[Biojava-dev] Biojava3 and BioSQL

Tue Jun 5 00:06:56 UTC 2012

Thanks you so much.
Good idea, I will create entities using standard JPA annotations in my
current project. It will be very useful and easy to maintain.

On 31 May 2012 10:19, Simon Foote <simon.foote at nrc-cnrc.gc.ca> wrote:

> Thought I'd throw in my 2cents also, even though I haven't worked
> extensively with the BioSQL in biojava for awhile.
>
> I have web-based genome browser that was written way back in the biojava 1
> days with it's original BioSQL support.
> The is still running happily along.
>
> I also dabbled into the newer BioSQL support that Richard Holland
> introduced into biojavax which was a prelude to Biojava3.
> This code is currently in biojava-legacy. This one uses Hibernate sessions
> to bind to the various db backends, and creates db model using hibernate
> mappings which are database specific (including Mysql, Oracle, Postgresql,
> HsqlDB).
>
> This code works quite well, and you can load Genbank files into the
> database in 20 lines of code.
>
> This maybe a good starting point for redesigning the interface to BioSQL
> within biojava3.
> Switching from hibernate based sessions to JPA sessions would allow
> seamless plugin of whichever Session manager one wanted (as mentioned by
> Bruno).
>
> The problem with that current design (biojavax), is that the database
> mappings are encoded within the hibernate configuration.
> One possible solution would be to build a BioSQL java class model using
> Java annotations. This way automatic database schema generation via one's
> chosen Session manager/Database backend could be used.
>
> Just a few thoughts,
>
> Simon
>
> --
> Bioinformatics Programmer
> National Research Council of Canada | Conseil national de recherches Canada
> Government of Canada | Gouvernement du Canada
> 100 Sussex Dr, Ottawa, Canada K1A 0R6
> Telephone | Téléphone 613-990-3600 / Facsimile | Télécopieur 613-952-9092
>
>
>
> On 05/30/2012 11:16 PM, Thiago Satake wrote:
>
>> 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>
>>> "<
>>> 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<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<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