Re: Dec 14 HCLSIG TC Minutes

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