monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza

https://monarchinitiative.org

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Add PomBase Phaf associations #2

Closed kshefchek closed 7 months ago

kshefchek commented 3 years ago

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

ValWood commented 3 years 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

ValWood commented 3 years ago

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

kshefchek commented 3 years ago

this is perfect - thanks!

kevinschaper commented 3 years ago

3 is a first pass at loading PomBase gene to phenotype associations. (with most of the work happening here: https://github.com/monarch-initiative/koza/pull/26)

kevinschaper commented 2 years ago

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?

ValWood commented 2 years ago

Penetrance isn't critical. Personally, I think it is better to get the data in.

kevinschaper commented 2 years ago

That's great, I think I can close this case then. Thank you @ValWood!

ValWood commented 2 years ago

Great so will the PomBase phenotype data be visible in the next version of Monarch?

kevinschaper commented 2 years ago

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?

ValWood commented 2 years ago

OK, tag me on the ticket, or let me know when visible and can give it a check over. Looking forward to seeing this!

cmungall commented 12 months ago

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

monicacecilia commented 7 months ago

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.

ValWood commented 7 months ago

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