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[bioontology-support] Hierarchy services

ben leinfelder leinfelder at
Mon Sep 13 14:36:43 PDT 2010

Trish - 
I have a few questions that relate to navigating concepts among different ontologies.

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:

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?
	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?
	d) Given two or more extension ontologies that import our OBOE ontology, do the extension ontologies 'share' the imported OBOE 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?

Any insight you can provide on this would be great.

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