Relation between ontology and database

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Relation between ontology and database

Julian Vincent-2
I’ve written an ontology which has been exhaustively tested and seems to work very well. However, the associated database section, which comprises a description of biological cases according to the classification of properties that the ontology encapsulates, keeps throwing up exceptions (owl: nothing) when I run the Reasoner (FaCT++) through the whole ontology+database. I’ve previously regarded this as a fault and spent long times trying to correct it (mostly by removing disjointness from the ontology - which obviously weakens it). But there are no ground rules to biology. So am I really only looking at this latter fact - that I should not expect biology to conform to the relations within the ontology? I am aware that the ontology is supposed to describe reality, but biology tends towards the English language in its organisation - few rules, lots of exceptions.

Comments, please.

Julian
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Re: Relation between ontology and database

Chris Mungall
Hi Julian

I think some concrete examples would help.

Btw, if the reasoner throws exceptions, that's an error in the reasoner.
Do you mean that the reasoner detects either unsatisfiable classes
(equivalent to Nothing) or inconsistencies, i.e. the ontology is
incoherent. You can use the explanations ("?" button) in protege to
debug these.

On 25 Apr 2017, at 5:00, Julian Vincent wrote:

> I’ve written an ontology which has been exhaustively tested and
> seems to work very well. However, the associated database section,
> which comprises a description of biological cases according to the
> classification of properties that the ontology encapsulates, keeps
> throwing up exceptions (owl: nothing) when I run the Reasoner (FaCT++)
> through the whole ontology+database. I’ve previously regarded this
> as a fault and spent long times trying to correct it (mostly by
> removing disjointness from the ontology - which obviously weakens it).
> But there are no ground rules to biology. So am I really only looking
> at this latter fact - that I should not expect biology to conform to
> the relations within the ontology? I am aware that the ontology is
> supposed to describe reality, but biology tends towards the English
> language in its organisation - few rules, lots of exceptions.
>
> Comments, please.
>
> Julian
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Obo-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/obo-discuss

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