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[HCLS] Circularity of Reasoning

From: Donald Doherty <donald.doherty@brainstage.com>
Date: Mon, 21 Aug 2006 15:39:53 -0400
To: "'w3c semweb hcls'" <public-semweb-lifesci@w3.org>
Message-ID: <006b01c6c559$93b4d1e0$6401a8c0@Brainstage>

Matt is right, of course. Circularity is always a danger when dealing with
semantics (bootstrap problem).

Let's say we use some sort of probabilistic reasoning to provide a measure
of semantic similarity to two elements existing in two ontologies. (For
instance, a Bolzman machine algorithm might do.)

How now to test the similarity link for veridicality? (That is, are they
really similar? ...and so on to infinity!)

So, perhaps we settle for a way to provide weights like in an artificial
neural network that may be continuously adjusted...

In other words, can we ever say "absolutely identical" and "absolutely not
identical" or should be instead come up with a standard that enables the
dynamic representation of relative sameness and difference?

Don

-----Original Message-----
From: Matt [mailto:matt.halstead@auckland.ac.nz] 
Sent: Sunday, July 30, 2006 8:47 PM
To: donald.doherty@brainstage.com
Cc: 'Eric Neumann'; 'Alan Ruttenberg'; 'w3c semweb hcls'
Subject: Re: URI thoughts

Donald's solution feels a little circular. The interpretation of  
these relations still need a formal specification, which OWL would do  
nicely for, but then OWL already defines similar constructs.

I think the "one true ontology" idea fails simply through open world  
semantics; I'm not sure the community should be aiming to formally  
agree on one true identity of something, but should formally agree on  
how to formally describe something so that reasoning/classification  
agents can provide the mechanism to highlight what is same or  
different identity.


On 31/07/2006, at 12:31 PM, Donald Doherty wrote:

>
> Eric,
>
> What you call "covering" below seems particularly important. In my  
> view,
> there can never be one true ontology, especially in science (unless  
> we're
> done and have reached complete knowledge...if that's possible). You  
> present
> an interesting solution...
>
> Don
>
> Donald Doherty, Ph.D.
> Brainstage Research, Inc.
> www.brainstage.com
> donald.doherty@brainstage.com
> 412-478-4552
>
>
> [snip]
>
> In the absence of any formal ontology that could cover all life
> sciences data records (e.g., Genes), a relational instance model might
> be more practical and appealing; A transitive rule could be proposed
> that states all data records referencing the same bio/chem-entity  
> would
> be viewed as "bio/chem entity" equivalent, regardless of what
> ontology/rdfschema were used to define each of them:
> (?data1 hcls:isDefinedAs ?ent) AND (?data2 hcls:isDefinedAs ?ent) ->
> (?data1 hcls:sameEntityAs ?data2 )
>
> This is an example of what I had suggested as a "Covering", since  
> there
> is no explicit need to use ontologies to map data records to common
> class-based concepts. owl:sameAs could be used hear, but  the
> 'sameEntityAs' relation could have more selective meaning for this
> community in terms of data records and 'things'. I leave it open for
> discussion...
>
> I'd be interested to hear how important and practical the points  
> raised
> here are. The main objective I have is to try and get our common
> discussion to focus on some basic, agreeable points that we can work
> together on over the next (hopefully) few weeks.
>
> cheers,
> Eric
>
>
> Eric Neumann, PhD
> co-chair, W3C Healthcare and Life Sciences,
> and Senior Director Product Strategy
> Teranode Corporation
> 83 South King Street, Suite 800
> Seattle, WA 98104
> +1 (781)856-9132
> www.teranode.com
>
>
>
>
>
>
Received on Monday, 21 August 2006 19:37:55 GMT

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