15:59:58 <RRSAgent> RRSAgent has joined #hcls
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16:00:00 <trackbot> RRSAgent, make logs world
16:00:00 <Zakim> Zakim has joined #hcls
16:00:02 <trackbot> Zakim, this will be HCLS
16:00:02 <Zakim> I do not see a conference matching that name scheduled within the next hour, trackbot
16:00:03 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
16:00:03 <trackbot> Date: 01 March 2016
16:00:05 <dbooth> Chair: David Booth
16:00:57 <dbooth> Agenda: http://wiki.hl7.org/index.php?title=ITS_RDF_ConCall_Agenda#DRAFT_Agenda_for_San_Antonio_Face-to-Face_Meetings
16:02:14 <Sajjad> Sajjad has joined #hcls
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16:05:59 <dbooth> Topic: FHIR RDF (Turtle) examples on HL7 github
16:06:00 <dbooth> https://hl7-fhir.github.io/allergyintolerance-example.ttl.html
16:12:47 <dbooth> Tony: _:example needs to be a named individual, because you cannot form reference to it.
16:13:39 <dbooth> eric: Could use inverse functional properties, but that's a pain and we would not be taking advantage of URIs.
16:14:20 <dbooth> lloyd: We can do that some of the times, but there are circumstances when resources will not have identifiers.  When you do a POST it has no identity.  The server gives you back a URI for it.
16:16:17 <dbooth> ACTION: Tony to try loading grahame's AllergyIntoloerance example (with _:example bnode root) in protege
16:16:17 <trackbot> Error finding 'Tony'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.
16:17:16 <dbooth> eric: should use the same root node in RDF as is used in FHIR XML or JSON
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16:28:23 <dbooth> lloyd: in fhir:AllergyIntolerance.substance grahame has added ' a sct:227493005;', but that's not always going to be on the wire.
16:29:48 <dbooth> ... grahame added it on some of the properties, but not all of them.
16:31:03 <dbooth> tony: the type code gets applied to AllergyIntolerance (type becomes Confirmed)
16:31:54 <dbooth> lloyd: sct:227493005 is a property of the AllergyIntolerance -- not a type of it.
16:32:29 <dbooth> ... Otherwise if there were both previousStatus and a different (current) status, they both of those types would be applied to AllergyIntolerance
16:32:45 <dbooth> ... Concept cannot exist independent of code
16:32:56 <dbooth> ... And VS is a set of codes that imply concepts.
16:33:55 <dbooth> tony: present and previous status, when applied to the concept structures, the concepts are distinct.
16:35:34 <dbooth> eric: elevating the type to the subject of the property does not work (e.g., currentlyConfirmed vs currentlySuspected).
16:36:11 <dbooth> ... But we could say that there's a set of properties, the concepts of which we can apply directly to the subjects.
16:36:37 <dbooth> ... Do you want to say that this house is a member of the class RedHouses or do you want to say that it has an attribute of red?
16:37:19 <dbooth> lloyd: The concept appears at two levels -- coding and codeableCOncept.
16:37:55 <dbooth> .. We started from everything being turned into a codeableConcept.  What grahame has said is that concepts appear at both levels, but I think that will cause us grief, but we'll see.
16:38:22 <dbooth> ... The binding ont from snomed to FHIR, it needs to know where to apply it.
16:38:38 <dbooth> tony: Yes, you really need to know the object property
16:39:19 <dbooth> lloyd: Can we come up with the ont that will enable that inference, that substance is an sct:227493005  and the coding is an sct:227493005 ?
16:39:50 <dbooth> tony: The big thing is the disjoint declarations that we had.  We'll have to take those out, because now we'll have codes that are also concepts.
16:43:13 <dbooth> dbooth:  The snomed types that grahame has added, such as ' a sct:227493005;', will not always be there, so we cannot count on it for round tripping.  It is misleading to have them there.
16:43:36 <dbooth> lloyd: Instances will not necessarily have these present, but if present they should be round tripped in the JSON or XML.
16:44:10 <dbooth> ... In many cases they will not be there.  But now they're present in order to test something, but should also appear everywhere.
16:44:22 <dbooth> ... Once we have completed our tests they can be dropped.
16:44:38 <dbooth> rob: How do deal with multiple codings?
16:45:00 <dbooth> lloyd: multiple concept assertions
16:45:31 <dbooth> harold: re everything having coding, at the moment we do not have a concept identifier for foo.  Is there a proposal for getting that in?
16:45:38 <dbooth> s/foo/food/
16:45:58 <dbooth> lloyd: What is the concept code for food?  We need one, but don't have one yet.
16:46:25 <dbooth> harold: Where is the equivalent of fhir:food (corresponding to snomed code)?
16:46:58 <dbooth> ... How does the target of the category rdf:type fhir:food get there?
16:47:31 <dbooth> lloyd: The transform happens based on ont knowledge, fixed value from a VS, implies food concept.
16:47:36 <dbooth> harold: Then why not for substance?
16:47:51 <dbooth> lloyd: For substance we don't have a fixed binding.
16:48:02 <dbooth> ... Substance could draw from 20 other code systems.
16:48:14 <dbooth> ... Also because it is not a fixed binding, it needs to draw from both.
16:49:18 <dbooth> lloyd: Right now we're asserting the concept for substance, but we need to (temporarily for testing) for status, criticality, etc. just like for substance.
16:50:42 <dbooth> let's get specific: https://docs.google.com/document/d/1XfktjntceKY4zDTmklkQTWuFbWC3tSY39Xh72Rl64hg/edit
16:55:36 <dbooth> changing fhir:AllergyIntolerance.status to:
16:55:37 <dbooth> [[
16:55:38 <dbooth>   fhir:AllergyIntolerance.status [
16:55:38 <dbooth>      a fhir:CodeSystem\/AllergyIntoleranceStatus\#confirmed ;
16:55:38 <dbooth>      fhir:value "confirmed"
16:55:38 <dbooth>   ];
16:55:39 <dbooth> ]]
17:04:00 <dbooth> Topic: 5pm call
17:04:06 <dbooth> We'll do one :)
17:10:55 <dbooth> Present: David Booth, EricP, Harold Solbrig, Lloyd McKenzie, Rob Hausam, Sajjad Hussain, Tony Mallia
17:11:01 <dbooth> rrsagent, draft minutes
17:11:01 <RRSAgent> I have made the request to generate http://www.w3.org/2016/03/01-hcls-minutes.html dbooth
19:53:16 <Zakim> Zakim has left #hcls
22:10:34 <dbooth> Topic: ============== 5pm Call ==================
22:12:34 <dbooth> Topic: Example FHIR RDF (Turtle)
22:14:28 <dbooth> lloyd: fhir:AllergyIntolerance.recorder is declared as a fhir:Reference .  Doesn't need to be declared.
22:17:32 <dbooth> lloyd: What about having the fhir:REference.reference include an actual URI of the thing that is referenced?
22:17:40 <dbooth> dbooth: Can it always have a URI?
22:18:15 <dbooth> lloyd: sort of.
22:18:26 <dbooth> dbooth: what about when you're POSTing and you have an internal reference?
22:18:42 <dbooth> lloyd: then it's relative to the server to which you're posting.
22:19:21 <dbooth> eric: An XML FHIR app will see a ref to Practitioner/example and take its own base URL and resolve that ref as ../Practitioner/example?
22:19:23 <dbooth> lloyd: Yes
22:19:38 <dbooth> ... it would prepend the base URL and go from there.
22:20:23 <dbooth> ... The tricky piece is that these are not true relative URLs.  there's some magic, but if you adhere to the magic it works.
22:20:34 <dbooth> eric: Can we emulate that magic on the RDF side?
22:21:03 <dbooth> dbooth: Will there *always* be a URI available?
22:21:34 <dbooth> lloyd: Will there always be a URI? yes.  Will it alwasy be available to the translation process?  IDK.  It would require that knowledge to be injected into the conversion process.
22:21:50 <dbooth> eric: Any XML tool traversing the ref would need the URI?
22:22:21 <dbooth> lloyd: Yes.  If you're doing a POST, and the recipient checks, it would look for baseUri/Patient/example to see if that exists.
22:22:49 <dbooth> ... The client is aware that the patient exists on the same server where the allergyIntolerance is being posted.
22:23:15 <dbooth> eric: So if we say that the translation process has the same burden, then we can do that, because JSON and XML will need to do that anyway?
22:23:49 <dbooth> lloyd: The info will be available to the systems, but not necessarily to the module doing the translation.  You may need to pass that info in through several layers.
22:24:04 <dbooth> ... From an ont perspective not having the link produces not useful data.
22:24:41 <dbooth> ... Without an expilcit ref to the patient, then finding the meds prescribed to the patient will be much more awkward for RDF types to write.
22:25:02 <dbooth> eric: You would have logic into the SPARQL: the logic of URI resolution.
22:25:44 <dbooth> ... If I say waht are all the med orders for this patient, it would have to figure out the ways to write down the ref to that patient.
22:26:46 <dbooth> lloyd: Instead of querying for meds for patient xyz, you have to query for a patient with a property with a string "xyz" OR . . . the various other ways of identifying the patient.
22:28:03 <dbooth> dbooth: Instead of using a URI for the patient, you would use one or more property paths?
22:28:15 <dbooth> lloyd: yes.
22:30:00 <dbooth> lloyd: the fhir:value of fhir:Reference.reference could be "Patient/example" or "http://example.org/fhir/Patient/example"
22:30:13 <dbooth> eric: Equivalence between http: and https: ?
22:30:28 <dbooth> lloyd: It was discussed, but don't know where it is document.
22:30:55 <dbooth> ... Yes, they refer to the same object.
22:32:08 <dbooth> ... But if you put a non-default port number on then it is different.
22:33:55 <dbooth> dbooth: Will there always be a URI
22:34:06 <dbooth> lloyd: There will always be a base, but not in the document.
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22:34:42 <dbooth> dbooth: If you're doing a POST, and you have not posted, you dont' know the base?
22:35:03 <dbooth> lloyd: if it's in memory and you haven't decided where to send it, then yes.
22:36:19 <dbooth> lloyd: The base URI does not exist inside the instance, but resources frequently know what their base is.
22:37:02 <dbooth> ... My inclination is to allow the URI to be optionally included in the instance.
22:37:40 <dbooth> Topic: Root URI
22:38:27 <dbooth> lloyd: Base URI will never appear inside the doc.
22:39:03 <dbooth> ... But if the doc lives on a server, then the server exposing that doc is aware of that base URI.
22:39:28 <dbooth> dbooth: And could sometimes include the URI in the doc?
22:40:12 <dbooth> lloyd: Could calculate absolute URIs for embedding in the doc.
22:40:25 <dbooth> ... My preference is to say that this is permitted but not required.
22:40:53 <dbooth> ... So transforms to RDF, XML or JSON could use an extension to keep that info if it's available.
22:41:32 <dbooth> dbooth: Trying to zero in on what we can ALWAYS count on.
22:42:20 <dbooth> lloyd: Cannot always count on an absolute URI in the doc.
22:42:45 <dbooth> dbooth: We need to figure out how to deal with that in RDF, because RDF uses *only* absolute URIs.
22:43:52 <dbooth> lloyd: Could use a post-processing step that would take the base URI to generate absolute URIs from properties.
22:45:15 <dbooth> dbooth: That sounds like it pushes us toward not requiring URIs in the RDF document.
22:48:33 <dbooth> eric: I haven't given up yet.  I hope we can have the baseUri available.
22:48:50 <dbooth> ... I also want to try leveraging Turtle's relative URIs.
22:49:37 <dbooth> lloyd: But for servers that don't care about RDF that use ref implementations might not want to be bothered to pass in the baseUri.
22:52:04 <dbooth> Topic: How to represent literals in Turtle
22:52:05 <dbooth> lloyd: In RDF, should things like dates be expressed as strings in turtle or not?
22:52:27 <dbooth> eric: Turtle literals are written as "foo"^^theType
22:52:47 <dbooth> ... So things like fhir:datetype can just be written that way.
22:53:58 <dbooth> dbooth: Could write "2012-06"^^fhir:datetype
22:54:34 <dbooth> lloyd: JSON people would not know or care if the date is xsd:date or xsd:datetype
22:54:59 <dbooth> eric: when using the JSON, you have to parse as all three and see which worked?
22:56:26 <dbooth> s/datetype/datetime/
22:56:38 <dbooth> s/datetype/datetime/
22:57:51 <dbooth> eric: I would prefer that the translator tries to parse the value all three ways, and then tag it with the type that worked.
23:03:24 <dbooth> dbooth: Query would either have to use: (a) a regex vs a datatype for all three types; and (b) cast all three to use them together.
23:04:54 <dbooth> ISSUE: How to represent fhir:datetime values?  Three different types?  Plain xsd:strings?
23:04:54 <trackbot> Created ISSUE-20 - How to represent fhir:datetime values?  three different types?  plain xsd:strings?.  Please complete additional details at <http://www.w3.org/2014/HCLS/track/issues/20/edit>.
23:06:43 <dbooth> ADJOURNED
23:16:47 <ericP> qualifiedBy
23:30:05 <dbooth> Topic: How to represent FHIR dateTime values in RDF?
23:31:02 <dbooth> Present+ EricP, David Booth, Lloyd McKenzie, Rob Hausam, Thomas Lukasik
23:42:38 <dbooth> [[
23:42:39 <dbooth> # fhir:dateTime is union of xs:dateTime, xs:date, xs:gYearMonth, xs:gYear
23:42:39 <dbooth> #
23:42:39 <dbooth> #########################################################
23:42:39 <dbooth> # If FHIR RDF literals are tagged with separate FHIR dateTime datatypes,
23:42:40 <dbooth> # filters would look like this:
23:42:41 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:gYear )
23:42:43 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:gYearMonth )
23:42:45 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:date )
23:42:47 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:dateTime )
23:42:49 <dbooth> #########################################################
23:42:51 <dbooth> # If FHIR RDF literals are xsd:strings ,
23:42:53 <dbooth> # filters would look like this:
23:42:57 <dbooth> FILTER regex(?lastOccurence,
23:42:59 <dbooth>   "^[0-9]{4}$")                     # YYYY
23:43:01 <dbooth> FILTER regex(?lastOccurence,
23:43:03 <dbooth>   "^[0-9]{4}\-[0-9]{2}$")           # YYYY-MM
23:43:05 <dbooth> FILTER regex(?lastOccurence,
23:43:07 <dbooth>   "^[0-9]{4}\-[0-9]{2}\-[0-9]{2}$") # YYYY-MM-DD
23:43:09 <dbooth> FILTER regex(?lastOccurence,
23:43:11 <dbooth>   "^[0-9]{4}\-[0-9]{2}\-[0-9]{2}T") # YYYY-MM-DDThh:mm:ss
23:43:13 <dbooth> #########################################################
23:43:15 <dbooth> # In both cases, the value would have to be converted in order
23:43:17 <dbooth> # to compare it to another FHIR dateTime value:
23:43:19 <dbooth> FILTER ( f:toDateTime(?lastOccurence) < ?someDateTime )
23:43:21 <dbooth> ]]
23:50:15 <dbooth> eric: But xpath  knows how to do datetime type conversions.
23:50:24 <dbooth> dbooth: Okay, so here's my updated comparison:
23:50:25 <dbooth> [[
23:50:32 <dbooth> # fhir:dateTime is union of xs:dateTime, xs:date, xs:gYearMonth, xs:gYear
23:50:32 <dbooth> #
23:50:32 <dbooth> #########################################################
23:50:32 <dbooth> # If FHIR RDF literals are tagged with separate FHIR dateTime datatypes,
23:50:33 <dbooth> # filters would look like this:
23:50:33 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:gYear )
23:50:35 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:gYearMonth )
23:50:37 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:date )
23:50:39 <dbooth> FILTER ( datatype(?lastOccurence) = xsd:dateTime )
23:50:41 <dbooth> # XPath knows how to convert between the different datetime
23:50:43 <dbooth> # representations
23:50:45 <dbooth> # https://www.w3.org/TR/xpath-functions/#casting-from-primitive-to-primitive
23:50:47 <dbooth> # so comparison can be done without an explicit conversion:
23:50:49 <dbooth> FILTER ( ?lastOccurence < ?someDateTime )
23:50:51 <dbooth> #########################################################
23:50:53 <dbooth> # If FHIR RDF literals are xsd:strings ,
23:50:56 <dbooth> # filters would look like this:
23:50:59 <dbooth> FILTER regex(?lastOccurence,
23:51:01 <dbooth>   "^[0-9]{4}$")                     # YYYY
23:51:03 <dbooth> FILTER regex(?lastOccurence,
23:51:05 <dbooth>   "^[0-9]{4}\-[0-9]{2}$")           # YYYY-MM
23:51:07 <dbooth> FILTER regex(?lastOccurence,
23:51:09 <dbooth>   "^[0-9]{4}\-[0-9]{2}\-[0-9]{2}$") # YYYY-MM-DD
23:51:11 <dbooth> FILTER regex(?lastOccurence,
23:51:13 <dbooth>   "^[0-9]{4}\-[0-9]{2}\-[0-9]{2}T") # YYYY-MM-DDThh:mm:ss
23:51:15 <dbooth> # To compare it to another FHIR dateTime value:
23:51:17 <dbooth> FILTER ( f:toDateTime(?lastOccurence) < ?someDateTime )
23:51:19 <dbooth> ]]
23:51:21 <dbooth> eric: Many more queries will be done than translations
23:51:38 <dbooth> ADJOURNED AGAIN :)
23:51:55 <ericP> ericP: many more queris written than translators implemented
23:51:57 <dbooth> rrsagent, draft minutes
23:51:57 <RRSAgent> I have made the request to generate http://www.w3.org/2016/03/01-hcls-minutes.html dbooth