RE: HCLS chartering/next steps Thur 26 May

In addition to having the "problem" based task forces, I would suggest that we establish sub-groups based on interest/technical capability with responsibilities to develop and maintain our efforts.


·         Terminology (to coordinate and maintain a shared vocabulary)

·         Knowledge Bases (to coordinate and maintain our scripts and triples stores)

·         Outreach (to develop and coordinate a strong external presence and to listen for opportunities)

m.


From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Matthias Samwald
Sent: Thursday, May 26, 2011 10:43 AM
To: Tim Clark; public-semweb-lifesci@w3.org
Subject: Re: HCLS chartering/next steps Thur 26 May

I agree with Tim's ideas. The different task forces should be problem-focused. This would also help to reduce the redundancy between task forces (for example, the original idea of BioRDF was mainly to convert biomedical data to RDF, but over the years this also became a major focus of other task forces such as LODD).

 - Matthias

From: Tim Clark<mailto:twclark@nmr.mgh.harvard.edu>
Sent: Thursday, May 26, 2011 3:55 PM
To: HCLS IG<mailto:public-semweb-lifesci@w3.org>
Cc: Mikel Egaña Aranguren<mailto:megana@fi.upm.es> ; Helena Deus<mailto:helenadeus@gmail.com>
Subject: Re: HCLS chartering/next steps Thur 26 May

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<mailto: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<tel:%2B1.617.761.6200> (Cambridge, MA)
[Note: limited access to European dial in numbers below]
Dial-In #: +33.4.26.46.79.03<tel:%2B33.4.26.46.79.03> (Nice, France)
Dial-In #: +44.203.318.0479<tel:%2B44.203.318.0479> (Bristol, UK)
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org<http://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<tel:%2B44%280%291582%20763133%20ext%202004>
andrea.splendiani@bbsrc.ac.uk<mailto:andrea.splendiani@bbsrc.ac.uk>





--
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com<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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