Re: HCLS chartering/next steps Thur 16 June

if "*Structured protocols* and experimental results" is added to the High
Level Use cases then in the Life Sciences domain there should also be:

Biomedical experimental data repositories:  although experimental
 protocols, methods and datasets are related, they are not always openly
accessible and interlinked.  data may be discoverable, researchers may
publish experimental information in the form of spreadsheets; however,
significant challenges remain in the reuse of the data, in particular
facilitating the necessary correlation, integration and synthesis of data
across levels of theory, techniques and disciplines. Biomedical experimental
data repositories should facilitate the reproducibility of experiments.



On Thu, Jun 16, 2011 at 4:56 PM, Helena Deus <helenadeus@gmail.com> wrote:

> Regrets, I cannot attend the call :-(
>
> A few points:
>
> 1. Suggest to change in the High Level Use cases
> - *Structured protocols* and experimental results
>
> I think we need to elaborate at least one of the use cases and describe
> them as a workflow (e.g. user needs to find about a pathway where two
> proteins are involved; user goes to uniprot to find the two proteins, finds
> the identified in kegg pathways and interactome, searches those databases,
> finds a list of other potential interacting proteins; uploads the data in
> string db, etc). This will help identify the gaps and help devise the
> deliverables around it.
>
> As it is, the use cases are more topics for exploring use cases.
>
> 2. We've been brainstorming about the mission statement here at DERI and
> here is what we came up with (based on the proposal by Tim Clark):
>
> The mission of the W3C HCLS IG is to exploit interdisciplinary, semantic
> web research so that stakeholders in health care and life sciences can
> collaborate and interoperate on a global scale.
>
> We enable this mission by actively adopting Web interoperability standards
> applicable to HCLS, and providing feedback to the standards development
> groups within the W3C based on our experiences. Our program is based on
> real-life requirements for the Web-based support of scientific and clinical
> activities, and a vision of 21st century research in biology and medicine.
> The evolving "web of data" is a critical component of this vision.
>
> The HCLS-IG actively supports the in-depth, practical involvement of
> multidisciplinary researchers in basic, clinical, and translational science
> in the application and development of these standards. Our activities
> include requirements and scenario formulation, tutorials, demonstrations and
> ontology development, hosting workshops, and dissemination in peer-reviewed
> journals and conferences.
>
>
>
> 3. We have also came up with a number of activities that may be interesting
> to explore beyond what is already in the charter
>
> Health Care domains
>
>
>    - Improved Diagnosis: Enable diagnostic decisions based on previous
>    evidence and aggregation of data from multiple electronic health record
>    system (EHR)
>    - Clinical Information Exchange: develop (semi-)automated ontology
>    building and alignment methods/tools for non-ontological healthcare
>    resources. Clinical information consists of different information parts
>    (e.g., medical history, lab observation) of a comprehensive patient record.
>    The clinical information uses several vocabularies and constraints to
>    describe their contents. Each of these vocabularies either described and
>    controlled by the standardisation committees or by local users. The use of
>    semantics for successful Clinical Information Exchange can reach to
>    full-potential by adopting domain specific methodologies and tool sets.
>    - Patient-Centric Care: develop context-aware and modular Semantic Web
>    framework. Patient's clinical information spans across different sites,
>    treatment occasions, diseases, medical situations (e.g., routine,
>    accidents), etc. It is important to arrange them in information modules and
>    integration should be centered according to point-of-care, that is, only
>    those information pieces should be combined or excluded that are appropriate
>    for any treatment situation.
>
> Life Sciences Domains
>
>    - Systems Biology: integration of multiple "omics" sciences
>    - Functional and Pathway Analysis of Expression Data: analysis of gene
>    expression results by categorizing results in terms of gene sets (there is
>    very little work going on in this area and a VERY big need. I know work
>    going on in the Netherlands where this area is under development.)
>    - Structure Bioinformatics/Chemoinformatics: integration of information
>    regarding chemical components (Egon has done most of the work in this
>    domain, time we help him a bit?)
>
> Best,
> Lena
>
> On Thu, Jun 16, 2011 at 1:58 AM, Eric Prud'hommeaux <eric@w3.org> wrote:
>
>> Hi again again. Since last we met, I pushed some documents around and
>> piled some words into others. The High Level Use Cases (AKA elevator
>> pitches) doc is now on the wiki:
>>  http://www.w3.org/wiki/HCLSIG/HighLevelUseCases
>> The on-deck charter remains where it was:
>>  http://www.w3.org/2011/05/HCLSIGCharter-proposal
>> Scott wrote up a brag sheet to show what we accomplished in this charter:
>>  http://www.w3.org/wiki/HCLSIG/Products
>> and I wrote a narrative version catering to pharmas:
>>  http://www.w3.org/wiki/HCLSIG/Products/TranslationalMedicine
>> Join me tomorrow at the usual time (11.00 EDT, 15.00Z)?
>>
>> * Eric Prud'hommeaux <eric@w3.org> [2011-06-01 22:06-0400]
>> > Hi all again. Last week we had some good idea exchange about what we
>> > should put into the next HCLSIG charter, i.e. what we tell the world
>> > we are doing. We agreed that we weren't done and that we'd like to
>> > meet in one week. I invite all to meet tomorrow, Thursday 2 June.
>> > Details at the bottom of the message.
>> >
>> > * Eric Prud'hommeaux <eric@w3.org> [2011-05-23 23:04-0400]
>> > > 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:xThursday,xMayx26,x2011x
>> >                 Thursday, June 2, 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 #: +33.4.26.46.79.03 (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=%23hclsfor
>> > > IRC access.
>> > > Duration: ~1 hour
>> > > Convener: Eric Prud'hommeaux
>> > > Scribe: TBD
>> > >
>> > > HCLS IG charter/strategy discussion
>> > > --
>> > > -ericP
>> >
>> > --
>> > -ericP
>>
>> --
>> -ericP
>>
>>
>
>
> --
> Helena F. Deus
> Post-Doctoral Researcher at DERI/NUIG
> http://lenadeus.info/
>
>


-- 
Alexander Garcia
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