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[bioontology-support] Hierarchy services

Trish Whetzel whetzel at
Wed Sep 22 15:01:18 PDT 2010

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:

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.


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