[BioSQL-l] Re: [Biojava-dev] Re: biosql

[Hilmar Lapp]

On Wednesday, March 17, 2004, at 12:58  PM, Len Trigg wrote:

> The problem is that when a BetweenLocation (and probably a whole bunch
> of others) get persisted, they get retrieved as regular
> RangeLocations. It would be straight forward to store a term
> corresponding to the location type in the term_id of the location
> table (currently unused in our binding).

This is what I proposed this foreign key for.

>  It's just a matter of determining what terms to use. Either (easiest 
> to hardest): a) the
> classname of the location type; b) whatever BioPerl uses (if it is
> capable of persisting the location type); c) jump through a few hoops
> and look up an appropriate obda name.

Please don't use classnames, although that would be easiest obviously, 
or otherwise bioperl (or any other language) won't interoperate with 
this properly.

As a matter of fact, bioperl-db doesn't use this currently, and 
therefore doesn't support fuzzy locations (which is what we call them 
in bioperl) to roundtrip to fuzzy locations (they'll become exact 
locations).

Note also that generally speaking the location_qualifier_value table is 
supposed to hold information from which you could infer the type of 
location. My point at the time was that querying 
location_qualifier_value every single time you obtain a location 
regardless of type is going to be a huge waste of time, given that 99% 
of locations are *not* fuzzy.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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