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error when loading GO process into GO database

Arnaud Kerhornou axk at sanger.ac.uk
Fri May 21 09:01:39 PDT 2004


ok, thanks for this

Arnaud

Daniel Barrell wrote:

> 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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