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

[Naama Menda]

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?

>
>
> 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.

>
> BTW please keep the Bioperl list in the loop, others may have insight too
> or be interested in the information.
>
> -hilmar
>
> --
>
Thanks!
-Naama

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