Full view extension presentation on phosphorylation phenotypes

[ValWood]

In these cases we could group

like
cdc2-33(A177T aa) affecting cdc18 modified residue T10A,T46A,T60AT104A,T134A
cdc2-33(A177T aa) affecting rap1 modified residue T378,S422,S513
etc

[kimrutherford]

Yep, we can do that. If I change the configuration so that residue extensions can be grouped together I get this:

https://desktop.kmr.nz/gene/SPBC11B10.09

We also have assay_using configured to group together so there are also summaries that look like this:

https://dev.pombase.org/gene/SPBC530.14c

Is that OK?

[ValWood]

Not sure. @PCarme is it clear that the residue belongs to the preceding ID in the list?

Also in the first figure, by grouping be residue, we lose

cdc2-33(A177T aa) affecting cdc13, orc2, sld3
cdc2-L7(P208S aa) affecting cdc13, orc2

grouping

ideally it would be
allele plus affecting + residue (when multiple residues, or single residue)
cdc2-33(A177T aa) affecting cdc18 modified residue T10A,T46A,T60AT104A,T134A
cdc2-33(A177T aa) affecting rap1 modified residue T378,S422,S513
cdc2-33(A177T aa) affecting xxx1 modified residue Txxx
THEN
all of the ones for the same allele which have no residue
cdc2-33(A177T aa) affecting cdc13, orc2, sld3

then the same for each allele

Is that possible?

I think people will primarily want the same allele together, then the most compacted version of that information.
At the moment you need to look at the entire list to see the affects of a single allele.

[PCarme]

is it clear that the residue belongs to the preceding ID in the list?

It is clear to me at least, although it feels a bit awkward.

ideally it would be allele plus affecting + residue (when multiple residues, or single residue)
cdc2-33(A177T aa) affecting cdc18 modified residue T10A,T46A,T60AT104A,T134A
cdc2-33(A177T aa) affecting rap1 modified residue T378,S422,S513
cdc2-33(A177T aa) affecting xxx1 modified residue Txxx
THEN all of the ones for the same allele which have no residue
cdc2-33(A177T aa) affecting cdc13, orc2, sld3

then the same for each allele

I agree, this would be a better solution overall

[kimrutherford]

Sorry, I realise that I got this wrong. The screenshot for cdc2 shows the residues grouped together but that was from when I had mis-configured my desktop site.

Adding the configuration to group by "modified residue" doesn't work in this case because (I now realise) it's not possible to group by two different extension relations in the same annnotation. The code doesn't support that. It's tricky code so I can't say how long this will take to fix. I've having a look now.

[kimrutherford]

Adding the configuration to group by "modified residue" doesn't work in this case because (I now realise) it's not possible to group by two different extension relations in the same annotation. The code doesn't support that.

I think I've fixed that, more or less. There might still be some situations where the grouping doesn't happen, but I think most cases will be covered. The change will be on pombase.org in the morning.

[kimrutherford]

[ValWood]

Fantastic. We will look it over and then we can also use the same configuration for other terms which have extensions and residues (if not already).

That would be all children of
abnormal protein modification (FYPO:0002494)
and
normal protein modification (FYPO:0002495)

[ValWood]

So in the figure above I still see 3 rows for cdc2-33 affecting cdc18
ie
T104A, T10A, T134A
T46A, T60A
T374A

[kimrutherford]

So in the figure above I still see 3 rows for cdc2-33 affecting cdc18

Yep, there are still have cases that aren't collected together. It's tricky to get it working in all situations, but I'll have a look at that one tomorrow.

[kimrutherford]

We will look it over and then we can also use the same configuration for other terms which have extensions and residues (if not already).

There will be a few changes to the GO summary too.

Current display:

Tomorrow's version:

[kimrutherford]

It's tricky to get it working in all situations, but I'll have a look at that one tomorrow.

I re-wrote the code to handle more cases. This change will be on pombase.org soon:

[kimrutherford]

This change will be on pombase.org soon

It's there now. Let me know if you spot any problems. It's new code which makes bugs more likely.

[ValWood]

Amazing. That's brillaint!