
Add tools in the yaml
…fectious-diseases-toolkit into update-hbd-data-sources
Add missing tools in the new way
@lauportell

Copy link
Copy Markdown
Contributor Author

READY TO BE MERGED! :)

@hedi-ee
hedi-ee merged commit 57b9985 into main Sep 19, 2023
@hedi-ee
hedi-ee deleted the update-hbd-data-sources branch September 19, 2023 11:26
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Data sources - Human biomolecular data

6 participants