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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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PomBase histone demethylases #3845

Closed pgaudet closed 3 years ago

pgaudet commented 3 years ago

From @ValWood in the ontology tracker, https://github.com/geneontology/go-ontology/issues/21089

I would like to be able to annotate to "histone demethylase activity" for family members with no experimental data. If these are like set domain we can't assume that all members have the same specificity.

The methyltransferase specificities: Systematic ID | Gene name | Product description SPAC29B12.02c | set2 | histone lysine H3-K36 methyltransferase Set2 SPCC297.04c | set7 | histone lysine H3-K37 methyltransferase Set7 SPCC306.04c | set1 | histone lysine H3-K4 methyltransferase Set1 SPBC428.08c | clr4 | histone lysine H3-K9 methyltransferase Clr4 SPCC4B3.12 | set9 | histone lysine H4-K20 methyltransferase Set9 SPAC22E12.11c | set3 | histone lysine methyltransferase Set3 SPCC1739.05 | set5 | histone lysine methyltransferase Set5 (predicted) SPBP8B7.07c | set6 | histone lysine methyltransferase Set6 (predicted)

pgaudet commented 3 years ago

Are these methylases or demethylases?

ValWood commented 3 years ago

These are methylases, but I was using to explain that the situation is similar for the demethylases. We don't know the specificity of all of the family members so we need to be able to annotate to the parent. We cant assume that all the family members have the same specificity. v

pgaudet commented 3 years ago

OK but I have not seen examples yet. We can edit once we find examples?

ValWood commented 3 years ago

jmj1 & 4 are the examples?

ValWood commented 3 years ago

I only want to annotate to "histone demethylase activity" I was using the methylases for comparison to show that they are usually modification specific. If the demethylases are the same, then we cannot be more specific than histone demethylase activity right now.