W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > December 2006

Re: Bench-to-Bedside definition & refs

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 07 Dec 2006 12:43:31 -0500
To: William Bug <William.Bug@DrexelMed.edu>
Cc: W3C HCLSIG <public-semweb-lifesci@w3.org>
Message-id: <457852C3.60400@yale.edu>

Hi Bill,

Thanks a lot for the reference which is very helpful.

Cheers,

-Kei

William Bug wrote:

> Hi Kei,
>
> This JAMA piece describing the $10M HHMI funding for special PhD 
> programs focussed on Bench-to-Bedside training. It also includes a few 
> citations regarding the need for B-to-B focussed research efforts.
>
> Cheers,
> Bill
>
> =
> ------------------------------------------------------------------------
>
>
>
>
> On Dec 7, 2006, at 11:18 AM, Eric Neumann wrote:
>
>> For the record...
>>
>> Begin forwarded message:
>>
>>> *From: *"kc28" <kei.cheung@yale.edu <mailto:kei.cheung@yale.edu>>
>>> *Date: *December 6, 2006 10:41:08 PM EST
>>> *To: *"Alan Ruttenberg" <alanruttenberg@gmail.com 
>>> <mailto:alanruttenberg@gmail.com>>
>>> *Cc: *"Tim Clark" <twclark@nmr.mgh.harvard.edu 
>>> <mailto:twclark@nmr.mgh.harvard.edu>>, helen.chen@agfa.com 
>>> <mailto:helen.chen@agfa.com>, "Matthias Samwald" <samwald@gmx.at 
>>> <mailto:samwald@gmx.at>>, bo.h.andersson@astrazeneca.com 
>>> <mailto:bo.h.andersson@astrazeneca.com>, canovaj@gmail.com 
>>> <mailto:canovaj@gmail.com>, dirk.colaert@agfa.com 
>>> <mailto:dirk.colaert@agfa.com>, donald.doherty@brainstage.com 
>>> <mailto:donald.doherty@brainstage.com>, "Eric Neumann" 
>>> <eneumann@teranode.com <mailto:eneumann@teranode.com>>, "Ivan 
>>> Herman" <ivan@w3.org <mailto:ivan@w3.org>>, "Jonathan A Rees" 
>>> <jar@mumble.net <mailto:jar@mumble.net>>, jluciano@cs.man.ac.uk 
>>> <mailto:jluciano@cs.man.ac.uk>, joerg.hakenberg@biotec.tu-dresden.de 
>>> <mailto:joerg.hakenberg@biotec.tu-dresden.de>, 
>>> kc28@email.med.yale.edu <mailto:kc28@email.med.yale.edu>, 
>>> kerstin.L.Forsberg@astrazeneca.com 
>>> <mailto:kerstin.L.Forsberg@astrazeneca.com>, marshall@science.uva.nl 
>>> <mailto:marshall@science.uva.nl>, ogbujic@bio.ri.ccf.org 
>>> <mailto:ogbujic@bio.ri.ccf.org>, ray.hookway@hp.com 
>>> <mailto:ray.hookway@hp.com>, "Susie Stephens" 
>>> <susie.stephens@oracle.com <mailto:susie.stephens@oracle.com>>, 
>>> "Vipul Kashyap" <VKASHYAP1@PARTNERS.ORG 
>>> <mailto:VKASHYAP1@PARTNERS.ORG>>, "June Kinoshita" 
>>> <junekino@media.mit.edu <mailto:junekino@media.mit.edu>>, "Elizabeth 
>>> Wu" <ewu@alzforum.org <mailto:ewu@alzforum.org>>, "Tonya 
>>> Hongsermeier" <thongsermeier@partners.org 
>>> <mailto:thongsermeier@partners.org>>
>>> *Subject: **Re: Another "one" liner*
>>>
>>> Hi,
>>>
>>> Sorry, Iím falling behind in terms of answering emails as Iíve been 
>>> having a very heavy teaching schedule this week (Iím also a little 
>>> bit sick). Anyway, I received the following one-liners:
>>>
>>> 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.
>>>
>>> Based on the above one-liners, I have a question about the following 
>>> terms:
>>>
>>> HCLS
>>> bench to bedside
>>> biomedical
>>> translational medicine
>>>
>>> Do they mean the same thing? Are they belong to one discipline 
>>> (http://www.amia.org/meetings/f02/call/intro.html)? 
>>> <http://www.amia.org/meetings/f02/call/intro.html%29?> For example, 
>>> when we talk about bench to bedside, are we talking about 
>>> translational informatics (intersection of bioinformatics and 
>>> medical informatics) or the range of activities in bioinformatics 
>>> and medical informatics. My impression is that the type of 
>>> activities that are going on within HCLS involve bioinformatics, 
>>> medical informatics and their bridge. So when we use the phrase 
>>> ďbench to bedsideĒ, I think we should define clearly what it means.
>>>
>>> Personally I prefer a balanced and synergistic approach to 
>>> describing different aspects of our HCLS group, including mission, 
>>> vision, progress, use cases, challenges, and semantic web 
>>> (introduction and strength and weakness). This may help different 
>>> authors who have different backgrounds/interests to contribute. We 
>>> can write up to 20 pages (in BMC format). When we talk about vision, 
>>> I think the vision should not be too ambitious. It should be a 
>>> deliverable/realistic vision (not a hype) given the strengths and 
>>> limitations of SW. Itís better to show some results (albeit 
>>> preliminary) to support our claims. We should avoid making claims 
>>> that cannot be substantiated. We have about two weeks left.
>>>
>>> Best,
>>>
>>> -Kei
>>>
>>>
>>> Alan Ruttenberg wrote:
>>>
>>>> I'm not great with one liners. Perhaps:
>>>>
>>>> HCLSIG: Exploring the challenges of using and sharing information 
>>>> in a semantic web connecting the life sciences.
>>>>
>>>> But the paragraph below is a better captures it. Think of it as a 
>>>> really long line :)
>>>> (hence the quotes around "one")
>>>>
>>>> -Alan
>>>>
>>>> On Dec 5, 2006, at 9:22 AM, kc28 wrote:
>>>>
>>>>> Hi Alan,
>>>>>
>>>>> Can you provide a one-line goal also? For example, description of 
>>>>> HCLS activities in applying semantic web technologies ...
>>>>>
>>>>> Best,
>>>>>
>>>>> -Kei
>>>>>
>>>>> Alan Ruttenberg wrote:
>>>>>
>>>>>> Here's a story that I think is both representative of who/where 
>>>>>> we are, and which creates a story that fits into the special issue.
>>>>>>
>>>>>> Everyone in this group is in a science or health care support 
>>>>>> role of one kind or another. They collect and provide information 
>>>>>> and strive to make connections across domains because they think 
>>>>>> it will help work of their group. This paper describes their 
>>>>>> shared activities in applying semantic web technologies to see if 
>>>>>> that helps. It describes
>>>>>> - The domains from which the information comes and the problems 
>>>>>> trying to be solved
>>>>>> - Technology and experiments that have been tried to represent, 
>>>>>> link and manipulate that information
>>>>>> - Problems that have been encountered, conceptual, social and 
>>>>>> technical
>>>>>> - Some of the things that they hope will be possible if/when the 
>>>>>> program is widely adopted.
>>>>>>
>>>>>> As such it is representative of the challenges that e-science 
>>>>>> practitioners will need to address when it comes to knowledge 
>>>>>> sharing and manipulation.
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>>
>> Eric Neumann, PhD
>> co-chair, W3C Healthcare and Life Sciences,
>> and Senior Director Product Strategy
>> Teranode Corporation
>> 411 1st Avenue South, Suite 700
>> Seattle, WA 98104
>> +1 (781)856-9132
>> www.teranode.com
>>
>>
>
> 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 - William.Bug@DrexelMed.edu 
> <mailto:William.Bug@DrexelMed.edu>
>
>
>
>
> =
Received on Thursday, 7 December 2006 17:43:45 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:20:21 UTC