[Biojava-l] BioJava with BioSQL schema on Oracle database

[Duangdaow Kanhasiri]

Thanks a lot Richard ...

While I'm waiting for your new improvement, in the
mean time, I'll look at the example you said and try
to do some work around with it...

Cheers,

Duangdaow


--- Richard HOLLAND <hollandr at gis.a-star.edu.sg>
wrote:

> Funny you should ask that...
> 
> ...for users of biojava-1.4, there is an FAQ on this
> at the BioJava in
> Anger website:
> http://www.biojava.org/docs/bj_in_anger/  - scroll
> down
> the page to the section on sequence databases and
> you'll find a page to
> help you out there...
> 
> ...but neither the file parsers nor the BioSQL
> interface are perfect,
> and they do strange things with the fields they
> load.
> 
> If you can bear to wait a while, we are currently
> rewriting the file
> parsers and BioSQL interfaces as part of the
> biojavax project. Once
> these are finished we will announce them here, and
> provide tutorials on
> how to use them. However they will be not-at-all
> compatible with the
> current contents of BioSQL databases loaded using
> biojava-1.4, so if a
> lot of data is involved and this is a new and
> not-urgent project, it may
> pay to wait a little while.
> 
> cheers,
> Richard
> 
> Richard Holland
> Bioinformatics Specialist
> GIS extension 8199
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> 
> > -----Original Message-----
> > From: biojava-l-bounces at portal.open-bio.org 
> > [mailto:biojava-l-bounces at portal.open-bio.org] On
> Behalf Of 
> > Duangdaow Kanhasiri
> > Sent: Friday, October 07, 2005 4:28 PM
> > To: biojava-l at biojava.org
> > Subject: [Biojava-l] BioJava with BioSQL schema on
> Oracle database
> > 
> > 
> > Hi,
> > 
> > I wonder if there's any one BioJava community has
> ever
> > used Biojava with BioSQL schema on Oracle
> database? I
> > really do need some advices...
> > 
> > Is there any BioJava program to load the whole
> genome
> > sequence files(e.g. genbank format) in to BioSQL
> > database like in BioPerl has load_ncbi_taxonomy.pl
> and
> > load_seqdatabase.pl?  Or anybody used to do the
> stuff
> > like this and has some tricks/work around for
> this?
> > 
> > My problem is that I used to use these BioPerl
> scripts
> > to load my genbank files into BioSQL schema in
> > PostgreSQL database; however, due to the hugh
> > increasing amout of my data (the whole complete
> > bacterial genome genbank files and Blast result
> files
> > from them), I have to move to Oracle instead of
> > PostgreSQL (in order to use the extra features
> that
> > don't have in PostgreSQL e.g. table partioning,
> > clustering, etc).  
> > 
> > When I use the load_seqdatabase.pl BioPerl scripts
> > directly with Oracle database (Oracle version
> 10.1.3),
> > it can load some genbank files into the database
> and
> > then it just dead with some STACK error.  I don't
> know
> > if the problem is due to the versions of the code
> in
> > BioPerl-db that change so fast... 
> > 
> > I did try to port data from PostgreSQL to Oracle
> but
> > there're problems with some fields in many tables
> that
> > has LOB type that I couldn't load these tables.   
> > 
> > By the way, I know some java but I'm just the
> newbie
> > with BioJava, any help would be very grateful...
> > 
> > Regards,
> > 
> > Duangdaow
> > 
> >   
> > 
> > 
> > 
> > 		
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