06:10:11 <RRSAgent> RRSAgent has joined #hcls
06:10:11 <RRSAgent> logging to http://www.w3.org/2006/10/04-hcls-irc
06:10:17 <ivan> rrsagent, set log world
07:11:36 <Joanne> Joanne has joined #hcls
07:21:07 <Helen> Helen has joined #hcls
07:21:47 <vipul> vipul has joined #hcls
07:24:57 <jar> jar has joined #hcls
07:26:46 <jar> eric presented a modal logic called KD45 as a way of talking about provenance (skepticism over truth value of statements)
07:27:08 <jar> jar said fine, another tool for the toolbox
07:27:41 <jar> eric suggested that trotting out KD45 as an epistemological stance might help us when we talk with folks from the AI community
07:27:57 <jar> then, discussion of best practices document
07:28:22 <jar> ivan said we need plans to make definite documents with definite editors, and assked what they were
07:29:04 <jar> a laundry list of problem is not good enough; we need to spell out what we tried, what the roadblocks were, what's needed to fix
07:30:02 <jar> jar suggested that everyone's practices are very interesting, and writing about these goes beyond just a problems document
07:30:18 <jar> and it's too early to know which practices are a"best" ones
07:30:48 <jar> eric is typing 'slides' as we talk and these should be included in the minutes
07:31:36 <jar> ivan: for any demo, what really important points do the demo demonstrate? this would be a good document
07:34:27 <jar> eric: until lunch, work on specifying these things (use cases, demos, problems) that we will write about
13:04:48 <RRSAgent> RRSAgent has joined #hcls
13:04:48 <RRSAgent> logging to http://www.w3.org/2006/10/04-hcls-irc
13:09:15 <eneumann> eneumann has joined #hcls
13:09:34 <eneumann> ScribeNick eneumann
13:10:42 <eneumann> ACPP Presentation- Helen Chen... 
13:12:58 <eneumann> ...new charter: http://esw.w3.org/topic/HCLS/ACPPTaskForce/UpdatedCharter#preview
13:13:28 <eneumann> ... Temporal reasoning etc.
13:14:04 <eneumann> ...notes: BP Note of SW for Adaptive Clinical Workflow (mid Nov 06)
13:14:43 <eneumann> ... Bench to Bedside demo around Parkinsons (BioONT)
13:15:40 <eneumann> ... artifacts: ACWF demo, Notes, use-cases: derived ontologies and rules
13:19:44 <eneumann> ... Working Draft of Notes, to be public, so will need to receive and respond to comments
13:20:08 <eneumann> Ivan for now is staff contact for adding publications
13:20:58 <ivan> -> pointer to the W3C Publication rules: http://www.w3.org/2005/07/pubrules
13:21:44 <eneumann> BioRDF+BioONT: Vipul presentation...
13:22:22 <eneumann> ... USe case nailed: "Shw me the location of receptors that bind..."
13:22:53 <eneumann> ... spans anatomy, neurosci, mol bio, pharma, clincial/medical
13:23:10 <eneumann> /spans DBS; HI DB  (OWL), Neuron DB, BioRDF
13:23:27 <eneumann> ... sources Cocodat...
13:24:05 <eneumann> .... Demo Tasks: specify SPARQL forms, annotations, merge warehouses...
13:26:29 <eneumann> ...start as one merged warehouse, then demonstrate distributed DBs
13:27:19 <eneumann> ... user interface? choices?
13:28:10 <eneumann> ...Architectural Alternatives (in Note): Data Warhouse , Mediator, etc
13:30:04 <eneumann> ...demo: april 2007
13:31:42 <eneumann> ... Report: use-cases, arch, value SW prop, UI, editors Kei-Cheung, Don Doherty, Susie Stephens -- Deadline Nov 06
13:32:02 <ivan> -> Found a reference to a system doing federated queries (but I have *no* experience with it): http://darq.sourceforge.net/
13:32:43 <eneumann> also...http://www.w3.org/2004/10/04-pharmaFederate/
13:33:10 <eneumann> and .. http://www.w3.org/2004/04/30-RDF-RDB-access/
13:35:03 <eneumann> ... Don Doherty editorial lead for BioRDF-BioONT report
13:35:36 <eneumann> Helen Chen will be editorial lead for ACWP Notes
13:40:15 <eneumann> ... BioRDF-BioONT next steps: joint TC/wiki, sessions map; where to have a demo machine(s) located?
13:40:45 <eneumann> ... possible inclusion of guidelines for Parkinson's ala ACPP
13:41:20 <eneumann> BioONT report, first draft Nov 08 ontology modeling and mapping
13:44:37 <eneumann> Alan's demo...
13:50:43 <eneumann> ... graph tool 'Prefuse' for graphing classes and instances
13:53:05 <Joanne> Joanne has joined #hcls
13:53:09 <eneumann> ... ontology instances for instance relations; use punning later Owl1.1
13:53:35 <Joanne> how (where) do i find the minutes on the web of yesterday and today?
13:54:17 <eneumann> joanne, there's a general form to use... will find later
14:03:27 <jar> hybrow is a great example of a potential consumer of semweb stuff
14:03:55 <jar> it's going to be very sensitive to the wild type/mutant distinction (i.e. what's true in nature versus what's been created in the laboratory)
14:04:52 <jar> and many knowledge bases don't make this distinction ==> BAD semweb practice.
14:06:02 <ivan> Joanne: the minutes of yesterday are at: http://www.w3.org/2006/10/03-hcls-minutes.html
14:06:09 <ivan> (still need to be cleaned)
14:06:16 <Joanne> Alan Ruttenberg gave demo - Alan, would you summarize?
14:06:24 <ivan> the ones of today will be at http://www.w3.org/2006/10/04-hcls-minutes.html when the time comes
14:06:25 <Joanne> Ivan, thanks!
14:10:36 <jar> http://www.hybrow.org/
14:17:13 <Joanne> is there a download site for alan's sw and/or presentations?
14:19:29 <jar> location of alan's software is on the hcls wiki: http://esw.w3.org/topic/AlanRuttenberg?highlight=%28lsw%29
14:19:48 <jar> for today's work we'll have to ask him
14:33:09 <Susie> Susie has joined #hcls
14:33:24 <eneumann> ACPP: 2 Notes: ACPP Ontology (Mid Nov. 06), Temporal Reasoning (Dec, 06)
14:34:25 <eneumann> BioONT+BioRDF: Parkinsons Use-Case: WorkingDraft Parkinson's Ontology
14:35:05 <eneumann> BioONT: Ontology Modeling and Mapping Note (Vipul)
14:35:21 <Susie> Notes from Eric Neuman’s presentation.
14:35:35 <Susie> Identify strong, feasible focus areas. 
14:35:44 <Susie> This in the clinical space, but connects to many other activities within HCLS. 
14:35:58 <eneumann> DSE:  CDISC's STDM from a SW Perspective
14:36:11 <Susie> The theme is translational research, which is cell cultures, animals and into clinical. 
14:36:59 <eneumann> ... (2) Retrospective DBs (JANUS) and SW based annotations and links
14:37:45 <eneumann> ...(3) Provenance and trust (non-reputability) and security
14:38:59 <eneumann> Alan Ruttenberg: URI resolution with ontologies (Jan 2007)
14:42:16 <eneumann> ... Jonathan Reese lead editor for URIs...
14:43:04 <eneumann> ... scheduled for Jan 2007 (maybe lucky sooner ; ) )
14:44:09 <eneumann> Demonstrations: ACPP Demo of adaptable clinical workflows
14:45:14 <eneumann> ... Bio+Ont+BioRDF Parkinson's Collab Demo (April 2007)
14:45:58 <Susie> Share information and knowledge across and within projects.
14:46:00 <eneumann> DSE Demo: STDM Table and XML models ala RDF (early 2007)
14:46:21 <Susie> Important to have state thinking about people and animals. 
14:46:27 <Susie> Are reactions to drugs favorable or not.
14:46:33 <Susie>  Lot of state information from biomarkers. 
14:46:41 <Susie> Biomarkers have strong link to the data sets that BioRDF has been working with. 
14:46:46 <eneumann> ... (2) DEMO: of retrospective DB (JANUS) using URI wrapping and annotations
14:46:53 <Susie> Important to map from animal to human. 
14:47:00 <Susie> Lot of people focus on genomics and functional genomics.
14:47:10 <Susie> Put data into repository and do mining. 
14:47:18 <Susie> Don’t just do this for 1 drug. 
14:47:27 <Susie> Are looking to learn from the experience, so can apply knowledge to future work.
14:47:36 <Susie> In mechanism space we are utilizing BioPAX.
14:47:59 <Susie> Domain semantics and flow of them have been defined. (slide 3).
14:48:07 <Susie> Relationship between HL7, CDISC, FDA. (slide 4)
14:48:16 <Susie> Overview of ontologies that relate to HL7, CDISC, etc. 
14:48:24 <Susie> It’s all about exchanging data sets. (slide 5)
14:48:39 <Susie> The FDA has large pool of clinical data, but can’t be analyzed because it’s not available. (slide 6)
14:48:47 <Susie> Proposed notes and activities. 
14:48:56 <Susie> SDTM exchange model has limitations. 
14:49:04 <Susie> Make it available in a Semantic Web representation.
14:49:12 <Susie> Goal is to create a note by November. 
14:49:20 <Susie>  Eric commits to getting it complete. 
14:49:29 <Susie>  Want to have demo by early 2007. 
14:49:39 <Susie> The demo would work with some set of SDTM data in the scenario of a simple experiment.
14:49:47 <Susie>  Latter action items are scheduled for mid to late 2007 (slide 7). 
15:04:17 <ivan> rrsagent, draft minutes
15:04:17 <RRSAgent> I have made the request to generate http://www.w3.org/2006/10/04-hcls-minutes.html ivan
15:04:24 <ivan> rrsagent, bye
15:04:24 <RRSAgent> I see no action items