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

[Hilmar Lapp]

On Mar 10, 2008, at 11:09 AM, Naama Menda wrote:

>
>
> On Sun, Mar 9, 2008 at 10:43 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> 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 :)
>
> I'll try to provide a patch for this. I'll let you know how it goes..

That'd be awesome! Don't hesitate to let us know if you hit bumps.

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