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RE: Evidence

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Mon, 18 Jun 2007 11:36:25 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D124428946@PHSXMB20.partners.org>
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>, <samwald@gmx.at>, <satya30@uga.edu>
Cc: "Waclaw Kusnierczyk" <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>, <phismith@buffalo.edu>, <public-semweb-lifesci@w3.org>


Alan, Satya, Matthias et. al...

Will be great if you could update the wiki with your comments.

Thanks,

---Vipul

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of Alan Ruttenberg
> Sent: Monday, June 18, 2007 2:30 AM
> To: samwald@gmx.at
> Cc: Waclaw Kusnierczyk; phismith@buffalo.edu; public-semweb-lifesci@w3.org
> Subject: Re: Evidence
> 
> 
> 
> On Jun 12, 2007, at 3:53 PM, samwald@gmx.at wrote:
> 
> >
> > Hi Waclaw,
> >
> >
> >> Matthias, if you look carefully at BFO, you'll see that roles are
> >> entities.  This means that evidences, as roles, are entities.
> >
> > Of course. I just wanted to differentiate that an experiment is not
> > an instance of any class called 'evidence' (in other words, an
> > experiment 'is not' evidence). Instead, it should be associated
> > with an 'evidence-role'.
> 
> The only problem with this is that roles inhere in continuants rather
> than in occurrents. One way around this is not to say that evidence
> is an experiment, but rather the results of an experiment.
> 
> In the protocol application branch we've been discussing the idea of
> "proxy". A common pattern in  biological experiments is that you want
> to measure one thing but in fact you measure another. In one of our
> use cases, we for instance look at chromium release cytoxicity assays
> (https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay)
> 
> In this case the desired measurement is the fraction of cells in a
> cell culture that have died.
> The cells are treated with a radioactive substance that is absorbed
> into their cytoplasm, only to be released when they die and the
> membrane is broken. So if you start with fresh medium and these
> cells, you can estimate the amount that have died by measuring the
> radioactivity of the medium.
> 
> In this case we plan to say that radioactivity of the medium is a
> proxy for the the number of cells that die.
> 
> Now if you ask what the evidence for the cytoxicity estimate the path
> leads via inverse proxy relations eventually to physical properties
> that are measured by some instrument. If we were doing an analysis of
> what could undermine the conclusion, each of these steps could be
> questioned.
> 
> In this case the inference isn't quite as mysterious - all of it is
> bottled up beforehand in the statement of the proxy relations.
> 
> -Alan
> 
> >
> > cheers,
> > Matthias
> >
> > cheers,
> > Matthias Samwald
> >
> > ----------
> >
> > Yale Center for Medical Informatics, New Haven /
> > Section on Medical Expert and Knowledge-Based Systems, Vienna /
> > http://neuroscientific.net
> > --
> > Psssst! Schon vom neuen GMX MultiMessenger gehört?
> > Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
> >
> 






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Received on Monday, 18 June 2007 15:41:58 GMT

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