[BioSQL-l] location type

[Hilmar Lapp]

For certain location types, specifically fuzzy locations, the 
additional attributes (min_start etc) are stored as 
Location_Qualifier_Value entries.

If you don't know in advance whether a location is a fuzzy location, 
you need to make an extra hit to the database for every location 
just to find out most of the time that there are no extra attributes.

To alleviate this I propose to add to SeqFeature_Location a FK to 
Ontology_Term denoting the type of the location. We'd need to agree 
on a standard ontology for location types too. E.g.,

	FuzzyLocation
	SplitLocation
	ExactLocation

Or, which thinking about it I'd even prefer, the location types 
known to Bioperl:

	EXACT
	IN-BETWEEN
	WITHIN
	BETWEEN

The problem with this is that you can have a fuzzy location of type 
EXACT (because position type and location type are not the same). 
Hence, one would have to extend this to make it a combination of 
location type and position types. E.g., <loctype>;<start-
type>;<end-type>:

	EXACT;EXACT;EXACT
	EXACT;BEFORE;EXACT
	WITHIN;EXACT;BETWEEN

and so on and so forth.

What do people think?

	-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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