- From: Eric Prud'hommeaux <eric@w3.org>
- Date: Thu, 12 Jun 2008 14:55:02 -0400
- To: public-semweb-lifesci@w3.org
- Message-ID: <20080612185502.GT5591@w3.org>
http://www.w3.org/2008/06/12-hcls-minutes
HCLS
12 Jun 2008
See also: [2]IRC log
Attendees
Present
Chime, Susie, Scott, EricP, +~25 folks
Regrets
Chair
Susie Stephends
Scribe
ericP
Contents
* [3]Topics
1. [4]Introduction to Co-chairs and Team contact - Chime, Scott,
Susie
2. [5]Group Structure - Scott
3. [6]Participation Expectations - Susie
4. [7]roll call
5. [8]Charter Overview - Chime
6. [9]Proposed Projects - Chime, Scott, Susie
7. [10]Q&A
* [11]Summary of Action Items
__________________________________________________________________
Introduction to Co-chairs and Team contact - Chime, Scott, Susie
* [12]HCLSIG Wiki Home Page
* [13]Introductions Wiki Page
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
Group Structure - Scott
* [14]integration of many data sources to answer scientific queries
* [15]TPAC Schedule
* [16]Main HCLS Mailing List
* [17]these minutes
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
Participation Expectations - Susie
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]
-> [18]http://en.wikipedia.org/wiki/Postel's_law Postel's Law
susie: i expect that following these guidelines will make a productive
group
Charter Overview - Chime
* [19]Health care and Life Sciences Interest Group (New) Charter
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
[20]RIF WG
<AdrianP> yes, we are working on such use cases
<AdrianP> e.g.
[21]http://www.w3.org/2005/rules/wiki/UCR#Ruleset_Integration_for_Medic
al_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
Proposed Projects - Chime, Scott, Susie
susie: acknoweldging the need for synergy beteen HCLS participation and
day jobs, we've selected some tasks
<chimezie> [22]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>
[23]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>
[24]http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLan
guages
<mscottm> oops - this one:
[25]http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLan
guages
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> [26]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>
[27]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> [28]http://esw.w3.org/topic/HCLSIG/Project_Ideas/Diseasome
susie: this has become a big focus area for lots of folks
<mscottm> [29]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> [30]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> [31]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> [32]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> [33]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:
[34]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> [35]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:
[36]http://whatizit.neurocommons.org/
mscottm: main questions are "how do you wnat to represent the info, and
how would you clean it up"
<mscottm>
[37]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> [38]http://tw.rpi.edu/wiki/index.php/Main_Page
Q&A
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> [39]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
Summary of Action Items
[End of minutes]
__________________________________________________________________
Minutes formatted by David Booth's [40]scribe.perl version 1.133
([41]CVS log)
$Date: 2008/06/12 18:53:34 $
References
1. http://www.w3.org/
2. http://www.w3.org/2008/06/12-hcls-irc
3. http://www.w3.org/2008/06/12-hcls-minutes#agenda
4. http://www.w3.org/2008/06/12-hcls-minutes#item01
5. http://www.w3.org/2008/06/12-hcls-minutes#item02
6. http://www.w3.org/2008/06/12-hcls-minutes#item03
7. http://www.w3.org/2008/06/12-hcls-minutes#item04
8. http://www.w3.org/2008/06/12-hcls-minutes#item05
9. http://www.w3.org/2008/06/12-hcls-minutes#item06
10. http://www.w3.org/2008/06/12-hcls-minutes#item07
11. http://www.w3.org/2008/06/12-hcls-minutes#ActionSummary
12. http://esw.w3.org/topic/HCLSIG
13. http://esw.w3.org/topic/Introductions
14. http://www.w3.org/TR/hcls-kb/
15. http://www.w3.org/2008/10/TPAC/Schedule
16. http://lists.w3.org/Archives/Public/public-semweb-lifesci/
17. http://www.w3.org/2008/06/12-hcls-minutes
18. http://en.wikipedia.org/wiki/Postel's_law
19. http://www.w3.org/2008/05/HCLSIGCharter
20. http://www.w3.org/2005/rules/wiki/RIF_Working_Group
21. http://www.w3.org/2005/rules/wiki/UCR#Ruleset_Integration_for_Medical_Decision_Support
22. http://esw.w3.org/topic/HCLSIG/Project_Ideas
23. http://esw.w3.org/topic/HCLS/ClinicalObservationsInteroperability
24. http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLanguages
25. http://esw.w3.org/topic/HCLSIG/Project_Ideas/DecisionSupportRuleLanguages
26. http://esw.w3.org/topic/HCLSIG/Project_Ideas/CDISC
27. http://esw.w3.org/topic/HCLSIG/Project_Ideas/ClinicalTrials
28. http://esw.w3.org/topic/HCLSIG/Project_Ideas/Diseasome
29. http://esw.w3.org/topic/HCLSIG/Project_Ideas/SIOC
30. http://esw.w3.org/topic/HCLSIG/Project_Ideas/PCMR
31. http://esw.w3.org/topic/HCLSIG/Project_Ideas/KB
32. http://www.w3.org/TR/2008/NOTE-hcls-senselab-20080604/
33. http://esw.w3.org/topic/HCLSIG/Project_Ideas/eScience
34. http://neuroweb3.med.yale.edu:8090/
35. http://myexperiment.org/
36. http://whatizit.neurocommons.org/
37. http://esw.w3.org/topic/HCLSIG/Project_Ideas/SemanticWikis
38. http://tw.rpi.edu/wiki/index.php/Main_Page
39. http://richard.cyganiak.de/2007/10/lod/
40. http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
41. http://dev.w3.org/cvsweb/2002/scribe/
--
-eric
office: +1.617.258.5741 32-G528, MIT, Cambridge, MA 02144 USA
mobile: +1.617.599.3509
(eric@w3.org)
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Received on Thursday, 12 June 2008 18:55:42 UTC