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[bioontology-support] Class equivalence in BioPortal

Ray Fergerson ray.fergerson at stanford.edu
Fri Nov 21 14:47:26 PST 2014


Erik,

OK, since you are actually using the first case, it is possible that we can 
fix this case (insert the reverse relation) without too much trouble. I will 
discuss it with the team.

Ray

-----Original Message-----
From: bioontology-support 
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Erik 
Fäßler
Sent: Thursday, November 13, 2014 11:28 PM
To: Ray Fergerson
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Class equivalence in BioPortal

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
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>

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