[BioSQL-l] load_ontology.pl Problem

[Hilmar Lapp]

Elastin has probably been obsoleted. My guess is that you don't have a  
term with ID GO:0001529, but you do have a term with name 'elastin' in  
the Gene Ontology, which is probably not obsoleted.

Obsolete terms need to be dealt with in some way in biosql, and you  
need to choose which way. Check out the load_ontology.pl POD where it  
talks about the options for obsolete terms. Also, depending on whether  
you want obsolete terms in the database (there are reasons for possibly  
wanting this, if that sounds strange) you may need to expand the unique  
key constraint on the term table to include the is_obsolete column.  
Check out the schema DDL, there is a commented out inclusion of that  
column documented.

BTW for GO upload to work properly you need to use the latest cvs  
snapshot from the 1.4 branch. I'm not aware that 1.4.1 has already been  
released, but maybe I'm confusing this. At least I can't find the  
release tag. As for bioperl-db, given the stack trace you are not using  
0.1, but rather the post-Singapore version.

Hth,

	-hilmar

On Tuesday, April 27, 2004, at 05:43  AM, Raphael A. Bauer wrote:

> Hi List,
>
> I encountered a problem parsing the Gene Ontology using Bioperl 1.2.1  
> and bioperl-db 0.1 (?).
>
> The parsing of the Gene Ontology Files into a BioSQL Schema worked  
> fine many times about 2 Months ago. Today I tried to parse the new GO  
> Files (26. April 2004) and got stuck with the follwing message:
>
>
> Loading ontology Gene Ontology:
>         ... terms
> Could not store GO:0001529 (elastin):
>
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Ontology::GOterm) failed to insert or to be  
> found by unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:270
> STACK (eval) load_ontology.pl:489
> STACK toplevel load_ontology.pl:471
>
> --------------------------------------
>
>
> If i try to override the problems with --safe I get about 150  
> Errors.(btw. Item GO:0001529 is not in my Biosql DB).
>
> We also tried to use the latest bioperl Version (1.4.1) and get the  
> same errors.
>
> Now I wonder what is wrong with my Bioperl Installtion.
>
>
>
> Many thanks in advance,
>
> Raphael
>
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------