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HCLS TC minutes 1-18-07

From: Eric Neumann <eneumann@teranode.com>
Date: Wed, 31 Jan 2007 20:08:51 -0500
Message-ID: <A3970D83EC72E84B8D2C2400CD6F0B9FE9B206@MI8NYCMAIL16.Mi8.com>
To: "W3C HCLSIG" <public-semweb-lifesci@w3.org>

Apologies for not having posted these earlier...

HCLS TC minutes 1-18-07

Susie S
Matthias S
Ted S
Bill Bug
Vipul K
Joanne L
Helen C
Olivier B
Tonya H
Eric N
Ivan H
Eric P

Scribe: Tonya Hongsermeier

Next Call is Feb 1st  --- Scribe will be determined

Agenda item 1)  Introduce Eric Prud'hommeaux .  We thank Ivan for his thoughtful
considerations and holding the fort.  Has worked in the RDF space for a while,
got interested in Lifesciences via Brian Wilbanks, worked on the SPARKL
language, and had forays into web services.  Joanne:  It's great to have you,
you have experience converting data to RDF.  Bill:  Have you worked in spaces
such as BIOMOBY or MOBY?   Worked on SOSDL spec, heard name MOBY but not sure
what it is... has lived in Paris, will move back to Boston after March (quel

Agenda item 2)  Task force review:

To complete this charter, it's time to refocus our efforts to complete
deliverables outlined in Amsterdam with demonstration POCs, best practices,
notes, artifacts, etc.  We'll renew our efforts to encourage progress.  We share
the Bench to Bedside vision, but the individual tasks will solve components of
that vision rather that the entire vision.

There is a set of actions that were defined :

There are some activities with dates past,  ACPP has artifacts in the sandbox
but lacks a narrative the describes the roles of these artifacts in solving
problems accompanying these files.

Bill:  If we have clear use cases, shouldn't those drive what we do?  We need
agreement on what we need to do,  the work to date such as the ACPP viewer,
publishing group...  Eric:  Didn't we agree on the use cases?   Joanne:  we
agreed on one of the use cases, Parkinsons?  don't remember... Bill:  Helen and
Don were to work together

Eric:  We are thinking about looking at the perspectives of the use cases, not
to "solve the disease", but rather to compartmentalize the parts of the, say,
Parkinson's disease use case that we can address...  we should reconsider
streamlining to something achievable.  Bill:  The word Use Case has been a messy
one,  I try to look at thinks in a hierarchical sense,  there is a general use
case, and then there specific use case components where we can define role of
ontologies/RDF to solve problems identified in the use case.  

Joanne:  which components have data and tools available to solve....

Vipul:  As we are developing the use cases,  we try to focus on how a data
source can solve a question,  But Bill and June said let's not do something that
has no value... 
EricN : work with Eric P. , Allan, Vipul, Matthias look back on the work
identified in Amsterdam, taking that example and work with Eric P   Joanne:
Should we (Bill, Tonya) identify criteria?  Bill:  I just published in a
manuscript, I'm comfortable helping here...    Susie:  BioRDF has made a lot of
progress, I'd like to update the group...  
Bill:  Let's vet a use case with scientists to validate that this is indeed of
practical value to them,  based on Matthias' comments,  those are two different
ways to approach the use case, infrastructural view may not surface relevance to
neuroscientists...maybe we need parallel lines?
Susie BioRDF update...  First goal was to convert datasets into RDF, look at
tools that assist with this,  recently focused on a use case/demo,  we've tried
to identify a Parkinson's use case, but since then, it was determined a single
question was insufficient,  then June identified some interesting Alzheimer
questions, then Bill discussed incorporation of images, then wanted to make sure
parkinson's is taken advantage of,  are there overlaps?  close to settling on a
use case,  then will identify the relevant data sets and ontology work...  to
remain motivated, we'd like to show the demo at ISMB and WWW 2007,   my concern
is we're focused on so many uses and fragmentation of the work...  Eric:  Susie
can you identify the data sets?  Susie: these are on the Wiki both use cases and
data sets...

Vipul:   in response to the fragmentation concerns:  we are now coordinated this
work across ACPP, BIORDF and BIO ONT...  Susie:  I'm confused, I thought we did
this during the BIO RDF calls...  Vipul:  there are two view points,  

Allan:  I think that we need a F2F to realistically get a demo done,  Eric: not
enough time...Allan:  there is going to be a number of people who must
contribute, debug, also, all the people working on this are working with
fragments of time,  not necessarily F2F of whole group, but at least
implementers and a couple people on scientific side... Eric;  let's suggest a
physical meeting of core participants with open TC line... would that work?
Tonya?  who are the core participants?  Allan:  Matthias can convert RDF sources
along with me,  Tim would put together around Alzforum use cases, Bill for
imaging, and Scott Marshall can help to...   Eric:  maybe we pull back from the
big picture and compartmentalize a doable part of the work     Allan;  there are
a bunch of isolated things, not even a single small one,  ie for a demo, a
script,   Eric:  what if you could show with info available right now how this
might associate Parkinsons with other disease, ie other neurodegeneratives...
Bill: the other issue, when I speak of a narrow use case, something that
translates into hypothesis backed by facts where we can link the hypothesis and
the facts,  Eric:  that is part of the longer picture, but not the demo we are
talking about...  Tonya:  need to decide on the topic for demo, then identify
logistical support for a mini-script/hack-a-thon... 

Allan:  I think I heard Susie say we have that, June has identified the sources
need?  Susie:  yes, Elizabeth Wu has identified the sources,  BioOnt can
identify the ontologies,   Allan:  if that is the case, let's get the folks who
implement to look this over and validate this by next BioRDF meeting,  Susie
could send links to the use case and sources, then we validate this,  ACTION
ITEM:  Susie will perform this,  
ACTION:  Joanne, Allan, Bill, will validate

Vipul:  F2F uses already has data sources ID'd,  Parkinson's I think is easier,
coming back to BioONT... Don Doherty is expecting,  so he's busy,  integrated
use case is going forward, then we will delve into ontologies and terminologies,
we've invited series of speakers on developing ontologies, ie Chimezie on EHR
ontology, later the SWANN folks, then Helen on the ACPP ontology, then Don
Doherty.  The agenda is to discuss motivating use cases, problems, design
choices, generalizability of best practices,    Eric:  focus less on how to
create a good conceptual model for a disease,  but rather what is the way to use
an ontology, how do you refer to instances and classes, what are approaches that
work?    As soon as Parkinson's and Alzheimer's cases become stable, we'll map
down to ontologies..  These talks are on alternate Tuesdays..

Helen:  we have regular attendence of Chimezie and Davide,  so there is an ACPP
ontology in N3 format, then we have come up with Notes, , will post draft to
wiki by end of this week,   Allan has helped us with presenting our ideas,  we
have concentrated on rule usage, ...Eric:  That is super,  Helen:  in addition,
we have put FACT recommendations and converted to ontologies,  we do not have
real data sets to play with,  we have sandbox without sand,  no data to validate
our rules, Eric: same problem as drug efficacy group, consider making it up...

Ivan :  comment,  if this is published as a W3C note, just realize that the news
will go on various home pages and blogs, so entire Semantic Web community will
jump at you... Helen:  that's why we need some help with writing....

ACTION ITEM: Eric N will look at providing logistical support for the
hacka/scripta thon for the demo...

Received on Thursday, 1 February 2007 01:14:18 UTC

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