[BioSQL-l] BioSQL at BOSC08 - Was Re: (no subject)

[Hilmar Lapp]

On Jul 24, 2008, at 12:33 PM, James Procter wrote:

> Hilmar Lapp wrote:
>>
>> On Jul 24, 2008, at 11:32 AM, James Procter wrote:
>>
>>> As a general question to the list - Were there any issues like this
>>> raised or discussed during or after the BioSQL presentation at  
>>> BOSC 08 ?
>>
>>
>> If you mean whether there were any questions about storing  
>> structure in
>> BioSQL, no.
> well - I was enquiring more generally - was there any discussion about
> extending the BioSQL model for other kinds of bioinformatic objects ?

This was among the examples I showed for actual usage. In fact, I  
suspect that that's a fairly common usage pattern of BioSQL. Many of  
the papers citing BioSQL are by groups who have data persistence needs  
and work on sequences and annotation plus something custom they  
generate themselves. They use BioSQL as their sequence and annotation  
"module" that instantly solves that piece and how to get data in, and  
they add custom tables to model whatever types of data or results they  
have that are associated with that.

One person wanted to accommodate pathway data (if I recall  
correctly?). I have so far been rather reluctant to add data types to  
the model that aren't really supported by at least one of the Bio*  
toolkits, as the main goal of BioSQL is to provide interoperable  
persistence for the Bio* toolkits rather than being a generic schema  
for all kinds of data. So I said I would look at it as soon as at  
least one toolkit has an object model for that kind of data.

I believe there are projects that aim to fill the latter need already  
and do so pretty well (Chado, as an example), and so rather than  
duplicating these efforts I thought that supporting Bio* persistence  
should take higher priority.

That said, I'm open to any kind of feedback or thoughts; please post  
if you have a different opinion, and I'd be interested to hear what  
people have to say on this.

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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