Hi Eric,
I think NCI Metathesaurus really should be placed under BioONT, if we
are to properly communicate how the BioONT & DSE TFs overlap.
Perhaps BioCyc could be replaced by NCI MT. Given the domain we are
covering, its important for NN to stay, I believe.
What do others think?
Cheers,
Bill
On Dec 18, 2006, at 7:04 AM, Eric Neumann wrote:
For Clinical Trials (DSE):
- CDISC (Clinical Data Onformation Standards Consortium)
- RCRIM (HL7 clinical trials)
- NCI Metathesaurus
- FDA's JANUS database
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of William Bug
Sent: Sun 12/17/2006 11:26 PM
To: Joanne Luciano
Cc: kc28; Alan Ruttenberg; W3C HCLSIG
Subject: Re: Dec 14 HCLSIG TC Minutes
Hi Joanne,
I like what you are trying to achieve in this figure, and I think you
do it well in a very small amount of space.
I've added just a quick "key" to the right-hand side, to give readers
a more concrete sense of what community resources the 4 Task Forces
have been focused on integrating. This should obviously not be
exhaustive, just examples to give folks a concrete sense of what each
task force has been examining. I provided examples for BioONT and
BioRDF drawn from the paper. I'd leave it to those who know better
than I what public resources fall under the purview of DSE & ACPP.
Just my $0.02.
Cheers,
Bill
?
On Dec 17, 2006, at 10:10 PM, Joanne Luciano wrote:
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: [EMAIL PROTECTED]
Joanne Luciano, PhD
Predictive Medicine, Inc.
45 Orchard Street
Belmont MA 02478-3008
Email: [EMAIL PROTECTED]
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
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 - [EMAIL PROTECTED]
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
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 - [EMAIL PROTECTED]
