Closed kshefchek closed 7 months ago
Hi @kshefchek what do you mean by URL without date info?
This is the stable link for download data, but there os no date info in the URL the release date will be the file date.
@kimRutherford
Ignore, I see the date is in the file name.
The data is copied daily to the ftp site https://www.pombase.org/data/annotations/Phenotype_annotations/ phenotype_annotations.pombase.phaf.gz
this is perfect - thanks!
I left this issue in something of a purgatory. The biolink model doesn't have a great place for us to capture the penetrance values, which might only be able to fit into a notes field ("~10%", ">50%", "10-20%" etc) without a big parsing effort. Since we aren't likely to make use of penetrance information, does it make sense to move this forward leaving that out?
Penetrance isn't critical. Personally, I think it is better to get the data in.
That's great, I think I can close this case then. Thank you @ValWood!
Great so will the PomBase phenotype data be visible in the next version of Monarch?
Oh, good question @ValWood - this is implemented now for the upcoming data ingest pipeline that it's in development, not for the existing pipeline. @kshefchek Should we copy the details on this ticket over and whip up a quick dipper version of this as well?
OK, tag me on the ticket, or let me know when visible and can give it a check over. Looking forward to seeing this!
I'm reopening this
I would expect the pombase data to be in the new UI:
https://next.monarchinitiative.org/explore
and I can't seem to enter FYPO terms in the search, e.g FYPO:0005502
The updated version of the new UI allows the use of FYPO identifiers. See https://monarchinitiative.org/explore?search=FYPO:0005502#search (and screenshot below).
Thanks for the heads up, @cmungall! This has been solved.
Excellent.
I don't know if ALL PomBase phenotype curation will be useful more globally, some of the detail may only be of use to fission yeast researchers. If you ever want to reduce the number of phenotypes that you load we could discuss and I could give some pointers. v
LinkML: https://biodatamodels.github.io/ontology-associations/PombasePhafAssociation/
Docs: https://www.pombase.org/downloads/phenotype-annotations
Data download (I assume this is best, would be good to find a url without date info): https://www.pombase.org/data/releases/latest/
cc @cmungall @valwood