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Get Yeast phenotypes directly from SGD #686

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kevinschaper opened this issue Apr 30, 2024 · 0 comments
Open

Get Yeast phenotypes directly from SGD #686

kevinschaper opened this issue Apr 30, 2024 · 0 comments
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@kevinschaper
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kevinschaper commented Apr 30, 2024

Based on this uPhenotizer discussion about SGD phenotypes in the Alliance phenotype ingest format, it seems like chemicals which are listed under conditions are actually part of the phenotype. Both uPhenotizer and monarch-ingest should pull directly from Yeastmine so that the chemicals can accurately be represented as part of the phenotype.

Here's a link to getting the phenotypes interactively from Yeastmine, we'll need to research a little more to turn that into a download url.
https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Phenotype_Tab_New&scope=all

This url seems to work for getting straight to tsv:
https://yeastmine.yeastgenome.org/yeastmine/service/template/results?name=Phenotype_Tab_New&format=tab&size=100000

(there are about 200k being returned from that url, so maybe tossing in another zero wouldn't hurt if it doesn't complain)

@kevinschaper kevinschaper added this to the 2024-06 Release milestone Apr 30, 2024
@kevinschaper kevinschaper self-assigned this Apr 30, 2024
@kevinschaper kevinschaper removed this from the 2024-06 Release milestone May 21, 2024
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