[Bioperl-l] Can I load ontologies into BioSQL?

[Florian Mittag]

Hi!

I wrote this under the subject of the DB2 driver, too, but this particular 
problem seems to also fit here.

I don't get the error message, but the same warnings as Achille, although I'm 
using the new OBO format. As you can see, the problems start right after the 
script gets to "relationships", before this there  are no warnings or errors.

(The lines between the warnings are debug information I added myself for a 
different problem.)

--- snip ---
[...]
        ... relationships
SELECT UK Bio::DB::BioSQL::TermAdaptoridentifier	
identifier : GO:0060058
SELECT term.term_id, term.identifier, term.name, term.definition, 
term.is_obsolete, cast(NULL as VARCHAR(255)), term.ontology_id FROM term 
WHERE identifier = ?

-------------------- WARNING ---------------------
MSG: GOC:dph exists in the dblink of _default
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: PMID:15282149 exists in the dblink of _default
---------------------------------------------------
SELECT UK Bio::DB::BioSQL::OntologyAdaptorname
name : gene_ontology
SELECT ontology.ontology_id, ontology.name, ontology.definition FROM ontology 
WHERE name = ?
SELECT UK Bio::DB::BioSQL::TermAdaptorname;ontology
ontology : 2
name : IS_A
SELECT term.term_id, term.identifier, term.name, term.definition, 
term.is_obsolete, cast(NULL as VARCHAR(255)), term.ontology_id FROM term 
WHERE ontology_id = ? AND name = ?
SELECT UK Bio::DB::BioSQL::TermAdaptoridentifier
identifier : GO:0043065
SELECT term.term_id, term.identifier, term.name, term.definition, 
term.is_obsolete, cast(NULL as VARCHAR(255)), term.ontology_id FROM term 
WHERE identifier = ?

-------------------- WARNING ---------------------
MSG: GOC:jl exists in the dblink of _default
---------------------------------------------------
SELECT UK Bio::DB::BioSQL::TermAdaptoridentifier
identifier : GO:0007429
SELECT term.term_id, term.identifier, term.name, term.definition, 
term.is_obsolete, cast(NULL as VARCHAR(255)), term.ontology_id FROM term 
WHERE identifier = ?

-------------------- WARNING ---------------------
MSG: GOC:mtg_sensu exists in the dblink of _default
---------------------------------------------------
[...]
--- snap ---

The command is:

perl load_ontology.pl --driver DB2 --dbname bioseqdb --dbuser <user>
        --dbpass <passwd> --namespace "Gene Ontology" --format obo
        /tmp/gene_ontology.1_2.obo


Any ideas?

Regards,
   Florian


On Saturday 04 July 2009 14:02, Hilmar Lapp wrote:
> according to Chris Mungall from the GO Consortium, the .ontology files
> have been deprecated by GO. You should use the .obo files instead, and
> BioPerl has a parser for that (and load_ontology.pl supports all
> formats that BioPerl supports).
>
> There has been a near identical issue report earlier (April 20 - I
> don't have the thread from the archives at hand). According to Chris,
> the BioPerl parser for the .ontology files appears to fail to deal
> with the new relations in GO, and so with the obsoletion of
> the .ontology format we have scheduled the respective parser for
> deprecation.
>
> 	-hilmar
>
> On Jun 22, 2009, at 10:12 AM, Achille Zappa wrote:
> > Hi guys
> >
> > I'm working with biosql and I try to figure out how to load ontologies
> > into biosql.
> >
> > I've tried to load the flat files gene ontologies :
> >
> > load_ontology.pl   --driver mysql --dbuser xxx --dbpass xxx --host
> > localhost --dbname biosql --namespace "Gene Ontology" --format goflat
> > --fmtargs "-defs_file,GO.defs"  function.ontology process.ontology
> > component.ontology
> >
> > as in the script info but I have an error,
> >
> > a lot of  ------------ WARNING ---------------------
> > MSG: DBLink exists in the dblink of _default
> > ---------------------------------------------------
> > and at the end
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: format error (file /home/user/Download/process.ontology)
> > offending line:
> >     -negative regulation of angiogenesis ; GO:0016525 ; synonym:down
> > regulation of angiogenesis ; synonym:down\-regulation of angiogenesis
> > ; synonym:downregulation of angiogenesis ; synonym:inhibition of
> > angiogenesis % negative regulation of developmental process ;
> > GO:0051093 % regulation of angiogenesis ; GO:0045765
> >
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw
> > /usr/lib/perl5/vendor_perl/5.10.0/Bio/Root/Root.pm:357
> > STACK: Bio::OntologyIO::dagflat::_parse_flat_file
> > /usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:627
> > STACK: Bio::OntologyIO::dagflat::parse
> > /usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:284
> > STACK: Bio::OntologyIO::dagflat::next_ontology
> > /usr/lib/perl5/vendor_perl/5.10.0/Bio/OntologyIO/dagflat.pm:317
> > STACK: load_ontology.pl:604
> > -----------------------------------------------------------
> >
> > could you help me?
> > is it possible to use the OBO format with the loader?
> > those GO flat files are deprecated by the Gene Ontology site
> > is there a list of format to use with the biosql perl scripts?
> >
> > thank you
> > regards
> > Achille