20 Aug 2019


Lusha_Cao, EricP, Harold_Solbrig, MarcT
David Booth



harold: Revisiting fhir.schema.org idea
... Is fhir.schema.org conflicting with medical schemas? I think not. fhirschema is about medical records.


Harold's slides: https://docs.google.com/presentation/d/1_yqpKWBhT8nTcPmRVm4nLtPIzdQ_nj8CpO9e8jIlNb4/edit#slide=id.p

harold: medical institutions such as Mayo Clinic annotate their web pages with medical info, and google uses it. They use micro-schema-like data for google to produce info boxes.
... That info is harvested both from Mayo clinic and NLM.
... This brings us to an interesting alignment question. Grahame has started to mark up FHIR with semantics. Some work pointing at SNOMED.
... Health and medical types potential are an alternative markup language for putting semantics into the FHIR language.
... Another one is bioschemas.org , which seems to be the same domain as FHIR. Not so much semantics, but what is in the medical record.
... FHIR schemas abut each other in schema.org space just as they abut each other in real life.
... interesting to look at a page: https://hangouts.google.com/_/elUi/chat-redirect?dest=http%3A%2F%2Ffhir.fhirschema.org%2F

here is the real URL: http://fhir.fhirschema.org/

harold: these are all the FHIR resources defined.
... Here is a URL for Observation.BodySite . There's a place for the Observation.code value, etc. Everything you can represent in FHIR, it gives you a set of URLs for it.
... skip to slide 6

<ericP> FHIRschema.org Obervation http://fhirschema.org/Observation

harold: FDA has structured product labels https://docs.google.com/presentation/d/1_yqpKWBhT8nTcPmRVm4nLtPIzdQ_nj8CpO9e8jIlNb4/edit#slide=id.g5f38253709_0_0
... We grabbed the HTML for their labels, and we're showing a use of fhirschema.org, and it has info about medical knowledge.
... WE put in the medical knowledge properties using a google testing tool for schema.org, and we show that you can pull the FHIR info, if you mark it up, from this medical knowledge database.
... Somebody is working on a direct transformation from the structured product label to the FHIR knowledge.
... Another use case on the slide 7 is a lipid panel. Not as pretty as on the Mayo web page. I can view it online. Today underneath is only HTML. But on the next slide we can include FHIR markup in the HTML.


harold: Mayo Clinic probably has this info directly in FHIR, but here we have a human-readable resource that is simultaneously FHIR data.

mark: Last I knew people in Mayo Clinic were ... They attached to each, a code for exchange with other systems.
... Are you thinking of adding such things?

harold: If Mayo puts in test codes they will put LOINC codes in.

mark: Most countries are mapping to SNOMED. There is semantic in LOINC code.

harold: Mark is saying that Mayo is talking about putting LOINC codes in published clinical records. If they do, that will give an interop component.
... If they do, the LOINC codes can be put into the microdata or RDFa markup, so that the patient does not have to see the codes. Most patients don't want to see them, but having them in the records enables others to know exactly which trigliceride test was used.
... Marc also says that wikipedia and other sources use the LOINC code as common anchor, so that gives a shared semantic link.

eric: Isn't FHIR planning to do the same thing?
... Everytime you have a codeable concept you have a bunch of codings, and each one has a codesystem and code, and in RDF they equate to URLs, and there was no resistence to using URLs there. That would give a gateway.

harold: And LOINC is leading the pack in having a sanctioned FHIR terminology with examples of how to get it. They are providing URLS for them.
... We want similar things to happen in the other common code systems that are used in FHIR. And as communities move into bioinformatics we're looking to the successor of the disease ontologies and various OBO ontologies.
... Back to slide 5: https://docs.google.com/presentation/d/1_yqpKWBhT8nTcPmRVm4nLtPIzdQ_nj8CpO9e8jIlNb4/edit#slide=id.g5f38253709_0_0
... fhirschema.org allows FHIR translation for medical knowledge
... Could also provide provenance. All FHIR examples have a text representation of what is in there.
... This could provide provenance of where it came from. If you do that, then the rest of the JSON could be superfluous. This could lead to an exchangeable format, which is interesting.

marc: HTML provides human readable. If we could use this in FHIR to make the text human readable.

harold: mayo, cleveland clinic and washington U are working on a joint project to make clinical records machine readable. Marc sees fhirschema.org as a big big jump from human readable to adding machine readable to it.
... Nice thing about schema.org idiom, as opposed to a formal FHIR resource with everything formalized, it allows things to be incrementally formalized.
... Good example was patient record. Inititially it did not lab codes. Gives an incremental entry to FHIR world.
... NLP markup ... having worked with Hung Fung Lee (sp?), they have ad hoc NLP to FHIR, and it requires annotating natural language text. fhir.schema.org would provide a standard for that.
... it gives a series of tags that are already defined in the FHIR space, and allows use of tools by google and others to extract the FHIR resources.
... Another area: IOP devices, and annotating the compact data records that come from heart rate monitors and smart watches, etc.
... There's a very active effort in IOT community to do a FHIR mapping.

david: Who is doing that?

lusha: Microsoft

harold: MS is working on maps bewteen the standard space and FHIR.
... Would be good to do a paper on this.
... slide 4: https://docs.google.com/presentation/d/1_yqpKWBhT8nTcPmRVm4nLtPIzdQ_nj8CpO9e8jIlNb4/edit#slide=id.g5f38253709_0_0
... We discussed with danbri about dots in identifiers. Microformats bans them. FHIR uses them everywhere.
... But banning them is kind of counter to the microdata spec. Danbri said microdata spec is outdated and suggested RDFa.
... On slide 7 https://docs.google.com/presentation/d/1_yqpKWBhT8nTcPmRVm4nLtPIzdQ_nj8CpO9e8jIlNb4/edit#slide=id.g5f38253709_0_0
... we only got dose form, not everything. So it looks like google tools handle the dots.

marc: But they will not display.
... It was discussed and they will keep the dots.

harold: Can you send a link to that discussion?

marc: If we could avoid the dots and make everyone happy . . . .

harold: draft spec on FHIR site there is a draft RDFa spec that uses dots. We played with it and looked at using CamelCase, but FHIR already uses CamelCase. We thought about hyphens, but that's an issue that will take work.
... Need to work with FHIR/RDF people. Hate to have two RDF specs.

david: How to follow up on that? What forum or people?

harold: I think FHIR/RDF spec will be at risk. Grahame said so far it is okay, but if things don't start happening it will eventually get pruned. First task is to show value.
... If we expand on these slides I think that is doable.

marc: Regarding discussion with danbri, what was final conclusion?

harold: Nothing final. danbri said he wasn't sure what the google parser would do. There was discussion but it got bogged down in the WG. He suggested using RDFa.
... I'd like to respond to danbri with more complete slides, to better outline the problem and maybe he can help.
... Another issue has to do with the JSON-LD @context. schema.org builds an @context that it uses.
... We have looked at JSON-LD [a few years ago] but it was not adequate at that time. JSON-LD 1.1 theoretically would address some of the key deficiencies. We run the risk of having two JSON-LD @contexts. One comes from fhir.schema.org, you get it for free. And it produces a different graph from what FHIR/RDF sanctions.
... Another thing that could bootstrap and ensure that RDF takes, if we could get JSON-LD @context, then the cost goes way down because it would only be a matter of pulling in a library for processing FHIR as RDF.

eric: The new JSON-LD 1.1 is context sensitive, which is one of the first things needed for FHIR/RDF. But another problem is it will never match what comes from fhir.schema.org

harold: Right, because fhir.schema.org is a path notation.

eric: There is no expectation in FHIR that the name fully identifies the item. The context is needed.

harold: We desperately need to work on that, the JSON-LD harmonization.

eric: Could work the microdata angle by giving danbri a copy of the fhir.schema.org with dots?

harold: Yes, we can do that.

<scribe> ACTION: Harold to respond to danbri on dots issue

marc: Is there a plan for an API that someone can use?

harold: Turning medical records into FHIR is hard if they are not marked up from the beginning.
... Our hope is that google wiil have done the bulk of turning marked-up HTML into structured data.
... But the hard part is marking it up from the beginning.
... This BBC thing mentions google's rich snippets: https://www.bbc.co.uk/ontologies/fo#terms_Food
... The top of that page mentions Google's Rich Snippets. How could FHIR inform Google's Rich Snippets?


Summary of Action Items

[NEW] ACTION: Harold to respond to danbri on dots issue

Summary of Resolutions

[End of minutes]

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