IRC log of hcls on 2014-12-23

Timestamps are in UTC.

15:55:53 [RRSAgent]
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logging to
15:55:55 [trackbot]
RRSAgent, make logs world
15:55:55 [Zakim]
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15:55:57 [trackbot]
Zakim, this will be HCLS
15:55:57 [Zakim]
ok, trackbot; I see SW_HCLS()11:00AM scheduled to start in 5 minutes
15:55:58 [trackbot]
Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
15:55:58 [trackbot]
Date: 23 December 2014
15:56:20 [Zakim]
SW_HCLS()11:00AM has now started
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bpech has joined #hcls
15:59:36 [Joshua_Phillips]
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16:00:34 [Zakim]
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+ +1.410.624.aaaa
16:00:56 [Joshua_Phillips]
zakim, aaaa is Joshua_Phillips
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+Joshua_Phillips; got it
16:01:10 [Ingeborg]
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16:03:38 [dbooth]
Talky is here:
16:04:24 [Zakim]
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+ +1.510.418.aabb
16:04:54 [dbooth]
zakim, aabb PeterHendler
16:04:54 [Zakim]
I don't understand 'aabb PeterHendler', dbooth
16:05:03 [dbooth]
zakim, aabb is PeterHendler
16:05:03 [Zakim]
+PeterHendler; got it
16:05:31 [dbooth]
We will try using for audio
16:05:33 [Zakim]
+ +1.727.501.aacc
16:05:37 [Zakim]
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+ +31.62.427.aadd
16:06:30 [dbooth]
zakim, aacc is Patricia
16:06:30 [Zakim]
+Patricia; got it
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16:07:23 [Zakim]
16:07:51 [Lloyd]
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16:08:27 [dbooth]
zakim, aadd is mscottm
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+mscottm; got it
16:09:06 [dbooth]
Talky is here:
16:09:36 [Zakim]
16:10:28 [Zakim]
16:10:53 [dbooth]
Talky is here:
16:12:44 [ericP]
Zakim, please dial ericP-mobile
16:12:44 [Zakim]
ok, ericP; the call is being made
16:12:45 [Zakim]
16:13:40 [Zakim]
16:13:51 [drjava]
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16:14:12 [Zakim]
16:14:33 [drjava]
Drjava is peter hendler
16:14:37 [mscottm]
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16:14:38 [Zakim]
16:14:50 [mscottm]
Zakim, who is here?
16:14:50 [Zakim]
On the phone I see DBooth, bpech, Joshua_Phillips, PeterHendler, Patricia, [IPcaller], [IPcaller.a], cecil, EricP, Ingeborg, mscottm, Tony
16:14:53 [Zakim]
On IRC I see mscottm, drjava, Lloyd, pknapp, Ingeborg, Joshua_Phillips, bpech, Zakim, RRSAgent, dbooth, TallTed, cloudcell, trackbot, ericP
16:15:10 [dbooth]
Topic: C-CDA as ORIM RDF (Eric Prud'hommeaux)
16:15:22 [dbooth]
16:15:30 [Zakim]
16:17:57 [dbooth]
Eric: Charlie and I created the ORIM -- translation of RIM to OWL.
16:18:04 [dbooth]
... a few years ago.
16:18:24 [GJiang]
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16:18:53 [ericP]
16:19:02 [ericP]
16:19:17 [dbooth]
... IThe translation into OWL was done via the above linked document.
16:19:30 [dbooth]
... It assumes that relation names in UML are not unique
16:19:36 [Zakim]
16:19:50 [dbooth]
... so it prefixes every relation name with the name of the class it came from.
16:20:17 [dbooth]
... So a predicate for a car with a registration would be car.registration.registrationDocument
16:20:27 [Zakim]
16:20:39 [dbooth]
... This makes predicate names very long, but they work.
16:20:57 [Claude]
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16:21:16 [Cecil]
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16:21:25 [dbooth]
... Lloyd did this for doing inference on the RIM model.
16:21:39 [dbooth]
... It's an enormous ontology.
16:22:08 [dbooth]
... My intention was that it be useful to turn CCDA XML into RIM, then turn RIM into RDF.
16:22:27 [Claude]
16:22:40 [dbooth]
... so this document: was my attempt to not be creative, but to produce the same RDF that anyone would.
16:23:02 [Zakim]
16:23:10 [dbooth]
... CCDA example came from Josh Mandel. In principle this xslt should work with any CCDA.
16:23:46 [RHausam]
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16:23:48 [dbooth]
Joshua: I'm specifically interested in including genomic and phenotypic data.
16:24:06 [dbooth]
... But basically want a concrete RDF representation that we can query using SPARQL.
16:24:11 [dbooth]
zakim, who is here?
16:24:11 [Zakim]
On the phone I see DBooth, bpech, Joshua_Phillips, Patricia, [IPcaller], [IPcaller.a], cecil, EricP, Ingeborg, mscottm, Tony, knapp, PeterHendler, rhausam
16:24:15 [Zakim]
On IRC I see RHausam, Cecil, Claude, GJiang, mscottm, drjava, Lloyd, pknapp, Ingeborg, Joshua_Phillips, bpech, Zakim, RRSAgent, dbooth, TallTed, cloudcell, trackbot, ericP
16:24:54 [Claude]
To David: Could you please paste the link again. I just installed an IRC client.
16:25:30 [dbooth]
The page eric is discussing:
16:25:57 [dbooth]
Eric: The main arcs of connectivity in RIM are ACT relations.
16:27:40 [dbooth]
... Using vocab from HL7 indicating severity, etc.
16:28:17 [dbooth]
... In principle those arcs make the RDF graph.
16:28:54 [dbooth]
... One way to make this more like what RDF people would use would be to turn these ACT relationships into RDF arcs, which means throwing out some information.
16:29:05 [dbooth]
... This would make a lean and RDF-friendly way to represent clinical data.
16:29:20 [dbooth]
... Then we could do RDF tricks from there.
16:29:40 [dbooth]
... Does it make sense to collapse the ACT relatinoships into predicates?
16:29:52 [dbooth]
Lloyd: No, because there are a lot more predicates attached to them.
16:30:14 [dbooth]
... Need to go through the TYPE codes to see which ones are identified.
16:31:26 [dbooth]
... When those other things are there, they are important.
16:32:08 [dbooth]
... My leaning is to have that detail there always, but have the shortcut there as well when it can be done.
16:32:30 [dbooth]
Cecil: What would be the use case for an RDF model that drops content?
16:32:55 [dbooth]
Eric: If the majority of ACT relationships were simple TYPE codes, then one could write SPARQL queries that use those
16:33:15 [dbooth]
... and when there was something else attached, then you would fall back to a more complex sparql query.
16:33:29 [dbooth]
cecil: to be safe for clinical use, you can't ever drop information.
16:33:48 [dbooth]
... Not safe to drop them ever.
16:34:08 [dbooth]
... But if our use of this is FHIR then why not use FHIR where it is flattened?
16:34:56 [dbooth]
... If you're going to model the RIM or CDA in RDF, you should not drop any of the model, because it would be dangerous to lose clinical content. Would risk clinically significant error.
16:35:32 [dbooth]
Eric: Not planning on discarding info, but using simple arc when there is ONLY a type code.
16:36:42 [dbooth]
... The other goal was to map this to FHIR RDF.
16:37:38 [dbooth]
... Wrote a script to spit out XSLT and ShEx code that will round trip FHIR XML to FHIR RDF
16:37:44 [Zakim]
16:37:45 [dbooth]
16:38:30 [ericP]
16:39:21 [john]
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16:39:24 [ericP]
16:39:33 [dbooth]
zakim, P13 is JohnMaddison
16:39:33 [Zakim]
sorry, dbooth, I do not recognize a party named 'P13'
16:39:42 [dbooth]
zakim, ??P13 is JohnMaddison
16:39:42 [Zakim]
+JohnMaddison; got it
16:39:57 [dbooth]
16:41:08 [ericP]
16:41:39 [dbooth]
Eric: ShEX is good for validating RDF, but also (slide 45) good for translating
16:42:01 [dbooth]
16:42:27 [dbooth]
Eric: This is a complex example. What's shown at the top is turned into what's shown at the bottom.
16:43:30 [dbooth]
... There are actions specified when the pattern on the left is matched.
16:43:56 [dbooth]
David: When the pattern on the left is matched, the %GenR action is run?
16:43:58 [dbooth]
Eric: Right.
16:44:38 [Zakim]
16:44:46 [ericP]
16:44:56 [dbooth]
Scott: the leading zeros are missing from the dates.
16:45:04 [dbooth]
Eric: yes, didn't fix that yet.
16:46:03 [dbooth]
David: now looking at the above link, shown Schema (ShEX) on the left and Data (Turtle) on the right.
16:46:24 [dbooth]
Eric: The left is the input, the right is the output, and below is the validation result.
16:47:12 [dbooth]
s/the input/the input schema/
16:47:24 [dbooth]
s/the output/the input instance data/
16:48:02 [dbooth]
Eric: when you click (at the bottom) "View GenR output as popup" then you see the output.
16:49:24 [dbooth]
... FHIR instance data could be combined with schema.
16:49:45 [dbooth]
... then you could conclude an allergy to bee stings
16:50:00 [Zakim]
16:50:39 [dbooth]
... Want to see if this would be good enough for use by the CDA work group at HL7.
16:52:33 [dbooth]
... Wanted to see whether we could migrate between different information models and combine that with validation, and this seems to do it.
16:52:57 [dbooth]
... Also the RDF Data Shapes working group is deciding what language to use, so comments on ShEx are invited.
16:53:25 [dbooth]
David: It reminds me of yacc rules.
16:53:42 [dbooth]
Paul: Is the intent of validation to determined a valid instance?
16:53:54 [dbooth]
Eric: Yes, validate an instance at an RDF graph level.
16:54:30 [dbooth]
... The semantic actions can do more business logic validation that the patterns cannot validate.
16:54:51 [dbooth]
Paul: Efficiency?
16:55:15 [dbooth]
Eric: Paper on Regular Bag Expressions looks at that.
16:55:40 [dbooth]
ACTION: Eric to supply link for paper on Regular Bag Expressions
16:55:40 [trackbot]
Created ACTION-14 - Supply link for paper on regular bag expressions [on Eric Prud'hommeaux - due 2014-12-30].
16:55:53 [dbooth]
John: Also interested in compelling complex examples
16:56:08 [ericP]
16:57:08 [dbooth]
ACTION: JohnMaddison to provide example CCDA for trying with ShEx
16:57:08 [trackbot]
Error finding 'JohnMaddison'. You can review and register nicknames at <>.
16:57:22 [Zakim]
16:57:27 [Zakim]
16:57:50 [dbooth]
zakim, who is here?
16:57:50 [Zakim]
On the phone I see DBooth, Joshua_Phillips, [IPcaller.a], EricP, Ingeborg, mscottm, Tony, knapp, PeterHendler, rhausam, JohnMaddison
16:57:52 [Zakim]
On IRC I see john, RHausam, Cecil, GJiang, mscottm, drjava, Lloyd, pknapp, Ingeborg, Joshua_Phillips, Zakim, RRSAgent, dbooth, TallTed, cloudcell, trackbot, ericP
16:59:57 [dbooth]
Topic: Approve minutes
16:59:58 [dbooth]
17:00:37 [dbooth]
Minutes unanimously approved!
17:01:37 [Zakim]
17:01:39 [Zakim]
17:01:42 [Zakim]
17:01:43 [dbooth]
17:01:44 [Zakim]
17:01:45 [Zakim]
17:01:54 [Zakim]
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17:04:43 [dbooth]
zakim, who is here?
17:04:43 [Zakim]
On the phone I see DBooth, [IPcaller.a], EricP, Tony, rhausam
17:04:45 [Zakim]
On IRC I see john, RHausam, Cecil, GJiang, mscottm, Lloyd, Ingeborg, Zakim, RRSAgent, dbooth, TallTed, cloudcell, trackbot, ericP
17:15:28 [dbooth]
17:16:45 [dbooth]
Chair: David Booth and Paul Knapp
17:16:53 [dbooth]
rrsagent, draft minutes
17:16:53 [RRSAgent]
I have made the request to generate dbooth
17:17:09 [Zakim]
17:18:22 [Zakim]
17:18:23 [Zakim]
17:18:29 [Zakim]
17:18:35 [ericP]
Zakim, who is here?
17:18:35 [Zakim]
On the phone I see Tony
17:18:37 [Zakim]
On IRC I see john, RHausam, Cecil, mscottm, Zakim, RRSAgent, dbooth, TallTed, cloudcell, trackbot, ericP
17:18:47 [ericP]
Zakim, please drop tony
17:18:47 [Zakim]
Tony is being disconnected
17:18:49 [Zakim]
SW_HCLS()11:00AM has ended
17:18:49 [Zakim]
Attendees were DBooth, bpech, +1.410.624.aaaa, Joshua_Phillips, Ingeborg, knapp, +1.510.418.aabb, PeterHendler, +1.727.501.aacc, +31.62.427.aadd, Patricia, [IPcaller], mscottm,
17:18:49 [Zakim]
... cecil, EricP, Tony, rhausam, JohnMaddison
17:19:13 [ericP]
(figuring tony's phone infrastructure failed to send the "all done")
17:20:24 [dbooth]
Present: Cecil_Lynch Claude_Nanjo David_Booth EricP GJiang Ingeborg John_Mattison Joshua_Phillips Lloyd_McKenzie Patricia Paul_Knapp Peter_Hendler Scott_Marshall Tony_Mallia Rob_Hausam
17:20:33 [dbooth]
rrsagent, draft minutes
17:20:33 [RRSAgent]
I have made the request to generate dbooth
17:21:13 [dbooth]
Present+ Peter_Hendler
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