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15:05:00 <trackbot> RRSAgent, make logs world
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15:05:02 <trackbot> Zakim, this will be HCLS
15:05:02 <Zakim> ok, trackbot
15:05:03 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
15:05:03 <trackbot> Date: 05 April 2016
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15:05:23 <dbooth> Present: David Booth, Lloyd McKenzie
15:06:11 <dbooth> Present+ Harold Solbrig
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15:07:28 <dbooth> Present+ Harold Solbrig
15:08:03 <dbooth> Agenda: http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda
15:10:35 <dbooth> Topic: Planning for May HL7 meeting in Montreal
15:10:38 <Tony> Tony has joined #HCLS
15:11:38 <dbooth> dbooth: Scheduled Tue Q2 in ITS group
15:11:50 <dbooth> http://www.hl7.org/events/wgm052016/
15:12:54 <dbooth> dbooth: Ken Lord, MDMI specialist, wants to present his work in order to align with RDF work.
15:13:19 <dbooth> tony: MDMI is an alternative to ShEx and XSLT
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15:14:45 <dbooth> dbooth: Ken and I have drafted 4 use cases.  We're organizing something about mapping for Montreal.
15:16:03 <dbooth> ... It would be good to encourage synergy.
15:16:49 <dbooth> lloyd: There's a new FHIR resource being defined to do what MDMI does, but not MDMI.  They evaluated MDMI and decided that somethign FHIR specific would be better.
15:16:54 <Marc_Twagirumukiza> Marc_Twagirumukiza has joined #hcls
15:17:16 <dbooth> ... If you look at StructureMap in the spec you'll see.
15:17:43 <dbooth> dbooth: Anything scheduled on it?
15:17:53 <dbooth> lloyd: Nothing official.  Don't know about BOF.
15:19:10 <dbooth> tony: Why FHIR specific?
15:20:36 <dbooth> tony: Maybe Ken could present the rationale for being FHIR specific.
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15:20:57 <dbooth> dbooth: Who will be in Montreal?
15:21:41 <dbooth> lloyd: Trying to get Grahame to come.  I won't be at the ITS section.
15:21:58 <dbooth> harold: Will do my best to be there.
15:22:08 <dbooth> tony: I won't be there.
15:22:45 <dbooth> rob: I'll be there.  Will bring teleconference gear.
15:23:52 <dbooth> dbooth: Status update, and review work products.
15:23:58 <Marc_Twagirumukiza> I will try to follow the TCon (thanks to Rob for organizing)
15:24:07 <dbooth> tony: And timelines.  DSTU3 in summer?
15:24:39 <dbooth> lloyd: Voting will be in Aug; reconciliation in Sept.
15:25:25 <dbooth> ... Deadline mid-July.
15:25:37 <dbooth> ... Question about whether we'll be able to call it DSTU.
15:25:47 <dbooth> tony: Still have some pieces we have not yet explored.
15:27:14 <dbooth> dbooth: RDF meeting in Montreal Will be 11-12:30 Tuesday.
15:27:33 <dbooth> sajjad: Would be good to send date/time in email.
15:28:44 <dbooth> Topic: Grahame's updates on hl7 github
15:28:46 <dbooth> https://hl7-fhir.github.io/allergyintolerance-example.ttl.html
15:29:52 <dbooth> dbooth: It uses fhir:nodeRole fhir:treeRoot; to indicate the root node.
15:30:03 <dbooth> tony: Looks close to what we discussed.
15:32:35 <dbooth> dbooth: Not sure that we've fully closed the question of what the root element URI should be or whether it should be a URI.
15:32:44 <dbooth> https://github.com/w3c/hcls-fhir-rdf/issues/18
15:33:06 <dbooth> tony: We could say http://example.org/ as the base URI
15:34:08 <dbooth> https://github.com/w3c/hcls-fhir-rdf/issues/3
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15:35:44 <dbooth> dbooth: resource may not have a URI if it is being submitted.
15:37:06 <dbooth> harold: example.org should also be in the references
15:39:13 <dbooth> tony: It's in the FHIR spec
15:39:16 <dbooth> https://hl7-fhir.github.io/http.html
15:39:29 <dbooth> dbooth: I see:   VERB [base]/[type]/[id] {?_format=[mime-type]}
15:40:06 <dbooth> dbooth: I'll close issue 3 then  :)
15:40:16 <dbooth> rrsagent, where am i?
15:40:16 <RRSAgent> See http://www.w3.org/2016/04/05-hcls-irc#T15-40-16
15:41:09 <dbooth> Topic: Draft rdf.html page on github
15:41:11 <dbooth> http://w3c.github.io/hcls-fhir-rdf/spec/rdf.html
15:41:36 <dbooth> eric: Changed to use the same source as hl7 github page.  That will make it easier to push changes.
15:44:05 <dbooth> eric: If we focus on the RDF for resources (not structures or valuesets) then we may be able to meet the July deadline.
15:45:07 <dbooth> ... One view is that we can translate resources like Observations, giving a  default mapping and exceptions.
15:45:21 <dbooth> ... Should we document that mapping or just hand it to people?
15:45:42 <dbooth> ... We'd like to be able to map an arbitrary resource with confidence.
15:46:07 <dbooth> tony: I'm worried about the number of resources we need to get into OWL.
15:46:28 <dbooth> eric: The code generates a lot of the OWL.  What else do we need to add to get more value added from the RDF?
15:47:42 <dbooth> tony: maybe we could do manual transformation for valuesets and structure defs.
15:47:57 <dbooth> ... Transformation from VS def in FHIR to the way it is expressed in OWL.
15:48:38 <dbooth> lloyd: We will add to the build process a generation that takes every VS and every structure def and output the OWL for them.
15:49:28 <dbooth> tony: Need to define what we want it to be.
15:50:18 <dbooth> dbooth: I think of the ont page as being for users of the ont, to tell them how to use it.
15:50:35 <dbooth> ... But it could also explain how the ont is generated.
15:50:43 <dbooth> lloyd: that should be in a secondary page.
15:51:16 <dbooth> eric: Harold, Josh and I are writing a JAMIA paper that explains we generated OWL.
15:51:55 <dbooth> ... FHIR does not publish how you map from a structure def to the XML schema.
15:52:24 <dbooth> dbooth: FHIR defines that mapping by example
15:54:08 <dbooth> eric: If people want to help on the JAMIA paper they're invited.  That paper might describe what tony wants -- defining the OWL corresponding to the structure def.
15:55:41 <dbooth> dbooth: Could we use the JAMIA paper as a starting point for a page that describes how the FHIR structure def is mapped to OWL?
15:55:45 <dbooth> eric: Yes
16:01:22 <dbooth> dbooth: Best path forward?  Look at examples and state the general rule?
16:04:14 <dbooth> dbooth: Maybe we should get Grahame to start generating some of the OWL, to see how it looks
16:04:44 <dbooth> ... Michael van der Zel also volunteered to generate the OWL
16:05:56 <dbooth> dbooth: Propose starting with AllergyIntolerance, since we have Tony's example of that
16:06:41 <dbooth> Topic: 5pm Call
16:06:46 <dbooth> Tony: cannot make it
16:07:08 <dbooth> can make it: eric, harold, rob
16:40:19 <dbooth> dbooth: I can also make the 5pm call.
16:40:24 <dbooth> ADJOURNED
16:42:22 <dbooth> rrsagent, draft minutes
16:42:22 <RRSAgent> I have made the request to generate http://www.w3.org/2016/04/05-hcls-minutes.html dbooth
16:42:48 <dbooth> Chair: David Booth
16:43:17 <dbooth> Present+ Marc T, Rob Hausam, Sajjad Hussain, Thomas Lukasik, Tony Mallia
16:46:18 <dbooth> RESOLVED: Close issue 3 as discussed at http://www.w3.org/2016/04/05-hcls-irc#T15-40-16
16:46:27 <dbooth> rrsagent, draft minutes
16:46:27 <RRSAgent> I have made the request to generate http://www.w3.org/2016/04/05-hcls-minutes.html dbooth
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19:20:17 <ericP> q+
19:20:45 <ericP> q+ to propose a map from what-it-does to spec
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21:04:02 <dbooth> trackbot, start meeting
21:04:04 <trackbot> RRSAgent, make logs world
21:04:04 <Zakim> Zakim has joined #hcls
21:04:06 <trackbot> Zakim, this will be HCLS
21:04:06 <Zakim> ok, trackbot
21:04:07 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
21:04:07 <trackbot> Date: 05 April 2016
21:04:38 <dbooth> Topic: =========== 5pm Teleconference =============
21:05:09 <hsolbrig> hsolbrig has joined #hcls
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21:05:21 <hsolbrig> Hi folks.  Lost track of time - just joining in
21:07:04 <hsolbrig> That said, the meeting number doesn't seem to work
21:07:22 <dbooth> [[
21:07:23 <dbooth> Tuesdays, 5:00pm Eastern US (Boston) time zone
21:07:23 <dbooth> Webex: https://mit.webex.com/mit/j.php?MTID=m5cd1bd8bb36825b9c4b369fd664bbb62
21:07:23 <dbooth>     Teleconference: +1-617-324-0000 Access code: 645 777 110
21:07:23 <dbooth>     Meeting password: 4257 ("HCLS")
21:07:25 <dbooth> IRC: irc.w3.org port 6665 channel #hcls
21:07:27 <dbooth> ]]
21:07:41 <hsolbrig> ah. I used 644 184 695
21:11:27 <dbooth> Topic: ValueSet server?
21:11:40 <dbooth> harold: Looking for a VS server for testing.
21:12:02 <dbooth> lloyd: Ping grahame.
21:12:35 <dbooth> Topic: schema.org
21:12:51 <dbooth> harold: Trying fhir:Observation in schema.org
21:13:13 <dbooth> ... Not sure of the value.  Original focus was shopping, using semantic markup of html.
21:15:08 <dbooth> dbooth: Discussion of schema.org in the FHIR group?
21:15:20 <dbooth> lloyd: A long time ago.  Don't remember where we landed.
21:16:23 <dbooth> harold: schema.org is branching out from primary application (html).  For stuff that got generated, you could use RDF markup for provenance.
21:16:53 <dbooth> ... But the more interested case would be moving unstructured or semi-structured data into FHIR -- blog or device data.
21:17:44 <dbooth> ... Promised the folks at biocaddie.org to try generating a schema.org extension.
21:18:10 <dbooth> ... You can tie the extensions into the schema.org core, but because it is so focused, I think we'd want to be cautious on doing that.
21:18:29 <dbooth> ... We're doing our own.  Classes, properties, etc.
21:18:43 <dbooth> ... They have lots of nice tools for generating documentation.
21:19:00 <dbooth> ... What we want to put into schema.org is coarser than what we want in FHIR.
21:19:27 <dbooth> ... Or breaking datatypes into components does not seem worthwhile for marking up HTML.
21:19:57 <dbooth> ... In contrast with what we're doing with RDF, we want to expose a subset of the differentials.
21:20:38 <dbooth> ... SpecificObservation specializes Observation . . . I only want to specify the differential.
21:21:24 <dbooth> ... But i'm finding in looking at some of the specialized Observations that, even though Grahame did not change the types, they were still being included in the differential.
21:21:39 <dbooth> lloyd: Instance data or profiles?
21:22:55 <dbooth> harold: VitalSigns profile specializes Observation profile.  In some of the bits in the differential section, they have types that are the same as in the Observation profile.
21:23:01 <dbooth> ... In the JSON
21:25:12 <dbooth> lloyd: Looking at the differential section
21:25:53 <dbooth> harold: I think the intent is the change the cardinality and fix code, but the type is there too.
21:26:17 <dbooth> lloyd: It's broken.  It's not slicing, but I would expect it to be slicing by system.
21:26:46 <dbooth> ... Please submit a change request.
21:28:11 <dbooth> Topic: Fhir modifying extensions and monotonicity
21:28:21 <dbooth> https://github.com/w3c/hcls-fhir-rdf/issues/9
21:28:39 <dbooth> https://www.w3.org/2014/12/02-hcls-minutes.html#item03
21:31:22 <dbooth> dbooth: I think we need to have the RDF express what the FHIR says, and before doing inference you need to do another step to check for unknown modifier extensions, and not try to inference over those sections.
21:31:37 <dbooth> lloyd: You need to first filter out unknown mod ext.
21:31:53 <dbooth> ... But how do you make the ones that you do recognize work in the ont?
21:32:17 <dbooth> ... You'll need to override some of the triples.
21:32:58 <dbooth> ... My leaning for the first release is to say that reasoning in the presence of known or unknown mod ext is challenging, and guidance will be provide when we get more experience.  i.e., punt.  :)
21:33:27 <dbooth> ... I'd like to try tackling from a real world perspective.  My guess is that there will be a few patterns that show up.
21:33:38 <dbooth> ... Maybe make recs once we learn.
21:34:28 <dbooth> dbooth: Don't want this to hold up getting a first release.
21:34:51 <dbooth> ... This means including the modifier extension statements in the FHIR RDF, and leave them up to the user.
21:35:06 <dbooth> lloyd: Should say that you cannot safely reason in the presence of mod exts.
21:36:40 <dbooth> dbooth: sounds good to me.  I don't think we can do more at this point.  it would mostly affect the descriptive pages rdf.html and ontology.html
21:37:30 <dbooth> RESOLVED: Include caveat about mod exts saying that you cannot safely reason in the presence of them.
21:37:49 <dbooth> rrsagent, where am i?
21:37:49 <RRSAgent> See http://www.w3.org/2016/04/05-hcls-irc#T21-37-49
21:38:45 <dbooth> Topic: If we treat observation.code as an instance of a class, should that class represent the disease itself or a *description* of the disease?
21:38:51 <dbooth> https://github.com/w3c/hcls-fhir-rdf/issues/11
21:39:06 <dbooth> https://www.w3.org/2015/04/22-hcls-minutes.html#item02
21:40:45 <dbooth> lloyd: Leaning to say it's not the code, it's a profile.  Because you'll need to take into account other things, such as status=refuted, rule-out status, entered-in-error, etc.
21:41:18 <dbooth> ... Class would be better handled in the profiling space.
21:41:46 <dbooth> harold: In the instance space, do we say that this is an instance of appendicitis.
21:42:31 <dbooth> ... OWL inferred that people had integers, and Jane cannot be both a person and a record describing something.
21:42:58 <dbooth> ... You'd be saying that a data record is really an instance of appendicitis, and that won't work.
21:43:14 <dbooth> ... Wouldn't hurt to have an rdf:about in the profile space, but it may be redundant.
21:43:50 <dbooth> ... It's a portion of the record.
21:44:12 <dbooth> dbooth: what would this affect?  what would we do differently if the answer were one thing vs another?
21:44:48 <dbooth> ... i.e., do we really need to solve this, or can we leave it to others?
21:47:34 <dbooth> ... Seems to me that this question shows up when you try to connect FHIR data to other ontologies like OBO that deal with real world entities.
21:47:56 <dbooth> ... But FHIR deals with records.
21:48:06 <dbooth> dbooth: What should we say?
21:48:38 <dbooth> lloyd: Say that we are representing records, and reasoners that want to reason about facts then additional logic may be need to extract the info that they need.
21:49:29 <dbooth> dbooth:  Would be nice to show an example of how it can be done.
21:49:43 <dbooth> rob: Same question applies to the SNOMED CT ontology.
21:50:09 <dbooth> dbooth: Maybe a better example would be to show connection to OBO.
21:51:02 <hsolbrig> oops - hit hang up rather than mute...
21:51:25 <dbooth> harold: Include tony's examples?
21:51:34 <dbooth> lloyd: On a time-available basis.
21:53:21 <dbooth> RESOLVED: Say that FHIR RDF is representing records, and reasoners that want to reason about facts may need to use additional logicto extract the info that they need.
21:53:41 <dbooth> RESOLVED: Include tony's bee sting inference examples as time permits
21:53:52 <dbooth> rrsagent, where am i?
21:53:52 <RRSAgent> See http://www.w3.org/2016/04/05-hcls-irc#T21-53-52
21:55:28 <dbooth> Topic: Should fhir:reference.reference->value be a string or an RDF URI node?
21:55:33 <dbooth> https://github.com/w3c/hcls-fhir-rdf/issues/16
21:55:50 <dbooth> lloyd: Should treat all URIs the same, not only Reference.reference
21:56:48 <dbooth> ... We cannot use the URI type, because we are not doing things in a pure URI way.  Relative references are not evaluated in a standard RFC 3986 way.
21:57:24 <dbooth> ... Rel ref is resolved according the URL of the resource containing the ref -- not the node that the ref is on.
21:57:58 <dbooth> ... Also when we have a local ref (hash) pointing to an ID, that is not resolved across the entire instance, it is only within the containing resource.
21:58:27 <dbooth> ... So we're better off treating them as strings in RDF.
21:59:53 <dbooth> dbooth: RDF itself has no relative referenced.  All URIs are absolute in RDF.
22:00:54 <dbooth> ... So it would be possible, but messy to capture them, because for round tripping we would also need a way to be able to turn them back into relative URIs.
22:01:23 <dbooth> harold: Making them strings would concern me, because URIs are so fundamental to RDF and LInked Data.
22:01:40 <dbooth> ... Could we deal with the funky FHIR rules and make it work?
22:01:56 <dbooth> lloyd: No way to make it work.
22:02:26 <dbooth> ... E.g., patient with a contained org, #1.   And a prescription with a contained med, also #1.
22:03:05 <dbooth> ... Then I query that causes them both to come back inside a bundle.  They are both digitally signed, so i cannot change the URIs.  No way to make the scoping document wide instead of resource wide.
22:03:56 <dbooth> lloyd: Fundamental problem is that XML always thinks about the document as immutable.  But we're generating documents and combining them.
22:04:38 <dbooth> dbooth: We'd be giving up value by not using URIs, because they're so fundamental to RDF.
22:05:15 <dbooth> lloyd: If we want to have a URI that points to something, we could have a property.
22:06:01 <dbooth> harold: It's not 'pointsTo' that matters, but the identity issue: is this the same as that, so that we can like the RDF together, regardless of whether it dereferences.
22:07:45 <dbooth> lloyd: May want an additional property that is the full URI of the reference.  Take the ref and if it's relative make it absolute.
22:08:12 <dbooth> dbooth: i.e., leave the relative URI but also have an absolute URI.
22:08:42 <dbooth> ... Sounds reasonable, but want to seen an example.
22:09:24 <dbooth> rrsagent, pointer?
22:09:24 <RRSAgent> See http://www.w3.org/2016/04/05-hcls-irc#T22-09-24
22:16:58 <dbooth> Present: 5pm call: David Booth, Harold Solbrig, Lloyd McKenzie, Rob Hausam
22:17:04 <dbooth> rrsagent, draft minutes
22:17:04 <RRSAgent> I have made the request to generate http://www.w3.org/2016/04/05-hcls-minutes.html dbooth