Integrate the 2 protein viewers

[ValWood]

We have one viewer focused on variants, modifications and all sequence features, that should only Pfam domains

then we have the protein domains and families feature table showing all Intero families and recording their details and links to other identical features below.

Ideally we would like to somehow integrate these better.

In the short term links between the 2 viewers will be added.

Pease add ideas of how to integrate below.

[ValWood]

ACTION ITEMS

DOMAINS & SEQUENCE FEATURES

• Relabel gene page left hand menu to "protein domains and features" which is the main content. We need to decide later what to do about properties
• Use the new style display for the protein domain and features section (it will only be possible to highlight from the viewer to the table/ not from the table to the viewer). Consider asking the developers to add that ability to hook into the viewer from a table
• The protein families and features display should include
  a) protein families and domains
  b) tmms
  c) signal peptides, transit peptides and other Sequence ontology features
  d) active sites binding sites
  e) low complexity, disordered and coiled coil
• Add link to ALL features view so that these features can be viewed in the context of modifications and mutants
  f) We talked about merging the PomBAse curated domains into the domain feature table but I will review these and decide which we need to keep

MODIFICATIONS

• Add a summary view of modifications to the top of the modification section

• Add link to ALL features view so that these features can be viewed in the context of protein features and mutants

@kimrutherford @PCarme
I think this was everything we discussed about integrating the views.
I left out the bit about moving the TMM link and the InterPRo link, we can decide that when we see the new pages
If you can think of anything else, or have any alternative suggestions please add these to the ticket

[kimrutherford]

As first step I'm testing loading all the InterProScan results into the fancy viewer to see how it looks.

This is only on my desktop for now: https://desktop.kmr.nz/gene_protein_features/SPAC22F3.06c

[kimrutherford]

I've been working on swapping using the new viewer widget in the Protein domains and properties section. It's works OK but there is still quite a bit of fine tuning needed, like using the MobiDB disordered regions instead of the existing features.

You can see it in action here: https://desktop.kmr.nz/gene/SPBC12D12.04c

The protein feature viewer widget at the top of the page is temporarily a bit broken on my desktop version.

[ValWood]

That is a lot neater than the existing view! and so nice that you can zoom in to see the amino acids.
The only down side is that you need to mouse over to see the label, but people will get used to that, and it will be better when the mouse over the domain highlights the row in the table - what functionality would we need to ask for to enable clicking the table and highlighting in the image?

[kimrutherford]

and it will be better when the mouse over the domain highlights the row in the table - what functionality would we need to ask for to enable clicking the table and highlighting in the image?

We should be able to implement highlighting in the same style as when you click on a feature. That's supported already in their code. The yellow bar here:

[ValWood]

You mentioned that it would be possible to click on the image and highlight the table, but it wouldn't be possible to click on the table and highlight the image without changes to the RCSB code.
We could ask for that, it would be good if they added it in the future, but not critical

[kimrutherford]

You mentioned that it would be possible to click on the image and highlight the table, but it wouldn't be possible to click on the table and highlight the image without changes to the RCSB code.

I was wrong about that. We'll need to do some re-implementing of the code for the table but it will
be possible to highlight a range of residues if we mouse-over a feature in the table.

[kimrutherford]

Work in progress, with the InterProScan output moved up and a track per Pfam entry:

https://desktop.kmr.nz/gene_protein_features/SPBC146.13c

[kimrutherford]

A lot of this work is finished now.

The next big task is re-writing the code for the table of InterPro domains so that it integrates with the new feature viewer. I think that's a job for Monday.

[ValWood]

Yes not one to begin on Friday evening. Great progress on this though! So much useful stuff.

[kimrutherford]

it will only be possible to highlight from the viewer to the table/ not from the table to the viewer

I've got the highlighting work from the viewer to the table (on my desktop) but no the other way yet. It needs a bit more work.

[kimrutherford]

from the table to the viewer

That's sort-of working now (on my desktop) but it's not very elegant. I'll improve it tomorrow.

[ValWood]

O I see the picture, it looks good!