See also: IRC log
<trackbot> Date: 23 December 2014
Talky is here: https://talky.io/hcls
We will try using https://talky.io/hcls for audio
Talky is here: https://talky.io/hcls
Talky is here: https://talky.io/hcls
<drjava> Drjava is peter hendler
http://www.w3.org/2013/C-CDA/IJ.xml
Eric: Charlie and I created the
ORIM -- translation of RIM to OWL.
... a few years ago.
<ericP> http://www.w3.org/2012/12/O-RIM/protege-tutorial/simple.omn
<ericP> http://www.omg.org/spec/ODM/1.1/PDF/
Eric: IThe translation into OWL
was done via the above linked document.
... It assumes that relation names in UML are not unique
... so it prefixes every relation name with the name of the
class it came from.
... So a predicate for a car with a registration would be
car.registration.registrationDocument
... This makes predicate names very long, but they work.
... Lloyd did this for doing inference on the RIM model.
... It's an enormous ontology.
... My intention was that it be useful to turn CCDA XML into
RIM, then turn RIM into RDF.
<Claude> Test
Eric: so this document: http://www.w3.org/2013/C-CDA/IJ.xml
was my attempt to not be creative, but to produce the same RDF
that anyone would.
... CCDA example came from Josh Mandel. In principle this xslt
should work with any CCDA.
Joshua: I'm specifically
interested in including genomic and phenotypic data.
... But basically want a concrete RDF representation that we
can query using SPARQL.
<Claude> To David: Could you please paste the link again. I just installed an IRC client.
The page eric is discussing: http://www.w3.org/2013/C-CDA/IJ.xml
Eric: The main arcs of
connectivity in RIM are ACT relations.
... Using vocab from HL7 indicating severity, etc.
... In principle those arcs make the RDF graph.
... 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.
... This would make a lean and RDF-friendly way to represent
clinical data.
... Then we could do RDF tricks from there.
... Does it make sense to collapse the ACT relatinoships into
predicates?
Lloyd: No, because there are a
lot more predicates attached to them.
... Need to go through the TYPE codes to see which ones are
identified.
... When those other things are there, they are
important.
... My leaning is to have that detail there always, but have
the shortcut there as well when it can be done.
Cecil: What would be the use case for an RDF model that drops content?
Eric: If the majority of ACT
relationships were simple TYPE codes, then one could write
SPARQL queries that use those
... and when there was something else attached, then you would
fall back to a more complex sparql query.
cecil: to be safe for clinical
use, you can't ever drop information.
... Not safe to drop them ever.
... But if our use of this is FHIR then why not use FHIR where
it is flattened?
... 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.
Eric: Not planning on discarding
info, but using simple arc when there is ONLY a type
code.
... The other goal was to map this to FHIR RDF.
... Wrote a script to spit out XSLT and ShEx code that will
round trip FHIR XML to FHIR RDF
https://www.w3.org/wiki/HCLS/ClinicalObservationsInteroperability/C-CDA
<ericP> ttp://www.w3.org/2014/Talks/1209-shex-egp/#(24)
<ericP> ttp://www.w3.org/2014/Talks/1209-shex-egp/#(24)
http://www.w3.org/2014/Talks/1209-shex-egp/#(24)
<ericP> http://www.w3.org/2014/Talks/1209-shex-egp/#(45)
Eric: ShEX is good for validating RDF, but also (slide 45) good for translating
http://www.w3.org/2014/Talks/1209-shex-egp/#%2845%29
Eric: This is a complex example.
What's shown at the top is turned into what's shown at the
bottom.
... There are actions specified when the pattern on the left is
matched.
David: When the pattern on the left is matched, the %GenR action is run?
Eric: Right.
Scott: the leading zeros are missing from the dates.
Eric: yes, didn't fix that yet.
David: now looking at the above link, shown Schema (ShEX) on the left and Data (Turtle) on the right.
Eric: The left is the input
schema, the right is the input instance data, and below is the
validation result.
... when you click (at the bottom) "View GenR output as popup"
then you see the output.
... FHIR instance data could be combined with schema.
... then you could conclude an allergy to bee stings
... Want to see if this would be good enough for use by the CDA
work group at HL7.
... Wanted to see whether we could migrate between different
information models and combine that with validation, and this
seems to do it.
... Also the RDF Data Shapes working group is deciding what
language to use, so comments on ShEx are invited.
David: It reminds me of yacc rules.
Paul: Is the intent of validation to determined a valid instance?
Eric: Yes, validate an instance
at an RDF graph level.
... The semantic actions can do more business logic validation
that the patterns cannot validate.
Paul: Efficiency?
Eric: Paper on Regular Bag Expressions looks at that.
<scribe> ACTION: Eric to supply link for paper on Regular Bag Expressions [recorded in http://www.w3.org/2014/12/23-hcls-minutes.html#action01]
<trackbot> Created ACTION-14 - Supply link for paper on regular bag expressions [on Eric Prud'hommeaux - due 2014-12-30].
John: Also interested in compelling complex examples
<ericP> http://researchers.lille.inria.fr/~staworko/papers/staworko-icdt15a.pdf
<scribe> ACTION: JohnMattison to provide example CCDA for trying with ShEx [recorded in http://www.w3.org/2014/12/23-hcls-minutes.html#action02]
<trackbot> Error finding 'JohnMattison'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.
http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_20141216
Minutes unanimously approved!
ADJOURNED
<ericP> (figuring tony's phone infrastructure failed to send the "all done")
This is scribe.perl Revision: 1.140 of Date: 2014-11-06 18:16:30 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) Succeeded: s/the input/the input schema/ Succeeded: s/the output/the input instance data/ Succeeded: s/Maddison/Mattison/g No ScribeNick specified. Guessing ScribeNick: dbooth Inferring Scribes: dbooth Default Present: 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, cecil, EricP, Tony, rhausam, JohnMaddison 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 Found Date: 23 Dec 2014 Guessing minutes URL: http://www.w3.org/2014/12/23-hcls-minutes.html People with action items: eric johnmattison[End of scribe.perl diagnostic output]