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Re: [BioRDF] BioSIOC / aTag task

From: Matthias Samwald <samwald@gmx.at>
Date: Wed, 7 Jan 2009 13:04:41 +0100
Message-ID: <FBD949E83CE74D41B823B2B20C11EC33@ms>
To: "Tim Clark" <twclark@nmr.mgh.harvard.edu>
Cc: "kei cheung" <kei.cheung@yale.edu>, <public-semweb-lifesci@w3.org>

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.

Matthias Samwald

DERI Galway, Ireland

Konrad Lorenz Institute for Evolution & Cognition Research, Austria

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 12:05:04 UTC

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