[Open-bio-l] Best practice for modelling data in GFF

[Leighton Pritchard]

On 06/07/2010 Tuesday, July 6, 13:11, "Dan Bolser" <dan.bolser at gmail.com>
wrote:

> I see... I guess this only applies because of the specific 'is_a'
> relationship. i.e. just because a nose is part_of a face and a mouth
> is part_of a face, you can't make inferences about relationships
> between nose and mouth.

Sounds like you get it.  To extend that analogy you can infer things about
nostrils and earholes, such as that putting a biro in a nostril is valid,
whether it's a left_nostril or a right_nostril, because nostril is_a orifice
- and that's why you can stick a biro in your ear, as well ;)
 
> Thanks very much for taking the time to provide such a detailed reply,
> and sorry for the dumb questions.

They weren't dumb questions.  I recently had a similar issue where I was
wondering how to represent sub-parts of protein domains that span exons in a
chromosomal reference frame.  It didn't seem right to have them span an
intron, as they derive from the polypeptide, but the ontology terms don't
have explicit subfeatures.  Happily the polypeptide_region feature provides
enough flexibility to get around this.

Cheers,

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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