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

[Duangdaow Kanhasiri]

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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