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RE: HCLS chartering/next steps Thur 26 May

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 25 May 2011 08:40:02 -0700
Message-ID: <791f311c1aa42cc039482eee61cc3244@mail.gmail.com>
To: "Eric Prud'hommeaux" <eric@w3.org>
Cc: public-semweb-lifesci@w3.org
hi eric,

thanks for all your hard work, it lets people like me nitpick from the
corners.  sorry i won't be able to make the teleconference.  comments

>   Terminology - identifying and integrating identifiers for biological
>   processes, gross anatomy and medical procedures to promote
>   unification of domain data.

"unification of domain data"

i'm not quite sure what this means, i don't think unification is quite the
right word.  i think "integration" is the right word, but you've used it
already and there's also "identifying"/"identifiers".  maybe:

"Terminology - promoting the discovery of relationships between biological
processes, gross anatomy and medical procedures by use of shared
identifying schemes to allow the integration of domain data."

or something like that

>   Scientific Discourse - representation and tracking of the changing
>   landscape of scientific knowledge and the driving theora and
>   experiments.


my meriam-webster doesn't recognize this word.  i think 'theories' is just
fine here.
on the use case page, the first column, Name,  is initially empty (ie9 and
firefox4) but when i click on a field in the table the name for that row
appears.  then it kind of is indeterminate if one moves around the page or
goes back and forth from another application whether that name is still

the use cases are good, brief introductions but i think they need to be
differentiated for each of the domains ('clinical data', 'personal health
care', etc) since the implications and relevance varies quite a bit.  the
title of the categories below the table the user is taken to by clicking
in the table don't really match up that well, i don't think.  for
instance, the row 'Electronic Lab Notebook', the three columns all go to
the '2. Structured Experimental Results' which doesn't mention notebooks
at all. structured experimental results, these days, wouldn't necessarily
go into a lab notebook, the reference to the where the raw data for the
gene expression experiment might be recorded in the notebook but the
actual raw data would be elsewhere.  the actual run of the experiment
might be recorded as a Taverna workflow in myExperiment or as a series of
R modules chained together and again only referenced by the lab notebook,
and so on.  and the use case for a notebook would be similar in
pharmaceutical development and biology but very different for a scientific

the general idea for table is mostly there, it just needs a bit more
thought, i think.
proposed charter looks great.  a couple of minor notes:

1. Scope--should there also be something about promoting use of existing
vocabularies and terminologies?  in 1.1, the first bullet is about
building consensus but doesn't mention where the "core taxonomies and
methodologies" will come from

2.3--"...from health care data which is easy to integrate with genomics,
bio informatics chem informatics and environmental data." should be "from
health care data which are easy to integrate with genomics,
bioinformatics, cheminformatics and environmental data."

the last paragraph of section 2, "Another topic of interest..." sort of
dangles out there, especially in relation to deliverables.


> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> lifesci-request@w3.org] On Behalf Of Eric Prud'hommeaux
> Sent: Monday, May 23, 2011 8:05 PM
> To: public-semweb-lifesci@w3.org
> Subject: HCLS chartering/next steps Thur 26 May
> 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 (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
> --
> -ericP
Received on Wednesday, 25 May 2011 15:40:35 UTC

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