[Bioperl-l] load_ontology and GO - progress!

Hilmar Lapp hlapp at gnf.org
Thu Apr 22 21:33:38 EDT 2004

Did you read the load_ontology.pl POD, in particular the documentation  
for the options that deal with obsolete terms?

Obsolete terms is not a trivial thing to deal with, and in the end you  
need to make some decisions for yourself. load_ontology.pl offers  
several choices but it's up to you what works best for you. There have  
been prior threads on this; e.g. reading  
http://bioperl.org/pipermail/bioperl-l/2004-February/014846.html may  
give you some additional information.

Note also that supplying --safe will make the script continue despite  
errors from the database.


On Thursday, April 22, 2004, at 04:39  AM, Dave Howorth wrote:

> Hi everybody,
> I'm very pleased to report that the upgraded branch-1-4 now passed its  
> tests to an acceptable/understandable level and has installed.  
> Furthermore, it has fixed the original trouble with the load_ontology  
> program.
> So big thanks to everybody who has put effort into helping me, fixing  
> problems and updating docs so quickly.
> There's always a gotcha, of course ...
> load_ontology is now failing with messages like this:
> Loading ontology Gene Ontology:
> 	... terms
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::TermAdaptor (driver) failed, values  
> were ("GO:0001529","elastin","OBSOLETE (was not defined before being  
> made obsolete).","X") FKs (2)
> Duplicate entry 'elastin-2' for key 2
> ---------------------------------------------------
> 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/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:207
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/local/share/perl/5.6.1/Bio/DB/BioSQL/> BasePersistenceAdaptor.pm:253
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/local/share/perl/5.6.1/Bio/DB/Persistent/PersistentObject.pm:270
> STACK (eval) load_ontology.pl:508
> STACK toplevel load_ontology.pl:490
> --------------------------------------
> What appears to be happening is that the GO.defs file defines two  
> terms called 'elastin' (0001528 and 0001529), one of which is used in  
> component.ontology and the other in function.ontology.  Both are  
> declared OBSOLETE.
> This isn't an isolated case; it occurs for 'collagen' as well, for  
> example.  Neither is it new in this release of the files; I found it  
> in an old copy I had.
> The GO flat file definition format document isn't very helpful in  
> describing what should be in the file, so my question is whether this  
> duplication is a legitimate occurence in GO?
> That is, is there a bug in the GO distribution (duplicate IDs) or a  
> bug in the biosql model (each of the three GO ontologies needs a  
> separate ontology ID)?
> Also of interest would be any ideas for a workaround :)
> Cheers, Dave
> -- 
> Dave Howorth
> MRC Centre for Protein Engineering
> Hills Road, Cambridge, CB2 2QH
> 01223 252960
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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