[Biojava-dev] Biojava3 and BioSQL

[Scooter Willis]

Thiago

The Biojava3-BioSQL module will be standalone so you should pick database tools like hibernate or others that make your implementation easy to support/robust. Did you check how other Bio languages support BioSQL? I would follow their API to allow for familiarity with already established packages.

Do you have a specific requirement for BioSQL support for code you are working on?

Scooter

From: Thiago Satake <maruco at gmail.com<mailto:maruco at gmail.com>>
To: Scooter Willis <hwillis at scripps.edu<mailto:hwillis at scripps.edu>>
Cc: Andreas Prlic <andreas at sdsc.edu<mailto:andreas at sdsc.edu>>, "biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>" <biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>>
Subject: Re: [Biojava-dev] Biojava3 and BioSQL

Hi,

I was wandering if I should use hibernate or not in my BioSQL module. In my point of the view we should avoid a lot of dependency to make things easy to set up. But I am not sure it would be good for everyone...

In this module I am thinking to create a data access object strategy typically exchange data with clients using Transfer Objects, and also, I believe we need to create DAOFactory to encapsulate multiple types of data source ( Oracle, Mysql and Postgres).

I will expose read() and write() functions using an session façade which will encapsulate reused biojava3 component an data access object.

Is everything making sense ? ;-)



Thanks


Thiago Seito Satake





On 29 May 2012 12:00, Scooter Willis <HWillis at scripps.edu<mailto:HWillis at scripps.edu>> wrote:
Thiago

If you get a chance can you look at the UniprotProxySequenceReader as a
potential model for BioSQL integration. The underlying sequence objects in
Biojava3-core don't care about the storage container for sequence data,
annotations etc. You should be able to do a BioSQLProxySequenceReader
which has knowledge of the BioSQL schema and connection parameters that
you pass into the appropriate Sequence object.

I think this makes the most sense to integrate BioSQL into Biojava3.

Let me know what I can do to help.

Scooter

On 5/28/12 9:34 AM, "Thiago Satake" <maruco at gmail.com<mailto:maruco at gmail.com>> wrote:

>Thanks Andreas,
>
>
>In my current project I will work with Java and BioSQL. I think that an
>biojava3-biosql API would be very useful. Now I am getting a good
>understanding of  biojava3 and deciding what is the best solution for
>that.
>Any suggestions would be good!!
>
>
>For now, I have created a simple project in my local environment called
>biojava3-biosql, after I've finished, I would like to share with all of
>you. Is possible include in BioJava project ?
>
>
>
>Thanks,
>
>
>Thiago Seito Satake
>
>
>
>
>
>
>On 26 May 2012 20:34, Andreas Prlic <andreas at sdsc.edu<mailto:andreas at sdsc.edu>> wrote:
>
>> No, biojava 3 does not have biosql bindings currently. Any patches are
>> welcome...
>>
>> Andreas
>>
>> On Sat, May 26, 2012 at 12:13 PM, Thiago Satake <maruco at gmail.com<mailto:maruco at gmail.com>>
>>wrote:
>> > Hi,
>> >
>> > I have noticed that there is a componet called biosql 1.8.1 which
>>works
>> > with biojava 1.8.
>> >
>> > Quick question, I would like to work with biojava3 and BioSQL. Is
>>there a
>> > componete for that ?
>> >
>> > Thanks
>> >
>> >
>> > --
>> > Thiago Seito Satake
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
>
>--
>Thiago Seito Satake
>Tel: (041) 88428444
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--
Thiago Seito Satake
Tel: (041) 88428444