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: [EMAIL PROTECTED]