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Re: blog: semantic dissonance in uniprot

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Wed, 25 Mar 2009 17:05:02 +0000
To: "Mark Wilkinson" <markw@illuminae.com>
Cc: "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
Message-ID: <87vdpx1qkh.fsf@newcastle.ac.uk>
"Mark Wilkinson" <markw@illuminae.com> writes:
>> If I remember correctly the original post that started this of Ben has
>> it about right. We need some tags which say "these two database records
>> are about the same protein, well, sort of, at least in this case, for
>> the purposes of what I am doing".
>
>
> I agree - the issue also came up at the BioHackathon last week... basically,
> as Tom Oinn phrased it, "if you're thinking of using  owl:sameAs... don't!"
>
> Another predicate is needed that is less "rigourous" - owl:kindOfLike  :-)


Well, I would say OWL is the wrong place for this. It is about it's best
making clear statements with a defined semantics. More or less by
definition, we are talking about an area where we lack knowledge. 


> Oh what a tangled "Web" we weave!  ;-)


My own feeling is that it's biology which wove the web; we're just
caught in the middle. What role for the web and semantics? Well, I think
we need a coordinated, controlled and defined way of expressing our
mutual confusion. I'd love to have a clear definition of gene (or
protein). In it's absence, a good way of expressing "err..." is probably
the best we can do. 


Phil
Received on Wednesday, 25 March 2009 17:05:44 GMT

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