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Re: Dec 14 HCLSIG TC Minutes

From: William Bug <William.Bug@DrexelMed.edu>
Date: Sun, 17 Dec 2006 23:26:41 -0500
Message-Id: <B47572C7-F364-4CF9-9E3D-A6E737F9FC8C@DrexelMed.edu>
Cc: kc28 <kei.cheung@yale.edu>, Alan Ruttenberg <alanruttenberg@gmail.com>, W3C HCLSIG <public-semweb-lifesci@w3.org>
To: Joanne Luciano <jluciano@predmed.com>
Hi Joanne,

I like what you are trying to achieve in this figure, and I think you  
do it well in a very small amount of space.

I've added just a quick "key" to the right-hand side, to give readers  
a more concrete sense of what community resources the 4 Task Forces  
have been focused on integrating.  This should obviously not be  
exhaustive, just examples to give folks a concrete sense of what each  
task force has been examining.  I provided examples for BioONT and  
BioRDF drawn from the paper.  I'd leave it to those who know better  
than I what public resources fall under the purview of DSE & ACPP.

Just my $0.02.

Cheers,
Bill



On Dec 17, 2006, at 10:10 PM, Joanne Luciano wrote:

>
> 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
>
>
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu





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Received on Monday, 18 December 2006 04:27:05 UTC

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