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RE: HCLS chartering/next steps Thur 26 May

From: Michel_Dumontier <Michel_Dumontier@carleton.ca>
Date: Thu, 26 May 2011 17:29:21 -0400
To: "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-ID: <E1784B0107E5634C8997868083EDE78061202FFEF2@CCSMBX10.CUNET.CARLETON.CA>
Hi all,

The way I see it we have 3 primary application areas:

1 - clinical
2 - translational 
3 - life sciences*

Each of these present concrete problems that need to be worked on, and I don't think we want to overspecify what those are as they will change with time and with the members that actively participate. The use cases that Eric and others have drawn up provide insight as to tantalizing areas/problems that *may* be addressed, and are effective if they describe the problems faced, the potential for SW, and the benefits/impact if addressed. At the same time, the three areas overlap in that they involve:

A - an understanding of the state of the art; to compare and contrast, identify strengths, weaknesses, opportunities and threats

B - accurate knowledge representation: terms and what they refer to + know-how to do this

C - effective knowledge management: data conversion/mapping, ontology development/mapping, text and data mining, queries & reasoning

D - outreach: establishing best practices, publishing original research, developing useable prototypes

E - maintenance

So, in terms of organization, I think the problems in 1-3 provide the motivation to do A-D, and encourage us to vertically integrate to solve challenging problems using several technology-oriented solutions. However, there is simultaneous value in recognizing the strengths of our members in regards to knowledge/technical capability - and that these members might also benefit by interacting at regular intervals e.g. a data-oriented sub-group might form from members doing data-oriented things in 1-3 and wrt A-D.  Such cross-pollination would help disseminate technically oriented factoids across the organization to the people who genuinely care about that level of detail, and together might help all facets move forward :)



* I included all basic sciences in this category inc. environmental science (unless it pertains to health, then it falls into translational).

> -----Original Message-----
> From: Rafael Richards [mailto:rafaelrichards@jhu.edu]
> Sent: Thursday, May 26, 2011 11:45 AM
> To: Michel_Dumontier
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: HCLS chartering/next steps Thur 26 May
> Michel,
> I concur.  As the overwhelming emphasis of the HCLS is in the lifesciences
> (biology, basic research, and other 'translational' areas), I would support
> the formation of a clinical applications task force  which would be
> relevant to practicing physicians. I would be happy to lead any efforts in
> this area.
> Rafael Richards M.D., M.S.
> Assistant Professor
> Department of Anesthesiology and Critical Care Medicine
> Johns Hopkins Medical Institutions
> On May 26, 2011, at 11:01 AM, Michel_Dumontier wrote:
> 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> [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<mailto: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 Egaņa 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 Egaņa 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 #: +<tel:%2B33.> (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 Egaņa 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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Received on Thursday, 26 May 2011 21:29:20 UTC

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