IRC log of hcls on 2024-02-22
Timestamps are in UTC.
- 15:58:17 [RRSAgent]
- RRSAgent has joined #hcls
- 15:58:22 [RRSAgent]
- 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
- 16:58:37 [RRSAgent]
- I have made the request to generate https://www.w3.org/2024/02/22-hcls-minutes.html dbooth
- 17:01:59 [TallTed]
- TallTed has joined #hcls