14:56:00 <RRSAgent> RRSAgent has joined #HCLS
14:56:00 <RRSAgent> logging to http://www.w3.org/2012/05/22-HCLS-irc
14:56:05 <ericP> Zakim, this will be hcls
14:56:05 <Zakim> ok, ericP, I see SW_HCLS()11:00AM already started
14:56:13 <ericP> Zakim, please dial ericP-office
14:56:13 <Zakim> ok, ericP; the call is being made
14:56:14 <Zakim> +EricP
14:56:20 <ericP> Zakim, who is here?
14:56:20 <Zakim> On the phone I see ??P30, EricP
14:56:22 <Zakim> On IRC I see RRSAgent, bobP, Zakim, matthias_samwald, mscottm, jerven, achille_zappa, egonw__, ericP
14:56:32 <ericP> Zakim, ??P30 jerven 
14:56:32 <Zakim> I don't understand '??P30 jerven', ericP
14:57:12 <Zakim> +Bob_Powers
14:57:36 <jerven> I might be ??P30 on the phone as well
14:59:34 <Zakim> +Kerstin_Forsberg
15:00:24 <Zakim> + +1.412.623.aaaa
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15:01:15 <iker> iker has joined #hcls
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15:01:45 <Zakim> + +46.7.08.13.aabb
15:01:56 <HarryH> Zakim - 412.623.. is me.
15:02:02 <HarryH> Harry Hochheiser
15:02:05 <Zakim> + +1.215.239.aacc
15:02:14 <HarryH> Who is 215?
15:02:25 <iker> is me
15:02:29 <Zakim> +??P29
15:02:41 <Zakim> + +1.916.596.aadd
15:02:44 <iker> Zakim +1.215.230.. is me
15:02:57 <mscottm> Zakim, +1.215.239.aacc is iker
15:02:57 <Zakim> +iker; got it
15:03:05 <iker> thx Scott
15:03:13 <JoanneLuciano> JoanneLuciano has joined #hcls
15:04:20 <JoanneLuciano> is there a skype way into zakim (is skype on zakim)?
15:04:27 <Zakim> +AndyS
15:04:41 <mscottm> no
15:04:45 <StuartTurner> StuartTurner has joined #hcls
15:04:49 <bbalsa> bbalsa has joined #HCLS
15:05:07 <JoanneLuciano> :-(
15:05:08 <mscottm> you can use skype out to call it but you knew that :)
15:05:19 <kalpana> this is kalpana i am on skype out
15:05:21 <JoanneLuciano> yes, was aiming to save my pennies
15:06:14 <mscottm> talked to ericP about it a while back. Problem is with Skype and proprietary APIs, no open source, etc.
15:06:16 <ericP> ericP has changed the topic to: FHIR debrief <http://www.w3.org/2012/Talks/0506-egp-EHRs/#%281%29>
15:06:26 <ericP> -> http://www.w3.org/2012/Talks/0506-egp-EHRs/ FHIR debrief
15:06:41 <jerven> there are some free sip software that you can use to call in for free
15:06:55 <jerven> such as jitsi
15:07:04 <StuartTurner> You're fine (a bit of background noise)
15:07:14 <StuartTurner> Yes, better
15:07:25 <Zakim> + +1.845.658.aaee
15:07:42 <ericP> Zakim, aaee is JoanneLuciano 
15:07:42 <Zakim> +JoanneLuciano; got it
15:08:17 <michel> michel has joined #hcls
15:08:24 <Zakim> +michel
15:08:25 <JoanneLuciano> @jerven  thanks!  I could probably use google voice too, now that i think of it.
15:10:00 <michel> Meeting: W3C HCLS – Health Care Forum
15:10:06 <michel> Chair: EricP
15:10:13 <michel> ScribeNick: Michel
15:10:46 <mscottm> btw, Stian Soiland-Reyes (Manchester) made a nice gadget which provides a URL to a skype chat: http://s11.no/s/
15:12:49 <michel> ericp: i2b2 - controls access to data to make sure that patients remain anonymous
15:12:56 <JoanneLuciano> i2b2 folks the ones (only ones) able to get the access to the clinical data.
15:14:02 <michel> ... shrine (sp?) interface to i2b2 data
15:14:32 <michel> ... need large data to uncover associations between genotype-phenotype, or treatments; huge cost to patient data protection
15:15:49 <michel> ... in SW modeling, pick schema(s) and encode data accordingly; form that readable as "sentences"; bob has blood pressure bp1; bp1 has a systolic component, etc, and a value with unit of. ..
15:16:27 <mscottm> mscottm has joined #hcls
15:16:53 <michel> ... every piece of infrastructure has a sophisticated map from the data they capture to the representation;
15:17:19 <michel> ... refer to other organizations for coding data - LOINC for lab data, SNOMED, etc
15:17:41 <matthias_samwald> matthias_samwald has joined #hcls
15:18:30 <bobP> http://allafrica.com/stories/201205220344.html
15:18:31 <ericP> -> http://www.w3.org/2012/Talks/0506-egp-EHRs/ FHIR debrief
15:18:36 <bobP> wrong, sorry!
15:18:56 <michel> zakim, who is here?
15:18:56 <Zakim> On the phone I see ??P30, EricP, Bob_Powers, Kerstin_Forsberg, +1.412.623.aaaa, +46.7.08.13.aabb, iker, ??P29, +1.916.596.aadd, AndyS, JoanneLuciano, michel
15:19:00 <Zakim> On IRC I see matthias_samwald, mscottm, michel, bbalsa, StuartTurner, JoanneLuciano, kalpana, iker, HarryH, kerfors, RRSAgent, bobP, Zakim, jerven, achille_zappa, egonw__, ericP
15:19:26 <HarryH> aaaa is HarryH
15:19:31 <Zakim> +??P42
15:19:37 <matthias_samwald> zakim, ??P42 is matthias_samwald
15:19:37 <Zakim> +matthias_samwald; got it
15:20:04 <bbalsa> Zakim, aabb is Bosse
15:20:04 <Zakim> +Bosse; got it
15:21:54 <michel> slide 4: observation - LOINC code for test and results
15:24:36 <michel> slide 5: for early TMO, we straightforward represented the test result
15:25:24 <michel> ... huge infrastructure depends on this explicit coding; RDF's scaling good for references to a number of terminologies
15:26:19 <michel> slide 6: first pass at an RDF version of FHIR (pronounced fire; HL7)
15:28:49 <michel> slide 7: HL7 produced a message passing for patient data, without specifying the nature of the data; coded terminologies handle that
15:30:13 <michel> ... small upper level ontology - patients, clinical encounters, labs, lab results, etc; constrained
15:31:19 <michel> ... mood code - whether something was a query, completed, order, medication prescription, - very complex 
15:31:41 <michel> ... v2 (ascii separated by pipe) while v3 more sophisticated
15:32:17 <michel> ... number of people who could understand and manipulate the RIM was very small - needed a model to accommodate every use case; so it became large and abstract
15:33:14 <michel> ... only 3 countries adopted rim / v3; refactoring now - more webby oriented - "based on REST"
15:33:54 <michel> ... not going to be transporting the record with all the details, but transactions now more targeted/focused using identifiers
15:35:06 <ericP> -> http://www.w3.org/2012/04/FHIR/labreport-short.xml FHIR lab report instance
15:36:42 <michel> slide 6: rdf version of the above xml file
15:37:47 <StuartTurner> FYI - Units of Measure (UOM) code system refers to UCUM (http://unitsofmeasure.org/)
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15:38:43 <michel> slide 7: rdf version of the v3 might look like; more data, but says the same as slide 6 in terms of content
15:39:15 <michel> ... the rest is template like; pretty easy to write SPARQL construct from one to the other
15:40:29 <michel> ... need bi-directional conversion because i) infrastructure similarity ii) this is the language of HL7;  e.g. this is a certain kind of event with mood code
15:40:52 <michel> ... so need to show how the abbreviated descriptions maps to the full entry
15:42:01 <michel> ... validation - open world-ness useful for knowledge representation, but these records contain current determinants, which need access to
15:42:33 <michel> ... need to find out what might be incompletene
15:42:43 <michel> ... incomplete
15:42:48 <StuartTurner> And also the reason for the ubiquitous use of NullFlavor in HL7
15:42:51 <StuartTurner> Great overview
15:43:08 <StuartTurner> http://www.hl7.org/v3ballot/html/infrastructure/vocabulary/NullFlavor.html
15:43:33 <michel> stuart: a null flavor captures the state (unknown, unavailable, pending, etc)
15:43:37 <JoanneLuciano> NullFlavor      [2.16.840.1.113883.5.1008] Description:  A collection of codes specifying why a valid value is not present.
15:44:00 <michel> ericp: different flavors to specify the null
15:44:56 <JoanneLuciano> Name of speaker?
15:45:02 <michel> jerven: software developer for swissprot / uniprot
15:46:10 <StuartTurner> Joanne: Recent HL7 discourse has been quoting Donald Rumsfeld's quote regarding "known unknowns" @ http://en.wikipedia.org/wiki/There_are_known_knowns
15:46:34 <michel> ... validation of RDF   :  i) is the message structure complete (are all values supplied); ii) are the supplied reasonable or correct 
15:46:56 <michel> ... SPIN allows you to do both - i) does a person have a birthday, ii) does the birthday fall within a certain range
15:47:24 <michel> ... SPIN can be seen as a collection of SPARQL queries to check with the records are complete or correct
15:48:21 <michel> ... e.g. a protein that contains a homeobox should have a DNA binding function; if find homeobox that doesn't have function, could be an error ; exceptions (non-functional homeoboxes)
15:48:41 <michel> ... SPARQL construct for violations - generates human-readable error message
15:50:27 <michel> ... SPIN rules as a syntax are not just SPARQL, but saves them as RDF.  You can then have SPIN rules about SPIN rules; e.g. organism dependence; if the organism id changes, then the rules will trigger an error
15:51:07 <michel> ... HL7 -> same kind of problems: want  to check that all the values that you need are there; that the ones that are there are within a reasonable range
15:51:23 <michel> ... if a human can derive the check, it can be encoded as a SPIN rule
15:51:42 <michel> ... 150 rules for uniprot - checking curation quality
15:52:45 <michel> ... infrastructure: interactive editor (assert homeobox  - complains of lack of functional annotation)
15:53:14 <michel> ... checking identifiers cross-links to external databases
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15:56:33 <matthias_samwald> Light-weight alternative to SPIN: 'Simple SPARQL Rules' http://purl.org/zen/ssr.ttl
15:56:47 <matthias_samwald> Example of such rules: http://safety-code.org/ont/cds.ttl
15:57:18 <michel> ericp: validation languages make use of grammar conditions - can specify the number of (one or more, etc) to check structure; is it possible to have such a grammar to generate the SPARQL rules?
15:57:30 <Zakim> -Kerstin_Forsberg
15:58:55 <michel> jerven: for message structure, I would write them as OWL; SPIN takes OWL in the closed world assumption and generates SPARQL; schema validation through OWL
16:01:21 <Zakim> -iker
16:02:30 <Zakim> -??P29
16:03:28 <jerven> This is the basic schema ontology we use http://www.uniprot.org/core
16:03:38 <kalpana> I have to run now but great discussion
16:03:45 <kalpana> thanks
16:03:57 <jerven> I also have to go
16:04:09 <Zakim> -AndyS
16:04:15 <jerven> feel free to send questions via twitter to jervenbolleman or help@uniprot.org
16:04:45 <kalpana> i will do that, we will have quite a we questions
16:05:08 <StuartTurner> Wanted to share that in the veterinary informatics realm, we have significant concerns about moving forward with HL7 (especially regarding the Clinical Document Architecture) in a number of projects. Much of this relates to IP/licensing issues as well as technical. 
16:05:16 <StuartTurner> We are interested in FHIR and its direction since it's nascent and there maybe opportunity to add and mitigate some of the modeling issues in HL7 regarding non-human animals (clinical as well as research).
16:05:21 <StuartTurner> We'll be meeting at our annual veterinary informatics symposium in August, so I may have more to report if interested. I'll be making a pitch for SemWeb approaches. Much of the emerging work is relatively unknown to that audience. 
16:05:50 <michel> michel: recap on OSCAR discussion from last week - two goals - real-time clinical narratives to parse out coded content for patient-problem tracking and visualization; and CDS (some discussion around SPARQL, JBOSS drools)
16:06:29 <Zakim> -Bosse
16:06:55 <HarryH> 7Thanks.
16:06:59 <jerven> bye
16:07:00 <Zakim> - +1.412.623.aaaa
16:07:02 <Zakim> -EricP
16:07:10 <matthias_samwald> http://safety-code.org/v0.1/qm70W00I2KZ0u-A01N103HmXRp0W80080zIe0oWW0vL4kC8441HTCCCfOA03U0uW020013mICe00I8wyFnk6Qo4m20e7Nq0m0500G03RG90e56407xu6O0000000000000000000000000000
16:07:38 <michel> link to a genetic profile a person from a 23andme result (above)
16:08:03 <michel> rrsagent, draft minutes
16:08:03 <RRSAgent> I have made the request to generate http://www.w3.org/2012/05/22-HCLS-minutes.html michel
16:08:03 <Zakim> - +1.916.596.aadd
16:08:04 <Zakim> -Bob_Powers
16:08:05 <Zakim> -??P30
16:08:07 <Zakim> -matthias_samwald
16:08:08 <Zakim> -michel
16:08:16 <michel> rrsagent, make log world-visible
16:08:34 <JoanneLuciano> nice update - unfortunate that Warfarin is late alphabetically
16:08:52 <Zakim> -JoanneLuciano
16:08:53 <Zakim> SW_HCLS()11:00AM has ended
16:08:53 <Zakim> Attendees were EricP, Bob_Powers, Kerstin_Forsberg, +1.412.623.aaaa, +46.7.08.13.aabb, +1.916.596.aadd, iker, AndyS, +1.845.658.aaee, JoanneLuciano, michel, matthias_samwald, Bosse
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