[not crucial] Preference of EDAM annotations

[matuskalas]

[not crucial] Preference of EDAM annotations

[beatrizserrano]

I've asked @bgruening for confirmation. And then I'll edit the text accordingly

[beatrizserrano]

@kostrykin @bgruening do you know this?

[kostrykin]

I think the confusion is due to two things being confused here 🤓

I remember that we had discussed this topic, and, as far as I remember, the bottom line of the discussion was indeed that the annotations in the XML have lower priority than those defined in Galaxy (there is a file, which defines the annotations for specific tools). I don't remember now which file this was, but, to my knowledge, this has nothing to do with bio.tools.

And then there is bio.tools. As far as I know, the EDAM annotations are fetched from bio.tools for tool wrappers, which do not have any annotations defined.

^{____________________________________
Update: I have minority revised the text above since it looks like I also have confused a few things 😅}

[matuskalas]

Quadrillion thanks @kostrykin 🙏🏽🙏🏽🙇🏽‍♂️ This is exactly how I remembered it too!

[matuskalas]

And sorry all, I forgot where to search for the "global Galaxy" list of annotations. Would you mind adding a link to it into the text here:

"We point out that there is a global list of precedential annotations with Bio.tools identifiers [@citesAsAuthority:usesDataFrom:biotools] in Galaxy (LINK HERE PLEASE), which ..."

I don't insist on this, but I think it would avoid others' confusion, and perhaps also our own in the future 😅

[beatrizserrano]

Could be this one?

[kostrykin]

I think it's it, but I'm not entirely sure and it would be good to verify somehow before pasting this link into the report.

Not quite sure now, however, how we could verify this.

[matuskalas]

Yes, that looks familiar! So I assume it's the correct one :D
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tool_util/ontologies/biotools_mappings.tsv
In the default branch, it is the above 👆🏽

[beatrizserrano]

Bjorn confirms that the link is correct

[matuskalas]

Million thanks all! 🙏🏽🙏🏽🙇🏽‍♂️👾🦑🐙
Submit?

[beatrizserrano]

I just finished the submission! But requires moderation, so won't have the doi for the BH project submission I guess :(

So, for now, all we have is this: https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/BH2023_preprint_project16.pdf

[matuskalas]

Billion thanks @beatrizserrano and all! 🙏🏽🙏🏽

In the end it was quite quick, https://doi.org/10.37044/osf.io/w8dsz.

What is the status of the BH proposal?

[beatrizserrano]

I submitted in the afternoon :)