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error when loading GO process into GO database

Daniel Barrell dbarrell at ebi.ac.uk
Fri May 21 08:48:57 PDT 2004


Hi,

There is a small format error in the file which the GO editorial team 
are fixing...

'[GO: jic]' -> '[GO:jic]'

Cheers

Dan

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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> 

-- 

Daniel Barrell
EMBL - The EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Phone: +44 (0)1223 492551
Email: dbarrell at ebi.ac.uk


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