21 Nov 2019


Nansu_and_Yue_from_Mayo_Clinic, Harold_Solbrig, Dan_Stone, EricP, Dazhi, Giorgio., hsolbrig, David_Booth
David Booth



harold: We have a test harness for testing conformance against R5 shex. They added a new attribute called 'link". We need to add that. The test tool is on the fhircat github.

harold's test tool: https://github.com/hsolbrig/fhir_model_generator

<ericP> https://github.com/ericprud/shex-to-jsonld-context/ -> repo

<ericP> https://github.com/ericprud/shex-to-jsonld-context/tree/master/build -> build products

<ericP> https://github.com/ericprud/shex-to-jsonld-context/blob/master/bin/shex-to-jsonld-context -> script

harold: First goal is to produce JSON-LD to match the current FHIR/RDF (including fhir:value etc.) We're calling that "R4 JSON-LD". "R5 JSON-LD" would not have the fhir:values.

JSON-LD @contexts

repo: https://github.com/ericprud/shex-to-jsonld-context/ build products: https://github.com/ericprud/shex-to-jsonld-context/tree/master/build script: https://github.com/ericprud/shex-to-jsonld-context/blob/master/bin/shex-to-jsonld-context

eric: We have FHIR/JSON already -- mature, lots of use, etc. RDF version doesn't get much love. With JSON-LD 1.0, we were not able to generate RDF from FHIR/JSON, because it did not have context-sensitive processing. JSON-LD 1.1 adds context-sensitivity., and allows lots of @contexts to be used in different contexts.
... I took a stripped-down AllergyIntolerance shex, with only a few properties, and ran a little script that takes all the ones without a dot and builds a new data structure file for them, then does some templating, looks at constraints, an dgenerates json-ld @context for each resource or datatype. (Will eventually be ~250 of these.)
... dateTime is expected to have that datatype, but the JSON does not have any datatype in the FHIR/JSON spec. But the JSON serializatoin does not tell you which type it is. It will have to be done by recognition.

harold: The way the RDF is put together, you can give something as xsd:date. But in JSON we only have the value and we have to infer the type from the value.

eric: There are two ways the type is presented. In one case the property gives the type, but dateTime is the other way -- you have to look lexically at the value.
... lastOccurrence is a union, but you can distinguish lexically between the choices.
... dateTime is misleading, because it is really a union of date, gMonth and gYear.

harold: Could either leave it in RDF as a string, or do pre/post processing to add the actual type. Which way should we go?

eric: RDF community likes things fully typed, to catch errors.

deepak: What is the plan? Generate these @contexts for all the resources?

harold: yes. By Jan FHIR Connectothon we want to have a first cut of all resources.
... But we'll evenually have to write an equivalent to shexj but in java, to add to the build process.

eric: It's an opportunity to look for places that I made assumptions but shouldn't have.

deepak: FHIR build process has to be extended with Java to gen the @contexts?

harold: Want to demonstrate that we can use JSON-LD 1.1 @context to produce today's R4 RDF. That will give us a benchmark for comparison as we evolve to R5.
... Shex generator is template driven. Should be easy enough to change the current java shex emitter to gen the @context files.
... Given that we cannot change the FHIR spec, we'll have to emit some parsing and shim code to do this also.
... In JSON-LD, anything that begins with an @ sign is reserved, so we could sneak processing instructions into it.
... But processors might reject them.
... One way or another we'll have to do lexical pre/post processing.

ISSUE: Should we add explicit types to the RDF where they are unions in the FHIR?

david: What do we want to show in January?

harold: Generate a complete library somewhere (maybe on github for the moment) of all of the @context files for FHIR.
... And accompany those with a pre/post processor that turns it into valid R4 FHIR/RDF.
... Those things in the pre/post processing are the primary things we want to reconsider for R5 FHIR/RDF?

deepak: Do we have a list of those things?

<hsolbrig> david: there will be some things that have to be a pre-processing step, such as numberic digits (5.5 vs. 5.50)...

<hsolbrig> ... you can't use a generic JSON processor to do this. It would be better to only do one step (pre) vs. splitting them

<hsolbrig> eric: We don't have to worry about this in RDF-land...

Pre or post processing the JSON?

<hsolbrig> ... in RDF, xsd:float 1.0 is different that 1.00

<hsolbrig> david: treeroot is another place info is lost, along with fhir:index

david: I realized that pre-processing may be helpful, for treeRoot, fhir:index and for retaining digits in numbers, and we could use the same blank node and fhir:value technique to add the extra datatype information, in the case of union types.
... That would allow all of the extra processing to be done in a single pre-processing step.

deepak: I would have to write that java pre-processor?

david: Yes. We would want to provide that for the commiunity, and JS and python versions.


Summary of Action Items

Summary of Resolutions

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