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RE: HCLS chartering/next steps Thur 26 May

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 26 May 2011 09:24:50 -0700
Message-ID: <7014dbef620a3c6f25eadf4c792fa4ad@mail.gmail.com>
To: Tim Clark <twclark@nmr.mgh.harvard.edu>
Cc: HCLS IG <public-semweb-lifesci@w3.org>
hi tim,

my feeling is that we have a problem 'Bio' (specifically gene expression at
this point but that focus can change) and we are actively using a semantic
web technology  'RDF' as the solution.  that is why we are a subgroup and
not the entire effort.  i believe our problem space gives us a lot to work



*From:* Tim Clark [mailto:twclark@nmr.mgh.harvard.edu]
*Sent:* Thursday, May 26, 2011 8:56 AM
*To:* Michael Miller
*Subject:* Re: HCLS chartering/next steps Thur 26 May

HI Michael,

As I said, problem focused activities hiding in solution-focused groups.
 The BioRDF group's very name is solution-focused.  Granted, over its recent
history there has been a strong problem focus in the actual activities, I am
thinking of the gene list work here.  But someone looking from the outside
can't necessarily see that, they see "RDF" in the name.



On May 26, 2011, at 11:36 AM, Michael Miller wrote:

hi all,

tim, your remarks confused me.  like lena, i have found BioRDF to be
problem-centric.  the fact that we are working on solutions to the problem
is what brings me to the table.  without that, BioRDF would be without me.

i stayed in the shadows for many years because i saw a lot of discussion and
nothing that would help me in my day to day job.  that has changed in the
last few years and has made me a more active member.  kudos to eric and
lena, and many others, with their focus on making these technologies
practical and accessible to solve problems, not just talk about them.



*From:* public-semweb-lifesci-request@w3.org [mailto:
public-semweb-lifesci-request@w3.org] *On Behalf Of *Helena Deus
*Sent:* Thursday, May 26, 2011 7:45 AM
*To:* Joanne Luciano
*Cc:* Tim Clark; HCLS IG; Mikel Egaņa Aranguren
*Subject:* Re: HCLS chartering/next steps Thur 26 May

Hi all,

I agree with a focus on creating "problem-centric" task forces - to be
honest, I always felt bioRDF to be a problem-centered group (i.e. trying to
solve a current problem in life sciences, not looking for a problem given a

I do believe, however, that we need to make sure that we are all in the same
page regarding goals. I propose that, for the next charter we agree on
a Mission Statement devised and agreed upon by the key players in each task

This will give us 1) focus;  2) requirements and 3) adequability of the task



On Thu, May 26, 2011 at 3:33 PM, Joanne Luciano <jluciano@cs.rpi.edu> wrote:


Thanks for your thoughts. I agree with you and would like to add an
evaluation criteria component - these efforts (imo) should be targeted at
having an impact on clinical outcome.



Joanne S. Luciano, PhD                            Rensselaer Polytechnic

Research Associate Professor                 110 8th Street, Winslow 2143

Tetherless World Constellation                Troy, NY 12180, USA

Department of Computer Science            Email: jluciano@cs.rpi.edu

Office Tel. +1.518.276.4939                         Global Tel.
+1.617.440.4364 (skypeIn)

On May 26, 2011, at 9:55 AM, Tim Clark 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.



On May 26, 2011, at 9:31 AM, Helena Deus wrote:


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.



2011/5/26 Mikel Egaņa Aranguren <megana@fi.upm.es>


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.


On og., 2011.eko mairen 26a 15:08, Andrea Splendiani wrote:


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

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.


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

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

 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

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

Andrea Splendiani
Senior Bioinformatics Scientist
Centre for Mathematical and Computational Biology
+44(0)1582 763133 ext 2004

Mikel Egaņa Aranguren, PhD

Marie Curie post-doc at Ontology Engineering Group, UPM

Helena F. Deus

Post-Doctoral Researcher at DERI/NUIG


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Helena F. Deus

Post-Doctoral Researcher at DERI/NUIG

Received on Thursday, 26 May 2011 16:25:15 UTC

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