W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2011

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

The main problem problem being addressed is false negatives and false
positives leading to inappropriate and ineffective therapies.


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 #: + (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/
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.

M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
Received on Thursday, 26 May 2011 15:52:27 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:46 UTC