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PomBase curation
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Reviewing genotype comments, #3684

Open ValWood opened 8 months ago

ValWood commented 8 months ago

Here are all the genotype comments, with links to the genotype pages: genotype_comments.txt

Here are some examples:

Originally posted by @kimrutherford in https://github.com/pombase/website/issues/2161#issuecomment-2022368873

ValWood commented 8 months ago

Historically we used "geneotype comment" in Canto for "geneotype comment" and "allele comment"

We can now capture "allele comments", we do them in this file pombe-embl/supporting_files allele_comments.txt (but they are not yet displayed because we don't have allele pages).

I had a scan of ~this~ the genotype comments list, and most look as though they can migrate to "allele comment". Certainly everything which is a valid comment, for a single gene where the expression is not assayed.

However, I see a lot of comments in here that should not be allele or genotype comments. C-terminal truncation catalytic site mutant these can be deleted

some are not absolutely necessary but we can keep them as allele comments because they are quite useful up in the overall alle or genotype description analogue sensitive non-hydrolyzable ATP kinase dead protease cleavable

Some probably predate us digging in to describe the genotype correctly AS inserted after initiator methionine, does not add anything, can be removed

Quite a few should be fixed to promoter syntax nmt-promoter, thiamine repressible promoter switch-off

Some should be part of the genotype nak1+ and orb6+ wild type product levels (check covered and remove)

Some are phenotypes Increased cortical tubular ER dynamics (check covered and remove)

etc

@PCarme if you could make a spreadsheet and

  1. Fix the promoters/ phenotypes/unecessary genotype descriptions etc and flag as "removed" (keep any comments that it will be helpful for people to see data glance in the allele /genotype description table)

  2. flag the ones that can migrate to "allele comment"

  3. flag the ones (genotype comment or allele comment) which only apply to a version of the genotype with a specific promoter, because these will need to be kept with the promoter as @kimrutherford suggested)-I don't think there will be many of these

ValWood commented 8 months ago

genotype_comments.txt

ValWood commented 8 months ago

@kimrutherford we will need a version of this file with the session ID that the comment is recorded in

kimrutherford commented 8 months ago

We can now capture "allele comments", we do them in this file pombe-embl/supporting_files allele_comments.txt

We also have a mechanism for adding allele "notes" in Canto that was added for FlyBase. We could use this system for adding comments.

image

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These notes aren't included in Chado yet but should be. I dropped the ball on that one.

There are already some sessions that have notes like this:

https://curation.pombase.org/pombe/curs/4488533ca5f8fdc3/genotype_manage/ro

image

image

ValWood commented 8 months ago

We can discuss what is best on next call. It maybe better to maintain these comments externally like "allele comments" if they do not apply to a specific session.

kimrutherford commented 8 months ago

we will need a version of this file with the session ID that the comment is recorded in

How's this: genotype_comments_and_sessions.tsv.txt

ValWood commented 8 months ago

We could use "note" for these kinds of comments:

285ddfe564bdf7e2 Error in Supp material (mentions twice LiL, but first one should be LiS). Small, medium, and large insertions in the FCCH loop of Uba1 (LiL, LiM, and LiL) were generated using PCR. Insertions are between positions 198 and 199 in Uba1 are composed of the following amino acid sequences: 'TG' for LiL, 'GRSRGTG' for LiM, and 'GRSRGRSRGTG' for LiL.

I guess the idea that "note" is only for curators? things that might be useful if we are ever looking back. (comments are publicly visible)

ValWood commented 8 months ago

How's this: genotype_comments_and_sessions.tsv.txt

Perfect, thanks

kimrutherford commented 8 months ago

I guess the idea that "note" is only for curators?

That's how FlyBase use them but we could use them as public allele comments if we wanted to.

PCarme commented 8 months ago

Here is the list after review of every comment. The comment at line 29 was unclear to me, so I didn't change anything about this one. The session codes in red are sessions listed for a specific comment where I couldn't find the comment (it seems to be curation sessions that contain an allele that is associated to the specific comment in another session). Ask me if anything needs clarification. genotype_comments_and_sessions.csv

ValWood commented 7 months ago

That's amazing, thank you. I reilise it was made more difficult by us not including the gene name.

Val

ValWood commented 7 months ago

We can discuss on Tuesday. We need to be clear precisely how we are using "notes" and if they are equivalent to allele comments (i.e. will be visible)

kimrutherford commented 7 months ago

Ask me if anything needs clarification. genotype_comments_and_sessions.csv

Hi Pascal. Do you need to make any more changes to this file before I move the "allele comment" lines over to the allele_comments.tsv file?

There is a one line that has "allele mutant" instead of "allele comment". What should we do with that?

Thanks.

PCarme commented 7 months ago

Hi Kim, I don't think I need to change anything to the file at this point. The "allele mutant" is an error and should be corrected to "allele comment" actually.

kimrutherford commented 7 months ago

OK, thanks.

I've now moved all of the "allele comment" details from genotype comments to the allele comments file.