base [sf#84]

[srynobio]

Reported by batchelorc on 2008-02-08 12:24 UTC Hello,

We don't currently have "base" in SO. Since we have zero-length features, junctions, it seems odd not to have bases in general (though we do have post-transcriptionally modified RNA bases).

Firstly, is there a case against including "base"?

Secondly, where would it go? Should modified_RNA_base_feature become a child of processed_transcript_region? I think it would be better for base to be a child of region, then its child, modified_RNA_base_feature would have a new 'quality', processed (to be distinguished from the existing one, SO:0000900, which applies to processed pseudogenes) so that the reasoner can work out what to do with it.

Thirdly, T/U?

Best wishes, Colin.

[srynobio]

Commented by eilbeck on 2008-02-08 17:05 UTC Logged In: YES user_id=742851 Originator: NO

Hi Colin, I think base is something that got overlooked in the beginning, and there is no reason why it should not be in SO. It should be in SO as a region with an extent of 1. I think this works for both space and base based coordinate systems.

I think your second suggestion is the right one. Many features can be processed - we need to define the different kinds of processing and apply those qualities to the right kinds of features.

Heres a list off the top of my head to start with: pseudogenes, all kinds of transcripts, bases...

--Karen

[srynobio]

Commented by batchelorc on 2008-02-18 14:18 UTC Logged In: YES user_id=1473024 Originator: YES

Something that occurred to me, if base is a "region with an extent of 1"---1 what?

Colin.

[srynobio]

Commented by eilbeck on 2008-02-25 21:24 UTC Logged In: YES user_id=742851 Originator: NO

I'm worried that this is all going to turn out to be circular but:

a base is a sequence_feature - corresponding to a single unit of a nucleotide polymer a region is composed of bases a junction is the boundary between bases

Not sure where this leaves amino acid. We would need to define this in terms of bases too.

--K

[srynobio]

Commented by batchelorc on 2008-02-26 15:24 UTC Logged In: YES user_id=1473024 Originator: YES

It makes sense for base to be a sibling of region and junction, yes.

Would amino_acid be a child of polypeptide_region (SO:0000839)? And how would it square with codon (SO:0000360)?

Colin.

[srynobio]

Commented by batchelorc on 2008-02-27 18:10 UTC Logged In: YES user_id=1473024 Originator: YES

OK. Done. Added amino_acid, which is a child of sequence_feature and part_of polypeptide_region.

Colin.

[srynobio]

Updated by batchelorc on 2008-02-27 18:10 UTC

• status: open --> closed