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[bioontology-support] Hierarchy services

Natasha F. Noy noy at stanford.edu
Tue Sep 28 14:09:19 PDT 2010


Ben,

On the mapping -- we run the mapping across all ontologies  
occasionally, but don't have it integrated into the workflow yet. Once  
you have some ontologies that you would like us to map, maybe you  
could alert us and then we'll run the mapping for them, without  
waiting for all the mappings to be updated.

Naturally, our plan is to have this integrated into our workflow, and  
to have the mapping kick off each time an ontology is uploaded.

Natasha


On Sep 23, 2010, at 5:07 PM, ben leinfelder wrote:

> Hi Trish -
> Thanks for your response. I imagine I'll have an even better  
> understanding once the ontologies are processed for use with the  
> hierarchy services.  Is the mapping algorithm a separate process and  
> does it require action on my part?
> It sounds like term mapping is meant to eek out equivalences that  
> are not formally defined in the OWL files rather than to aid  
> navigation among children of a shared superclass. We'll likely want  
> to take advantage of this sort of mapping feature as more and more  
> domain-specific extensions to OBOE are created where the authors  
> have [unwittingly] defined equivalent/overlapping concepts.
> In terms of "ontology groups", I've gone ahead and placed both of  
> the OBOE ontologies in the "Semtools" BioPortal project. While this  
> doesn't enforce any formal relationship, at least it keeps the group  
> organized. Perhaps someday I can use the search services to return a  
> subset of ontologies by project.
> -ben
>
> On Sep 22, 2010, at 3:01 PM, Trish Whetzel wrote:
>
>> Hi Ben,
>>
>>> 1. How can I get my ontologies processed so that the hierarchy  
>>> services can be invoked on them. Here is an example service call I  
>>> might use for my OBOE SBC ontology: http://rest.bioontology.org/bioportal/concepts/children/44257/Sample
>>
>> We routinely process ontologies for use with the Hierarchy web  
>> services. I'll double-check with the developers, but I believe OBOE  
>> SBC should be processed in the next round.
>>
>>
>>> 2. How are imports handled?
>>> 	a) As we've discussed previously, our project uses a base "OBOE"  
>>> ontology that various ontologies are meant to extend (via import).  
>>> The classes in the extension ontology are subclasses of the base  
>>> ontology and I'd like to be able to access these children no  
>>> matter which extension ontology defines them (assuming they are  
>>> registered in BioPortal). So far I've uploaded the OBOE base  
>>> ontology and the OBOE SBC ontology that extends it.
>>> 	b) When invoking hierarchy services must I use the ontologyId in  
>>> which the concept was _defined_ or can the concept be defined in a  
>>> parent ontology that is imported?
>>
>> For OWL ontologies that use the import statement, the ontology  
>> loaded into BioPortal will also include the import and it's content.
>>
>>> 	c) Incidentally there is yet another level of indirection in that  
>>> 'Entity' (defined in oboe-core as imported in oboe) is one example  
>>> of a superclass of which I'd like to get all children. These  
>>> children should be gathered from any registered extension ontology  
>>> that has subclasses of 'Entity'. Is this the behavior of BioPortal?
>>
>> The Get all children web service is based on the ontologyId or  
>> ontology version id depending on which variation of the web service  
>> is used.  The child terms returned will be those found in the  
>> version of the ontology specified in the web service call.
>>
>>> 	d) Given two or more extension ontologies that import our OBOE  
>>> ontology, do the extension ontologies 'share' the imported OBOE  
>>> ontology?
>>
>> If the import was designated in Protege with the import statement,  
>> then each extension will contain the contents of the imported  
>> ontology.
>>
>>> 	e) Currently there does not appear to be any formal BioPortal  
>>> relationship between OBOE and the OBOE SBC extension (other than  
>>> what is in the OWL files themselves). Perhaps this will change  
>>> once the ontologies are processed for use with the concept  
>>> hierarchy services?
>>
>> Correct, there is not a formal relationship between OBOE and OBOE  
>> SBC as they are loaded as separate ontologies. Processing for use  
>> with the Hierarchy web services will not provide this linkage. When  
>> the ontologies are processed via our term mapping algorithm, the  
>> terms that are common between the ontologies will be displayed in  
>> the mappings tab.
>>
>> I've added Natasha to this thread as well for additional thoughts  
>> on the idea you previously suggested WRT to "groups" of ontologies.
>>
>> Trish
>>
>>
>>
>




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