Begin forwarded message:
From: Tim Clark <[EMAIL PROTECTED]>
Date: December 10, 2006 10:03:00 PM EST
To: kc28 <[EMAIL PROTECTED]>
Cc: June Kinoshita <[EMAIL PROTECTED]>, Alan Ruttenberg
<[EMAIL PROTECTED]>, Eric Neumann <[EMAIL PROTECTED]>,
[EMAIL PROTECTED], Matthias Samwald <[EMAIL PROTECTED]>,
[EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED], [EMAIL PROTECTED], Ivan Herman
<[EMAIL PROTECTED]>, Jonathan A Rees <[EMAIL PROTECTED]>,
[EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED], Susie Stephens <[EMAIL PROTECTED]>,
Vipul Kashyap <[EMAIL PROTECTED]>, Elizabeth Wu
<[EMAIL PROTECTED]>, Tonya Hongsermeier
<[EMAIL PROTECTED]>, William Bug <[EMAIL PROTECTED]>
Subject: Re: Another "one" liner
PS I will also take responsibility for writing up the SWAN pilot
project
Tim
On SundayDec 10, 2006, at 9:48 PM, kc28 wrote:
Hi All,
Again the one-line goals are listed below.
Vipul: Present a vision of the Bench to Bedside and the value
proposition provided by SW Technologies through use case examples.
Ivan and Helen: This is a vision paper for the application of
semantic web technology in biomedical research and development.
Joanne: HCLSIG's role in facilitating the vision of translational
medicine (aka bench to bedside)
Matthias: A paper that is 1/3 about the vision, 1/3 about the work
we have done so far and 1/3 a review of our thoughts about the
pros/cons of Semantic Web technologies."
Scott: A clear report explaining the HCLS mission and progress to
date.
Alan: HCLSIG: Exploring the challenges of using and sharing
information in a semantic web connecting the life sciences.
I agree that it'd be very difficult to fit all of these goals into
a single paper given the limited size/time. Vision and B2B are
mentioned in several of these goals. Given what we have written so
far and the approaching deadline, my assessment is that we will
have a better chance to meet the deadline if we focus this paper
more on the B2B vision and use cases and relate the progress-to-
date (shorter version) to the vision and use cases. I talked to
the organizers of the supplement issue, they said there may not be
an editorial section for this supplement issue. So, we'll have to
keep the SW introduction in our paper. They also said it should be
no problem for us to post the paper if accepted by BMC.
Regarding the current paper, I have the following suggestions:
1. In section 1.1, some references (e.g., the ones mentioned by
Vipul, Bill Bug and myself) should be included to define
translational research (B2B). We might want to point out some of
the important components/issues in the translational pipeline.
June also pointed out another important factor in the
translational pipeline, which is the process by which new
treatments enter into standard of care guidelines.
2. Section 1.2 should be shortened
3. Section 1.3 (SW introduction) should be shortened. I wonder if
we can merge the strengths/advantages discussed in the conclusion
section into section 1.3. Fig. 1 should probably be included in
this section.
4. I think the use case section is very good. Tim, Don, June,
Elizabeth can continue to work on their AD/PD use cases to
illustrate how SW can help achieve the B2B vision. If possible, I
would also suggest to add references to the use case description
to add credability.
5. Section 1.5 is fine.
6. The Methods section should give a brief overview of each of the
task forces including the goals and the approaches taken to
achieve these goals. It would be great if some of these goals/
approaches can be tied to the use cases
7. In the results section, we should probably include some
preliminary results in relation to the use cases (e.g., biordf
datasets, PD ontologies, SWAN pilot project, demo queries, etc).
8. In the conclusion section, we might want to discuss some issues
and challenges involved in fully realizing the B2B vision. For
example, we can discuss current limitations of SW, how to increase
the level/types of activities on the clinical side, and limited
interaction/intersection with the neuroscience community as well
as other communities (e.g., NCBO)
The above are just my suggestions. Others might have more or
different suggestions. Also, we need to think about how to proceed
in of writing in the next week. Should we assign different
sections to different individuals to avoid overwriting each other
parts?
Even though we cannot fit all the goals into one paper, in the
near future, we might want to consider writing another paper (4-5
pages) to discuss the goals/ideas that are not included in this
paper. For example, Nature publishes short commentary or status
paper that we might want to consider in the near future (see below).
http://www.nature.com/nature/authors/sitemap.html
Best,
-Kei
June Kinoshita wrote:
I believe another important factor in the translational pipeline
is the process by which new treatments enter into standard of
care guidelines. It's very frustrating when you have a body of
research that supports a treatment approach, but the physician
won't or can't prescribe it because it's not in the guideline.
June
On Dec 7, 2006, at 3:35 PM, Kei Cheung wrote:
In today's discussion, we basically agreed on the use of "bench
to bedside" for describing our vision. In addition to articles
suggested by Bill and Vipul, I found the following articles
quite helpful in terms of helping us understand translational
research:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15496233&query_h
l=3 &itool=pubmed_docsum
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15974245&query_h
l=3 &itool=pubmed_docsum
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16174693&query_h
l=3 &itool=pubmed_docsum
One of the articles highlighted issues such as Institutional
Review Board (IRB), Health Insurance Portability and
Accountability Act (HIPAA) compliance, data standardization,
sample procurement, quality control (QC), quality assurance
(QA), data analysis, preclinical models and clinical trials are
critical in the translational pipeline.
Best,
-Kei
Alan Ruttenberg wrote:
On Dec 6, 2006, at 11:54 PM, Eric Neumann wrote:
Alan,
1. Coming from a a practical point of view, I would suggest
to you not to try and force rationality on terms created
originally to inspire ideas and movements; very few examples
exist where logic helped define initial paths in business
and politics. B2B is out there and has some good points to
it, but it is unquestionably incomplete (and I'm OK with that)!
I'm not trying to force rationality on them. I'm trying to
force understandability.
