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Re: [BioRDF] BioSIOC / aTag task

From: Kei Cheung <kei.cheung@yale.edu>
Date: Wed, 07 Jan 2009 13:55:55 -0500
To: Matthias Samwald <samwald@gmx.at>
Cc: Tim Clark <twclark@nmr.mgh.harvard.edu>, public-semweb-lifesci@w3.org
Message-id: <4964FABB.6090801@yale.edu>

Hi Matthias, Tim,

I'll be happy to work with both of you to establish synergistic 
activities between BioRDF and Scientific Discourse task forces. I think 
it might be better coordinated if Tim and I first discuss this.



Matthias Samwald wrote:
> Hi Tim,
> Of course, I will take every measure to coordinate what I am doing 
> with the scientific discourse task, as well as the BioRDF and LODD 
> tasks. I am trying to participate on all of the conference calls of 
> these tasks, even though it can be a bit difficult sometimes. I think 
> having an overly strong division between the different tasks did not 
> work that well in the last charter of the HCLS IG (where we started 
> out with several tasks, which mostly converged to a single task during 
> the course of the two years). Therefore I try to follow all of the 
> task forces (with the exception of COI in the recent months, but that 
> might change).
> BioRDF seemed like a better choice for being an official umbrella for 
> that work, since it involves the conversion of large amounts of 
> biomedical datasets into RDF/OWL, does not involve discourse 
> representation (but connects to it) and is not specifically focused on 
> drug information. I will discuss and coordinate any part of the 
> project that might be relevant for scientific discourse and drug 
> information with the Scientific Discourse and LODD task force members 
> in the respective conference calls.
> Cheers,
> Matthias Samwald
> DERI Galway, Ireland
> http://deri.ie/
> Konrad Lorenz Institute for Evolution & Cognition Research, Austria
> http://kli.ac.at/
> --------------------------------------------------
> From: "Tim Clark" <twclark@nmr.mgh.harvard.edu>
> Sent: Wednesday, January 07, 2009 12:14 PM
> To: "Matthias Samwald" <samwald@gmx.at>
> Cc: "kei cheung" <kei.cheung@yale.edu>; <public-semweb-lifesci@w3.org>
> Subject: Re: [BioRDF] BioSIOC / aTag task
>> Hi Matthias,
>> My concern is not redundancy of content, or of technical  
>> implementation, but of potential semantic redundancy and/or mismatch  
>> between two formulations of the same basic idea.
>> This problem could arise precisely because the form in which the  
>> content is expressed - i.e. scientific assertions - would have  
>> different technical implementations, despite being semantically  
>> identical at a fundamental level.   Therefore I think your proposed  
>> work should it be carefully coordinated with SWAN-SIOC both before 
>> and  during development to ensure alignment - if it is to be part of 
>> an  official HCLS task.
>> When you initially proposed your idea on the Scientific Discourse  
>> call, I felt confident this coordination could occur, if and when 
>> the  work was started, because it was being done in the same task 
>> group as  the other Discourse tasks.  Now that you have proposed it 
>> again in  BioRDF,  I am not confident this coordination will occur 
>> spontaneously  unless we make it happen - therefore I suggest you and 
>> Kei and I spend  some time exploring the ramifications of starting 
>> this task in another  group and how to achieve alignment.  Perhaps 
>> Susie could lend a hand  in this discussion as well.
>> If it later turns out I am wrong and it turns out, after discussion,  
>> that there is no need for any pre-alignment or coordination of your  
>> work with the Discourse tasks, we will still have had the chance to  
>> understand your ideas better, and have shared our thinking, which is  
>> all good.
>> Best
>> Tim
>> On Jan 7, 2009, at 4:33 AM, Matthias Samwald wrote:
>>> Dear Tim,
>>> The project I have in mind is not redundant with SWAN-SIOC, both in  
>>> its technical implementation and the biomedical content that will be 
>>> represented. The statements will not have discourse relationships  
>>> among themselves, and indeed such relationships would be better  
>>> represented through the vocabulary that SWAN can add to the basic  
>>> SIOC vocabulary.
>>> This project could also demonstrate the value of the alignment of  
>>> SWAN and SIOC, showing that information represented in basic SIOC  
>>> can be easily aligned with information represented in the more  
>>> expressive SWAN vocabulary, via the SWAN-SIOC alignment. This is  
>>> important for demonstrating the advantages gained (in terms of  
>>> interoperability) by the SWAN-SIOC alignment.
>>> Cheers,
>>> Matthias Samwald
>> Tim Clark
>> Director of Informatics, MassGeneral Institute for Neurodegenerative 
>> Disease
>> Instructor in Neurology, Harvard Medical School
>> 617-947-7098 (mobile) 
Received on Wednesday, 7 January 2009 18:56:42 UTC

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