[BioSQL-l] Location with lt, gt

[Hilmar Lapp]

Sorry for the delay in responding. Peter's suggestion of  
location_qualifier_value is good but only half of the truth.

More specifically, location_qualifier_value can be used to store the  
minimum and maximum start and end coordinates for the start and end  
positions of a location. The model that BioPerl uses for fuzzy  
locations is in Bio::Location::FuzzyLocationI. Basically, on top of  
the canonical start and end, a fuzzy location has a min_start,  
max_start, start_pos_type ('BEFORE', 'AFTER', 'EXACT','WITHIN',  
'BETWEEN','UNCERTAIN') and similarly for the end position. How to  
determine the canonical start and positions from these is left to a  
CoordinatePolicy object, i.e., subject to different possible  
interpretations (e.g., conservative, maximum range, etc).

In addition, locations have a type: 'EXACT', 'WITHIN', or 'IN- 
BETWEEN'. This would be set using the term_id foreign key from the  
location to the term table.

Does this make sense?

I have to admit that Bioperl-db doesn't implement round-tripping of  
fuzzy locations yet, so there actually isn't a reference  
implementation yet that you could look at (but Biojava sounded like it  
roundtrips those?).


	-hilmar

On Oct 10, 2008, at 6:40 AM, Raoul Jean Pierre Bonnal wrote:

> Il giorno ven, 10/10/2008 alle 10.58 +0100, Peter ha scritto:
>> On Fri, Oct 10, 2008 at 10:46 AM, Richard Holland
>> <holland at eaglegenomics.com> wrote:
>>>
>>> BioJava refers to the < and > notation as fuzzy locations. See:
>>>
>>> http://www.biojava.org/wiki/BioJava:BioJavaXDocs#Working_with_RichLocation_objects 
>>> .
>>>
>>
>> Biopython also calls them fuzzy locations and has special location
>> objects to hold this in memory.
> Ok BioRuby too but ...
>
>> Raoul, were you asking how these are stored in the tables in BioSQL  
>> itself?
> YES.
>
> --
> Ra
>
>
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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