[Biojava-dev] Biojava3 and BioSQL

[Thiago Satake]

Hi Scooter,

I have worked with bioperl-db before and I have a good understanding about
that, but now I need to work with Java, it is my first time I am working on
biojava3 and I could not find any support to BioSQL.

Basically, I am going to create a web interface using JEE. My first task I
need to read GenBank, GFF and Fasta file and store the data into the BioSQL.

In order to maintain my JEE application easy to support/robust I am using
Spring and Hibernate. However, I could not find Hibernate or Spring support
in BioJava3 and I thought that it would not sound good for everyone,
because we need to have a good knowledge of external API.

If hibernate will help the application to be robust I believe that I need
to use Spring too.  Easy to maintain, but the architecture will be more
complex.

I can change my decision and use hibernate if everyone likes :-)



Thanks

Thiago Seito Satake


On 30 May 2012 23:43, Scooter Willis <HWillis at scripps.edu> wrote:

> 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>
> To: Scooter Willis <hwillis at scripps.edu>
> Cc: Andreas Prlic <andreas at sdsc.edu>, "biojava-dev at lists.open-bio.org" <
> 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> 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> 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> 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>
>> >>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
>> >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> >>
>> >
>> >
>> >
>> >--
>> >Thiago Seito Satake
>> >Tel: (041) 88428444
>> >_______________________________________________
>> >biojava-dev mailing list
>> >biojava-dev at lists.open-bio.org
>> >http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>>
>
>
> --
> Thiago Seito Satake
> Tel: (041) 88428444
>



-- 
Thiago Seito Satake
Tel: (041) 88428444