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

[Elia Stupka]

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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