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

Suzanna Lewis suzi at fruitfly.org
Sat Jun 5 23:36:55 PDT 2004


I would guess this is the problem that Jen/I/&others were
discussing. The duplicated synonym differs only by case.
The way things were settled was that differences of
appearance/format (case in this case) would be ignored
and thus the 2 synonyms are the same.

Anyway, deleting the duplicates was the right thing to do

On Jun 3, 2004, at 5:14 AM, Jane Lomax wrote:

> 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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>
>
>
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