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[Go-database] Re: error when loading GO process into GO database

Jane Lomax jane at ebi.ac.uk
Thu Jun 3 05:14:20 PDT 2004


Hi Martin,

I've just taken out those two synonyms - not sure why this has been 
happening - those synonyms have been in the ontololgy for a while. If 
you're using process.ontology, you should see those changes by tomorrow 
(the old flat file format is now updated once a day),

thanks,

Jane

On Thu, 3 Jun 2004, Martin Aslett wrote:

> Hi,
> 
> We're still getting the error that Arnaud reported below, using the
> process.ontology file from the anonymous CVS.
> 
> DBD::mysql::st execute failed: Duplicate entry '6383-Smt3-dependent
> protein degradation' for key 1 at
> /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/SqlWrapper.pm
> line 818, <GEN0> line 30057.insert into term_synonym (term_id,
> term_synonym) values (?, ?) Duplicate entry '6383-Smt3-dependent protein
> degradation' for key 1 at
> /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/SqlWrapper.pm
> line 818 GO::SqlWrapper::insert_h('DBI::db=HASH(0x1409c1ea8)',
> 'term_synonym', 'HASH(0x14128e9f0)') called at
> /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/Handlers/DbStoreHandler.pm
> line 337
> 
> Cheers,
> 
> Martin
> 
> On Fri, 21 May 2004, Arnaud Kerhornou wrote:
> 
> > Hi
> >
> > We're having troubles in loading the GO process ontology into our local
> > GO database. We use the process.ontology file from the anonymous CVS. It
> > seems to stop while trying to load a synonym that is already loaded.
> >
> > ------------>
> > DBD::mysql::st execute failed: Duplicate entry '6291-Smt3-dependent
> > protein degradation' for key 1 at
> > /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/SqlWrapper.pm
> > line 818, <GEN0> line 26766.
> > insert into term_synonym (term_id, term_synonym) values (?, ?)
> >     Duplicate entry '6291-Smt3-dependent protein degradation' for key 1
> > at
> > /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/SqlWrapper.pm
> > line 818
> >     GO::SqlWrapper::insert_h('DBI::db=HASH(0x1409c2150)',
> > 'term_synonym', 'HASH(0x141265100)') called at
> > /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/Handlers/DbStoreHandler.pm
> > line 337
> > ...
> >
> > GO::Parsers::GoTextParser::parse_file('GO::Parsers::GoTextParser=HASH(0x14070ed08)',
> > '/nfs/pathsoft/databases/go_cvs/ontology/process.ontology', undef)
> > called at
> > /nfs/pathsoft/external/go-dev_oracle_mod_perl/apps/db-loading/load-go.pl
> > line 52
> >     ...propagated at
> > /nfs/pathsoft/external/go-dev_oracle_mod_perl/perl-api/GO/Parsers/BaseParser.pm
> > line 240, <GEN0> line 26766.
> > <-----------
> >
> > grep 'Smt3-dependent protein degradation' process.ontology
> >          %SMT3-dependent protein catabolism ; GO:0019950, GO:0019946 ;
> > synonym:SMT3-dependent protein degradation ; synonym:Smt3-dependent
> > protein catabolism ; synonym:Smt3-dependent protein degradation
> >         %SMT3-dependent protein catabolism ; GO:0019950, GO:0019946 ;
> > synonym:SMT3-dependent protein degradation ; synonym:Smt3-dependent
> > protein catabolism ; synonym:Smt3-dependent protein degradation
> >
> > It looks like the synonym is duplicated three times ? Can someone look
> > at this please ?
> >
> > cheers
> > Arnaud
> >
> >
> > --
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