15:11:23 <RRSAgent> RRSAgent has joined #HCLS
15:11:23 <RRSAgent> logging to http://www.w3.org/2012/03/27-HCLS-irc
15:13:08 <ericP> eric@w3.org, public-semweb-lifesci@w3.org
15:15:50 <mscottm> mscottm has joined #hcls
15:15:54 <cme> cme has joined #hcls
15:16:49 <ericP> -> http://www.w3.org/2012/03/CSTE_TB.ppt Cecil's slides
15:17:12 <Stuart> Got them, thanks
15:17:41 <cme> cme has joined #hcls
15:18:14 <iker> thx ericP
15:18:18 <ericP> ericP has changed the topic to: Cecil Lynch's SemWeb in Health Care slides: http://www.w3.org/2012/03/CSTE_TB.ppt
15:20:32 <ericP> scribenick: ericP
15:20:38 <ericP> [slide 3]
15:20:56 <cme> cme has joined #hcls
15:21:07 <Joanne_Luciano> slides aren't numbered :-(
15:21:32 <Joanne_Luciano> ah, but the browser numbers them!
15:22:00 <egombocz> If you look at them not in show mode, you can see the numbers on the side thumbnails
15:22:00 <ericP> Cecil: antibiotic-resistent airline passenger promted review on Tuberculosis Information Management System (TIMS)
15:22:44 <ericP> ... reporting a TB case required passing a brittle set of messaging and business rules
15:23:12 <ericP> [slide 4: Message Processing Integration]
15:23:23 <ericP> Joanne_Luciano: each state wanted their own standard?
15:23:33 <ericP> Cecil: CDC wanted a standard
15:23:43 <ericP> ... states would take anything which makes reporting easier
15:23:52 <ericP> Cecil: [re: slide 4]
15:24:21 <ericP> ... choices about how to import messages to CDC
15:24:30 <ericP> ... .. after message had some processing
15:24:38 <ericP> ... .. as a Web Service RPC
15:24:51 <ericP> [slide 5: Deployment Architecture]
15:25:08 <Zakim> +??P7
15:25:09 <ericP> Cecil: going with existing CDC infrastructure
15:25:22 <ericP> ... staring from left:
15:25:22 <michel> michel has joined #hcls
15:25:47 <ericP> ... .. some source, usually state or large counties (53 jurisdictions) reports
15:25:57 <Joanne_Luciano> is going with the CDC one of those three options on slide 4 or is it another one (not listed on slide 4)?
15:26:10 <ericP> ... .. goes into data messaging broker, which validates syntax
15:26:33 <Joanne_Luciano> looks like it's option 1 on slide 4
15:26:36 <ericP> ... .. if a valid TB message, off to content validation queue
15:27:02 <ericP> ... .. also split into components for e.g. line listing of incoming cases
15:27:31 <ericP> ... .. after validation, email with contents of alert sent to CDC's TB group
15:27:47 <ericP> Joanne_Luciano: this is slide 3 option 1?
15:28:09 <ericP> Cecil: this is slide option 3 (RPC)
15:28:39 <ericP> ... we had tried driving real-time alerting from biosense
15:29:11 <ericP> ... we took messages off the first transport, never queued in DMB [slide 4 left]
15:29:25 <ericP> s/[slide 4 left]/[slide 5 left]/
15:29:38 <ericP> Cecil: the HL7 2.x standard is fairly loose
15:29:45 <ericP> ... flexible, can take any payload
15:29:51 <ericP> ... can be structured in any way
15:30:21 <ericP> ... segments are well-defined, but segment structure requires point to point negotiation
15:30:59 <ericP> ... p2p neg is a guideline
15:31:00 <ericP> charlie: HL7 2.x is a syntactic standard and a semantics guideline
15:31:16 <ericP> [slide 6: Message Content Validation Architecture]
15:31:32 <Joanne_Luciano> JMS?
15:31:38 <ericP> Cecil: after leaving broker, falls into JMS interface
15:32:08 <ericP> ... because this has the 2.5 validation, we don't need the 2.x syntactic validation
15:32:21 <ericP> ... so we don't do the validation
15:32:39 <ericP> ... before we went live, we validated and found 2 errors in HL7 messaging
15:32:51 <ericP> ... (was a benefit of 2-tier validation)
15:33:03 <ericP> ... once live, we don't do syntacit validation
15:33:16 <ericP> ... but we do parse out components
15:33:50 <ericP> ... questions like birthday and date of problem were found via OBX extractions
15:33:51 <Zakim> +Tony.aaaa
15:34:03 <Zakim> -mayo
15:34:28 <ericP> ... an OWL ontology tells us how to process a message
15:34:40 <ericP> ack me
15:35:34 <ericP> Cecil: the ontology links all the knowledge
15:36:01 <ericP> ... it guides parsing the message by aligning the OBX-extracted facts with an RDF graph
15:36:26 <ericP> ... we can then use the JESS reasoner for evaluating these facts
15:36:53 <ericP> ... JESS (Java Expert System Shell) is a rules FW/BW chaining rules engine
15:37:09 <ericP> ... has a protege plugin, interprets SWRL
15:37:38 <ericP> ... good commercial tool for high-volume processing
15:38:10 <ericP> ... payed for by tax dollars, only free for government use
15:38:32 <ericP> ... ($75K)
15:39:03 <ericP> ack me
15:39:15 <Stuart> Drools
15:39:17 <iker> DROOLS
15:39:23 <mr_sticky> Drools is from JBoss
15:39:41 <mr_sticky> http://www.jboss.org/drools
15:39:48 <ericP> Cecil: we tried Drools, which has FW/BW chaining and similar fact structure
15:40:05 <ericP> ... use JESS if you're processing millions of facts
15:40:12 <ericP> Joanne_Luciano: and Jena?
15:40:19 <ericP> Cecil: no experience with it
15:40:39 <ericP> ack me
15:42:04 <ericP> Cecil: at OTR, we pass what we expect to see and what we got as two graphs
15:42:53 <ericP> ... the choreography of the OTR framework works out that something is a question about an e.g. resistance pattern of anitbiotic
15:43:10 <ericP> ... we have a set of "listeners" (patterns)
15:43:36 <ericP> ... we built this on V3 semantics, but mapped back to V2 syntax
15:44:09 <ericP> ... once we've matched the graph against the patterns, we pass it to jess
15:45:04 <ericP> ... we give jess the profile for an e.g. normal patient, MDR (multi drug resistant) patient, XDR (extensive drug resistant) (potential super-spreader)
15:45:33 <ericP> ... the reasoning framework decides if an event needs action
15:46:13 <ericP> ... another listener strains through alerts from JESS for outbound messaging
15:46:33 <ericP> ... we also use the output for visualization
15:47:03 <ericP> ... folks don't need to need to use SAS to extract this data from mid-tier, instead just using graph representations
15:47:44 <ericP> ... with agreement from CDC, we could have sent output messages back to reporters
15:47:53 <ericP> ... output:
15:47:58 <ericP> ... .. drug resistant
15:48:17 <ericP> ... .. appropriateness of drugging (per WHO codes)
15:48:39 <ericP> ... .. predictive analysis of whether someone is likely to fall off treatment based on patient history
15:48:54 <ericP> [slide 7: Types of problems that could be solved by extending the TB framework]
15:49:16 <ericP> Cecil: had to bend to time and budget limitations
15:49:44 <ericP> ... we could have added a d2rq interface to retrofit the pre-existing data
15:49:50 <ericP> ... a lot we could have done
15:50:02 <ericP> [slide 8: The use of an OWL ontology]
15:50:05 <ericP> Cecil
15:50:53 <ericP> [slide 9: HL7 Message Artifact Taxonomy]
15:51:11 <ericP> Cecil: this is how we mapped the OBX structure to the ontology
15:52:13 <ericP> [slide 11: Rule Processing]
15:52:33 <ericP> [slide 12: Message Content Validation Rule Implementation]
15:52:49 <ericP> Cecil: this demonstrates the advantage of using OWL
15:53:00 <ericP> ... the blue is what we deleted
15:53:08 <ericP> ... (from TIMS)
15:53:25 <ericP> ... went from 358 to 175
15:53:42 <ericP> ... reduces frustration of reporters facing conflicting rules
15:54:26 <ericP> ... beyond OWL being able to do syntax, vocabulary, rule processing, we see the advantage of declarative rules
15:54:40 <ericP> [slde 13: Message Content Validation Rules]
15:55:23 <ericP> Cecil: with tons of volume and response time requirements, you need a more efficient bw-chaining system (JESS)
15:55:36 <ericP> [slide 14: Message Content Validation Results View]
15:55:43 <ericP> Cecil: sample output
15:55:58 <ericP> [slide 15: Processing Results]
15:56:11 <ericP> Cecil: average processing time 3.5s round trip
15:56:26 <ericP> ... far faster than a human, and more accurate
15:56:38 <ericP> ... scales up to ~350k messages/day
15:57:03 <ericP> ... ~300K TB messages/year
15:58:09 <mscottm> q+ on summary of SemWeb advantages
15:58:34 <ericP> Cecil: could scale to influenza
15:59:00 <ericP> ... at worst case (4 month window), 50-75M, so ~ 200K message/day
15:59:17 <ericP> ... in a surveillance, you're also looking at folks who don't have it
16:00:13 <ericP> ... feeds from 800 VA hospitals, + laps a quest and labcore, ...
16:00:23 <ericP> ... congress says we need response in 2 mins
16:00:50 <ericP> ... had to put everything in memory
16:01:03 <ericP> ... biosense lost funding
16:01:18 <mscottm> q-
16:01:51 <ericP> mscottm: summary of SemWeb advantages is very different from our usual tech demos in HCLS
16:02:05 <ericP> ... what are your SemWeb wins?
16:02:16 <ericP> ... what could be improved?
16:03:00 <ericP> charlie: would like formal continuation
16:03:13 <ericP> ... to help us find focal points in HCLS
16:03:43 <ericP> Cecil: SemWeb is a flexible way to extract knowledge
16:03:59 <ericP> ... we were given a TB messaging system and a deadline
16:04:25 <ericP> ... 7 days before deadline, CDC said we'd like to upgrade a 1.2 of our implementation guideline
16:04:39 <ericP> ... had around 35 new rules and 100 terminology changes
16:05:05 <ericP> ... because everything CDC gave us was in the OWL. expected to do it in 4 days
16:05:36 <ericP> ... made it on 4 days with no additional charge to CDC
16:06:00 <ericP> ... big commercial motivation is the flexibility at responding to rapidly changing knowledge
16:06:23 <ericP> ... at NCI, i wanted to build an EMR system
16:06:37 <ericP> ... NCO SHARP projects kind of get to this
16:06:49 <ericP> ... win 1: rapid software engineering
16:07:00 <ericP> ... win 2: rule validation
16:07:13 <ericP> ... win 3: can infer things that a human has problems inspecting
16:07:47 <mscottm> Nice to hear that experience in the field confirms my main sales pitch about advantage of SemWeb tech for software: easier maintenance and change, agile development, effectively lower cost.
16:07:51 <ericP> ... .. (large systems (e.g. BRIDG's UML) hard to swap into a brain)
16:08:27 <Zakim> -Tony.aaa
16:10:05 <Zakim> -Tony.aaaa
16:11:43 <iker> +1 April 4th
16:13:30 <Zakim> -??P7
16:13:40 <Zakim> -Tony.aa
16:14:01 <Zakim> -Tony
16:14:13 <michel> zakim, who is here?
16:14:13 <Zakim> On the phone I see Tony.a, charlie, egombocz, bosse, Joanne_Luciano, Cecil, mscottm, StuartTurner, iker, Bob_Powers, ericP, [IPcaller]
16:14:15 <Zakim> On IRC I see michel, mscottm, RRSAgent, Stuart, qiip, iker, Cecil, mr_sticky, troy, egombocz, Zakim, amrapali, Bosse, Guoqian, bobP, MacTed, ericP
16:14:23 <michel> rrsagent, draft minutes
16:14:24 <RRSAgent> I have made the request to generate http://www.w3.org/2012/03/27-HCLS-minutes.html michel
16:14:29 <michel> rrsagent, make log world-visible
16:16:04 <Zakim> -iker
16:16:23 <Zakim> -[IPcaller]
16:16:35 <Zakim> -charlie
16:16:36 <Zakim> -Joanne_Luciano
16:16:36 <Zakim> -mscottm
16:16:37 <Zakim> -bosse
16:16:37 <Zakim> -Bob_Powers
16:16:39 <Zakim> -StuartTurner
16:16:40 <Zakim> -egombocz
16:16:41 <Zakim> -Tony.a
16:16:42 <Zakim> -Cecil
16:16:43 <Zakim> SW_HCLS()11:00AM has ended
16:16:45 <Zakim> Attendees were Bob_Powers, Tony, EricP, charlie, egombocz, bosse, +1.518.276.aaaa, Joanne_Luciano, +1.415.537.aabb, mscottm, +1.301.443.aacc, Cecil, +1.507.269.aadd, mayo,
16:16:48 <Zakim> ... StuartTurner, iker, [IPcaller]
16:19:06 <egonw> egonw has joined #HCLS