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

Please provide feedback on the figure too.


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

Hi Joanne,

I'll work with Alan and others based on your suggestions.



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


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.


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).



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.


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

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
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