See also: IRC log
harold: It is working out pretty
well, though also finding some bugs.
... I2B2 is almost an RDF system. Similar.
... They don't allow infinite nesting level of predicates, but
they allow two levels. And it's not unreasonable to map FHIR
ont URIs into I2B2, and that puts us into the position to map
raw FHIR directly into I2B2 and get useful stuff out.
... Very exciting.
... Nice thing is that every researcher can have their own
optimized data model.
... That's good until you want to combine data, because then
you have to map either to your own model or an existing
model.
... Most orgs are already mapping into FHIR. So if we can map
FHIR into I2B2 we can save a lot of people a lot of
money.
... That mapping is working well because of the work we've done
in this group.
... You need standard URIs for all of the data elements -- FHIR
ont -- and the second thing you need is data that uses those
tags. That's the other bit that we've done and we've got
operating.
... One of the challenges that we face is that, as yet, HAPI
FHIR server does not have RDF.
... The HAPI tooling is just different enough to be difficult
to see how the transformations occur.
dbooth: Two versions of open source FHIR implementations handle FHIR JSON/XML to FHIR RDF translations: Grahame's Delphi implementation and Michael Van Der Zel's .NET implementation.
harold: Still need to map the
datatypes into I2B2 analogs.
... Another issue is what to do with codes. I2B2 tends to use
concept codes as first class identifiers.
... Instead of the code being a value it is a tag on a fact.
But that only works on small finite codesets.
... Not feasible for SNOMED -- too big.
... But for small code sets, want to use the same approach as
for blending FHIR RDF.
<inserted> https://github.com/BD2KOnFHIR/i2FHIRb2
harold: I've put out a pre-alpha.
<hsolbrig> https://github.com/w3c/hcls-fhir-rdf/tree/gh-pages/fhirowl
https://github.com/w3c/hcls-fhir-rdf/tree/gh-pages/fhirowl
From harold:
[[
The files represent what would appear in the FHIR publish directory and its children.
The java module that generated the objects can be found at:
https://github.com/w3c/hcls-fhir-rdf/tree/gh-pages/fhirowl/java
]]
harold: That includes all the new
things that I would add to the FHIR publish dir.
... We're using the FHIR ont and the W5 ont in anger here.
Finding a few bugs.
... Grahame wants to approve all changes to the FHIR ont. I
think I have the fixes cleared though.
... We really need to clean up the hcls-fhir-rdf github
ISSUE: need to clean up the hcls-fhir-rdf github
<trackbot> Created ISSUE-42 - Need to clean up the hcls-fhir-rdf github. Please complete additional details at <http://www.w3.org/2014/HCLS/track/issues/42/edit>.
harold: If you look inside the java dir, this is what would change if we run this script. Need to decide whether to publish this on the FHIR site or put it in a terminology service. Need to discuss that with Rob Hausam.
ISSUE: Talk with Rob Hausam about whether to publish this on the FHIR site or put it in a terminology service
<trackbot> Created ISSUE-43 - Talk with rob hausam about whether to publish this on the fhir site or put it in a terminology service. Please complete additional details at <http://www.w3.org/2014/HCLS/track/issues/43/edit>.
(Harold shows codesystem-diagnostic-report)
harold: Still need to add
skos:prefLabel
... First question is what do the FHIR group think of these
URIs?
... Second question: Do we want a top level node in these
ontologies? Right now they are flat.
... Right now the parent of 'partial' is owl:Top
... One common FHIR idiom is "all codes in codesystem X".
... A root class would addres that.
... A third question: Two approaches used to ont. HL7 itself
has a mess of tiny ont. A lot of tooling around HL7 has taken a
different approach, with one gigantic ont with the leaves being
individual codes.
... The UMLS and the ___ has done with HL7v3 has one code
system -- top level node. I don't think we want to do that, but
it's a question.
... Also in v3 there's a code for every codesystem. So I
represented a v3 act class, but I don't think I match lloyd's
v3 URIs. I think v3 might have been the same without a
hash.
eric: The problem is that there are a zillion of them. He stuck the full history in there, so there are many.
<ericP> i used <http://hl7.org/owl/rim#> in https://www.w3.org/2013/C-CDA/IJ.xml but i don't remember how diligent I was
harold: Interesting in v3 is that
they have classes that are used for organizing but cannot be
used for codes. They start with an underscore.
... Another question: I've been using a .owl suffix. We've been
using .ttl for other things.
... But it is turtle inside.
... Fixed a bug in naming.
... Also I had 4 different predicates for diagnosis with
different ranges, and we turned them all into
diagnosisComponent. (This is issue #53)
... fhir:ItemComponent combines 4 different classes. Does not
cause a problem.
... Proposal I made: Instead of calling it ItemComponent call
it ClaimItem. Grahame wanted naming to be consistent, so the
names are getting pretty long.
... But it seems to work fine for the display, because we only
see the last part.
... One other fix made was that we didn't subclass xsd:string
as part of fhir:Primitive
... Also, fhir:Money has no elements inside it. Need to fix
that.
eric: This is the ont that backs the FHIR resources?
harold: This is the FHIR metadata
vocabulary.
... I'm using the domain and range statements in what I'm
doing. Not using the OWL part.
... But the brilliance of this is that we have URIs for
things.
... Huge amount of benefit.
harold: I would have to see a
sample of what was going on.
... Assuming by "profile" you mean a regular FHIR profile.
gopi: I've been playing with a forge tool for making profiles. Was wondering about using protege.
harold: one interesting thing in
rdf: You can add bits and pieces. Start with a
DiagnosticReport, and narrow the cardinality, etc. Seems like
it would be an interesting experiment.
... In some ways RDF is better suited to profiles than the FHIR
profiling language.
... I'd be interested in seeing someone try it and see how far
they could get.
... Still need to add FHIR profiles in RDF.
gopi: Other question: right now you use a separate conformance server. Can we use shex?
harold: WHen we started, one
pushback was "why do you need shex?". FUndamental answer is
that OWL uses the open world assumption.
... There was quite a debate early on, about "Couldn't we close
the world on OWL?" But it was trying to use a tool for a
purpose for which it was not designed.
... shex might not be unreasonable to think of as a good closed
world owl.
eric: SHACL might be
closer.
... Spoke to the guy who maintains protege about shex, and he
said that a lot of people want data validation.
harold: Irony is that protege was originally a frames-based model.
eric: Matthew Horridge
ADJOURNED
This is scribe.perl Revision: 1.152 of Date: 2017/02/06 11:04:15 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: Irssi_ISO8601_Log_Text_Format (score 1.00) Succeeded: i|I've put out a pre-alpha|https://github.com/BD2KOnFHIR/i2FHIRb2 Present: Gopi Harold_Solbrig EricP David_Booth No ScribeNick specified. Guessing ScribeNick: dbooth Inferring Scribes: dbooth Found Date: 11 Jul 2017 Guessing minutes URL: http://www.w3.org/2017/07/11-hcls-minutes.html People with action items:[End of scribe.perl diagnostic output]