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

[Dan Bolser]

On 6 July 2010 15:29, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
> 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.

Perhaps there is scope for a 'best practices' catalogue after all?

P.S. How did you know (about the biro that is).

Dan.


> 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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