[Bioperl-l] biosql,das,gmod,gfd integration

[Lincoln Stein]

This sounds right.  There are going to be some modifications necessary in GMOD 
to allow the configuration file to specify which DasI-compliant object to 
initiate, but it is a straightforward task.  When you have a chance, take a 
look at the current configuration files and tell me how you'd like to modify 
the database-related options in order to be fully generic.  Possibly 
something like this?

	[GENERAL]
	adaptor_module = NameOfDasIModule
	database = "some symbolic way of addressing the database"
	adaptor_parameters = name1 value1
					name2 value2
					name3 value3

The configuration file lets you insert perl subroutines for option values, so 
this is pretty flexible.

The GadFly people should weigh in on this too.

Lincoln

On Wednesday 10 July 2002 04:24 am, Elia Stupka wrote:
> We have installed GMOD and want to work on getting it to work with our
> biosql sequence repository and GFD (generic feature database, more
> info at BOSC) to display the results of analyisis stored in GFD, sequences
> coming from biosql.... the generic feature database basically is a
> relational database for features and sequences with arbitrary
> nested relationships....
>
> The model to make this work from what I understand would be:
>
> -write a DasAdaptor for bioperl-db which is compliant with the DasI
> interface and can fetch sequences using that interface
>
> -use the "a la ensembl" system, and add a method
> add_External_Feature_Factory to this DasI compliant object, so that we can
> add the GFD EntityAdaptor and add features from GFD to the sequence.
>
> So you would initiate the Bio/DB/DasAdaptor.pm, add GFD/EntityAdaptor,
> then pass this to GMOD, and when GMOD would ask for the features of a
> segment this would seemlessly fetch a sequence from bioperl-db, look for
> features in GFD, and return the features...
>
> Does it all make sense?
>
> Elia
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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