IRC log of hcls on 2014-12-16

Timestamps are in UTC.

15:58:04 [RRSAgent]
RRSAgent has joined #hcls
15:58:04 [RRSAgent]
logging to
15:58:06 [trackbot]
RRSAgent, make logs world
15:58:06 [Zakim]
Zakim has joined #hcls
15:58:08 [trackbot]
Zakim, this will be HCLS
15:58:08 [Zakim]
ok, trackbot, I see SW_HCLS()11:00AM already started
15:58:09 [trackbot]
Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
15:58:09 [trackbot]
Date: 16 December 2014
15:58:28 [Zakim]
15:58:39 [dbooth]
zakim, who is here?
15:58:39 [Zakim]
On the phone I see +1.604.250.aaaa, +1.978.794.aabb, DBooth
15:58:41 [Zakim]
On IRC I see RRSAgent, knapp, Tony, dbooth, TallTed, cloudcell, trackbot, ericP
16:01:01 [Ingeborg]
Ingeborg has joined #HCLS
16:01:09 [mscottm]
mscottm has joined #hcls
16:01:13 [Zakim]
16:01:33 [dbooth]
Regrets: Lloyd_McKenzie Hans_Cool
16:01:50 [Zakim]
+ +1.801.949.aacc
16:01:52 [Zakim]
+ +1.678.999.aadd
16:01:56 [Zakim]
+ +1.202.528.aaee
16:02:02 [Kerstin_Forsberg]
Kerstin_Forsberg has joined #HCLS
16:02:02 [dbooth]
zakim, aaaa is knapp
16:02:03 [Zakim]
+knapp; got it
16:02:10 [dbooth]
zakim, aabb is Tony
16:02:11 [Zakim]
+Tony; got it
16:02:24 [dbooth]
zakim, aacc is rhausam
16:02:27 [Zakim]
+rhausam; got it
16:02:43 [dbooth]
zakim, aadd is Brian_Peck
16:02:44 [Ingeborg]
zakim aaee is ingeborg
16:02:44 [Zakim]
+Brian_Peck; got it
16:02:56 [Zakim]
16:02:59 [dbooth]
zakim, aaee is Ingeborg
16:02:59 [Zakim]
+Ingeborg; got it
16:03:05 [bpech]
bpech has joined #hcls
16:03:22 [RHausam]
RHausam has joined #HCLS
16:03:27 [dbooth]
zakim Brian_Peck is really bpech
16:03:36 [dbooth]
zakim, Brian_Peck is really bpech
16:03:37 [Zakim]
+bpech; got it
16:03:57 [Zakim]
+ +
16:03:57 [Zakim]
+ +1.415.537.aagg
16:04:11 [dbooth]
zakim, aaff is Charlie
16:04:11 [Zakim]
+Charlie; got it
16:04:40 [ericP]
Zakim, aagg is cecil
16:04:40 [Zakim]
+cecil; got it
16:04:40 [dbooth]
zakim, aagg is Cecil
16:04:42 [Zakim]
sorry, dbooth, I do not recognize a party named 'aagg'
16:04:53 [Zakim]
+ +31.88.445.aahh
16:05:10 [ericP]
Zakim, aahh is mscottm
16:05:10 [Zakim]
+mscottm; got it
16:05:11 [Cecil]
Cecil has joined #HCLS
16:05:19 [Zakim]
16:05:23 [charlie]
charlie has joined #HCLS
16:05:24 [dbooth]
zakim, who is here?
16:05:24 [Zakim]
On the phone I see knapp, Tony, DBooth, Kerstin_Forsberg, rhausam, bpech, Ingeborg, ericP, Charlie, cecil, mscottm, [IPcaller]
16:05:27 [Zakim]
On IRC I see charlie, Cecil, RHausam, bpech, Kerstin_Forsberg, mscottm, Ingeborg, Zakim, RRSAgent, knapp, Tony, dbooth, TallTed, cloudcell, trackbot, ericP
16:05:36 [ericP]
charlie, [IPcaller] is claude
16:05:54 [dbooth]
16:06:21 [ericP]
scribenick: ericP
16:06:22 [dbooth]
Topic: Approval of Minutes
16:06:23 [dbooth]
16:07:06 [ericP]
RESOLVED: approve as a record of the dec 9 call
16:07:43 [dbooth]
Topic: Action Item Review
16:07:51 [dbooth]
ACTION: Tony to find out more details about how iCat handles ICD-11 ont and report back [recorded in] -- PENDING
16:07:51 [trackbot]
Error finding 'Tony'. You can review and register nicknames at <>.
16:08:04 [dbooth]
ACTION: Guoqian to figure out whether he can share URI conventions for ICD-11 [recorded in] -- PENDING
16:08:04 [trackbot]
Created ACTION-12 - Figure out whether he can share uri conventions for icd-11 [recorded in] -- pending [on Guoqian Jiang - due 2014-12-23].
16:08:53 [Zakim]
+ +1.617.498.aaii
16:08:56 [dbooth]
ACTION: Kerstin and Ingeborg to prepare a status and future state ideas for PhUSE-FDA work [recorded in] -- PENDING
16:08:56 [trackbot]
Error finding 'Kerstin'. You can review and register nicknames at <>.
16:09:00 [ericP]
dbooth: i have Frederick @@1 to speak on @@2
16:09:15 [Vipul]
Vipul has joined #HCLS
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Zakim, +1.617.761,6200 is Vipul
16:09:41 [Zakim]
sorry, Vipul, I do not recognize a party named '+1.617.761,6200'
16:09:47 [dbooth]
ACTION: Tony and all to decide on a wiki for Term Info work [recorded in] -- DONE
16:09:48 [trackbot]
Error finding 'Tony'. You can review and register nicknames at <>.
16:09:53 [ericP]
-> C-CDA -> RDF page
16:09:55 [Vipul]
Zakim, help
16:09:55 [Zakim]
Please refer to for more detailed help.
16:09:56 [dbooth]
Rob: I did that action
16:09:58 [Zakim]
Some of the commands I know are:
16:09:58 [Zakim]
xxx is yyy - establish yyy as the name of unknown party xxx
16:09:58 [Zakim]
if yyy is 'me' or 'I', your nick is substituted
16:09:58 [Zakim]
xxx may be yyy - establish yyy as possibly the name of unknown party xxx
16:09:58 [Zakim]
I am xxx - establish your nick as the name of unknown party xxx
16:09:58 [Zakim]
xxx holds yyy [, zzz ...] - establish xxx as a group name and yyy, etc. as participants within that group
16:09:59 [Zakim]
xxx also holds yyy - add yyy to the list of participants in group xxx
16:09:59 [Zakim]
who's here? - lists the participants on the phone
16:09:59 [Zakim]
who's muted? - lists the participants who are muted
16:09:59 [Zakim]
mute xxx - mutes party xxx (like pressing 61#)
16:09:59 [Zakim]
unmute xxx - reverses the effect of "mute" and of 61#
16:10:00 [Zakim]
is xxx here? - reports whether a party named like xxx is present
16:10:00 [Zakim]
list conferences - reports the active conferences
16:10:01 [Zakim]
this is xxx - associates this channel with conference xxx
16:10:01 [Zakim]
excuse us - disconnects from the irc channel
16:10:01 [Zakim]
I last learned something new on $Date: 2013-03-03 19:18:47 $
16:10:08 [Claude]
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16:10:28 [Vipul]
Zakim, +1.617.761.6200 is I
16:10:29 [Zakim]
sorry, Vipul, I do not recognize a party named '+1.617.761.6200'
16:10:30 [Claude]
16:10:45 [Claude]
Please join the gotomeeting
16:10:48 [dbooth]
ACTION: Tony and Rob to report their plan on High-level concept mapping to RDF work [recorded in] -- DONE
16:10:48 [trackbot]
Error finding 'Tony'. You can review and register nicknames at <>.
16:10:52 [Vipul]
Zakim, +1.617498.8797 is Vipul
16:10:52 [Zakim]
sorry, Vipul, I do not recognize a party named '+1.617498.8797'
16:11:01 [Vipul]
Thanks Claude
16:11:17 [dbooth]
Topic: FHIR Ontology review with Cecil Lynch
16:11:22 [Claude]
16:12:18 [dbooth]
ACTION: Eric and Joshua to report on C-CDA RDF representations work plan [recorded in]
16:12:18 [trackbot]
Created ACTION-13 - And joshua to report on c-cda rdf representations work plan [recorded in] [on Eric Prud'hommeaux - due 2014-12-23].
16:12:29 [dbooth]
16:12:40 [dbooth]
Tony: Will send email to the list.
16:13:06 [RHausam]
16:13:07 [ericP]
topic: Cecil Lynch's FHIR Ontology review
16:13:31 [ericP]
16:14:15 [dbooth]
s/-< http/-> http/
16:14:22 [ericP]
Cecil: followed lloyd's point that we need an automated, repeatable way to do this
16:16:15 [ericP]
... i've used TBC to import XML Schema into RDFS and OWL
16:16:24 [dbooth]
cecil: I imported XML Schema of FHIR into RDF/OWL using TopBraid Composer.
16:16:37 [Claude]
To David: Could we reserve 5 min at the end of the meeting to discuss plans for Jan meeting in San Antonio?
16:16:48 [dbooth]
claude, good idea
16:16:56 [RHausam]
Sorry, Eric - must be dyslexic this morning. :)
16:17:40 [ericP]
... you can tell composer to import schema and optionally instance data
16:17:55 [ericP]
... i pointed all of the FHIR XSDs in a package
16:18:02 [dbooth]
cecil: I pointed it to all of the XSDs and it imported all of them.
16:18:13 [ericP]
... you can have it prefix the object properties with a "has..."
16:18:20 [dbooth]
... Also imported all of the datatypes
16:18:43 [ericP]
... everything drills down to privimage types like [21090] Code
16:18:43 [dbooth]
... It's faithful to the XML Schemas, in an automated way.
16:18:58 [ericP]
... follows lloyd's goal to completely import the FHIR spec
16:19:07 [dbooth]
... The potential downside is that it brings in EVERYTHING, giving a complex model.
16:19:11 [ericP]
... downside: you get a complex model
16:19:38 [dbooth]
... We've built tooling around HL7, OWL interface to Jena API, and we want all the detail.
16:19:44 [ericP]
... at accenture, we've built tooling to use this with NLP, with links to Jena API
16:19:51 [dbooth]
... But for human mapping you might not want all of this complexity.
16:20:06 [ericP]
... you need to examine whether you need this level of detail
16:20:51 [ericP]
... [examining AdverseReaction]
16:21:01 [dbooth]
q+ to ask about round tripping
16:21:42 [ericP]
charlie: i'm just staring with a company in paris which is the medication info provider for the french government
16:21:50 [dbooth]
Charlie: I'm just starting with a Paris company, medication provider for French Gov, committed to semantic infra, using TBC.
16:22:02 [dbooth]
... Will be talking about importaing FHIR specs.
16:22:17 [ericP]
... we have a call tomorrow with john hayden to talk about about the import from FHIR specs
16:22:39 [dbooth]
... Asked cecil if FHIR spec XSDs can be imported directly.
16:22:57 [dbooth]
... Also emailed Eric about his approach.
16:23:37 [dbooth]
Eric: I'm driving this from XML Schema and Cecil is, so the only differences (aside from cosmetics) should be where I've customized toward the RDF-natural way to do things.
16:23:55 [dbooth]
Cecil: I had it add "has" to predicates.
16:24:01 [ericP]
... does ericP/Josh's instance map correspond to Cecil's schema?
16:24:25 [ericP]
ericP: in principle, apart from our customizations and coin flips in the parameters
16:24:29 [ericP]
Cecil: agreed
16:24:35 [dbooth]
Tony: I looked at TBC and didn't use it, but got the specs on the XML->RDF transforms that they use.
16:24:45 [ericP]
Tony: i haven't seen a transform for a sequence yet
16:24:59 [ericP]
... sequence is interesting.
16:25:19 [dbooth]
Tony: I suspect that we need to transform both the schema and the profile, to get more specific.
16:25:21 [ericP]
... looking at the high level, we need to transform the schema and the profile.
16:25:59 [dbooth]
... If you define a link as being a reference, which is the explicit XML, what you want is that it's resolved to the patient.
16:26:00 [ericP]
... if you define a link as a reference (which is the explicit XML), what you want is that it's resolved to the patient
16:26:06 [egonw]
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16:26:09 [dbooth]
s/patient/patient resource/
16:26:15 [ericP]
Cecil: the patient resource.
16:26:40 [ericP]
Tony: so the resource is the referent in the XML the way the XML defines the reference.
16:26:53 [ericP]
... so we need it to be reasoner-friendly
16:27:15 [dbooth]
Cecil: I did generate an ont to do it that way, but you need to bring in the target resource.
16:27:46 [dbooth]
Eric: I have a lab test for a patient, XML reference strcuter with attribute having a URL for that subject.
16:27:54 [ericP]
Cecil: i did that using TBC
16:28:15 [ericP]
Tony: the question is how do you get a reference that the reasoner can actually deail with
16:28:28 [ericP]
... this should be fine apart from the specific resource
16:28:36 [ericP]
... i believe those are in the profile
16:28:38 [dbooth]
Tony: This looks fine other than the specific type of Resource -- how to restrict it to a patient reference.
16:28:49 [dbooth]
cecil: Let me switch to a different ontology.
16:29:01 [ericP]
Cecil: looking at a 2.5 message spec
16:29:12 [ericP]
... looks a little different, but same idea
16:29:18 [ericP]
... sucked in the schema
16:29:21 [dbooth]
cecil: this is an HL7 2.5 spec
16:29:31 [ericP]
... you have PID segemtn and patient content
16:29:48 [ericP]
... this was build to model the lab domain for biosurveillance
16:29:54 [dbooth]
... This was built to model the data for biosurveilllance
16:30:05 [ericP]
... so i have an OBX and instance data that fits this model.
16:30:21 [ericP]
... that's done with terminology bindings
16:30:41 [ericP]
16:31:12 [ericP]
Cecil: drilling down on the instance data, i see the properties of that LOINC code
16:31:23 [ericP]
... this is how you'd bind that instance data to the schema
16:31:36 [ericP]
... this is fully machine-processable
16:31:55 [ericP]
... in practice, we don't do with with inference 'cause it would take forever
16:32:19 [dbooth]
cecil: once you have validated your ont, you can do instance data inference some other way.
16:33:09 [dbooth]
eric: A difference from the way Tony versus Josh and I took, in one case we did mechanical transformation and we did not dig into the coding systems -- terminology layer.
16:33:48 [dbooth]
... But in Tony's we dug in, for obs coding system, snomed code, allergic reaction that is bee sting.
16:34:28 [dbooth]
... What we're looking at here is a combination of mechanical transformation of obs records, followed by extra rules that could be modeled as OWL equiv classes
16:34:48 [dbooth]
cecil: Correct, and i have a tool in sourceforge
16:35:12 [ericP]
Cecil: i put a tool up in sourceforge that translate e.g. presence findings into a normal form
16:35:25 [ericP]
... it has lots of swtiches:
16:35:46 [ericP]
... .. taking a top-level SNOMED concept and turning things into instances or classes
16:35:49 [dbooth]
... tool lets you build vocabularies (with switches to include skos, etc.), set top level class with terms of instances, and it auto imports snomed, rxnorm, loinc from their native files.
16:35:58 [ericP]
... .. imports terminologies from their native files
16:36:14 [dbooth]
... You point it to whatever comes and it imports terminologies.
16:36:26 [ericP]
Tony: i use the SNOMED export to classes
16:36:33 [dbooth]
... This allows you to export as classes or as instances.
16:36:50 [dbooth]
Tony: That's been a debate: the two ways to represent concepts (as classes vs instances).
16:36:58 [ericP]
... this brings up the question of modeling classes or instances
16:37:10 [dbooth]
cecil: It's a matter of how to model it to use it in a production system.
16:37:37 [dbooth]
eric: Is there a clear winner about the better approach?
16:37:42 [ericP]
Cecil: yeah, question of how to model for your use case
16:37:42 [dbooth]
cecil: Depends on the use case.
16:38:13 [dbooth]
... TB surveillance system used classes, because in that case there is a generator that writes rules for them, and we use backward chaining in JESS
16:38:18 [ericP]
... i've modeled as classes for the CDC's turberculosis to then backward-chain in jess
16:38:27 [ericP]
... everything in that system is classes
16:38:40 [dbooth]
... CDC has a set of OWL classes and we validate against medications the person is taking
16:38:45 [ericP]
... we validate against instance data for e.g. medication the patient was taking
16:39:29 [dbooth]
... But this one uses instances because it is building value sets where i use a top level concept and I want everything to be an instance: does that value appear in that field?
16:39:48 [ericP]
... this one is a little different because it's building value sets where i don't care about hierarchy
16:40:15 [ericP]
ericP: so if you're doing a leaf closure, you go straight to instances
16:40:23 [ericP]
dbooth: @@1
16:40:50 [ericP]
Cecil: the real question for the group in general is what are we aiming for?
16:40:56 [ericP]
... some target use of the ontologies?
16:41:11 [dbooth]
david: Like the difference between instance data validation as the RDF Validation WG is working on, versus class level inference like OWL reasoners do.
16:41:29 [ericP]
... 'cause if you're using it for large-scale data processing, you won't use reasoners.
16:41:33 [dbooth]
cecil: None of the OWL reasoners are robust enough for production processing.
16:41:51 [ericP]
... i'd wrap it up in a jar and add it as a SPOUT in SPARK
16:42:08 [dbooth]
Tony: Could also use punning, so we have both instances and classes
16:42:11 [ericP]
Tony: we could be looking at puns where the instance in one is a value in another
16:42:37 [ericP]
Cecil: yep, the code value is the owl:individual
16:42:37 [dbooth]
cecil: I did use punning, and that makes it a lot easier to navigate from a machine processing viewpoint.
16:42:59 [ericP]
Tony: so in an instance, you can reference either IRI
16:43:19 [ericP]
topic: FHIR requirements
16:43:24 [dbooth]
Topic: FHIR Ontology requirement
16:43:37 [dbooth]
16:44:14 [ericP]
dbooth: any comnents about FHIR ontolog reqs?
16:44:26 [ericP]
q+ to say we need to think about sales
16:44:40 [ericP]
Vipul: these reqs are about syntax
16:44:55 [dbooth]
Vipul: These requirements are primarily targeted at syntax. Should look at use cases and then look at requirements.
16:44:57 [ericP]
... we should go back to real-world use cases and then go to reqs
16:45:08 [ericP]
... that approach was successful in the COI group
16:45:34 [dbooth]
1. It must be possible to round-trip instance data from XML/JSON through RDF representation
16:45:57 [dbooth]
16:46:44 [dbooth]
Eric: We have one shot to impress people with how cool RDF is in the clinical domain, if we want to focus our efforts, we want to pick something that is achievable and differentiates the value proposition that shows benefits of using RDF over XML or JSON, etc.
16:46:59 [Vipul]
16:47:07 [ericP]
dbooth: 1 seems like MUST
16:47:11 [ericP]
16:48:03 [Tony]
16:48:10 [ericP]
ericP: is this met by round-tripping just to XML, counting on the compiles XML-JSON mapping
16:48:19 [ericP]
Vipul: can it be lossless?
16:48:59 [ericP]
dbooth: whether it's lossless or not has to be viewed through the lense of what is semantically significant according to the spec
16:49:16 [ericP]
Tony: the translated XML instance data has to be parsable
16:49:17 [RHausam]
16:49:34 [ericP]
... e.g. TBC sequences doesn't parse
16:49:53 [dbooth]
2. We want to be able to represent instances as RDF and Profiles as OWL/RDFS
16:49:58 [ericP]
16:50:08 [dbooth]
16:51:42 [dbooth]
3. Syntax needs to be "safe" when dealing with modifier extensions
16:51:44 [ericP]
16:52:12 [dbooth]
QUESTION: What is meant by "syntax"? RDF has several serializations. What syntax do you mean?
16:53:05 [dbooth]
Eric: You can have extensions, so before interpreting results you need to check whether there are modifying extensions.
16:55:03 [dbooth]
Topic: January HL7
16:55:34 [Vipul]
Does anyone know the FHIR Link for "Version 2" - on Claims and Adminstrative Processes?
16:55:46 [Vipul]
Can someone please post this here?
16:55:49 [Vipul]
16:57:11 [dbooth]
Paul: We could do Q1 or Q2 Monday for RDF subgroup.
16:57:15 [dbooth]
Tony: Remote access?
16:57:31 [dbooth]
Tony: We can try, with skype, but HL7 doesn't provide it.
16:57:43 [dbooth]
Rob: I have audio hardware I can bring.
16:58:09 [dbooth]
David: Who will be coming to San Antonio?
16:58:21 [dbooth]
Answers: Claude, Paul, Cecil, Charlie, David
16:58:36 [dbooth]
... Rob
16:58:37 [Zakim]
16:58:44 [dbooth]
... Brian
17:00:18 [Zakim]
17:00:45 [dbooth]
Tony: Out Dec 23
17:00:52 [dbooth]
Charlie: Out Dec 23 and 30
17:01:09 [Zakim]
- +1.617.498.aaii
17:01:36 [Zakim]
17:01:40 [Zakim]
17:02:23 [dbooth]
Eric: I won't be able to attend the San Antonio, but I would love for people to be able to run the FHIR transformations that either Cecil or I have done.
17:02:48 [Zakim]
17:02:51 [Zakim]
17:02:58 [Zakim]
17:02:59 [Zakim]
17:03:03 [dbooth]
17:05:43 [dbooth]
zakim, who is here?
17:05:43 [Zakim]
On the phone I see DBooth, ericP, mscottm (muted), [IPcaller]
17:05:45 [Zakim]
On IRC I see Claude, Vipul, charlie, Cecil, RHausam, bpech, mscottm, Zakim, RRSAgent, knapp, dbooth, TallTed, cloudcell, trackbot, ericP
17:06:31 [ericP]
-> from
17:07:00 [ericP]
-> to
17:07:19 [ericP]
-> to
17:08:01 [Zakim]
17:08:03 [Zakim]
17:08:03 [Zakim]
17:08:04 [Zakim]
17:08:04 [Zakim]
SW_HCLS()11:00AM has ended
17:08:04 [Zakim]
Attendees were +1.604.250.aaaa, +1.978.794.aabb, DBooth, Kerstin_Forsberg, +1.801.949.aacc, +1.678.999.aadd, +1.202.528.aaee, knapp, Tony, rhausam, ericP, Ingeborg, bpech,
17:08:04 [Zakim]
... +, +1.415.537.aagg, Charlie, cecil, +31.88.445.aahh, mscottm, [IPcaller], +1.617.498.aaii
17:11:33 [dbooth]
rrsagent, draft minutes
17:11:33 [RRSAgent]
I have made the request to generate dbooth
17:12:18 [dbooth]
Chair: David Booth and Paul Knapp
17:15:09 [dbooth]
Present: David_Booth, Kerstin_Forsberg, Paul_Knapp, Tony_Mallia, Rob_Hausam, EricP, Ingeborg, Brian_Pech, Charlie_Mead, Cecil_Lynch, Scott_Marshall, Claude_Nanjo, Vipul_Kashyap
18:08:41 [dbooth]
rrsagent, draft minutes
18:08:41 [RRSAgent]
I have made the request to generate dbooth
18:56:40 [dbooth]
i/Topic:/Screen shots from Cecil's FHIR ontology discussion:
18:57:44 [dbooth]
rrsagent, draft minutes
18:57:44 [RRSAgent]
I have made the request to generate dbooth
19:37:08 [Zakim]
Zakim has left #hcls
19:51:43 [dbooth]
s/Topic: FHIR Ontology review with Cecil Lynch//
20:14:53 [dbooth]
s/topic: FHIR requirements//
20:14:56 [dbooth]
rrsagent, draft minutes
20:14:56 [RRSAgent]
I have made the request to generate dbooth