[Bioperl-l] DB2 driver for BioPerl

Florian Mittag florian.mittag at uni-tuebingen.de
Thu Jul 2 09:28:21 UTC 2009


I previously posted a message on the BioSQL mailinglist regarding a BioSQL 
schema for DB2 and we are several steps closer to completion now.

We were able to adapt the "load_ncbi_taxonomy.pl" script from BioSQL to fill 
our DB2 database with taxonomy data, but loading the gene ontology with 
BioPerl's "load_ontology.pl" is somewhat harder.

We created the Package Bio::DB::BioSQL::DB2 and copy-pasted the contents of 
the Oracle package into it. Then we changed the (what we thought) appropriate 
methods whenever we encountered an error, but now we are a bit frustrated.

We execute the command:
perl load_ontology.pl --driver DB2 --dbname bioseqdb --dbuser user
--dbpass passwd --namespace "Gene Ontology"
--format obo --debug gene_ontology.1_2.obo

It first ran a few minutes processing the file and then died after the 
following SQL-command was prepared and executed:

"SELECT term.term_id, term.identifier, term.name, term.definition, 
term.is_obsolete, NULL, term.ontology_id FROM term WHERE identifier = ?"

I don't know if the "NULL" column is supposed to be there, but DB2 doesn't 
like it. After ours of digging into the code, I gave up and simply commented 
out the line that added the NULL column in 

        if((! $attr) || (! $entitymap->{$tbl}) ||
           $dont_select_attrs->{$tbl .".". $attr}) {
#            push(@attrs, "NULL");
        } else {

The script completed with a few warnings, like:
"no adaptor found for class Bio::Annotation::TypeManager"
"-------------------- WARNING ---------------------
MSG: PMID:15012271 exists in the dblink of _default"

so we don't know, if it really worked. Since removing this one line will 
probably break compatibility with other databases, it is not a real solution 
and we would appreciate any hints pointing us to the real cause.

We would really like to contribute to the BioPerl project by adding DB2 
support, but we need some help here, since none of us has experience with 
either Perl or BioPerl ;-)

Keep up the good work!


Dipl. Inf. Florian Mittag
Universität Tuebingen
WSI-RA, Sand 1
72076 Tuebingen, Germany
Phone: +49 7071 / 29 78985  Fax: +49 7071 / 29 5091

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