Fwd: Another "one" liner

Tim,
add the pubsem mailing list to the future cc's.

Joane

Begin forwarded message:

> From: Tim Clark <twclark@nmr.mgh.harvard.edu>
> Date: December 10, 2006 10:01:23 PM EST
> To: kc28 <kei.cheung@yale.edu>
> Cc: June Kinoshita <junekino@media.mit.edu>, Alan Ruttenberg  
> <alanruttenberg@gmail.com>, Eric Neumann <eneumann@teranode.com>,  
> helen.chen@agfa.com, Matthias Samwald <samwald@gmx.at>,  
> bo.h.andersson@astrazeneca.com, canovaj@gmail.com,  
> dirk.colaert@agfa.com, donald.doherty@brainstage.com, Ivan Herman  
> <ivan@w3.org>, Jonathan A Rees <jar@mumble.net>,  
> jluciano@cs.man.ac.uk, joerg.hakenberg@biotec.tu-dresden.de,  
> kc28@email.med.yale.edu, kerstin.L.Forsberg@astrazeneca.com,  
> marshall@science.uva.nl, ogbujic@bio.ri.ccf.org,  
> ray.hookway@hp.com, Susie Stephens <susie.stephens@oracle.com>,  
> Vipul Kashyap <VKASHYAP1@PARTNERS.ORG>, Elizabeth Wu  
> <ewu@alzforum.org>, Tonya Hongsermeier  
> <thongsermeier@PARTNERS.ORG>, William Bug <William.Bug@drexelmed.edu>
> Subject: Re: Another "one" liner
>
> Hi Kei,
>
> Having done much of the writing in section 1 already, I volunteer  
> to clean it up and get it ready for prime time.  We can avoid  
> stepping on each other if others do likewise for large sections.  I  
> would suggest that people with changes to suggest to section 1  
> beyond what you have written below, email me their suggestions  
> rather than changing the text directly.  Same applies to other  
> sections once people sign up to "own" them.
>
> Best
>
> Tim Clark
>
> 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.
>>>>
>>>>
>>>>
>>>>
>>>
>>
>>
>