Create CV term for methylation of a nucleic acid

[noedelta]

We need a term to attach a methylation as a feature of a nucleic acid.

E.g. pmid: 12379844

Reported by: bmeldal

[noedelta]

Des it mean PTM branch will have to be revived ?

Original comment by: lukasz99

[noedelta]

Can't be a PTM - you don't have a post-translation product of a nucleic acid. I'll have to think of another phrase. But yes, MOD is totally protein centric so we'll have to do something.

Original comment by: orchard

[noedelta]

PTM can also stand for Post-Transcriptional-Modification :oP it might actually make sense to create a term common to protein and nucleic acid modifications with two child terms - one delegated to protein mods, the other to nucleic acids... didn't some nucleic acid oriented people come up with their own CV to handle these ?

Original comment by: lukasz99

[noedelta]

Actually the Sequence ontology has the necessary terms e.g. SO:0000306
Name: methylated_DNA_base_feature

which has base-specific child terms so probably simpler to leave it to them and just refer out as we do with MOD.

Original comment by: orchard

[noedelta]

oh... there would have to be another term for DNA as it is modified without transcription. post-transcriptional would hold for RNAs of various sorts though...

Original comment by: lukasz99

[noedelta]

Actually the Sequence ontology has the necessary terms are they grouped into one CV branch that can be referred to within MI ?

Original comment by: lukasz99

[noedelta]

Sequence feature - region - biological region - base

if we can come in from 'base' downwards, we are covered for all the modifications to DNA and RNA.

Original comment by: orchard

[noedelta]

I think we've done as much as we can here - raise at PSI meeting if necessary

Original comment by: orchard

[noedelta]

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Original comment by: orchard