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error when loading GO process into GO database

Arnaud Kerhornou axk at sanger.ac.uk
Fri May 21 06:16:03 PDT 2004


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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