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The PomBase community curation tool
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PHIbase deletion mutant notation #2070

Open ValWood opened 5 years ago

ValWood commented 5 years ago

So far, I have been defauting these if the gene name is not in Swiss-prot

Screenshot 2019-10-14 at 20 02 13

Maybe I should add the real allele name Chia1delta in these cases?

I will do this now, but this raises the question about how these are updated if the names change. Is there a system in place for refreshing from uniprot. This only probably works to update gene names and allele names would not be updated?

kimrutherford commented 5 years ago

I will do this now, but this raises the question about how these are updated if the names change. Is there a system in place for refreshing from uniprot. This only probably works to update gene names and allele names would not be updated?

Only the gene names will display differently if there is a UniProt change. As long as it's clear for you, I don't think it matters too much what you or Canto call the deletions because a deletion is a deletion. In PHI-Canto (and PomBase) they can be displayed using whatever the current gene name is and the Canto deletion name can be ignored. i.e. if the gene name changes after curation the deletion can be displayed differently automatically. As discussed on the call it's different for the non-deletion alleles where it makes sense to record the allele name from the paper.

ValWood commented 5 years ago

OK that makes sense.

Gene names are updated. Alleles are unaffected.

I just wanted to confirm because I wasn't even sure that gene names updated automagically.

This also means that our decision today to not necessarily align alleles with gene names makes total sense.

kimrutherford commented 5 years ago

I just wanted to confirm because I wasn't even sure that gene names updated automagically.

I skipped over some details. :-)

We need to do a bit of work on this. Canto caches the details from UniProt so that the pages load fast. So at the moment if the gene name changes in UniProt you won't see it immediately. Clearing the local cache is straightforward we just need to decide how often to do it. Maybe nightly?

ValWood commented 5 years ago

Oh gosh, monthly would be fine I think.... weekly a bonus but, it doesn't need to be totally up date...

kimrutherford commented 5 years ago

monthly would be fine I think

That's good. The less often, the better because sessions will load slowly straight after we clear the ID cache.

ValWood commented 4 years ago

I think this can close.

Summary Alleles are named as described in the paper Gene names are taken from Uniprot and periodically refreshed.

kimrutherford commented 4 years ago

Clearing the local cache is straightforward we just need to decide how often to do it.

@jseager7 did we have a chat about this a while ago? We added a cache refreshing script (#2107). Are you using that on the server?

jseager7 commented 4 years ago

The PHI-base team hasn't made any decisions about how often we want the cache refreshed (we might not have even discussed it in detail), so I haven't automated anything yet. I'll check with @CuzickA when she's around. Would it simply be a case of running the script on a schedule? I'm assuming the script can be run while Canto is live.

kimrutherford commented 4 years ago

I'm assuming the script can be run while Canto is live.

Sort of. :-)

The cache clearing and reloading runs in a transaction. The reloading is slow so Canto is likely to hang until the process completes.

We should be able to improve that. I've re-opened #2107 and I'll work on it.