Re: [Obo-discuss] Drosophila Phenotype Ontology

[Alan R. <ala...@gm...>]

Hi David. 

Could you please submit this as a ticket to the operations working group tracker. 

For what it's worth, I think you could just submit a namespace request as usual. I don't think there's any requirement that the IDs in the file at that location actually use the prefix. It's the other way around, if the prefixes used them at Ontology should be found at that location that includes those terms. At least that's my current understanding of what we've said. 

-Alan

On Jul 25, 2013, at 8:12 AM, dosumis <do...@gm...> wrote:

> Hi there,
> 
> It's been a couple of weeks since I sent this mail.  Wondering if anyone has any thoughts on it.  Can DPO be listed on the foundry despite not having its own foundry IDSPACE?
> 
> Cheers,
> David
> 
> 
> On 12 Jul 2013, at 10:35, David Osumi-Sutherland wrote:
> 
>> Dear Foundry,
>> 
>> I'd like to submit the Drosophila Phenotype Ontology  (DPO) to the OBO Foundry.  It consists of about 190 terms for commonly encountered and/or high level Drosophila phenotypes.  It has significant formalisation - utilising terms from GO, CL, PATO and the Drosophila anatomy ontology.  It has been used by FlyBase for > 159000 annotations of phenotype.   We are not aware of any other ontology that covers this domain, so there are no orthogonality issues. We have an open term tracker, wiki page and repository. A forthcoming paper (submitted to JBMS) will describe the DPO in detail.  
>> 
>> The one wrinkle, and the reason the DPO has never been submitted before, is that it shares the IDSPACE FBcv with a mix of other CVs/ontologies used by FlyBase (collectively released as http://purl.obolibrary.org/obo/fbcv/fbcv.owl).  The chances of persuading FlyBase, so far the only user of this ontology, to invest the time and resource required to shift their phenotype annotations to a new IDSPACE are low.  So I have kept the IDSPACE while releasing the the ontology separately from the rest of fbcv using foundry standard URIs:
>> 
>> http://purl.obolibrary.org/obo/fbcv/dpo.owl
>> http://purl.obolibrary.org/obo/fbcv/dpo-non-classified.owl
>> http://purl.obolibrary.org/obo/fbcv/dpo-simple.obo
>> etc
>> 
>> I hope that difference between the ontology name and IDSPACE is not a block to acceptance of this ontology to the obo library and ultimately to the Foundry.
>> 
>> Please note that the current URI pattern fits with the Foundry ID policy for derived ontologies, but I would much prefer the simpler URI patterns that other foundry ontologies have:
>> 
>> http://purl.obolibrary.org/obo/dpo.owl
>> http://purl.obolibrary.org/obo/dpo/dpo-non-classified.owl
>> etc
>> 
>> Would this be possible?  Any decision on changing (simplifying) the URI will need to be quick as we will need to modify our upcoming paper to reflect this prior to publication.
>> 
>> Regards,
>> 
>> David
>> 
>> David Osumi-Sutherland, PhD
>> Ontologist at FlyBase & Virtual Fly Brain
>> Department of Genetics, University of Cambridge,
>> Downing Street, Cambridge, CB2 3EH, UK
>> Tel: +44 (0)1223 333 963, Fax: +44 (0)1223 766 732
>> http://www.virtualflybrain.org
> 
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