Meeting minutes
Introductions
joe: Work for Chris Chute, term and infra mgmt sys. Goal is a FHIR server w latest features, including OWL/RDF stuff. Work a lot w med terminologies and HL7 stuff.
daniel: Working at Mayo as part of standards research, FHIR and FHIR RDF.
Concept IRIs
gaurav: We have 6 votes and need 15 votes, plus additional quorum requirements.
https://
… Our 3 votes have 2 votes each. Not sure of next step. Nobody responded to zulip post.
… Already brought this to the vocab mtg, but might be able to bring it back to terminology group to get more votes.
… This is not really R5 change, but if it doesn't go through then we'd have to revert to either using extensions or making an R5 change.
dbooth: Sounds like you need to continue to beat the bushes for votes.
gaurav: We have two FHIR proposals for R5, both have been resolved. They're just waiting for the change to be made. I'll do them.
https://
gaurav: For 39604 change I'm running into validation errors when it does its auto checks when I put in the PR.
… It's telling me the XML is malformed.
… I forgot to change the short desription.
gaurav: Third change: I think I need to open a UTG ticked for the iri-stem type.
https://
gaurav: I will ask Rob.
FHIR Build process
gaurav: Update from Jim: He's in an all-week meeting. He's working on changing property names.
… Trying to figure out this code: https://
… He can fix this easily by getting rid of all this code and just using the short name, but he's not sure what all of this code here. Why are bundles and parameters being treated differently from everything else?
… Wants to walk through this code with someone who understands it.
eric: seems like a good idea.
… I had to throw exceptions for bundles in the Playground, but don't remember why I had to do special code for bundles.
… Also happy to dispense w parameters.
… I've been telling Deepak to come up w shex for clinically operational resources.
… All the meta structures we (Claude and I) think it's not worth worrying about them now.
… If we don't do the shex for the meta properties, we can always add them later. But for Jim's work, the examples will be generated anyway.
eric: Two courses of action: 1. Figure it out. Look at structure defs that come out. 2. Not worry about it and update it later. Priority is to get the clinical stuff right.
gaurav: In other words, use short properties, but then make corrections later if that causes problems with bundles and parameters.
eric: Right.
… Keep a pointer to the old code with a git permalink.
dbooth: Sounds good, but should first look at it togther to see if we can figure it out.
eric: IDK who wrote that code. git blame might tell us.
dbooth: eric and jim should get together (top priority), but copy Deepak and Daniel and me, in case we can join. But don't wait for us.
gaurav: Jim is also working on RDF lists. Hasn't touched the de-currying, but thinks he's found some of the relevant code.
Ontology generation
daniel: Still trying to figure out what the changes mean.
… Trying to find time to connect w Jim. Found that editing the turtle parser in the HAPI code affects the example files.
… Already changed fhir:value to fhir:v
FHIR FAQ
chris: Will check w Davera
How to use CURIEs for foreign concepts
joe: How to implemente CURIEs for foreign concepts?
eric: What's your objective? Are you trying to do inference?
joe: No inference, just serving content. Not aware of use case for inference yet.
eric: When you use it for classification, when you have a code system and code, you end up adding a type arc.
… But not sure we can give guidance WRT CURIES. You need to tell the world that your codes start with "ro:", and tell your friends that it means a certain thing.
… But you probabl ywant to enable the classification use case.
joe: where would a prefix map go?
eric: We didn't arrive at a conclusion for dealing w that. We haven't defined a way to expand CURIEs.
joe: Is the group planning to address that issue?
dbooth: How about using full URIs instead of CURIEs?
ACTION: joe to email problem description to dbooth for inclusion in these minutes
joe: I guess we could.
gaurav: Lean toward using the full URI - -unambiguous, and can be translated to concepts outside of FHIR.
… Also we need to come up with a way to standardize this.
… FHIR doesn't see CURIEs. Once you've defined the code somewhere, you can reference it from elsewhere.
… All uberon codes could start with "uberon:"
joe: We changed periods to underscores in the URIs because they were causing a problem with Lucene indexing.
dbooth: Codes can normally have periods in them though.
dbooth: Also, you mentioned the code system being implicit. Can it be made explicit?
chris: He was looking at the terminology def itself.
HAPI
eric: Still hoping to have time
ADJOURNED
Example of CURIE problem
From Joe Flack:
Attached is the example snippet of the JSON I was showing at the meeting. One of the RO references is a CURIE, and another one is a URI, just as an illustrative difference. I found which CodeSystem / ontology it was taken from. It is from Mondo, actually. If you have any need, that file is called CodeSystem-mondo.json and can be downloaded here: https://github.com/HOT-Ecosystem/owl-on-fhir-content/releases
The example:
{
"code": "UBERON:0004455",
"display": "neurula embryo",
"property": [
{
"code": "parent",
"valueCode": "UBERON:0000922"
},
{
"code": "RO:0002202",
"valueCode": "UBERON:0004734"
},
{
"code": "http://purl_obolibrary_org/obo/RO_0002491",
"valueCode": "UBERON:0000110"
}
]
},
Oops, here's the message from Joe Flack again, better formatted:
Attached is the example snippet of the JSON I was showing at the meeting. One of the RO references is a CURIE, and another one is a URI, just as an illustrative difference. I found which CodeSystem / ontology it was taken from. It is from Mondo, actually. If you have any need, that file is called CodeSystem-mondo.json�~@~K and can be downloaded here: https://github.com/HOT-Ecosystem/owl-on-fhir-content/releases
ADJOURNED AGAIN