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.
<<attachment: HCLSIG_paper.jpg>>
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: [EMAIL PROTECTED]
