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