IRC log of hcls on 2024-02-22

Timestamps are in UTC.

15:58:17 [RRSAgent]
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logging to https://www.w3.org/2024/02/22-hcls-irc
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
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I have made the request to generate https://www.w3.org/2024/02/22-hcls-minutes.html dbooth
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