Re: [GUSDEV] Extending the Schema to add a schema for pathway data

[Angel P. <an...@ma...>]

If you want to use GUS objects and write GusApplication plugins for 
these tables, then you need to convert the BioPax schema. If you want to 
just query the data (SQL or WDK) and assign your GUS entities to these 
pathways, you can get away without translating the schema to GUS 
conventions and adding materialized view relating them (or querying on 
the fly for the associations).  Your answer really depends on the needs 
of your application and your available coding resources.

In either case, I would replicate the BioPax database in a different 
schema, since translating from DB to DB is slightly easier in a plugin 
than flat file to DB transformations.

Angel

Dhivya Aras wrote:

> Hi,
>  
> I'm trying to add a new schema to GUS to add pathway data. I plan to 
> implement the biopax pathway data model on GUS. To do this, can I just 
> add the tables as they are given in Biopax? Or do I need to follow the 
> superclass(imp class)-subclass(view) relationship that is used in GUS?
>  
> I need to import data into the schema later on which is in BioPax 
> format, so I feel it would be easier to maintain the data model as 
> given in Biopax. But I just wanted to know if it would cause problems 
> since I'll be violating the subclassing relationships followed in GUS.
>  
> thanks
> dhivya
>
>
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-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
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