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PomBase curation
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Capturing half life data #3522

Open ValWood opened 1 year ago

ValWood commented 1 year ago

Would would require a tab delimited format with

Systemtic ID mandatory gene optional RNA/protein (Madatory) number (in mins?) conditions? Evidence (mandatory) Publication date Anything else ?

We could make it spreadsheet submission only Display would be an additional table in the expression section

ValWood commented 1 year ago

Datasets (we can put out a call)

Juan: PMID: 25375137 table s7 PMID: 22466169 There may be newer datasets using sequencing, but I can’t find them

ValWood commented 1 year ago

Conversation with SGD, they display: https://www.yeastgenome.org/locus/S000000364/protein#experiment And make queries available in Yeastmine (we could do similar in Advanced search)

They provide queries Gene --> Protein Half-life Retrieve Protein half-life for a given gene(s). This study had reported value of >=100 hours for the most stable proteins. To facilitate sorting and searching this values have been substituted '10000' hours.

Retrieve --> Proteins with half-life in a given range Retrieve proteins with half-lives ranging from minutes to >100 hours. To facilitate sorting and searching for the most stable proteins, where half-lives were reported as >=100 hours, values were substituted with '10000' hours. For the complete set, combine results via saved Lists of min (0.0 - 60) and hr (1 - 10000) template queries.

We need to be mindful of the units we select to make sure we can do queries across a range of values. I'm not sure what would. be best to cope with minutes and hours!