new page type. All alleles of this gene

ValWood commented 5 years ago

Discussed on group call that such a page would be a useful addition.

Antonialock commented 5 years ago

can these not be summarised in the phenotype section?

ValWood commented 5 years ago

this is basically going to be a long list, so I think a separate page might be better.

kimrutherford commented 4 years ago

Is this related: #1325?

ValWood commented 4 years ago

This is a bit different. but related. I guess it was just so people could look easily through the list of alleles. At the moment you can control F to search for one. But you might not know the name. I can see it would be useful to have a list of all the alleles to browse:

cdc2-r4 (D90N aa) cdc2-Y15F (Y15F aa) cdc2-22 (unknown) cdc2-D152N (D152N aa) cdc2-E51D (E51D aa) cdc2-N22 (E42K aa)

etc

grouped by 'type' with some ordering There are 100's for some genes now (it feels like, I might be exaggerating but lots for cdc2!)

ValWood commented 4 years ago

Would another filter on the gene page help? We could filter by allele type.

This is less about the type (this would just be a convenient way to group) and more about being able to scan the range of alleles quickly.

I can imagine this question. "I want to see ALL of the alleles of cdc2" At present it is difficut to scan because even if you could look down the page there is so much redundancy.

mah11 commented 4 years ago

I would find this useful, but not a super-high priority.

ValWood commented 4 years ago

.. it would be nice for scanning all the alleles. I would use it.

Jurg and Jacky didn't reply though...

I agree, not super high priority, but if it's easier to do with allele pages....

ValWood commented 4 years ago

JB We briefly discussed this in lab meeting, and the consensus is that it would be a useful addition. The wild strains would of course have many new gene alleles but these may be more difficult to implement.

(I'm not sure that the second part is strictly related)

kimrutherford commented 4 years ago

this is basically going to be a long list, so I think a separate page might be better.

It would be a dull page though wouldn't it? Would it be just a list of allele names and descriptions?

ValWood commented 4 years ago

It will not make exciting reading true, but sometimes dull is useful...

kimrutherford commented 4 years ago

Would it be just a list of allele names and descriptions?

After discussion, for each allele we'll need:

name
description
allele type
possibly a list of associated genotypes

mah11 commented 4 years ago

also want any synonyms & comments (see https://github.com/pombase/pombase-chado/issues/752 & https://github.com/pombase/pombase-chado/issues/753 as well as synonyms entered in Canto)

ValWood commented 3 years ago

It seems that we decided what to do here so I am removing the "discuss" label. However, I think we wanted Is this related: ~#1325~ (edit by kmr: maybe #1294?) to happen first, so I'll put this at "low priority' for now.

ValWood commented 3 years ago

This also might be useful to report in the publication if could be done alongside "allele pages" .It's kind of 'on topic' for improving accessibility to huge amounts of phenotype data.

kimrutherford commented 3 years ago

this is basically going to be a long list, so I think a separate page might be better.

I'm still not sure about this. We already have some long lists on the gene pages. And a table of alleles won't be that long will it? It should be a lot shorter than the phenotype annotation table for example.

If the list was its own page we'd need to link to it from the gene page. Where would the link be in the page? Would it get lost on a long gene page?

ValWood commented 3 years ago

Maybe a link at the top of the phenotype section, tucked away to the right

[Single allele phenotype]
-----------------------------------------------------------------[ Link : All alleles of this gene] [Gene Deletion Viability: Inviable]

mah11 commented 3 years ago

To me, the fact that it'll be a long and dull list for some genes is actually part of the case for hiving it off onto its own page. But a list on the gene page might also do, if it can toggle between expanded and collapsed, and defaults to collapsed.

ValWood commented 3 years ago

I would prefer the list to be on it's own page, I think (in case I wasn't clear).

kimrutherford commented 3 years ago

I've had a first attempt at this: https://www.pombase.org/gene_alleles/SPBC11B10.09

There are no links to these pages yet. You'll need to edit the URL to try other genes.

mah11 commented 3 years ago

This looks good. A few follow-up thoughts:

Can you make "delta" resolve to Δ in the Name column?

I think it's OK that it sorts by Type, but it would be cool if you can add the sort-by-column controls. I bet people would like to be able to sort on at least the Name column; not sure anyone would want to sort by Description but I dunno.

I like that you can see genotypes that use the allele right on the page, although I think the behavior will need to be documented thoroughly (otherwise it could be unexpected and maybe even confusing that the first click shows more on the allele page, but the next click on any genotype description goes to a different page).

On a related note, is it feasible to have the display of genotypes toggle on and off?

ValWood commented 3 years ago

Looks good. As an aside

I wonder if these are really 2 copies of cdc2? cdc2-33 (A177T aa) cdc2-L55M (aa) cdc2-33 (A177T aa) cdc2-T167E (aa) cdc2-33 (A177T aa) cdc2-E179R (aa) cdc2-33 (A177T aa) cdc2-T167Y (aa) and a few more I will open a curation tracker ticket to check that.

kimrutherford commented 3 years ago

Can you make "delta" resolve to Δ in the Name column?

Yep, I'll do that.

it would be cool if you can add the sort-by-column controls

I'll do that too.

kimrutherford commented 3 years ago

Can you make "delta" resolve to Δ in the Name column?

Yep, I'll do that.

it would be cool if you can add the sort-by-column controls

I'll do that too.

All done for the morning.

kimrutherford commented 3 years ago

On a related note, is it feasible to have the display of genotypes toggle on and off?

So have a button that hides the "Show genotypes.." link?

mah11 commented 3 years ago

On a related note, is it feasible to have the display of genotypes toggle on and off?

So have a button that hides the "Show genotypes.." link?

Actually, I was thinking more of having "Show genotypes" change to "Hide genotypes" after you click "Show" to, well, show them. Sorry if that wasn't clear.

kimrutherford commented 2 years ago

Actually, I was thinking more of having "Show genotypes" change to "Hide genotypes" after you click "Show"

There's a button to hide all the genotypes. Will that do?

mah11 commented 2 years ago

having "Show genotypes" change to "Hide genotypes" after you click "Show"

There's a button to hide all the genotypes. Will that do?

I'll have a think. It does do the job of hiding any genotypes I've shown, but I'm not quite sure it meets the need behing my request. After I'd clicked to "open" the view of genotypes for one allele, my instinct was to look for a toggle near where I'd just clicked, so I could hide those genotypes. Also, the show all/hide all controls are up at the top, and therefore not visible if you scroll down a long page.

ValWood commented 2 years ago

There's a button to hide all the genotypes. Will that do?

[ ] I would also prefer to be able to toggle off the genotypes I just looked at. Particularly for long lists (like the first example on the cdc2 page). The toggle all will not be so useful as I suspect users will open these one at a time (i.e for the specific alleles of interest). The page becomes unwieldy when all are open. I also failed to see the hide all genotypes button (maybe because it isn't close to the 'show genotypes' options.
[ ] could the default view put deletion, then WT to the top?
[x] In the genotype lists could the 'single allele genotype' be at the top of the list, followed by 'multi', then 'diploids'?
[ ] include a synonyms column

ValWood commented 2 years ago

[ ] Midori also mention comments above. These would be useful too. Mainly things like "temperature-sensitive" " kinase-dead" "loss of function" etc so would be useful for people browsing this list. Hopefully there aren't and very long descriptions?
[ ] Decide how to link from the gene pages

kimrutherford commented 2 years ago

Coming back to this after a few months, I have a suggestion.

I don't like the way the page works at the moment. The genotype lists are long and ugly, especially when more than one is shown. How about instead of the "Show genotypes.." link, could we link to the allele pages once they're done? We could have the list of genotypes at the top of the allele page.

kimrutherford commented 2 years ago

We can discuss on Thursday. Low priroty if it is complicated high priority if it is quick :)

I think it's probably quick but it depends on what's needed. :-)

Here's an example of how the pages currently look, for discussion: https://www.pombase.org/gene_alleles/SPAC1782.09c (Or here for latest: https://desktop.kmr.nz/gene_alleles/SPAC1782.09c)

How about instead of the "Show genotypes.." link, could we link to the allele pages once they're done?

I still think that's a good idea. I've (possibly temporarily) changed the allele name to be a link to the test allele pages (see https://github.com/pombase/website/issues/1294#issuecomment-1170757811) for discussion.

kimrutherford commented 2 years ago

Decide how to link from the gene pages

I've added a temporary link on the dev site gene pages, mostly so it's easier for me to get to the alleles pages while testing. It's at the top of the phenotype annotation tables for now because I wasn't sure where else to put it.

ValWood commented 2 years ago

II think that's a good place for now. Unless there are better suggestions @manulera

ValWood commented 2 years ago

Note that most pages will look better than this. http://dev.pombase.kmr.nz/gene_alleles/SPBC1347.10

because they will have more concise descriptions.

ValWood commented 2 years ago

[ ] Maybe we will need to line wrap the descriptions at around 50 chars?. How many very long .ones do we have? (note the ones above will be shorter tomorrow, I don't think very many are this long)
[ ] The genotypes look a bit confusing when displayed: It isn't really very clear where one ends and the next one begins:

kimrutherford commented 2 years ago

The genotypes look a bit confusing when displayed:

I think we should consider removing the expression and genotype columns from these pages and linking to the allele pages instead. We show the genotypes on the allele pages in a better format.

ValWood commented 2 years ago

I think we should consider removing the expression and genotype columns from these pages and linking to the allele pages instead. We show the genotypes on the allele pages in a better format.

yep,

manulera commented 2 years ago

I agree with Kim, that the genotypes should not be displayed in this page. My only doubt is about the expression level for wild type products.

Say that I am a new comer and I would like to see the phenotypes of overexpression or shutdown of a gene. It may not be obvious to me that I will find them in wild_type. So maybe it's good to say something like "wild type knockdown or overexpression" instead of "wild_type", since anyway it is not possible to have a wild_type allele without an expression qualifier.

ValWood commented 2 years ago

I think we are agreed not to display genotypes of each allele.

We can probably make this page available after the link is added.

ValWood commented 2 years ago

We should include synonyms on this page though, I think...

kimrutherford commented 2 years ago

We should include synonyms on this page though, I think...

No problem. Is an extra column OK? It's mostly going to be empty though.

ValWood commented 2 years ago

Maybe we shouldn't include them here. I think we discussed this previously and decided not to.

I had a use case - I went to this page to see if I could find which allele a synonym belonged to. If the simple search on a. synonym leads you to the allele page that is not necessary.

kimrutherford commented 2 years ago

I've found a bug. There are no alleles on this page: http://dev.pombase.kmr.nz/gene_alleles/SPCC736.12c

kimrutherford commented 2 years ago

I've found a bug. There are no alleles on this page

Fixed for Sunday morning.

kimrutherford commented 2 years ago

I've collected all the "to do" items here. Some are done and some we decided not to implement.

[x] How about instead of the "Show genotypes.." link, could we link to the allele pages once they're done? We could have the list of genotypes at the top of the allele page. YES
[ ] ~This also might be useful to report in the publication if could be done alongside "allele pages"~
[ ] ~I think we should consider removing the expression and genotype columns from these pages and linking to the allele pages instead. We show the genotypes on the allele pages in a better format.~
[x] We should include synonyms on this page - add a new column YES
- also add allele comments:
- "comment: ... synonyms: ..."
[x] could the default view put deletion, then WT to the top?
- move deletion and WT alleles out of table to top of page
[ ] ~I would also prefer to be able to toggle off the genotypes I just looked at.~
[x] Maybe we will need to line wrap the descriptions at around 50 chars?. How many very long .ones do we have? (note the ones above will be shorter tomorrow, I don't think very many are this long) YES - truncate at 50 characters

ValWood commented 9 months ago

This could maybe go ahead to get it off the list. I think its quite a useful feature, and it was pretty much completed?

ValWood commented 9 months ago

Are there any outstanding questions?

kimrutherford commented 9 months ago

I think we can go ahead but it won't be so useful without links to the alleles. It will be more useful once we we allele pages: pombase/website#1294

ValWood commented 9 months ago

We can wait until allele pages are available, but I it could be useful just to see all of the alleles of a gene.

kimrutherford commented 9 months ago

I've added a link to the "alleles of this gene" page from the gene page and disabled the links to the allele pages (on the main site):

pombase / website

new page type. All alleles of this gene #1255