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Re: [ontolog-forum] [bfo-discuss] Re: Heterarchy & Hierarchy, oh my my

To: bfo-discuss@xxxxxxxxxxxxxxxx, Phillip Lord <phillip.lord@xxxxxxxxxxxxxxx>
Cc: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>, obo-relations@xxxxxxxxxxxxxxxxxxxxx
From: Alan Ruttenberg <alanruttenberg@xxxxxxxxx>
Date: Mon, 12 May 2008 23:15:54 -0400
Message-id: <71276CEE-2D06-41FD-99B0-FC545D44057E@xxxxxxxxx>
On May 6, 2008, at 11:54 AM, Phillip Lord wrote:
>>>>>> "Alan" == Alan Ruttenberg <alanruttenberg@xxxxxxxxx> writes:
>   Alan> I've seen the disadvantages of multiple asserted  
> inheritance when
>   Alan> reviewing, e.g. the Cell ontology in OBO, where it was  
> demonstrated
>   Alan> (by the authors) that it was quite easy to find mistakes of  
> the sort
>   Alan> where all of the properties described in the definition of  
> (multiple,
>   Alan> and transitive) superclasses were not true of instances of  
> the class
>   Alan> in question. Regarding (c) what is perhaps being referred  
> to is that
>   Alan> if one practices "normalization" in the sense that Alan Rector
>   Alan> proposes [1] then the component single inheritance  
> ontologies from
>   Alan> which more complex terms are constructed are more likely to  
> be able to
>   Alan> be reused by other projects. Certainly that's the intention of
>   Alan> creating and using PATO. I've found the exercise of factoring
>   Alan> definitions in this manner is often helpful and is  
> conducive to
>   Alan> helping the sorts of people I work with think carefully when
>   Alan> constructing ontologies.
> I think that we need to be clear here; there is a fundamental  
> distinction
> between normalisation as according to Alan Rector and to the idea  
> of single
> inheritance is a correct reflection of reality.    (01)

I think I've been clear on this. What I consider interesting is that  
the same conclusions about the pragmatics of ontology construction  
arise from two different approaches. For me, since I have respect for  
the purveyors of these two approaches, this strengthens the case that  
this is a good way to go about doing things.    (02)

> While you are correct that allowing multiple inheritance increases  
> the risk of
> some common errors, it also allows modelling that is not possible  
> otherwise;
> in particular it can be used to avoid a combinatorial explosion of  
> terms.    (03)

Example?    (04)

> My take; single inheritance can be easier and simpler sometimes,  
> but not always;    (05)

Curious about the not always. And not sure about the easier or  
simpler either. "I would have written a shorter letter if I had  
time", etc. But I think it leads to better quality results.    (06)

> using a computationally amenable languages and normalisation allows
> you to get some of the advantages of both.    (07)

+1 on that one.    (08)

-Alan    (09)

(the *other* Alan R ;-)    (010)

> Phil
> ps, I started of writing this email referring to Alan Rector as  
> "Alan". Then I
> had to correct it to "Alan R" to disambiguate from you. Then again.  
> Eech.    (011)

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