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RE: Thickness of lines in this figure

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Thu, 11 Mar 2010 13:25:12 -0500
To: Eric Miller <subscriptionbox@squishymedia.com>, Michel_Dumontier <Michel_Dumontier@carleton.ca>
CC: Oliver Ruebenacker <curoli@gmail.com>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-ID: <E1784B0107E5634C8997868083EDE7805CCD8C16F5@CCSMBX10.CUNET.CARLETON.CA>
Hi Eric,
  There's no ambiguity. This is a simple map of dataset interconnectivity in Bio2RDF. In datasets that refer to people, Bio2RDF uses FOAF relations and types.  Whether there are multiple names for the same individual or that the name refers to different people is an age old problem which we don't attempt to solve.

m.


-----Original Message-----
From: Eric Miller [mailto:subscriptionbox@squishymedia.com] 
Sent: Thursday, March 11, 2010 1:19 PM
To: Michel_Dumontier
Cc: Oliver Ruebenacker; public-semweb-lifesci@w3.org
Subject: Re: Thickness of lines in this figure

Hi all,

As a user interface person, I worry about this sort of ambiguity.  (a  
la Karger's "Pathetic Fallacy" paper from a couple years back)

Example: yes, there are conceptual connections between Pubmed and the  
FOAF vocab, and the weight of the line implies a strong and important  
connection between the two.  But that's a superficial mapping of  
fields, not a true description of interoperability.   Pubmed doesn't  
normalize authors, so you'd presumably have one FOAF record for "A. Q.  
Smith" and another one for "Adam Q. Smith" and no authoritative way to  
reconcile them.   We've run into this problem in one of our  
projects.   (If I'm wrong here, please speak up, it would solve a big  
problem for us!)

In other words, we should be aware of the informational consequences  
of these sorts of abstractions....

Eric

||  Eric Miller
||  503.488.5951 (office) or  503.780.1847 (mobile)
||  skype: squishymedia

On Mar 11, 2010, at 8:52 AM, Michel_Dumontier wrote:

> Hello,
>  It comes from the number of relations between the datasets.
>
> m.
>
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-request@w3.org 
> ] On Behalf Of Oliver Ruebenacker
> Sent: Thursday, March 11, 2010 8:35 AM
> To: public-semweb-lifesci@w3.org
> Subject: Thickness of lines in this figure
>
>     Hello,
>
>  Can any one explain what in this figure determines the different
> thicknesses of lines? Thanks!
>
>  http://sourceforge.net/apps/mediawiki/bio2rdf/nfs/project/b/bi/bio2rdf/4/4a/Bio2rdfmap_blanc.png
>
>     Take care
>     Oliver
>
> -- 
> Oliver Ruebenacker, Computational Cell Biologist
> Systems Biology Linker at Virtual Cell (http://vcell.org/sybil)
> Turning Knowledge Data into Models
> Center for Cell Analysis and Modeling
> http://www.oliver.curiousworld.org
>
>
Received on Thursday, 11 March 2010 18:25:39 GMT

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