EDAM terms for Circos, Jbrowse

[hexylena]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

xref galaxyproject/galaxy#10592

[bgruening]

Can you maybe also add the bio.tools identifier? https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-xrefs

Thanks @hexylena!

[hexylena]

@bgruening sure, added to jbrowse.

I've also added the "real" circos ID to the circos tool which only had our 'galactic circos' identifier. Is that correct to do? Or should we keep it with just the 'galactic circos' id?

(the rest of the tools are custom scripts or simply not registered in bio.tools.)

[hmenager]

Thanks a lot for pushing this @hexylena !
Here are a few recommendations, up for discussion:

• EDAM topics I would have the same for all circos wrappers, since they designate the general subfield that the tool is concerned with. I would annotate circos with Comparative genomics (topic_0797)and Data visualisation (topic_0092) just like in bio.tools, unless there is a specificity in Galaxy circos which would have it diverge significantly from this. For jbrowse, the topic in bio.tools is Genomics and I would add Data visualisation (topic_0092).
• As a general rule, try to avoid topic_0003 (which is the Topic terms root) for tool annotation.
• EDAM operations look fine to me, nothing to say 😃
• xrefs are fine, but I would only keep galactic_circos (and not circos) since from what you say @hexylena it is an overlay on circos.

Please tell me if there is anything else I can do to help out.

[hmenager]

One thing that comes to my mind is that some of these remarks I made could be useful as documentation. I can help out with that as well.

[hexylena]

Hey @hmenager, that's incredibly useful advice! Thank you !

remarks I made could be useful as documentation

Yes, definitely!

[hmenager]

Yes, definitely!

@hexylena Would a PR for this documentation page the most appropriate location?

[hexylena]

Yeah that's definitely a good place for it! man. 2. nov. 2020, 17:36 skrev Hervé Ménager <[email protected]>:

…

Yes, definitely! @hexylena <https://github.com/hexylena> Would a PR for this documentation page <https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#> the most appropriate location? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3269 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADP7O3LWLPB3UAZFI3J6TDSN3NYVANCNFSM4TEYYQCQ> .

[bernt-matthias]

As a follow up: I just found this old one: #1897 .. could be interesting to get EDAM for more tools

[bgruening]

@hexylena is that one ready?

[hexylena]

Yep

[bgruening]

Danki!