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Re: blog: semantic dissonance in uniprot

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Sun, 22 Mar 2009 09:26:57 -0400
Message-ID: <5639badd0903220626y3b00baccwd41ab511c233c57@mail.gmail.com>
To: W3C HCLSIG hcls <public-semweb-lifesci@w3.org>
     Hello, All,

  We just started a discussion on identifying compounds at the last
meeting of the BioPAX OBO Workgroup and will continue at the next
meeting, to which any one interested is invited. We meet both locally
and virtually. Either stop by at 346 Stata MIT or log into Skype and
ask a participant (e.g. me) to invite you to text and voice chat. Next
meeting is this week, Tuesday, 4pm to 6pm EST.

  Action item for next meeting: Getting familiar with PRO.

  The topic lies at the center of the pathway community and has been
subject to bitter battles. Usually, a pathway is defined in terms of
connected smaller processes which are defined in terms of
participating compounds and their roles. Connected means that a
participant of process A is the same as (owl:sameAs?) a participant in
process B. As important as knowing what is connected is knowing what
is disjoint (owl:disjointWith?). Inevitably, there is tension between
simplicity and rigour, between those who want to make it easy to stuff
data into databases and those who demand stricter criteria to make
pulling the data out again more useful. The community spans all the
way from the experimenter to the modeller to the drug designer, from
the qualitative to the quantitative, the conceptual to the precise.

     Take care
     Oliver

On Fri, Mar 20, 2009 at 1:35 PM, M. Scott Marshall
<marshall@science.uva.nl> wrote:
> FYI:
> http://i9606.blogspot.com/2009/02/semantic-dissonance-in-uniprot.html
>
> I thought that the above blog entry would interest some of you (it
> apparently already has interested a few of you that have added comments :)
> ). The blog is from Benjamin Good (from Mark Wilkinson's Lab) and was
> referenced during a napkin discussion I had with Marco Roos and Ben about
> how one could best refer to a protein in text-mined triples. One of the best
> options seemed to be to use a PURL that referred to a record associated with
> the protein. Sound familiar? Those of you who have been with us for more
> than a year will think so. See http://sharednames.org for an attempt to
> approach the issue.
>
> -Scott
>
>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
Received on Sunday, 22 March 2009 13:27:34 UTC

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