See also: IRC log
David: Need 1 or more use cases to drive the rewrite of the Linked Data Module pages.
eric: At SWAT4LS I combined info
model with clinical model and searched for terms more broadly
than how they were coded, using subsumption.
... It didn't require much of FHIR ont. More about combining
FHIR RDF with rich terminology model.
... Use cases for a FHIR ont beyond that will be mostly around
workflow.
dbooth: Written up?
eric: yes.
harold: We had to make one
significant change, which we need to make in the FHIR RDF
spec.
... Want to change fhir:concept ID to a type.
dbooth: Other use cases?
michael: I've been working on
technical stuff of converting FHIR to RDF and back.
... Also working on ISO 11179 stuff to do mapping between
models and maybe even a query using SNOMED CT.
... Want to be able to figure out what is already represented
in FHIR.
eric: I haven't figured out how to exploit the ont in the info model.
harold: I was originally going to
use FHIR RDF to find iso-semantic models, or models whose info
content was a subset of another model.
... But decided not to do that because it was too geeky for
SWAT4LS folks.
... it would give you the ability to deal with models of
different granularity, such as pre vs post coordinated.
eric: Or when FHIR has more specific resource for something, but a general purpose Observation could have been used.
harold: Linda and Grahame are
working on the ability to transform local DBs to FHIR and
back.
... Like the Yosemite model. But you need to align the
terminology for it to work.
... probably need to get more closely connected to Linda Byrd
and Grahame's work, re mapping FHIR into SNOMED using a
combination of the mapping tool and templates.
... Instead of dealing with RDF they're doing it with the idiom
that Grahame's mapping tool presents. What is the relationship
between Grahame's mapping tool and RDF?
... Claude Nanjo and Cognitive group have been implementing
Grahame's mapping spec. Might want to touch base with him at
some time and see how it relates.
eric: If we consider a hierarchy of Observation, AdverseReaction, Intolerance, you are supposed to use the most specific one, but being able to recognize it using Harold's work would be good.
harold: At the moment Grahame and
Linda are using the SNOMED template language. Either FHIR will
have to come closer to SNOMED, or the SNOMED language would
have to broaden to cover other terminologies.
... The templating language has a set of slots and fillers that
align with different description models in SNOMED. THey're
focusing on Observable right now.
... it has a primary object of observation, finding site, thing
being measured, etc. -- about 10-12 facets.
... Individual SNOMED concepts are instances of that generic
model. It's job is to fill in th eslots, so that you can put in
the diagnosis, laterality, body site, etc.
... So that you can take a SNOMED concept or a logic
description and get something that you can put into a
spreadsheet.
... Template language on the SNOMED site includes a sort of
valueset def -- a list of values that can go into the slots, so
there is a bit of validation creeping in.
... Linda was intially trying to support all the nuances of
FHIR, but decided we needed a two step process.
... First step is from FHIR-specific to template
grammar,.
... Template grammar itself is very SNOMED specific. Nobody
looking at using Disease Ontology, for example.
... Need to look at relationship between this mapping language
and ShExMap
<ericP> http://rawgit.com/shexSpec/shex.js/backtick/doc/shex-simple.html
eric: Once we deal with SNOMED
stuff you might be interested in this, that I did.
... Click on protein record, then delete green box contents and
do control-enter to see schema.
... If we had an Obs in SNOMED, turned it into an RDF graph
that has relationship that come from the SNOMED OWL, then we
could use those in this back-tick language and validate that
graph.
harold: Other use cases we've
touched on: not all the world is FHIR.
... We looked at connecting clinical data with environmental
data and other stuff in the LOD cloud, but we were disappointed
with lack of LOD data.
... Might want to look at that again.
michael: Also need to look at
logical models. FHIR now also has logical models -- differnt
way to present the data.
... Can express other data as FHIR logical data and then use
it.
dbooth: Make up your own structure definitions?
michael: yes.
dbooth: Using FHIR as a schema language.
<mvdzel> https://fhirblog.com/2016/10/17/logical-models-in-fhir/
eric: The logical models have several expressions (JSON, XML, RDF), and RDF is closest to capturing the logical model directly.
dbooth: Okay to use Eric's example to rewrite the Linked Data module pages?
harold: Another good example would be connecting with the LOD cloud, like in the Yosemite vision.
<mvdzel> http://build.fhir.org/structuredefinition.html#logical
dbooth: Good! I need a working example for it.
eric: FDA data from 3 ROund
Stones is now available.
... Could get toxin data from that.
... Need the location of the patient or encounter.
... Find the time and releases of toxins, and locations of
clinics (from dbpedia?), and the clinics appeared in the FHIR
encounters, then you could look at the incidence of a
respiratory disorder 3 weeks after chemical release versus
other times.
... These studies happen all the time anyway. This would make
the task easier in RDF.
<scribe> ACTION: Eric to ask Daniella Meeker to see if she has ideas for chem release use case [recorded in http://www.w3.org/2017/01/03-hcls-minutes.html#action01]
<trackbot> Created ACTION-73 - Ask daniella meeker to see if she has ideas for chem release use case [on Eric Prud'hommeaux - due 2017-01-10].
dbooth: What should we try to do there?
harold: I could demo the SWAT4LS
example.
... Classifying an instance to decide if a diagnosis is for
cancer, using subsumption.
... For example, to enlist patients for studies.
dbooth: Sounds good.
<scribe> ACTION: dbooth to find out the day and time of f2f meeting [recorded in http://www.w3.org/2017/01/03-hcls-minutes.html#action02]
<trackbot> Error finding 'dbooth'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.
ADJOURNED
<ericP> https://www.w3.org/2016/Talks/1205-swat4ls-egp/reasoning
<ericP> (dbooth)
thanks!
This is scribe.perl Revision: 1.148 of Date: 2016/10/11 12:55:14 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) No ScribeNick specified. Guessing ScribeNick: dbooth Inferring Scribes: dbooth Present: David_Booth EricP Michael_van_der_Zel Harold_Solbrig Found Date: 03 Jan 2017 Guessing minutes URL: http://www.w3.org/2017/01/03-hcls-minutes.html People with action items: dbooth eric[End of scribe.perl diagnostic output]