W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2007

Re: Advancing translational research with the Semantic Web

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 17 May 2007 09:08:58 -0700
Message-Id: <p0623092bc2722d233347@[192.168.1.4]>
To: samwald@gmx.at
Cc: public-semweb-lifesci@w3.org

>  > Just catching up on reading papers :-)
>>
>>  <http://www.biomedcentral.com/1471-2105/8/S3/S2>
>>
>>  "It is also useful to know who believes something and why. However, there
>>  is no standard way of expressing such information about a statement [...]"
>>
>>  Reification?
>
>To return to the original question: In many of the biomedical 
>ontologies we are currently using or developing most of the 
>biological relations that matter ARE already reified.

? See below

>For example, most current ontologies would not contain the statement 
>"<A> <binds_to> <B>", rather they would contain the two statements 
>"<binding_process> <has_participant> <A> . <binding_process> 
><has_participant> <B>".

OK, but that's not reification. Its what is often called role-based 
descriptions. It introduces the binding process into the vocabulary 
which is almost certainly a good idea,  but it doesn't give you a way 
to talk about the assertion itself.

>Statements about believe, evidence and provenance can be easily 
>attached to "<binding_process>".

Hmm. They could, but that isn't really internally coherent. If this 
is supposed to be the name of a process, then its doesn't make sense 
to say that it has a provenance or that it is subject to belief. If 
on the other hand it's a propositional kind of thing, then it doesn't 
make sense to say that it has participants.

>We have already done this for some ontologies we developed for the 
>Banff demo. I think that this approach will proof to be sufficient 
>for most use cases,

It will work for a while, then it will break when things get more 
complicated. Its a hack; hacks work, but one shouldn't forget that 
they are hacks, and will need to be re-done properly eventually.

Pat Hayes

>and that the need for reification or fine-grained labeling of graphs 
>is generally quite low (but I guess there are exceptions).
>
>-- Matthias Samwald
>
>Yale Center for Medical Informatics, New Haven /
>Section on Medical Expert and Knowledge-Based Systems, Vienna /
>http://neuroscientific.net
>
>
>
>.
>--
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Received on Thursday, 17 May 2007 16:09:06 UTC

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