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Re: Dec 14 HCLSIG TC Minutes

From: Joanne Luciano <jluciano@predmed.com>
Date: Sun, 17 Dec 2006 22:10:28 -0500
Message-Id: <C52AF310-4ABB-4B48-AE0F-31A5DDCB18A5@predmed.com>
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, W3C HCLSIG <public-semweb-lifesci@w3.org>
To: kc28 <kei.cheung@yale.edu>

Please provide feedback on the figure too.

Joanne

On Dec 17, 2006, at 2:53 PM, kc28 wrote:

>
> Hi Joanne,
>
> I'll work with Alan and others based on your suggestions.
>
> Thanks,
>
> -Kei
>
> Joanne Luciano wrote:
>
>> Hi Kei,
>>
>> I made my edits on the google page this morning, so this becomes  
>> a  belated request for deadline extension.
>>
>> Included here:
>>
>> 1.3.2. Standards as Applications of Semantic Web Technologies  
>> (Joanne)
>>
>>
>> There is a tacit assumption within the Semantic Web community  
>> that  every type of data sets and ontologies will be  
>> interoperable. The  reality is that a multitude of different  
>> conceptualisations and  formal representation of data exist. A key  
>> part of the Health and  Life Sciences SIG's vision is that  
>> standards need to be established  and accepted sufficiently widely  
>> within the community so as to allow  that necessary  
>> interoperability between data sets, application and  workflows. A  
>> relatively early effort in this direction was the BioPAX   
>> initiative [REFS] which aimed to provide a common framework for  
>> the  disparate data sources and multiple conceptualisations of  
>> cellular  pathways. Its major success was in increasing public  
>> awareness and  persuading a community of researchers that the  
>> integration of data  was possible and would result in major  
>> research and discovery  advantages. It highlighted the multiple  
>> conceptualizations existing  within the domain of cellular  
>> pathways and made people aware of the  significant investment  
>> needed to achieve interoperability at not only  a syntactic level  
>> but also at a semantic one. A considered critique  of the effort  
>> with suggestions of the way forward is presented in  [REF to  
>> Luciano and Stevens] in this issue.
>>
>> In the medium term future, the efforts for standardization need a   
>> much more careful analysis of the user requirements so as to be  
>> able  to get the end users (wet lab scientists) to buy into the  
>> approach  and its benefits. A greater understanding is needed both  
>> of the  conceptualisations needed which will be reflected in a  
>> number of  ontologies and the boundary which lies between what is  
>> possible and  useful in OWL based ontologies given the  
>> capabilities of the current  generation of reasoners, and on the  
>> other hand the ambitions and   needs of clinical researchers to  
>> integrate and interpret their data.
>>
>> The HCLSIG has an interesting role in the SW community because   
>> potentially there is a far greater commitment to resourse  
>> curation  and the need for standard formats and data integration,  
>> thus making  it a much more likely candidate for being a poster  
>> child for the  success of Semantic Web technologies.
>>
>> Added to Section 2:
>>
>>
>> The following figure shows the respective relationship between  
>> the  different task forces and their role in the bench to bedside  
>> vision.
>>
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>>
>> and added my contributions to the section at the bottom:
>>
>>
>> JL Joanne Luciano, Havard Medical School, Universtity of  
>> Manchester  (UK), BioPathways Consortium, BioPAX
>>
>> Affiliation:
>>
>> JL Joanne Luciano, Havard Medical School, Universtity of  
>> Manchester  (UK), BioPathways Consortium, BioPAX
>>
>> To Acknowledgment
>>
>> (after Kei's) JL was supported by NSF grant IIS-0542041.
>>
>> ---Joanne
>>
>>
>> On Dec 15, 2006, at 10:58 AM, Kei Cheung wrote:
>>
>>>
>>> Just want to add that the google doc editing deadline is 12:00  
>>> am  (mid-night EST), Dec 15. If people still need a little bit  
>>> more  time, please let us know as soon as possible. We might be  
>>> able to  extend it to 12:00 noon, Saturday Dec 16 (but not  
>>> anymore since the  deadline is very close).
>>>
>>> Thanks,
>>>
>>> -Kei
>>>
>>> Alan Ruttenberg wrote:
>>>
>>>>
>>>> Correction: Helen, Vipul will send whatever they haven't   
>>>> integrated  into the googledoc to Alan over the weekend for   
>>>> integration. Alan  will edit and send to Kei at weekend's end.
>>>>
>>>> -Alan
>>>>
>>>> On Dec 14, 2006, at 6:14 PM, Eric Neumann wrote:
>>>>
>>>>> [NEW] ACTION: Content will be moved off from googleDoc to Word   
>>>>> COB  Dec 15; to be serially edited by Alan, Helen, Vipul, and   
>>>>> returned  to Kei Dec 20. [recorded in http://www.w3.org/  
>>>>> 2006/12/14-hcls- minutes.html#action01 <http://www.w3.org/  
>>>>> 2006/12/14-hcls- minutes.html#action01> ]
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>> Joanne Luciano, PhD
>> Predictive Medicine, Inc.
>> 45 Orchard Street
>> Belmont MA 02478-3008
>> Email: jluciano@predmed.com
>>
>>
>>
>
>
>

Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: jluciano@predmed.com
Received on Monday, 18 December 2006 03:10:39 UTC

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