I see it this way: translational / \ / \
life clinical sci* (aka health care) (aka bio) and life sci includes all the life sciences - metatenomics, environmental, etc. carbon based = organic = life science On May 26, 2011, at 5:29 PM, Michel_Dumontier wrote: > 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 :) > > Cheers, > > m. > > * 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:rafaelricha...@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-requ...@w3.org<mailto:public-semweb-lifesci- >> requ...@w3.org> [mailto:public-semweb-lifesci-requ...@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- >> life...@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:twcl...@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:meg...@fi.upm.es> ; Helena >> Deus<mailto:helenad...@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 <meg...@fi.upm.es<mailto:meg...@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.splendi...@bbsrc.ac.uk<mailto:andrea.splendi...@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/ >> >> >> >> >> 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 . 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