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Finding contradictions in research statements (SenseLab example)

From: <samwald@gmx.at>
Date: Wed, 18 Apr 2007 17:47:51 +0200
Cc: public-semweb-lifesci@w3.org
Message-ID: <20070418154751.291660@gmx.net>
To: Alan Ruttenberg <alanruttenberg@gmail.com>

> It's been my experience that the cases of the data being wrong, or at  
> best incomplete, in bio databases, vastly outnumber of the cases of  
> the evidence actually
> being contradictory. I'd be curious to have a look at papers  
> supporting contradictory answers that you identified. 

See http://senselab.med.yale.edu/senselab/NeuronDB/ndbEavSum.asp?id=3978&mo=4&re=

then look for "I Na,t" currents in the soma. One publication states 

"Depolarisations beyond -40 mV activated a fast transient TTX-sensitive inward current. Once activated, INa declined exponentially to zero following a single exponential." [1]

the other one states

"no Na+ currents could be elicited in voltage clamp experiments." [2]

> Is is possible  
> that upon rereading of the paper we will be able to find something in  
> the biological context that will distinguish them.

Of course we can. For example, one experiment used frog as a model system, the other one used rabbit. We could also find other biological differences, or differences outside the biological context, e.g. the employment of slightly different methods of measurement. We could even go as far as saying that the two outcomes are different becomes the experiments were made by different persons (this happens in biology...).

However, such differences are not modeled in SenseLab and therefore our OWL ontology. We have to set certain rules on how we generalize from certain findings, otherwise we end up being unable to make generalizations at all -- and trying to make generalizations is the goal of doing experiments and publishing the results.

Matthias Samwald

[1] Bardoni R and Magherini PC and Belluzzi O. (1995) Sodium current in periglomerular cells of frog olfactory bulb in vitro. Brain Res. 703:1-2:19-25.
[2] Bufler J, Zufall F and Franke C and Hatt H. (1992) Patch-clamp recordings of spiking and nonspiking interneurons from rabbit olfactory bulb slices: membrane properties and ionic currents. J Comp Physiol [A]. 170:2:145-152.

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Received on Wednesday, 18 April 2007 16:47:54 UTC

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