14:57:03 RRSAgent has joined #hcls 14:57:08 logging to https://www.w3.org/2025/09/04-hcls-irc 14:57:08 rrsagent, make logs public 14:57:12 Meeting: FHIR RDF 14:57:15 Chair: David Booth 15:07:32 Topic: Issues with using FHIR R5 ShEx 15:07:38 https://github.com/w3c/hcls-fhir-rdf/issues/172 15:09:35 tim: bnodes are a problem. Want IRIs for the structure defs. 15:10:08 ericp: We now have IRIs for the top of the structure def, based on the IDs. 15:11:42 jim: https://github.com/w3c/hcls-fhir-rdf/issues/172 15:14:16 tim: Still need to link the class using rdfs:isDefinedBy , as described in issue 133. 15:15:01 ericp: The FHIR examples are not compliant w the FHIR REST protocol. It would be nice if they were resolvable. 15:19:09 tim: I can work on linking the classes. 15:19:28 jim: The roots of the structure defs now have IRIs, in the latest. And in the examples. 15:19:37 ... But they were accidentally bnodes before, in R5. 15:20:44 tim: There's still a problem w imports: Issues with using FHIR R5 ShEx 15:20:52 ... The first two there. 15:21:36 s|Issues with using FHIR R5 ShEx|https://build.fhir.org/fhir.shex 15:22:19 tim: Also it looks like it uses shex 2.2 . It would be good to what version of shex it uses. 15:22:42 ericp: It uses a version we haven't yet merged back into jena. 15:23:10 ... We're still working on usability for it. 15:23:34 tim: Also he FHIRPath constraints are not in the pubic shex. 15:23:49 ericp: Yes, the need a lot of debugging. 15:24:17 ... Also the jena shex version that iovka put together is much faster, so we hope to use that one. 15:24:45 tim: So far I've been getting around these issues. 15:24:56 ... I'm using it for encoding more of the valueset bindings. 15:25:08 ... this issue: https://github.com/w3c/hcls-fhir-rdf/issues/167 15:25:40 ... using a reasoner with valuesets 15:25:56 ... I think I have a solution for doing that w an ontology, e.g., SNOMED 15:27:00 ... Basically because of the OWA you need to use shex for the validation part. 15:27:09 ... Did you consider: What was the status on making a SHACL version? 15:27:31 ericp: Probably possible, but wouldn't give you as good validation because of no notion of closed shapes. 15:27:42 ... Would probably work for base resources, but not well for profiles. 15:28:04 ... You'd have to customize it for each profile. 15:28:57 ... SHACL was meant to be easy to implement; ShEx was meant to be easy on users. 15:29:48 Topic: FHIR R5 RDF Support broken 15:29:54 https://github.com/w3c/hcls-fhir-rdf/issues/174 15:30:08 detlef: Want to receive FHIR R5 and convert it to FHIR R5 RDF. 15:30:24 ... But found that HAPI does not contain a real R5 parser. 15:30:34 ... Tim said I should look at the FHIR core for the real parser. 15:30:42 ... But then we ran into multiple issues. 15:31:14 ... Went back to HAPI FHIR base, and found that this parser is generic, and creates the correct RDF and JSON in R5 but not R4. 15:31:48 ... And we asked it for a FHIR context for R5, but it turns out it is a hybrid version that uses R4 syntax but has some R5 contexts. Broken. 15:32:14 ... tried to replace it w the R5 parser, but has implementatoin of 28k lines in one class. 15:32:27 ericp: That's grahame's implementaion. 15:32:36 detlef: I was guessing it was generated. 15:32:56 ... Also serializatoin is completely missing. 15:33:08 ... Lots of comments of implementation missing. 15:33:34 ... My colleague changed the generic parser to support proper R5 (we think). That work is ongoing. 15:34:01 ... HAPI FHIR base has some tests for it. Converted XML to RDF and see if that creates the correct XML again. 15:34:28 ... ANd my colleage was checking agains the examplex, but they're created from a third implementation. 15:35:26 ... My colleague collected issuee believing he would get an R5 parser. E.g., still uses fully qualified property names, still uses the R4 list syntax, etc. 15:36:07 ... Looks like nobody actually implemented the R5 parser. Should have caused an exception if it isn't implemented. 15:36:19 tim: We switched to using a class called turtle parser. 15:36:28 https://github.com/w3c/hcls-fhir-rdf?tab=readme-ov-file#rdf--shex-generation 15:36:38 tim: Decent examples of how to use it https://github.com/hapifhir/org.hl7.fhir.core/blob/master/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/TurtleGeneratorTests.java 15:37:09 ... The maintainers of this repo have not done a good job of clearly separating R5 code from R4 code. That has causd me some confusion. 15:37:19 ... There's also a turtle generator classe. 15:37:25 jim: But that's only serialization. 15:38:08 ericp: I think I have the generic parser updated for R5 rdbch. 15:38:34 s/rdbch/rdvch/ 15:40:15 ericp: https://github.com/fhircat/hapi-fhir/tree/update-rdf-parser-to-rdvCh 15:40:31 tim: This work should go into the core llibrary, because it's not specific to HAPI. 15:41:11 ... THat would allow it to be shared by the FIHR build and HAPI. 15:41:33 ericp: There's a test that does round tripping. 15:42:31 ericp: https://github.com/fhircat/hapi-fhir/tree/update-rdf-parser-to-rdvCh 15:43:13 tim: So the 28k like class should be replaced by what ericp has. 15:43:25 ... But the code is up to date, but in the turtle classe. 15:43:42 detlef: We like that the FHIR base is integrated. 15:44:12 tim: The core lib is hosted in HAPI's repo (the hapi fhir prefix), but the namespace is just core fhire. 15:45:03 ... But the updated parser https://github.com/fhircat/hapi-fhir/tree/update-rdf-parser-to-rdvCh should be brought into FHIR core. 15:45:34 ericp: i'm confused by why 15:45:34 https://github.com/hapifhir/hapi-fhir/tree/master/hapi-fhir-base/src/test/java/ca/uhn/fhir/parser 15:45:34 doesn't have the test for 15:45:34 https://github.com/hapifhir/hapi-fhir/blob/master/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/RDFParser.java 15:46:34 ericp: If detlef's colleague wants to work togheter over signal, we can get the properly merged into FHIR core. 15:51:03 ericp: In japan Sep 12-24. 15:51:14 s/24/22/ 15:52:48 gaurav: Out next week 15:53:08 ADJOURNED 15:54:39 Present: Eric Jahn, EricP, Erich Bremer, Detlef Gritner, David Booth, Jim Balhoff, Guarav Vaidya, Tim Prudhomme 15:54:46 rrsagent, draft minutes 15:54:47 I have made the request to generate https://www.w3.org/2025/09/04-hcls-minutes.html dbooth