14:58:48 RRSAgent has joined #hcls 14:58:48 logging to https://www.w3.org/2022/11/03-hcls-irc 14:58:56 rrsagent, make logs public 14:59:00 Meeting: FHIR RDF 14:59:07 Chair: David Booth 15:01:25 Topic: Introductions 15:02:20 Joe: At Johns Hopkins, working w Chris Mungall 15:02:29 Chris: Working at U Colorado 15:03:52 Present: Joe Flack, Chris Roeder, Jim Balhoff, Rob Hausam, EricP, David Booth 15:05:40 Present+ Houcemeddine Turki, Gaurav Vaidya 15:07:29 Topic: OWL usage 15:08:06 joe: Have some questions on how to represent things. 15:09:08 ... Working on PR for ont access kit. We have a FHIR server and want to load content from a number of sources. Need to convert to FHIR, some data already in OWL/RDF. Not sure how to structure it. 15:09:36 ... There's a github w existing OWL converter, but it's leaving out a lot of content. 15:10:33 https://github.com/aehrc/fhir-owl The Australian e-Health Research Centre 15:11:03 joe: Working on a PR: https://github.com/INCATools/ontology-access-kit/pull/320 15:11:26 ... How to represent CURIEs? How to include classes from external code systems? Synonym structuring? 15:11:36 ... Is-a hierarchy -- want to check it. 15:12:24 jim: Two issues in converting OWL. In our IRI stem proposal, we assume lots of code with one prefix. But a lot of OBO ont include terms from a number of namespaces. 15:13:06 ... Also, our proposal assumes that the code is a local code and not a CURIE. 15:13:36 ... RDF group has expectations about how that should work? 15:14:05 eric: Converting OWL to FHIR? joe: Yes. 15:14:40 joe: Converting OWL ont to FHIR code system resource. Suppose some content maps could be involved. 15:14:55 dbooth: Your intent is to use those with FHIR data later? 15:15:12 chris: Yes. 15:15:51 gaurav: Not sure how pyrophen is related, but it looks like it could be useful: https://pyrophen.readthedocs.io/en/latest/example-json.html It highlights the problem we have. 15:16:21 chris: It was written by the phenopackets guy. 15:16:58 https://pyrophen.readthedocs.io/en/latest/representation.html 15:22:47 jim: For a code like "HP:000300", if we prepend an IRI stem directly, then it won't match the OBO IRIs, that OBO assigns. 15:23:28 joe: i like those CURIEs in there but Idk if that's conformant? 15:23:45 joe: code: Indicates that the value is taken from a set of controlled strings defined elsewhere (see Using codes for further discussion). Technically, a code is restricted to a string which has at least one character and no leading or trailing whitespace, and where there is no whitespace other than single spaces in the contents xs:token JSON string 15:23:45 Regex: [^\s]+( [^\s]+)* 15:23:45 This datatype can be bound to a ValueSet 15:24:01 joe: i don't mind using a fhir extension element for the prefix/namespace, but whenever extensions come into play that is certainly an area where we'd want to have a consensus or explicit standard 15:24:12 joe: I'm thinking like: CodeSystem.extension.curie_map 15:24:24 joe: CodeSystem.concept.extension.uri maybe 15:25:11 eric: The code should just be the number part. You can still have valuesets that draw from multiple code systems. 15:25:22 gaurav: We could ask everybody to use either: 15:25:28 ... { system: OBO, code: “HP:101” } OR { system: HPO, code: “101” } 15:25:38 houcemeddine: An excellent practice will be the use of OBO Ontologies instead of SNOMED-CT. 15:26:27 joe: I was thinking one OWL file should generate one FHIR resource. 15:27:27 jim: If you're making a FHIR resource for Mondo, maybe it should only have the Mondo terms. 15:28:15 gaurav: So then { system: MONDO, code: “UBERON:101” }? 15:29:59 eric: If there's no need to unify codes w other ontologies, then ... if you have hp: on the front of each, and take those off, but leave others off, you'd effectively be making aliases for them in your code system. 15:30:31 ... But the cleanest way to do it is to emit one code system for each prefix. 15:30:44 rob: Agreed. 15:32:13 joe: Suppose I have one with only one term. Would that confuse? 15:33:02 eric: I don't think so. It would be more confusing if you kept the prefixes. 15:33:23 chris: Want to check with Peter. 15:35:08 jim: Our goal is that it comes out looking how people expect it to look. 15:36:12 joe: Tooling available for FHIR RDF? 15:36:19 jim: The playground. 15:37:12 eric: Also Harold's demo of using SNOMED and reasoning with FHIR RDF. 15:37:13 https://yosemiteproject.org/tutorial-fhir-rdf-as-a-bridge-to-the-semantic-web-in-healthcare/ 15:38:14 gaurav: Also concept IRI https://github.com/fhircat/fhir-rdf-playground/pull/12 15:39:06 dbooth: Also HAPI server does FHIRRDF R4. Not yet R5. 15:39:54 ... and the playground: https://fhircat.github.io/fhir-rdf-playground/ 15:41:59 gaurav: Given that FHIR thinks of codes as system-code pair, and RDF uses IRIs. We're planning to use the HL7 terminology website to host the IRI stems. 15:42:09 https://jira.hl7.org/browse/UP-364 15:42:17 https://bit.ly/fhir-rdf-concept-iris-july-2022 15:42:41 eric: hapi-fhir RDF tests: https://github.com/hapifhir/hapi-fhir/blob/master/hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/RDFParserTest.java 15:43:12 gaurav: We've made the proposal to the terminology group, and want to start adding actual IRI stems. 15:49:28 dbooth: And the underscore should be a part of the IRI stem, because it isn't a part of the code. 15:50:49 joe: For sysnonyms, if it's exact, shoudl I use "designation"? 15:50:56 rob: Yes, that sounds right. 15:51:39 ... For broader/narrower, it could be done with a property. 15:53:46 Topic: Other updates 15:53:56 gaurav: No progress on concept IRIs 15:54:09 jim: No word from grahame. 15:55:32 dbooth: Eric, HAPI progress? 15:55:50 eric: Need time to work on it. 15:58:15 dbooth: And simplifying the playground URI? 15:58:19 eric: James is doing that. 15:59:09 ... Might want an OWL-friendly option. So it might be useful to keep those optoins somewhere. 16:00:36 ACTION : DBooth to check with James about trimming the playground UI 16:09:41 ADJOURNED 16:09:56 rrsagent, draft minutes 16:09:56 I have made the request to generate https://www.w3.org/2022/11/03-hcls-minutes.html dbooth