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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 26 Mar 2009 11:21:58 -0500
Cc: Oliver Ruebenacker <curoli@gmail.com>, Mark Wilkinson <markw@illuminae.com>, W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
Message-Id: <98C6D26B-A3C6-476E-9DAE-C505F910925E@ihmc.us>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>

On Mar 26, 2009, at 10:45 AM, Phillip Lord wrote:

>
> Pat Hayes <phayes@ihmc.us> writes:
>>> Besides which, the issue being discussed here is one of equality.  
>>> When
>>> are two proteins the same protein?
>>
>> TWO proteins are never the same protein. Two mangelwurzels are  
>> never the same
>> mangelwurzel, either. What 'same' means, is that there is ONE   
>> thing with two
>> names. Being the same as is never a relationship  between two  
>> different
>> things.
>
>
> This is obvious; the question is about types of proteins. A statement
> like: "every protein molecule in the world is different from every  
> other
> protein molecule" is true, but more or less totally useless.

I agree, but I have no idea why you keep harping on about molecules. I  
didn't mention molecules.

>
> We are talking about proteins not protein molecules

Indeed, we are. Glad we have that clear.

> ; if I give you a
> solution of protein molecules, all the same, and you split it into two
> halves, do you now suddenly have two proteins?

No, of course not. You have two pieces of the same material. (This is  
all very standard ontological stuff, by the way: mereology 101)

>
> Protein is a mass term. You would agree that two glasses of water both
> hold the same substance; just so for protein.

Quite.

> The question is, then,
> when are two samples of protein, samples of the same protein.

I don't know the answer to that (not being a chemist) but I do know  
what it *means to say* they are the same protein, which is all we need  
for writing ontologies.

> A
> secondary question is, how do we represent this computationally.

You could use, for example, owl:sameAs. Provided of course that  
'proteins' were in your ontology.

I fail to see what you see as being any problem here. These 'issues'  
about mass terms were all fully worked out decades ago.

Pat

>
> We are going around in circles here; I think that I have said enough.
>
> Phil
>
>

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Received on Thursday, 26 March 2009 16:23:16 UTC

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