[BioSQL-l] BioSQL and ontology "standards".

[Leighton Pritchard]

On 04/12/2008 15:04, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> On Thu, Dec 4, 2008 at 1:25 PM, Leighton Pritchard <lpritc at scri.ac.uk> wrote:
>> With apologies if I'm misinterpreting the tide of discussion, but I would be
>> disappointed to see a default behaviour of "bung everything under
>> 'Annotation Tags', typos and all" become a 'standard' of any sort, rather
>> than a placeholder for future development of ontology-aware Bio* code that
>> queries and populates BioSQL appropriately.
> 
> Overall, I agree.  It isn't ideal, but the current ad-hoc "ontology"
> is useful in that its looseness allows any parsable GenBank file to be
> imported into the database.

I think that this may be a matter of perspective: you see an advantage, I
see an accident waiting to happen ;)
 
>> I see the situation as pretty much analogous to the effective requirement
>> for NCBI taxon data in BioSQL, when using Biopython: you need to load in the
>> NCBI taxon data before your own data can be imported in a taxon-aware
>> manner.
> 
> This is going off topic, but that's not really true any more.

Ah... Good point - my bad.

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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