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Re: HCLS chartering/next steps Thur 26 May

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Thu, 26 May 2011 17:51:59 +0200
Message-ID: <BANLkTi=RmUkqJWcRkpFaJ6dyDFyyDjjh4Q@mail.gmail.com>
To: Tim Clark <twclark@nmr.mgh.harvard.edu>
Cc: HCLS IG <public-semweb-lifesci@w3.org>, Mikel Egaña Aranguren <megana@fi.upm.es>, Helena Deus <helenadeus@gmail.com>
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 Egaña 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 Egaña 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 15:52:27 GMT

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