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Re: HCLS chartering/next steps Thur 26 May

From: Tim Clark <twclark@nmr.mgh.harvard.edu>
Date: Thu, 26 May 2011 11:56:56 -0400
Cc: HCLS IG <public-semweb-lifesci@w3.org>, Mikel Egaņa Aranguren <megana@fi.upm.es>, Helena Deus <helenadeus@gmail.com>
Message-Id: <44C41E74-04F0-4DC0-808D-BEDEBB3A5E2C@nmr.mgh.harvard.edu>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
Agree - again, same as I said in remarks to Michael Miller.  

On May 26, 2011, at 11:51 AM, M. Scott Marshall wrote:

> Hi Tim,
> 
> I agree with the principle. Just want to point out that the
> Terminology task force has been looking at a very specific problem -
> detecting discrepancies between clinical reports from radiology and
> pathology:
> http://www.w3.org/wiki/HCLSIG/Terminology/PathRadCorrelation
> 
> The main problem problem being addressed is false negatives and false
> positives leading to inappropriate and ineffective therapies.
> 
> Best,
> Scott
> 
> On Thu, May 26, 2011 at 3:55 PM, Tim Clark <twclark@nmr.mgh.harvard.edu> wrote:
>> Dear HCLS colleagues
>> I guess my comment would be, setting Translational Medicine as a major
>> priority = ok, making it the only priority = not ok.
>> TM applications are important, and do potentially integrate many of the
>> things we have all been working on. But they are far from covering all the
>> bases, and far from covering all the use cases of critical concern to people
>> in my Task Group, Scientific Discourse.
>> I'll just observe that since we launched the multiple task groups we have
>> ended up with two kinds of groups:
>> (1) Problem Centric, e.g. TM and Scientific Discourse
>> (2) Solution Centric, e.g. LODD, BioRDF, Terminology
>> My personal recommendation would be to formulate the charter around
>> accelerating biomedical research and promoting cross-discipline sharing,
>> across the full scientific and clinical life cycle.  I would begin by
>> dividing into several distinct problem focused areas. I would lose the
>> solution-based Task Groups and reformulate them as problem-based.
>> for example, BioRDF has been working on gene lists for transcriptomic
>> experiments, we might recharter that Task Group to work on Genomic
>> Experiments, for example, or whatever concept area the Task members like and
>> is a logical step from what they are doing now, but with a PROBLEM FOCUS ...
>> you see the point.
>> I think each of the solution centric groups has a potential problem centric
>> group hiding inside it, waiting to come out.
>> Best
>> Tim
>> On May 26, 2011, at 9:31 AM, Helena Deus wrote:
>> 
>> Hi,
>> That is a very good point, thanks Mikel and Andrea!
>> Do you have pointers to such type of data? Shall we consider an IG for
>> "basic" life sciences?
>> The LS part of HCLS has indeed been gaining adepts rapidly and it may make
>> sense to reflect that in the charter.
>> 
>> Cheers,
>> Lena
>> 2011/5/26 Mikel Egaņa Aranguren <megana@fi.upm.es>
>>> 
>>> Hi;
>>> 
>>> I should attend the conference call but I just want to add that I concur
>>> with Andrea in that the HCLS IG should consider the environmental realm,
>>> since loads of new ecological/environment data, with new challenges to be
>>> addressed, are waiting to be represented semantically. That's precisely one
>>> of the lines we are trying to open here at OEG-UPM.
>>> 
>>> Cheers
>>> 
>>> On og., 2011.eko mairen 26a 15:08, Andrea Splendiani wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> I see myself as more involved in the next incarnation of the charter ;)
>>>> Unfortunately, today is a travel day and I cannot attend the conference
>>>> call.
>>>> 
>>>> I have two questions/ideas, which don't really map to the current
>>>> sub-groups, but just in case they ring some bell:
>>>> 
>>>> -) Is the HCLS exclusively oriented on HeathCare ? (that is, is the "and"
>>>> in
>>>> Heath Care and Life Sciences IG and AND or an OR ?). Here in Rothamsted,
>>>> we
>>>> are just starting to evaluate the Ecological/Agricultural/Environmental
>>>> connections to Life Sciences. Does this fall into the remit of the IG
>>>> group
>>>> ?
>>>> 
>>>> -) Does the evaluation/ coordination of development of systems which link
>>>> information representation and analysis side fall within the remit of the
>>>> IG
>>>> ? I think interfaces to linked data, as well as tools which can analyze
>>>> linked data are important to improve the acceptance of Semantic Web
>>>> technologies in the Life Sciences.
>>>> 
>>>> ciao,
>>>> Andrea
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Il giorno 24/mag/2011, alle ore 04.04, Eric Prud'hommeaux ha scritto:
>>>> 
>>>>> Hi all, as some of you reallize, the charter ends at the end of this
>>>>> month. I've been polling around to see what alternative formulations
>>>>> would give us the most resources and impact. In the process, I wrote
>>>>> up some of our high-level use cases (elevator speeches) to help us
>>>>> approach the relevant parties in pharmas, health services and
>>>>> research:<http://www.w3.org/2011/05/HCLSIGUseCases>.
>>>>> 
>>>>> I'd like to discuss the landscape and potential strategies with the
>>>>> community. I'd particularly like to invite those who have been active
>>>>> or see themselves as being active in the next incarnation of the group.
>>>>> We'll discuss the current, fairly conservative draft charter
>>>>> <http://www.w3.org/2011/05/HCLSIGCharter-proposal>, as well as ways to
>>>>> optimize both its message and the paths for dissemination. An example
>>>>> of a messaging alternative would be to characterize the HCLS IG work
>>>>> in terms of e.g. overarching translational medicine use cases:
>>>>> "
>>>>>  The W3C Semantic Web in Health Care and Life Sciences Interest Group
>>>>>  focuses on translational medicine use cases. The group will continue
>>>>>  the aggregation of cutting edge and traditional scientific knowledge
>>>>>  to meet use cases for researchers, care givers, patients and
>>>>>  regulatory agencies. Due to the scope and diversity of expertise
>>>>>  required to meet translational needs, the HCLS IG work is broken
>>>>>  down into discrete task forces focused on particular data
>>>>>  acquisition, modeling and integration requirements:
>>>>> 
>>>>>  Terminology - identifying and integrating identifiers for biological
>>>>>  processes, gross anatomy and medical procedures to promote
>>>>>  unification of domain data.
>>>>> 
>>>>>  LODD - curation of compounds, clinical trials and outcomes.
>>>>> 
>>>>>  BioRDF - modeling of biological processes and actors.
>>>>> 
>>>>>  Scientific Discourse - representation and tracking of the changing
>>>>>  landscape of scientific knowledge and the driving theora and
>>>>>  experiments.
>>>>> 
>>>>>  Translational Medicine - the oversight and high-level ontology that
>>>>>  connects these disciplines together in order to meet immediate and
>>>>>  long term needs from pharma, health care and other vested parties.
>>>>> "
>>>>> . Perhaps you all have some other ideas about how to tell a story
>>>>> about our work which will serve to both draw people to our work and
>>>>> our products and to help already interested parties find the task
>>>>> forces which interest them. I of course want to draw an optimal
>>>>> balance between doing work which motivates the participants and
>>>>> focusing on tasks which will accelerate education and adoption by
>>>>> important organizations.
>>>>> 
>>>>> I'm sure you are all aware of my preference for technical work, but I
>>>>> feel that this outreach can make us all ultimately more effective. I
>>>>> will use the Thursday 26 May HCLS slot (11:00 EDT) to reach out to the
>>>>> current HCLS IG community, and whomever else you folks elect to bring
>>>>> along. Of course, I'll reserve extra teleconference slots, but please
>>>>> RSVP to me privately so I can make a guess at how many ports to
>>>>> reserve. Also, please provide what feedback you can before the
>>>>> conference. Anything we take care of before will make the meeting more
>>>>> efficient.
>>>>> 
>>>>> Conference Details
>>>>> 
>>>>> Date of Call: Thursday, May 26, 2011
>>>>> Time of Call: 11:00 am Eastern Time, 4 pm UK, 5 pm CET
>>>>> Dial-In #: +1.617.761.6200 (Cambridge, MA)
>>>>> [Note: limited access to European dial in numbers below]
>>>>> Dial-In #: +33.4.26.46.79.03 (Nice, France)
>>>>> Dial-In #: +44.203.318.0479 (Bristol, UK)
>>>>> Participant Access Code: 4257 ("HCLS")
>>>>> IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for
>>>>> details, or see Web IRC), Quick Start: Use
>>>>> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for
>>>>> IRC access.
>>>>> Duration: ~1 hour
>>>>> Convener: Eric Prud'hommeaux
>>>>> Scribe: TBD
>>>>> 
>>>>> HCLS IG charter/strategy discussion
>>>>> --
>>>>> -ericP
>>>>> 
>>>> Andrea Splendiani
>>>> Senior Bioinformatics Scientist
>>>> Centre for Mathematical and Computational Biology
>>>> +44(0)1582 763133 ext 2004
>>>> andrea.splendiani@bbsrc.ac.uk
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> --
>>> Mikel Egaņa Aranguren, PhD
>>> http://mikeleganaaranguren.com
>>> 
>>> Marie Curie post-doc at Ontology Engineering Group, UPM
>>> http://www.oeg-upm.net/
>>> 
>>> 
>> 
>> 
>> 
>> --
>> Helena F. Deus
>> Post-Doctoral Researcher at DERI/NUIG
>> http://lenadeus.info/
>> 
>> 
>> 
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> 
> 
> 
> -- 
> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> http://staff.science.uva.nl/~marshall
> 
> 
> 
Received on Thursday, 26 May 2011 15:57:25 GMT

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