IRC log of hcls on 2022-11-03

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14:58:56 [dbooth]
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Meeting: FHIR RDF
14:59:07 [dbooth]
Chair: David Booth
15:01:25 [dbooth]
Topic: Introductions
15:02:20 [dbooth]
Joe: At Johns Hopkins, working w Chris Mungall
15:02:29 [dbooth]
Chris: Working at U Colorado
15:03:52 [dbooth]
Present: Joe Flack, Chris Roeder, Jim Balhoff, Rob Hausam, EricP, David Booth
15:05:40 [dbooth]
Present+ Houcemeddine Turki, Gaurav Vaidya
15:07:29 [dbooth]
Topic: OWL usage
15:08:06 [dbooth]
joe: Have some questions on how to represent things.
15:09:08 [dbooth]
... 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 [dbooth]
... There's a github w existing OWL converter, but it's leaving out a lot of content.
15:10:33 [dbooth]
https://github.com/aehrc/fhir-owl The Australian e-Health Research Centre
15:11:03 [dbooth]
joe: Working on a PR: https://github.com/INCATools/ontology-access-kit/pull/320
15:11:26 [dbooth]
... How to represent CURIEs? How to include classes from external code systems? Synonym structuring?
15:11:36 [dbooth]
... Is-a hierarchy -- want to check it.
15:12:24 [dbooth]
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 [dbooth]
... Also, our proposal assumes that the code is a local code and not a CURIE.
15:13:36 [dbooth]
... RDF group has expectations about how that should work?
15:14:05 [dbooth]
eric: Converting OWL to FHIR? joe: Yes.
15:14:40 [dbooth]
joe: Converting OWL ont to FHIR code system resource. Suppose some content maps could be involved.
15:14:55 [dbooth]
dbooth: Your intent is to use those with FHIR data later?
15:15:12 [dbooth]
chris: Yes.
15:15:51 [dbooth]
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 [dbooth]
chris: It was written by the phenopackets guy.
15:16:58 [dbooth]
https://pyrophen.readthedocs.io/en/latest/representation.html
15:22:47 [dbooth]
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 [dbooth]
joe: i like those CURIEs in there but Idk if that's conformant?
15:23:45 [dbooth]
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 [dbooth]
Regex: [^\s]+( [^\s]+)*
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This datatype can be bound to a ValueSet
15:24:01 [dbooth]
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 [dbooth]
joe: I'm thinking like: CodeSystem.extension.curie_map
15:24:24 [dbooth]
joe: CodeSystem.concept.extension.uri maybe
15:25:11 [dbooth]
eric: The code should just be the number part. You can still have valuesets that draw from multiple code systems.
15:25:22 [dbooth]
gaurav: We could ask everybody to use either:
15:25:28 [dbooth]
... { system: OBO, code: “HP:101” } OR { system: HPO, code: “101” }
15:25:38 [dbooth]
houcemeddine: An excellent practice will be the use of OBO Ontologies instead of SNOMED-CT.
15:26:27 [dbooth]
joe: I was thinking one OWL file should generate one FHIR resource.
15:27:27 [dbooth]
jim: If you're making a FHIR resource for Mondo, maybe it should only have the Mondo terms.
15:28:15 [dbooth]
gaurav: So then { system: MONDO, code: “UBERON:101” }?
15:29:59 [dbooth]
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 [dbooth]
... But the cleanest way to do it is to emit one code system for each prefix.
15:30:44 [dbooth]
rob: Agreed.
15:32:13 [dbooth]
joe: Suppose I have one with only one term. Would that confuse?
15:33:02 [dbooth]
eric: I don't think so. It would be more confusing if you kept the prefixes.
15:33:23 [dbooth]
chris: Want to check with Peter.
15:35:08 [dbooth]
jim: Our goal is that it comes out looking how people expect it to look.
15:36:12 [dbooth]
joe: Tooling available for FHIR RDF?
15:36:19 [dbooth]
jim: The playground.
15:37:12 [dbooth]
eric: Also Harold's demo of using SNOMED and reasoning with FHIR RDF.
15:37:13 [dbooth]
https://yosemiteproject.org/tutorial-fhir-rdf-as-a-bridge-to-the-semantic-web-in-healthcare/
15:38:14 [dbooth]
gaurav: Also concept IRI https://github.com/fhircat/fhir-rdf-playground/pull/12
15:39:06 [dbooth]
dbooth: Also HAPI server does FHIRRDF R4. Not yet R5.
15:39:54 [dbooth]
... and the playground: https://fhircat.github.io/fhir-rdf-playground/
15:41:59 [dbooth]
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 [dbooth]
https://jira.hl7.org/browse/UP-364
15:42:17 [dbooth]
https://bit.ly/fhir-rdf-concept-iris-july-2022
15:42:41 [dbooth]
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 [dbooth]
gaurav: We've made the proposal to the terminology group, and want to start adding actual IRI stems.
15:49:28 [dbooth]
dbooth: And the underscore should be a part of the IRI stem, because it isn't a part of the code.
15:50:49 [dbooth]
joe: For sysnonyms, if it's exact, shoudl I use "designation"?
15:50:56 [dbooth]
rob: Yes, that sounds right.
15:51:39 [dbooth]
... For broader/narrower, it could be done with a property.
15:53:46 [dbooth]
Topic: Other updates
15:53:56 [dbooth]
gaurav: No progress on concept IRIs
15:54:09 [dbooth]
jim: No word from grahame.
15:55:32 [dbooth]
dbooth: Eric, HAPI progress?
15:55:50 [dbooth]
eric: Need time to work on it.
15:58:15 [dbooth]
dbooth: And simplifying the playground URI?
15:58:19 [dbooth]
eric: James is doing that.
15:59:09 [dbooth]
... Might want an OWL-friendly option. So it might be useful to keep those optoins somewhere.
16:00:36 [dbooth]
ACTION : DBooth to check with James about trimming the playground UI
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ADJOURNED
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