[Bioperl-l] Bio::Ontology::OntologyI

Hilmar Lapp hlapp at gmx.net
Mon Mar 10 02:43:13 UTC 2008

On Mar 9, 2008, at 10:26 PM, Naama Menda wrote:
> On Sun, Mar 9, 2008 at 10:13 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
> On Mar 9, 2008, at 9:34 PM, Naama Menda wrote:
>> My main problem is that go-perl does not handle updates, so if I  
>> want to update GO I need an empty schema. We find it more  
>> complicated to re-load our annotations than to update cvterms and  
>> their related data.
>> Our loading script compares an existing load of an ontology to the  
>> obo file and updates/insets/deletes accordingly.
> load_ontology.pl in bioperl-db should have all this functionality,  
> though of course that doesn't give you the typedef support (yet).
> Will you add this support to obo.pm? I had a look at it and it  
> seems easy to implement.
> Will there be a patch? Or in the next Bioperl release?

If you have ideas for how to implement this we'd be thrilled if you  
can provide a patch.

Most changes in BioPerl happen because and by people who have an itch  
to scratch. Seems like this one is right down your alley?

I'd in principle be interested in doing this too but can't give any  
promises as to when I might have time (unless I need it myself :)

>> We are now in the process of committing this code to GMOD
> Cool - obviously load_ontology.pl doesn't work off of Chado but  
> instead uses BioSQL as the schema (though the ontology model is  
> *very* similar between the two).
> We  store ontologies in Chado, and that was the reason for writing  
> a new loader.

Looking at it it seems you wrote a whole new language binding? Did  
you find it too difficult to build on one of the existing ones (which  
use Class::DBI if I recall correctly, though Scott will have the  
details here)


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

More information about the Bioperl-l mailing list