[Biopython-dev] [Bug 2677] BioSQL seqfeature enhancements

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2677





------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-28 07:05 EST -------
(In reply to comment #7)
> (In reply to comment #6)
> > (From update of attachment 1072 [details] [details])
> > I think this is still a big improvement, but that the
> > (sub)feature.location_operator issue could wait.  We'll
> > need to discuss on the
> > BioSQL mailing list how this should be handled consistently.
> > 
> > Leaving this bug open.
> 
> Further to the "where to put the (sub)feature.location_operator" (eg. "join",
> "order") question, this comment appears in the BioPerl MySQL schema for the
> location_qualifier_value table:
> 
> -- location qualifiers - mainly intended for fuzzies but anything
> -- can go in here
> -- some controlled vocab terms have slots;
> 
> So, this would seem a suitable place to store the attribute.
> 

Yes, but if we record something in the location_qualifier_value table we can't
use a NULL term_id (possibly a schema limitation).  We therefore need to use a
particular ontology, which is where some co-ordination with the other BioSQL
projects is needed (so that we all default to the same ontology).  I'd meant to
send of an email about this to the BioSQL mailing list but didn't get it done
before I had to leave for a trip.


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