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[bioontology-support] OBOE

ben leinfelder leinfelder at nceas.ucsb.edu
Wed Aug 18 21:21:12 PDT 2010


Paul - 
Thanks for following up with me. I must admit that I submitted these ontologies to BioPortal mostly in an exploratory fashion as I evaluate the various ontology repositories out there. OBOE itself is relatively stable at this point - at least for v1.0, but the SBC (Santa Barbara Coastal) extension remains in constant development.

I'm curious about the distinction between views and extensions/imports. Our structure is such that: 
- 'oboe' imports 'oboe-core', extending the core ontology with additional classes.
- 'oboe-sbc' imports 'oboe' (as well as 'oboe-units' and 'oboe-context') and defines subclasses of various classes defined in 'oboe'/'oboe-context'/'oboe-units'.

What is the recommended approach for registering these ontologies? Some options, as far as I can tell, might be:
1. Register each individual owl file as a distinct ontology
2. Register a top-level ontology (oboe-core) and then create views off of it (oboe, oboe-sbc**)
	**how is the "grandchild" view treated (ie, oboe-core -> oboe -> oboe-sbc)?
3. Register a somewhat-top-level ontology (oboe) and create views off of it (oboe-sbc)

Typically we'd be looking at a scenario in which communities of researchers author a domain-specific ontology much like oboe-sbc. The various core ontologies will remain relatively small and static, whereas versioning, exploration, and discovery will be paramount considerations for these domain-specific, researcher-defined extensions to oboe.

Any insight or additional resources you can point me to will be much appreciated.
Thanks,
-ben

On Aug 18, 2010, at 5:40 PM, Paul R Alexander wrote:

> Ben,
> 
> We noticed that you have recently tried to submit OBOE and OBOE-SDC to BioPortal and likely encountered an error. Due to a recently-resolved bug we've been able to process your request. You can see your ontologies in BioPortal here:
> http://bioportal.bioontology.org/ontologies/44257
> http://bioportal.bioontology.org/ontologies/44258
> 
> The two ontologies obviously have some differences, but it looks like one is perhaps an extended version of another. Generally we handle extensions like this by creating a "view" on the ontology that's being extended. For example, Gene Ontology has several views associated with it (http://bioportal.bioontology.org/ontologies/44308#views).
> 
> Views are generally treated the same as other ontologies in BioPortal, but they won't be processed by the Annotator and Resource Index and they won't appear individually in our main ontology list. Could you let us know how you'd like these handled?
> 
> Thanks! Sorry for any inconvenience and please let me know if you have any questions.
> 
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research




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