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isb-cgc / ISB-CGC-Webapp

ISB CGC Webapp
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Gene names and folding source data #315

Open Gibbsdavidl opened 8 years ago

Gibbsdavidl commented 8 years ago

After creating a new list of genes, they should be made all capital letters. Especially, since when creating a new list of gene, the user can type small case letters, which match the gene name, and it's shown as capitals in the list, but then the list of genes is shown in a mix of capital and lower case letters.

When working on a worksheet (making plots), it would be really nice to be able to fold down the list of genes and variables.

s-paquette commented 7 years ago

@Gibbsdavidl Blast from the past on this one, but I have a question regarding the first request. We're going to be putting miRNAs into our gene lists, and it's my understanding those names should not be capitalized, is this correct?

Gibbsdavidl commented 7 years ago

I had to check: http://www.mirbase.org/help/nomenclature.shtml "...it is unwise to rely on capitalisation to confer information..."

So, correct. Avoid caps. :-)

s-paquette commented 7 years ago

@Gibbsdavidl Got it. And one more question, this more related to the functionality - it's actually very easy to have the system capitalize gene (and not miRNA) names once the list is formally made, but not so much right after they've typed it in. So eg. if you type in 'tnn' and decline to select it from the suggestion list, it will display as 'tnn' while you're building your list, but be saved as 'TNN' once you're done and have saved the favorites. Does that work alright for functionality? Or would you want it to correct the capitalization while you're still building the list as well?

smrgit commented 7 years ago

we definitely don't want to force anything to all caps, but if the user inputs some gene symbols, maybe we could do a case-insensitive comparison and then substitute in the proper "spelling" based on our stored-list ...

which is, I think, what @s-paquette just suggested above ;-) I don't think it needs to correct capitlization while the user is typing/building the list, but afterwards/downstream would be good

s-paquette commented 7 years ago

The downstream one's very easy to do, and in fact was necessary to have the miRNAs display correctly anyways, so that'll be in the next patch.

mdmiller53 commented 7 years ago

this is to echo @smrgit on being case insensitive to the user's input. in fact, in reading what @Gibbsdavidl points out, i read that not so much as lower case is correct as that case shouldn't be depended on. the rest of the comment mentions databases that use some caps and databases that don't. for our app, going with the convention of lower case certainly makes sense.

s-paquette commented 7 years ago

@mdmiller53 I assume you mean for miRNAs, because in our database genes are done as HGNC compliant so they're fully upper-cased.

mdmiller53 commented 7 years ago

@s-paquette yes! i should have been clearer