IRC log of HCLS on 2012-03-27
Timestamps are in UTC.
- 15:11:23 [RRSAgent]
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- 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]
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- 15:15:54 [cme]
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- 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]
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- 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]
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- 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]
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- 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]
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