David Booth, Deepak Sharma, Emily Pfaff, EricP, James Champion, Jim Balhoff
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
ITS meeting Wed Feb 22, 3pm Boston time
ACTION: David to send out meeting details
ACTION: David to make slides
eric: Does HAPI work need to be done?
david: Not as far as I know.
eric: If I can translate JSON into Turtle, and ShEx validate them against the schemas, then that's good.
dbooth: IDK the HAPI code acceptance criteria.
deepak: If Rob reviews our changes, maybe he can vote for us? … Raises their level of confidence. … I emailed the latest schema and resources. … They include constraint conjunctions, and also some that are unmapped. … If you cannot find a mapping, you surround it with underscore-shex.
eric: Just don't serialize those. Does it parse, using shex scala?
deepak: Yes, if I remove that token.
eric: You can put the original text in comments.
deepak: Ok, I'll make that code correction.
eric: Could be done as semantic actions, but that would be a new work item.
HAPI
eric: Implemented everything except the polymorphic types and RDF lists.
FHIR Build
jim: Asked Grahame about updating the validator parser. He discovered that it hadn't be working for a while, so I haven't been working on FHIR RDF parser. … I wonder if we should run the generated FHIR RDF examples through deepak's shex validation.
david: Yes, absolutely.
ACTION: Deepak to run shex validation against the generated FHIR RDF examples from jim
eric: The HAPI test harness validates them as POJOs.
Daniel Stone, David Booth, EricP, Gaurav Vaidya, Jim Balhoff, Rob Hausam
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
RDF validator parser
jim: I could work on it, but as a longer-term effort
FHIR ontology
daniel: Need to look it over
eric: Try loading it into protege
Shex
dbooth: Followup needed: still needs testing against examples
eric: Jose is not sure that relative imports work. Will check.
eric: Also refactoring my code to make it more efficient.
ACTION: DBooth to follow up w Deepak.
HAPI
eric: Got it working, but no PR yet. … Haven't got it working w both R4 and R5. … Any deadline?
rob: No, it's de-coupled from R5 deadline. … There's already a milestone build of R5. It should be structurally the same as the ultimate release. Only minor tech changes.
dbooth: Are you doing both RDF parsing and generation?
eric: Yes. It's all one module.
dbooth: Testing w POJO models?
eric: Yes.
Concept IRIs and IRI stems
gaurav: Got another vote on IRI stem for LOINC. Still need v3 voter. Will reach out to jean dutaeau. … Also need a THO task for adding IRIs to the list of known ID systems.
rob: Too late for dev days participation, but might be able to do a sidebar. … Amsterdam, early June. … Like BOF groups … Could also put an article in HL7 newsletter.
dbooth: Could post on lists, eg W3C and JAMA list
eric: Might wait for tools to be ready. Maybe at FHIR connectathon (First week in May)
dbooth: There's an AMIA list also.
rob: Examples are not good to see in protege, because they don't show anon individuals at all.
jim: Would be helpful to skolemize bnodes.
eric: Might be nice to have a FHIR-specific tool.
dbooth: Using shexmap? Eric: Maybe.
eric: We did a tutorial at SWAT4LS.
dbooth: Should update harold's tutorial to R5.
ACTION: Eric to reach out to FAIR-data-somethign-something group
David Booth, EricP, Houcemeddine Turki, Jim Balhoff, Rob Hausam
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
Adding validation to the Playground
houcemeddine: Shex doesn't work without BASE.
dbooth: Without BASE it's looking from where the playground was loaded.
dbooth: Should we have a settable BASE in the playground?
eric: Shex is generated internally from the structure defs.
dbooth: Leaning toward only having user select the FHIR version, and the playground uses those schemas that are internally generated.
eric: ok
(Eric shows Houcemeddine where to find the internal shex that was generated.)
HAPI
dbooth: What's remaining to do?
eric: Need to geek w Grahame or someone about how to lay out the tests. Need to make all my changes parametric for the version. … Then need to figure out how to test it.
dbooth: Probably shouldn't bug grahame yet.
rob: Also try James Agnew.
What's new in FHIR RDF R5
dbooth: Could do a page describing what's new, a webinar? Would be nice to update Harold's tutorial to R5.
eric: Should finish our bug fixes first. … Shex can do minimal checking, but could be extended for more checking. … E.g., could point it to a profile, and validate against that. … Deepak already parses the extensions, but we disabled that because it's hard to say what use case it fits. … Hard to imagine someone using all the FHIR-defined extensions. … That code is most useful if you point it at your own profile.
rob: Typicaly people require certain extensions, but do not restrict others.
rob: IG = Implementation Guide
dbooth: Need to follow up w Deepak about whether he could take this on.
ACTION: David to ask deepak whether he could extend the shex effort for specified profiles/extensions
rob: should be able to specify what profile to use, in validating.
Validation parser
jim: No progress at the moment. Grahame's busy. I'll come back to it at some point.
eric: Should ask FHIR folks whether we could make shex files case sensitive.
ACTION: Eric to ask Grahame about using mixed case shex filenames
eric: No update on HAPI yet. … Want to get the shex parser usable for deepak. … Applied for a grant for bio hackaton in japan beginning of July, to add sparql support to HAPI FHIR.
ShEx testing of examples
eric: Deepak is working on a paper. Also it was taking too long to run the shex parser. That's why I worked on Jison to dramatically improve the speed.
Concept IRIs
gaurav: Just sent reminder email to jean and Reuben. Will poke them on zulip if I don't hear back from them. We have 10 of 15 votes needed for LOINC proposal.
gaurav: Rob promoted our proposal, and now have the votes we need, but not yet met the quorum requirements. … Will follow up w Rob
gaurav: on our other propopsal, to add IRIs to the externakl known ID systems. This needs voting again. But there's a question about who will be responsible for providing the IRIs.
Adeel Anari, AllenFlynn, Avanti Paturkar, Claude Nanjo, David Booth, EricP, Gaurav Vaidya, Jim Balhoff, Philippe_Rocca-Serra, Rob Hausam
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
Introducttions
dbooth
ericP: Worked w Josh Mandel on FHIR RDF. Was W3C contact a long time.
jim: At U NC. Work on bio ont, and applying OWL.
Gaurav: Also at UNC. Working on sem web stuff for 5-6 years.. General research software dev. int in how to represent data in RDF and make it easier to connect data. Want to do it in large scale data like wikipedia.
Allen Flynn: Prof U mich. Was in pharma, then EHR, Trinity health. 2018 PHD in CS, got me into sem web. Working on algo that are evidence based for healthcare. Did work on metadata, packaging algo. Lots of work informed by Linked data ideas. … Published one ont on describe things w parts. Working on joint project w C mental health in toronto.
avanti: informatic student, working w Allen.
adeel: Work at Ctr for addiction and mental health in toronto. In ontario there's a push to use FHIR, so we're trying to create a data sharing platforme, for EHR, imaging, wearable, use FHIR and RDF and other vocabs.
phhilippe: U of Oxford, prev astra zeneca. OBO foundry.
U Mich & Ctr for Addict and Mental health
allen: want to deploy functions in the graph env that can compute over it and add value. … W're in the middle of that process now. Multiple sources of data, already in a graph DB. … Inside the dashed line is our work. Gray pipeline Adeel is building. … Current focus is 3 resources: 1. library resource from FHIR standard. Using that to describe individ computer functions, eg, medical calculators, predictive models, etc. … Inside the graph DB we're adding descriptions of fns. Assuming they're already in there, the pipeline extracts one pt data and relevant params, then calls a fn to gen new pt features as the outcome, eg, risk score. … Two things come along w that: want to describe the fn call itself. Landed on an exploration of the service request FHIR resource -- not originally intended for that use. … Then onthe output we're using the FHIR Observation resource. Then it gets pushed back to the graph DB. … We keep a record of the request and the output.
dbooth: Nice clean computing flow model.
eric: Did you use SMART?
allen: I don't think so.
eric: e.g. using it as the executoin env, such as auth and auth.
adeel: The flow we're exploring is more automated, not user driven.
(slide 2)
allen: the library resource is close to what we want to describe. Good fit for purpose. … The FHIR RDF Observation is okay. Status field isn't too painful. Not aware of anything better, so we're using it for now. … FHIR RDF service request is not the best fit. Prob not the originalintent for that. … in the lower part of this slide, want to use URLs everywhere. @contexts are getting longer. … Helped a lot by the paper from Solbrig and all. Playground has been a super resource. … We Started saying we were using FHIR. Earlier were using the Function ont and the Prov ont. Still looing to include them, even though we're most focuse on FHIR so far.
eric: re service request, you mentioned the terminology doesn't line up well. Want to say "I want a resource w a value in this terminology" … A diagnosis, allergy, etc tries to be more specific than Observation. … If you were doing some coding that was producing a bunch of values...
allen: Questionnaire and response has aome relevance here, but need something a little more general.
eric: When you talk about FHIR RDF lib, what's your input. If there were a svc req for this, it will find code for it?
allen: Yes. Want fn assoc w those things. We have a record and triples. That's why the slide shows iterations. … Anticipate having many hudreds of fns, and when it runs, point back to what was run.
eric: There's some prov stuff in Domain resource I think. You want to use the Service Request to use DRY principles.
eric: Is writing that in FHIR land useful, because you can interop w yourself, but not others.
allen: Might have gone to strongly on FHIR.
dbooth: Re Harold's observations about R4 problems, Struggled w trying to get rid of the extra bnode, but concluded that we couldn't.
eric: Working on NHS project, using SOLID. Similar motivation to your work. Also working w Claude Nanjo on U Utah project for CDS. … Goal of SOLID is for all pers data that can be shared or not, under the individuals control -- FHIR in and FHIR out.
gaurav: For this group, I'm working on Concept IRIs. Working to get FHIR UTG group to include that in their repo.
jim: Gaurav and I get involved in this through Emily Pfaff on NIH grant. Helped on R5 changes, and implementation and java code. Emily has plans to apply RDF to integrate ont w diseases. Export to FHIR RDF and then query and aggregate.
claude: At U of Utah, clinical informaticist. Working on dev CDS appllication for disease mgmt, used in production. Also int in the FHIR RDF work and ShEx and ShexMap work. Part of our knowledge base, looking at boundary of rule-based knowledge vs KB that should not be written as rules.
HAPI
eric: It's upgraded to R5, passing tests, but have not yet added switches to allow you to switch between R4 and R5.
Concept IRIs
gaurav: now have 16 votes, but not sure we have all the quorum req met yet. On the other one, Reuben hasn't replied yet to my response.
rob: We discussed the UTG tickets on Term infra co-chairs call, for planing agenda. Agreed to put thse tickets on the agenda, try to get them over the finish line this afternoon, 3;30pm Eastern.
What works for RDF reasoning?
eric: What works? What doesn't? What Arch features would you want to provide the ecosystem you want? … I interpreted the U Mich work as simillar to SMART on FHIR: doing computes and injecting things back in. … And Claude is injecting things back, like med request. … So far U Mich work doestn' need Auth and Auth, becuaes it's internal.
allen: Yes, but if we want to open beyond firewall is a good one.
eric: And when you're doing computes, are you infrancing over term. Any machine learning?
allen: No maching learning yet. Fixed computing fn. But it's picked up separately.
adeel: Currently the sys doesn't do inferencing. Fns are writtin in JS or python.
allen: Blue brain has been used in community to add reasoning. Think that's coming, but we haven't used it yet.
eric: What did crystal daniele use? Claude: IDK. … She used CCDA on her own.
ADJOURNED
Minutes manually created (not a transcript), formatted by scribe.perl version 210 (Wed Jan 11 19:21:32 2023 UTC).
gaurav: One proposal is still 'sent for implementation'. … The other proposal is up to 9 votes out of 15. Will tag others who voted on the first proposal.
gaurav: Will be out next week.
HAPI
eric: No new progress. Worked on shex. Also working on shex-jena, which is needed for HAPI.
ADJOURNED
Minutes manually created (not a transcript), formatted by scribe.perl version 210 (Wed Jan 11 19:21:32 2023 UTC).
Adeel Ansari, Avanti Paturkar, Daniel Stone, David Booth, EricP, Jim Balhoff
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
ShEx for FHIR RDF
adeel: Want to use python for shex validation of FHIR.
eric: Doesn't yet have the ExTEND stuf, though it is in the works … It is needed for the latest FHIR RDF stuff. … Typescript/JS library handles it though. That would be the best starting point at the moment.
adeel: If we add attributes from other ontologies, would it throw an error?
eric: As written yes, it is all closed shapes. It's geared toward interchange, such as into HAPI. … But if your use case is shex plus some stuff, I might be able to put a switch in the ShexJS implementation to ignore the closed-ness of shapes.
Updating Harold's tutorial on SNOMED with FHIR RDF
daniel: Found the latest files.
dbooth: First step is to update the github materials … Suggest forking R4 to make R5.
avanti: I might be able to help on this also
jim: I can also help on OWL pieces.
HAPI
eric: Still working on shex for jena, which is needed for it.
Validation parser for FHIR RDF
eric: Wait until after I have the HAPI stuff done, then ask Grahame if the other code is still useful.
SNOMED / FHIR RDF tutorial (more)
daniel: looking at some of the new examples, not sure if it is correct.
jim: R4 example has root node that is IRI, but in R5 it's a blank node. Should look into it.
eric: I think the R5 behavior is correct. Guessing that Grahame was appending the id to the resource source.
eric: Still working on the jena shex for it. No ETA yet. Need to get semantic actions back in. Very fast validation now, but harder to figure out how it knows what to execute a semantic action. Also need to add extends support, needed for FHIR shex.
Questions from U Michigan
allen: Avanti starting to look at FHIR RDF Playground work
allen: Working with 3 kinds of data. We were working w the FHIR ServiceRequest, but also interested in Prov ont. … Want to take inputs, compute a resutlt and log that result as a FHIR object. … Adeel is building a pipeline for it, producing FHIR as output. … We'll be producing a JSON-LD @context object. want to make endpoint URLs in our results that point directly to where terms are defined. … Therefore we need several URIs in our @context. … How should we deal with this?
dbooth: Why are you using JSON-LD?
allen: JSON-LD data objects are loaded
dbooth: how are the JSON-LD objects being created by your functions?
eric: Sounds like you are trying to do JSON?
allen: Trying to do both JSON and JSON-LD. … Python write statements are used to generate the JSON-LD.
eric: When you try to make JSON-LD represent arbitrary RDF, then you have @graph at the root and a bunch of triples, and it would not be friendly to JSON users. … But it sounds like you want something appealing to JSON users.
allen: yes.
eric: Perfectly reasonable to write everything out in JSON-LD. You'll have to decide how to reference things. JSON-LD works well for tree, but when you reference something in a non-tree structure, you'll need full URI for it. … I'd expect to have extra prefixes in the @context, or full URLs in the data. … But if you're pointing to HTML, and look at the ServiceRequest page and look at Turtle examples... … How is fhir:SRD: being used in your URLs?
allen: In the data model for the provenance (our second question), in the Prov spec https://build.fhir.org/provenance.html … We've looked at ProvO, and want to bring in Activity, Entity and Agent. Trying to declare entities assoc w the computational processs we're doing.
eric: The FHIR model has entities have a role and an agent attribute, as well as a "what" attribute.
allen: ProvO target is the thing that the provenance is for or about. We're trying to figure out the target entity.
allen: When we use RDF for health data, we were directly using ProvO -- not FHIR Provenance. If there's already an established RDF vocab, would we expect it to inform FHIR resources? Or would we expect FHIR to point to ProvO?
eric: You'll face pain either way. … If you follow ProvO, ProvO people will understand it, but you won't be able to automatically dump it into FHIR. … If you go the other way, you need to map the FHIR idioms onto ProvO.
allen: So we'll need to map to/from FHIR.
dbooth: I think that's inescapable.
allen: once we produce these JSON-LD resource and put them into bluebrain, we want to do sparql queries on them, so might not need to go into FHIR.
eric: And need to look down the road to ask "will we want to dump the data as FHIR"?
dbooth: important arch question to consider: what do you want your native data representation to be? FHIR or general RDF?
allen: We're taking FHIR resources, unpacking them, using them as input parameters to a function, produces a computed result. Wondering: what if it were FHIR all around?
eric: if you want FHIR all around, you might want to work natively in FHIR. … Wondering why you were considering doing it all in FHIR?
allen: Our stakeholders are building FHIR expertise. Wondering about leveraging that. … The center does treatment, but also research.
dbooth: Should consider what kinds of questions you want to ask of the data, and how you want to ask them.
allen: We can look at some of the questions they've previously asked.
dbooth: What other data or ont do you want to pull into the mix?
allen: ProvO and function ont. … Want a flexible way to add functions.
dbooth: Should look at what clinically relevant data or ont you might want to add.
allen: Comparative effectiveness.
eric: Guessing that the Prov stuff will be important to researchers, in terms of FHIR provenance.
allen: Version is important.
dbooth: If you only care about FHIR data, then you might as well stay in the FHIR world. But if you want clinically relevant data or ont from other sources, that changes the calculus of whether to use general RDF.
ADJOURNED
Minutes manually created (not a transcript), formatted by scribe.perl version 210 (Wed Jan 11 19:21:32 2023 UTC).
Diagnostics
Succeeded: i/Working with 3/https://lists.w3.org/Archives/Public/public-semweb-lifesci/2023May/0005.html
David Booth, EricP, Gaurav Vaidya, James Champion, Shahim Essaid
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
Intros
shahim: U of Colorado, working w Melissa Haendel. Been working w FHIR for 3 years. Also working on brining terminology into FHIR, and OWL ontologies.
HAPI
eric: Now adding extends support to jena shex. Code was migrated to use a better valdation algo. … Going to the DBCLS bio hackathon in japan end of June / beginning of July. … That will be to add SPARQL support to FHIR, with Claude Nanjo.
Concept IRIs
gaurav: one proposal is now "queued for next impl". The other one is now "sent for impl" … One other UTG proposal 377< proposal to add IRI stems to MESH. Not sure if we should submit this next. Or should we go through UTG to determine how many are needed?
eric: Doing a few should help give us momentum.
dbooth: If MeSH doesn't define IRI stem, ask them for it.
dbooth: Worth scoping what others will be needed.
gaurav: Should wait for LOINC to be complete before doing MESH.
David Booth, EricP, Gaurav Vaidya, Jim Balhoff, Shahim Assaid
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
HAPI
eric: Still working on jena shex. Got "extends" working. Yobka's working on semantics for "extends". After that we'll be able to validate all of deepak's shex against the FHIR examples. … Claude also make progress on shexJ. … Got travel plans for Japan, where CLaude and I wll work on adding SPARQL support to HAPI.
dbooth: Any coordination needed w larger FHIR group, about API?
eric: THere's a DB way to ask FHIRpath querie. … If we can compile SPARQL queries into FHIRpath objects, then we'll be able to talk to whatever.
gaurav: Wrote a scala program that looks at repo that lists all code systems and naming sytems, so we can figure out what needs IRI stems. … There's a whole bunch of things inthe UTG repo that are solely intended for use in FHIR. They can mint their own IRI stems. These are hl7 code systems, even if they're from other orgs. We can mint IRI stems for those. The bigger thing is external code systems -- outside of FHIR. We'll need to work with those orgs on those.
eric: How much should we emphasize that those are resolvable? Should we wait for them to be resolvable before making them official?
gaurav: After we identify code sys / naming sys w IRI stems, we'll be making UTG proposals to put them in. And we should prioritize the ones that are resolvable or on wikidata.
eric: Should decide how much to push them for stable resolvable URLs.
dbooth: Would be interesting to know what is the rate of increase of terminologies on terminology.hl7.org
ADJOURNED
Minutes manually created (not a transcript), formatted by scribe.perl version 210 (Wed Jan 11 19:21:32 2023 UTC).
Allen Flynn, David Booth, EricP, Gaurav Vaidya, Max Burton
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
Introductions
max: From Medtronic, building interactions w FHIR and EHRs. Investigating using RDF for representing our data. Primarliy work on arch. Saw the video w Harold on uing JSON-LD into RDF.
dbooth: Still plannig to use JSON-LD?
max: Yes, using the framing apect of JSON-LD -- framing service for JSON data. … RDF comes into the backend side for transferring.
eric: Is your framing target isomorphic to the graph structure.
max: IDK yet.
eric: JSON-LD does not invent nodes.
Concept IRIs
gaurav: No progress since last week. … Still wrinting a prog to pull all the code sys and naming sys from the repo.
HAPI
eric: Resurrected the HAPI server. Still focused on jena shex. Also working w Deepak on validating the examples against the shex. … There's a bug in Jim's generated RDF. For codings, the datatype is a fhir:code, and the XML of that is an xsd:token, but they were represented as xsd:strings, so they were rejected in the validation. … But since it was only codes, deepak hand edited the schema for code to allow either string or xsd:token.
OWL to FHIR transformers
gaurav: THere were some old ones aehrc/fhir-owl , and there is now some discussion in zulip on a new effort. … Foundational model of anatomy
#narrow/stream/179202-terminology/topic/AMA.2C.20HL7.20Partner.20on.20FHIR.20CPT.20Integration.20to.20Drive.20Interop … It sounds like AMA agreed to let CPT to be shared in FHIR.
eric: Only as a code system, or also logical models?
gaurav: Code sys. … FMA is not going to terminology.hl7.org. Someone just wanted to use it. … I think as a code system. … I think that's what the OWL-to-FHIR tools do.
eric: As giant valuesets?
gaurav: The new tool was demoed, and it turned it into a massive code set -- one term every every term in the ont. … They were working on HPO ont.
eric: The OBO Foundry has formal rules about modeling things. FMA is Foundational Model of Anatomy -- about what is a part of what. … CPT is from AMA. … There was a press release saying that AMA is partnering w HL7.
gaurav: They're also looking at how they can put the terminology into terminology.hl7.org, but might have a licensing issue.
eric: what use cases?
gaurav: If the terms exist in HTO then presumably they could validate
FHIR ShEx
eric: it has about 1500-2k shapes, and you need a dedicated shape for every list, because it needs to be able to point to itself, so it needs a label. … Is there willpower and energy to add templates to ShEx to allow you, instead of creating ListOfX, to say you have a llist template w parameter X. … Purpose would be to get that done before finishing shex "extends", to get it into the IEEE standard.
dbooth: Like a macro expansion?
eric: That's one of the big questions. Could be a syntax trick. Or it could be built into the semantics of the language, and gives more power and allows round tripping. … To do it right would require someone think hard about it.
dbooth: Sounds worthwhile.
ADJOURNED
Minutes manually created (not a transcript), formatted by scribe.perl version 210 (Wed Jan 11 19:21:32 2023 UTC).
gaurav: Also looking at coding system, to find IRI stems for all of them. Found the publisher field. We cannot always ignore HL7 publisher field, because sometimes they're referencing external vocabs. … But good for most. … If I filter out everything that's a draft or retired, that leaves 755 code systems and 424 naming systems.
gaurav: next step may be 1. figure out the number of systems needing IRI stems. That will scope the work. … Another option: 2. Make larger and large change requests for adding the IRI stems. … From that approach, maybe we should come up with a short list of the ones most needing IRI stems.
dbooth: Sounds like a good start. … Maybe ramp up to 10-20 next
fhir:link missing from MedicationStatement.subject #121
eric: The problem is that the root node is a blank node, so it doesn't have a base URL for creating the subject URL.
eric: We could make them relative URLs, so wherever people put them, they'll work. … Or we could use example.org
eric: If we use relative URL, for a patient, it will become "../Patient/123"
dbooth: example.org seems like a less risky approach.
eric: Examples are not set up to be an imitation FHIR server, because they're all in the same dir. … But we could put them into their own directories -- 190 directories.
eric: The XML and JSON examples could also be set up that way.
dbooth: Seems like it's worth raising an issue with FHIR in general.
ACTION: DBooth to ask on zoom about putting the examples in subdirectories
dbooth: Should solicit more community input before going with option 1. … or 2
eric: If I get a bundle, that link is useful. … One of the observations in the bundle may have an abs url, and another in the bundle may have only a fragment. I want to know if they point to the same thing.
dbooth: Need to first find out if the vertical bar can appear after the hash. That will determine whther it is always an IRI.
ACTION: eric to look for a canonical with a vertical bar and frag ID
ACTION: eric to ask on zulip about hash and vertical bar in a canonical
dbooth: In this example http://build.fhir.org/rdf.html#2.1.6.6.2 , in the fhir:Quantity … Should `fhir:value [ fhir:v "185"^^xsd:decimal ];` also have a type arc, even though this is not a value[x] property?
allen: For a fhir:Quantity, the fhir:value subproperty MUST be type decimal, so an additional type arc is not needed.
allen: If we add a type arc to that, we might need to look at what else might be similar.
AGREED: Leave that one as is.
Playground RDF validation
houcemeddine: Could work on it if it's simple.
ShEx Validation
allen: Was excited to see Deepak's validation work. … Interested in early testers. … Want to show some of our work. Interested in 3 types of FHIR RDF resources: library, provenance, Observation. … Library is more like code library. … Provenance is modeled after W3C PROVO ont, but now there's a resource in the FHIR space. … Going with the FHIR provenance resource. … There are several projects on FHIRCat github. Started w Deepak's Shex validation repo. … Cloned the repo and tried to run it on a mac.
dbooth: The proposed change (moving the fhir:link insitde fhir:reference) would break existing code
eric: fhir:reference is allowed to be version specific
dbooth: Does that make it not be a URI/IRI?
dbooth: I think we need to ask the zulip crowd whether pipe (when a version is in the fhir:reference) is to be percent encooded and used in the URL … And a secondary question is whether the JSON and XML represenations percent-encode the pipe.
ACTION: DBooth to ask on zulip about including a version in a fhir:reference
dbooth: For a fhir:canonical, the json is a URI + | + version, but if it is sent in a GET request, the vertical bar must be percent encoded. … So the example in the FHIR spec is wrong, and I'll file aa jira ticket to correct it.
eric: So when we generate a fhir:link in FHIR RDF, we need to percent encode it. DBooth: Right.
dbooth: how do we want to convert one of these fhir:reference strings to an RDF node? … And that string is syntactically a URI
eric: But its meaning is different, because it uses a different base. We need to prepend "../" to the relative URI. … and if it's just a frag ID, then it'relative to the current base (not "../")
jim: Writing a script to load an FHIR XML example and output FHIR RDF. But to run them I need a worker context.
dbooth: Try asking on zulip?
jim: away on vac next week.
U Mich work
allen: Got ShEx.js working over the weekend. … Making some progress. Goal is to validate certain FHIR RDF resources at will. Now that we have the test running, both on Mac and PC, trying to be able to run it at will.
dbooth: Looks like EricP is not able to join today. We need him to continue on the outstanding issues, so we'll adjourn and try to continue next week.
ADJOURNED
Minutes manually created (not a transcript), formatted by scribe.perl version 210 (Wed Jan 11 19:21:32 2023 UTC).
eric: Do those show up in the examples? Want to have the generator add the stems to the examples.
dbooth: Would be nice to have them pulled automatically from the terminology website.
gaurav: Candidates radlex, human phenotype ont, mondo disease ontology. … We still have MeSH pending. … Will also look in to dicom and some others. … Might run into issues of prefixes like hp_ , it won't work with codes starting hp: . … (Issue raised by Melissa Haendel's group) … Should get back in touch with them to determine their current position.
ACTION: Gaurav to write an issue for this
ACTION: Gaurav to ask Melissa Haendel's group about underscore prefixes
Guoqian Jiang's passing
gaurav: Emily is reaching out to Bob Freimuth to coordinate … Expect an update next friday.
eric: I sent Bob a status. Haven't heard back yet. Also not sure yet whther Claude and I have funding for an AMIA tutorial. … Tutorial is Aim 2 stuff.
ShEx FHIR validation
allen: We're in midstream. Hoping to show next week.
David Booth, Gaurav Vaidya, Jim Balhoff, Rob Hausam
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
Concept IRIs
gaurav: Had proposals accepted. Everything looking good. Three minor corrections needed. For namingSystem we used a type of Other. NOw need to change it to IRIStem.
w3c/hcls-fhir-rdf#132 … Also, in one place we have a reference to build.fhir.org/... . Needs to be updated. … Will do tickets for them. … Also we prposed IRIs for naming system, but it's linked to another ticket that is still queued.
Allen Flynn, David Booth, EricP, Gaurav Vaidya, Rob Hausam, Tim Prudhomme
Regrets
-
Chair
-
Scribe
dbooth
Meeting minutes
Intros
Allen: U Michigan. Project started joining these meetings. Working on project here with Toreoto center for mental health. Deployed a triple store, using FIHR and RDF. … Worked on ShEx this summer, validating new FHIR resources.
tim: Indep software consultant. Workd on opthalmology stds, NL7 dicom. Past 3 years working w ont, OWL, RDF. … Used some FHIR RDF to create prototype healthcare app. Exciting because it gives me the whole core structure of the app. Validate w shex.
gaurav: U of NC. Working on FHIR RDF tooling. Currently working on Concept IRI, converting FHIR codes to IRIs used in RDF.
Concept IRIs.
gaurav: No update.
U Michigan shex validation
allen: Avanti worked on this. … Got a shex validator working.
(showed a simple example)
allen: Next week we'll have another session with Deepak at Mayo.
gaurav: Could look to see if there are any curies in examples.
eric: I thnk breaking this will not break anything in the world. … I.e., in favor of option 1.
gaurav: People like curies. Might not want only the code. Also, you can strip the code out, but you cannot jjust concatenate after that, because it's mondo_ (with underscore).
David Booth, EricP, Jim Balhoff, Rob Hausam, Tim Prudhomme
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
FHIR build
jim: Mostly getting the FHIR build working. … It validates examples, and some of them fail. I would have expected them to be fixed before merging. … So far, it's just been extra spaces. … Goal was to get a script to convert a single XML file to RDF. … But it requires setting up some context. Trying to figure out how to do that. … Trying to replicate a test from the FHIR build. This is the org.h77.fire core. … Not HAPI FHIR
eric: After converting, it would be good to do a shex validation, which would require jena.
w5 ontology version IRI is stored as a string #131
jim: Looks like an easy fix.
eric: The w5 bindings are in the resource definitions, along side of SNOMEd and othe rbindings.
Intros
tim: Working on prototype helathcare app using FHIR RDF. Background on opthomology.
jim: Core generates the examples. Kindling generates the ontologies. … But there's another code base that generates turtle from FHIR. When it's done I'd rather use that one, becaues it uses jena.
eric: It's probably working, if you want to use it. It's in a clone. I haven't done release engineering on it yet.
eric: New examples are in XML.
jim: The execution happens in another repo called FHIR.
jim: Whole site build takes about 20 minutes. Trying to make a script to generate a single example from XML.
Update the SPARQL scripts to add the OWL ontology declarations #126
Allen Flynn, David Booth, EricP, Houcemeddine Turki, Jim Balhoff, Rob Hausam, Tim Prudhomme
Regrets
-
Chair
David Booth
Scribe
dbooth
Meeting minutes
Transforming FHIR examples to FHIR RDF
jim: Made a little progress. Dounloaded an npm package and made an object from it. But different FHIR types have versions in them. Version doesn't match. Trying to figure out how to instantiate them from the code base.
eric: FHIR pkg is resources or code?
jim: I think it's resources.
Add a link to our HL7 page from this repo's front page or README #105