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[bioontology-support] Class equivalence in BioPortal

Erik Fäßler erik.faessler at uni-jena.de
Thu Nov 13 23:27:59 PST 2014


Ray,

thanks for your answer. I’m talking of the first case that is used a few times in OBOE. I just saw what you meant with “partially handled”:

OBOE states

“Hectopascal is equal to Millibar”; Protege automatically creates the reverse relation. I was confused because in BioPortal I did not see the reverse relation: the class “Millibar” in BioPortal does not state it would be equivalent to another class. However, in BioPortal, the class “Hectopascal” DOES state that it is equivalent to Millibar. So everything is all right, I just happened to look in the wrong direction. Sorry for that! :-)

Thanks again and best regards,

Erik

P.S.
Regarding your question whether I would have this case often: It’s not a case I would come across very often, but OBOE - and with it the OBOE-SBC ontology in BioPortal - makes frequent use of the feature.

> On 14 Nov 2014, at 00:31, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
> 
> Erik,
> 
> It is the case that we do not try to display anything with handle equivalent 
> classes now. There are two cases. The first, simpler case, is to handle 
> "class-A is-equivalent-to class-b". The second is "class-A is-equivalent to 
> ...some class expression...
> 
> Currently BioPortal does nothing with class expressions. We do actually 
> partially handle the first case though. (In the details for class A you can 
> see "is-equivalent-to" class B.). It is not really clear how often this 
> first case comes up though. Certainly the second case is much more common.
> 
> Do you have a situation where you commonly have equivalent classes without a 
> class expression?
> 
> Ray
> 
> -----Original Message-----
> From: bioontology-support 
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Erik 
> Fäßler
> Sent: Thursday, November 13, 2014 6:42 AM
> To: support at bioontology.org
> Subject: [bioontology-support] Class equivalence in BioPortal
> 
> Dear BioPortal-Team,
> 
> in my current work with the OBOE ontology I came across the OBOE-SBC 
> ontology in BioPortal. When I download this ontology and open it in Protege, 
> I see that there are some equivalence relations in there, for example 
> “Hectopascal is equivalent to Millibar”. However, when I browse the ontology 
> within the BioPortal homepage, I don’t see anything hinting to this 
> equivalence. Is BioPortal somehow expressing this equivalence relation or 
> can I only get it by parsing the downloadable OWL file? I did not find a 
> respective mapping, either. Can this information be retrieved using the REST 
> API somehow?
> 
> Thank you and best regards,
> 
> Erik
> _______________________________________________
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 



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