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[bioontology-support] BioPortal metadata ontolgy

Todd Detwiler det at
Wed Aug 12 09:39:17 PDT 2009

Thanks Natasha. Regarding my need for direct access to all the 
instances, given your last message (about how to get all ontologies that 
are in OWL), I don't really need this access. If it had turned out that 
it was a question that I couldn't ask via the service, then I would have 
been looking for an alternative access mechanism. I can imagine 
operations that would be easier given the instantiated ontology, but so 
far nothing I need is inaccessible through the services.

For the moment I am just trying to determine which ontologies we could 
potentially provide (extended) SparQL query service for. This will only 
work on the OWL ontologies, not those in OBO format.


Landon Todd Detwiler
Structural Informatics Group (SIG)
Biological Data Integration and Analysis Group (Bio-DIAG)
University of Washington

Natasha Noy wrote:
>> Under the hood, does BioPortal populate the BioPortalMetadata 
>> ontology with actual instances of ontologies (their metadata I mean)?
> Yes. Go to
> and select "BioPortal Metadata Ontology". Once there, select the 
> Individuals tab and the OMV:Ontology class for a sample of instances.
>> If so, can you query the service for a copy of the ontology, complete 
>> with instances (for custom processing not supported by the api)?
> no, sorry :( We haven't yet figured out a clean way to do it.
>> I have a copy of the metadata ontology, but it doesn't have any 
>> instances of classes ontology or ontology view (for example).
> Yes, you'll have to use the public rest services to get to  that 
> information. Once we have the release with the views (last week of 
> August), there will be services similar to the service in your 
> previous email that would get you to the information about the views.
> Why do you feel you need direct access to all the instances? Is there 
> some additional functionality that maybe we can expose to you through 
> services?
> Natasha

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