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15:58:22 <dbooth> rrsagent, make logs public
15:58:27 <dbooth> Meeting: FHIR RDF
15:58:30 <dbooth> Chair: David Booth
16:05:12 <dbooth> Topic: Kindling PR
16:06:03 <dbooth> DBooth: Think it's getting unstuck.
16:06:31 <dbooth> Topic: DICOM
16:06:47 <dbooth> erich: They're goingn to give me a copy of their software in begin of march.
16:08:54 <dbooth> jim: Met with Emily last friday.  Working on plans to finish out the grant, including the Java stuff.
16:09:19 <dbooth> dbooth: If Deepak is unable to continue the shex testing, then we'll need someone to work on that.
16:09:56 <dbooth> eric: Tests need to be run again..  The examples are incompatible w the shex at present.
16:10:24 <dbooth> ... You can run it in two modes, with more or fewer checks.
16:10:57 <dbooth> ... Want to be able to hit a button to gen the examples or the shex, and hit another button to validate them all.
16:11:14 <dbooth> ... If we were set up to do that, we'd have a lot fewwer PRs and it woudl speeed us up.
16:12:04 <dbooth> dbooth: And you'll want a way to gen a single exmaple.
16:13:19 <dbooth> ... Also need to update Harold's tutorial to R5.
16:15:24 <dbooth> eric: Harold tried to do it just with Protege.  I just did it with OWL QL (manchester syntax).  That meant I couldn't compare dates.
16:15:51 <dbooth> ... There aren't any plugins you can use with protege doing owl and SPARQL.
16:16:22 <dbooth> ... You might need to enhance the expressivility of the thing that rewrites sparql queries.
16:17:35 <dbooth> ... And claude and I want help w the shexmap stuff.
16:18:42 <dbooth> ... Would be fun to explain the shexmap process to Jim.  I need to push the notion of a threaded regex engine to the whole shape expression.
16:19:12 <dbooth> jim: shexmap is an addon to shex?
16:20:04 <dbooth> eric: Shex has an annotation system and an extension system.  You can attach a semantic action to a rule.
16:20:29 <dbooth> ... You add var names (as URLs)
16:20:59 <dbooth> ... Then when you validate one, you get bindings for the var, then you use that when you synthesze to the target.
16:21:21 <dbooth> ... When you're validating you wind up w a hierarchy
16:21:59 <dbooth> ... Capture the tree and then synth a new doc by walking that tree.
16:22:16 <dbooth> jim: Comparison to sparql construct?
16:22:32 <dbooth> eric: The complexity of optional parts in a query make it complex.
16:22:54 <dbooth> ... If you try to do it piecemeal, and you have bnodes, you wind up with discontinuous things.
16:24:50 <dbooth> Topic: ShexMap
16:25:15 <dbooth> gaurav: There might be people from the SSSOM team who are interested in interconverting with this: https://github.com/mapping-commons/sssom
16:26:12 <dbooth> ... SSOM is a simple way to map ont, developed by Monarch group.
16:27:47 <dbooth> jim: They're int in complex mappings.
16:28:21 <dbooth> ... Eg if you map a species-specific mapping term, to a more general one, you might want the mapping to be an OWL expr.
16:29:35 <dbooth> ... And LinkML is working on their own transformation system.
16:29:48 <dbooth> ... I think of them all being RML-adjacent.
16:30:29 <dbooth> gaurav: https://github.com/linkml/linkml-transformer
16:30:34 <dbooth> ... I’ve previously used YARRRML to do these kinds of transformations, but I think LinkML is working on something more sophisticated: https://github.com/rmlio/yarrrml-parser
16:31:07 <dbooth> ... All will rely on mappings that exist in SSSOM.
16:32:27 <dbooth> Topic: Concept IRIs
16:32:54 <dbooth> gaurav: Small update: got MeSH change request approved by ITS, is now submitted.
16:33:27 <dbooth> ... Minor fixes for LOINC update is now queued for manual content check.
16:33:52 <dbooth> ... On vac next weekj.
16:34:39 <dbooth> ... Might do a bunch of OBO ont at once next.
16:35:32 <dbooth> .. Might need OBO ont to officially  say what the IDs are.
16:35:57 <dbooth> ... SNOMEd mapping stuff we were doing is quite int.  Hope we can get it moving again.
16:36:34 <dbooth> Topic: SHExMap
16:36:47 <dbooth> (demo by ericP)
16:43:16 <dbooth> Present: Rob Hausam, David BOoth, EricP, Erich Bremer, Gaurav Vaidya, Jim Balhoff
16:44:40 <dbooth> rob: FHIR BP requires LOINC
16:44:53 <dbooth> ... Also the coding needs one more level of nesting.
16:45:48 <dbooth> DBooth: We used this in a research project to transform one form of RDF to another form of RDF.
16:47:32 <dbooth> ericP: It has some limitations, which I'm working to fix.
16:48:47 <dbooth> erich: What if it doens't find a particular mapping?
16:49:34 <dbooth> eric: It will fail the materializer.
16:53:08 <dbooth> dbooth: IF you need to map to/from FHIR, this could help, because you already have all of the shex shemas for FHIR generated for you.
16:56:12 <dbooth> ericP: You can also provide annotations by reference.
16:57:51 <dbooth> ADJOURNED
16:58:30 <dbooth> i/Met with Emily last friday/Topic: Future FHIR RDF work
16:58:36 <dbooth> rrsagent, draft minutes
16:58:37 <RRSAgent> I have made the request to generate https://www.w3.org/2024/02/22-hcls-minutes.html dbooth
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