See also: IRC log
Susie: principal research
scientist at Eli Lilly
... involved in RDF since 2002
... chaired BioRDF
chimezie: lead architect on SemanticDB at Cleveland Clinic
mscottm: postdoc researcher at Univ AMS
mscottm: work with lab for
E-Science on knowledge management/capture
... involted with semweb
... compsci background, who has worked with biologists for a
while
<Susie> Eric Prud'hommeaux sem web since 98, and team contact at W3C
<Susie> Happy to help with questions
Susie: encourage folks to post their intros on the wiki
mscottm: in 2002 there was a big meeting where people aired what they wanted out of the SemWeb in the areas of health care and life sciences
mscottm: an ambitious group, focused on data integration in health care, life science, biological modeling, tranlsational medicine
mscottm: crosses many databases
mscottm: first incarnation of the
group started several task forces around areas of work
... in this incarnation, we expect to have several projects
with weekly calls
... continuing from last charter, we have BioRDF task force and
Clinical Observations Interoperability
... would like to gather project descriptions
... face to face meeting: 20-21Oct during the W3C Technical
Plenary
mscottm: meeting is in Mandelieu
ericP: How do you manage a phone
call with 40 or 50 people? We use IRC and some derivative of
Robert's Rules of Order.
... we have a web-based IRC client which is available to
Members and Invited Experts (more later)
<eneumann> Anyone except Susie from pharma on this call?
<mscottm> Therese Vachon from Novartis might show up when another TC is done.
<Zakim> ericP, you wanted to say something clever
ericP: there are some other tricks for managing agenda and that sort of thing.
<AdrianP> Hi, just joined
<mscottm> Hi Adrian
ericP: The W3C site is backed by
a revision control system called CVS.
... A lot of these documents are edited by elected editors,
responding to comments in publc mailing lists.
... Wiki's have their own form of concensus (most prolific
wins).
... So W3C also has wiki space for things which invite that
group dynamic.
... W3C is a member-based industry consortium
... that is, we invite participation from folks appointed by
representatives of the various members.
... for this group, we'll have lots of invited experts
susie: note the email alias team-hcls-chairs
<mscottm> team-hcls-chairs@w3.org
susie: work expectations:
... .. participation is public, but we expect the majority will
be members of W3C
... .. non-members can explore the IE path
<mscottm> IE = "Invited Expert"
susie: .. better to be a member,
access to more resources
... .. we'll be pruning the mail list shortly to include
members and IEs
... .. would recommend assigning a minimum of 10% time to the
group
... .. appreciate that work preempts
... .. there will be less exploration than the first HCLS
group; we expect the participants to be able to work on
deliverabless
... .. deliverables will include conferences and papers
... .. meeting records will document action items, decisions,
...
... commitments:
... .. it's important to be clear when you can do
something
... .. also important to respect other participants at all
levels
... .. [ref Postel's Law]
-> http://en.wikipedia.org/wiki/Postel's_law Postel's Law
susie: i expect that following these guidelines will make a productive group
chimezie: Charter defines the
mandiate and scope of an interest group
... scope, goals, deliverables, liasons
... goals:
... .. 1st: advocate, develop tools, and suporting documents
for SemWeb in health care, life science
... .. document use cases
... use cases useful for defining what we need to do and when
we've succeeded
... will develop implementations that meet these use
cases
... develop high-level vocabularies
... diseminate this info to govornments, other bodies...
... charter lays out separation of the primary domains of this
group: biology, health care, trans therap
... primary value proposition is in integrating diverse
databases
... Trans Therapeutics: working on "bench to bedside":
preclinical trial data to affect patient medication
... health care
... coordiation with other groups:
... .. many of the standards in this area are sill
develping
<AdrianP> would propose a liaison with W3C RIF
chimezie: another group to liase with is RIF
<AdrianP> yes, we are working on such use cases
<AdrianP> e.g. http://www.w3.org/2005/rules/wiki/UCR#Ruleset_Integration_for_Medical_Decision_Support
chimezie: relevent recently
closed groups: SPARQL, GRDDL
... this IG is charterd for 3 years (starting 1 June)
... want to work with HL7, CDISC, those managing SNOMED -GT
eneumann: lots of nearby
activities that aren't SemWeb-based
... the folks working BRIDG wanted to get more involved
... BRIDG working with CDISC, HL7, National Cancer
Instituted
... they are now aware that there is an OWL version of
BRIDG
chimezie: how does these liasons
work
... we often invite them to speak to tasks forces
marco: how open are you to new
use cases?
... if you work 10% of your time, it needs to be in sync with
your interests
susie: acknoweldging the need for synergy beteen HCLS participation and day jobs, we've selected some tasks
<chimezie> Project Ideas
susie: we ask your advice on
these tasks and invite new proposals
... if there projects that you are working on, you may enter it
in the wiki page (Project Ideas)
<AdrianP> I already started to add to this projects
susie: alternatively, you can send email to the public-semweb-lifesci@w3.org list, or to the team-hcls-chairs@w3.org if you just want input from the chairs
tx AdrianP
<mscottm> http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability
chimezie: Clinical Osbervations
Interoperability task force (ongoing) lead by Vipul
... re-purposing existing clinical models and developing new
ones
... lots of recent activity
susie: Vipul will give us a 20 minute overview during the next HCLS call (2 weeks from today)
chimezie: we encourage SNOMED to distribute in OWL
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLanguages
<mscottm> oops - this one: http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLanguages
chimezie: ISTC is now planning
to distribute as a secondary deployment
... RIF is a language for exchanging rules
... we can give them use cases in the area of Clinical Decision
Support
... we can see how well these rules can support these use
cases
... [task] identify archetypal data that comes up a lot in
health care scenarios to push for standards in those small
areas of KR
AdrianP: [editor of the RIF UC&R document] I can easily add your use cases to the UC&R doc
susie: CDISC creates clinical interchange standards approved by the FDA
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/CDISC
susie: [task] work with CDISC to
create ontology of data elements withing the SDTM
... [task] (similar to drug safety and efficacy) labeling and
modeling biomarkers
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/ClinicalTrials
<AdrianP> I'm also working on several use cases which exploit rules in HCLS
susie: [task] clinicaltrials.gov
documents clinical trials around the world
... lillytrials.com includes lilly trials
... FDA publishes the Orange Book
... sometimes the data is available in HTML
... sometimes it's all trapped in PDFs
... project would involve picking a therapeutic area to mining
the data in those papers
... [task] diseasome written up in nature, new england journal
of medicine
... barabassy interested in working with us to publish
diseasome in RDF/OWL
... [task] how can SIOC benifit the scientific/medical
communities?
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/Diseasome
susie: this has become a big focus area for lots of folks
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/SIOC
susie: harvard just won a large
grant for this
... create a graph of who's publishing with whom
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/PCMR
susie: [task] (less certain how
to persue this just now) personally managed health care
records
... clinical trials subjects get their genome scanned, but
don't keep that information
... both google and microsoft are working on storage for this
area
... we can be ahead of the curve (or leading edge) on this
mscottm: [covering life
science/bio projects]
... some of these could form basis of projects that have
already be defined
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/KB
mscottm: my top interest is
enchancing the HCLS Knowledge Base
... could include adding diseasome data from barabassy
... would this find genetic reasons for diseases that are
related to each other'
... [project] add chemical structures (KB currently biased
towards neurology)
... can add other things like anatomy and physiology
... [task] distribution of the KB across multiple
locations
... fairly challenging, people ask "can it be distributed?"
<AdrianP> we could probably host another triple store here at the Biotec Center in Dresden
mscottm: require nitty gritty work on query engines
<AdrianP> or a verbalized language, a controlled english interface
mscottm: [task] enhance the query interface to make it easier to compose queries without having to know all the namespaces
mscottm: similarly to getting to know the contents of a KB requires the same work
<mscottm> http://www.w3.org/TR/2008/NOTE-hcls-senselab-20080604/
<kidehen_> ericP: Does a query interface exist?
<ericP> kidehen_, only have SPARQL endpoints so far
<kidehen_> ericP: is the a link to something I can see?
<kidehen_> ericP: s/the/there
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/eScience
<matthiassamwald> kidehen_, some of us have built UIs that access parts of the Knowledge Base, such as Entrez Neuron: http://neuroweb3.med.yale.edu:8090/
<ericP> kidehen_, i think it's in the hcls-kb doc
mscottm: [task] add e-science to our work, including grid computing
mscottm: web services are a way
for us to collaborate
... you can use Taverna (SP?) to compose workflows out of
multiple web services
<mscottm> http://myexperiment.org/
mscottm: sharing workflows is
getting easier
... you can trigger web services by clicking on something on a
web page
... should look for synergy between these projects and other
HCLS projects
<AdrianP> there is a synergy with the Rule Responder project, which allows to describe rule-based workflows
mscottm: e.g. exporting diseasome
in RDF would be usefully shared
... e-science allows you to, e.g. export text-mined medline in
RDF -- surprisingly in-reach
<matthiassamwald> shameless self-promotion of a prototype RDF/OWL wrapper for a text mining service: http://whatizit.neurocommons.org/
mscottm: main questions are "how do you wnat to represent the info, and how would you clean it up"
<mscottm> http://esw.w3.org/topic/HCLSIG/Project_Ideas/SemanticWikis
mscottm: also want to explore the use of semantic wikis
<dingl> we may look at some work on semantic media wiki at RPI
<dingl> http://tw.rpi.edu/wiki/index.php/Main_Page
AdrianP: how do we get folks to work on a project?
susie: document the project, and
if there's sufficient interest, off you go
... the lead person will pick task force meeting times, and
report during the HCLS calls
... these projects will have indepencence and their own
lifespan
... expect most to be done within a year
mscottm: if you have project
ideas, try to keep in mind that synergy with other projects
helps your goal
... helps to aim for a particlar demo/implementation
kei: could expand the KB with,
e.g. herbal medicine
... china has dbs about these herbs
ericP: I expect that Huajun will be spearheading something like that
<Huajun> yes, I am working with kei together on this project actually
susie: western pharmaceuticals are interested in easter meds
<matthiassamwald> http://richard.cyganiak.de/2007/10/lod/
matthiassamwald: would be great
aim to turn our projects into something that creates a coherent
datastructure
... many independent participants in linked open data follow
some rules to create an aggregated project
susie: reminds me that we'd like
projects with common threads through the different silos
... don't want isolated projects; want to bridge them all
together
... don't expect they'll all link together right from the
start, but if you use e.g. the same compound as an example, we
can link them together
Next call: two weeks June 26
susie: tx to all participants, tx for your participation