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Re: Evidence

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Mon, 18 Jun 2007 02:29:35 -0400
Message-Id: <1BD2A1E1-C475-40A1-A269-2D05F51D8C69@gmail.com>
Cc: Waclaw Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>, phismith@buffalo.edu, public-semweb-lifesci@w3.org
To: samwald@gmx.at


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
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Received on Monday, 18 June 2007 06:29:42 GMT

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