List of actions from group call 15-Oct-2024

[ValWood]

• PRINTS, only report start and end in table
• PRINTs, display features as con-joined in viewer
• Move domains /families to the top and other features to the bottom
• Check IDs are included in pop-ups
• Put Pfam at the top one per row and label thre domains on the right-hand side
• Future, we need to make a decision whether to include or exclude unintegrated families
• Check if Pfan-N and Pfam-B are available for import

Also, not on the call, but I noticed that the MOBIDB said "provided by InterPRO". Probably this should say "Imported from InterPro" since that is where we get them from, but InterPro do not create them.Maybe in these cases we should be more explicit ->
e.g Provided by MOBIDB via InterPRO?

[kimrutherford]

MOBIDB said "provided by InterPRO".

Could you add a screenshot? I can't find that.

[kimrutherford]

See also:

• Integrate the 2 protein viewers #2203 (comment)

[ValWood]

I think I imagined it!

But we should change this to say "Imported from"

[kimrutherford]

But we should change this to say "Imported from"

OK, I've changed that on my desktop.

[kimrutherford]

PRINTs, display features as con-joined in viewer

Should we do that? InterPro has them as them as separate features:
https://www.ebi.ac.uk/interpro/protein/reviewed/Q9Y7Z8/

[ValWood]

I think we shoudn't follow interPro on this one. Its clearer as single conjoined feature.
@PCarme do you agree?

[PCarme]

Yes, in term of visualisation I think it makes more sense as a single feature

[kimrutherford]

Check if Pfan-N and Pfam-B are available for import

The InterProScan output gives no hint about this. The InterPro website only mentions Pfam-A:
https://www.ebi.ac.uk/interpro/download/pfam/

There is a Pfam-B file on the FTP site:
https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/

This old blog post says that Pfam-B is not included in the main Pfam website so maybe it's not included in InterPro:
https://xfam.wordpress.com/2020/06/30/a-new-pfam-b-is-released/

[ValWood]

Pfam-b not urgent. but useful if we can link it to the interpro to see other 'members'