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14:57:11 <trackbot> Zakim, this will be HCLS
14:57:11 <Zakim> I do not see a conference matching that name scheduled within the next hour, trackbot
14:57:12 <trackbot> Meeting: Semantic Web Health Care and Life Sciences Interest Group Teleconference
14:57:12 <trackbot> Date: 25 August 2015
15:00:46 <Tony> Tony has joined #HCLS
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15:04:34 <dbooth> Topic: ValueSets
15:05:40 <dbooth> Scribe: rhausam
15:06:07 <ericP> en route
15:06:26 <rhausam> david: defer minutes until we have quorum - no chair yet
15:07:02 <rhausam> tony: presented to ARB last Thursday on FHIR mapping to O-RIM
15:07:38 <rhausam> tony: issues with value set bindings - how do we declare the code system and concepts?
15:08:02 <rhausam> tony: divergenge with FHIR
15:09:06 <rhausam> tony: in RDF/OWL code system  is a namespace where a code is unique
15:09:40 <rhausam> tony: code is a fragment of a URI - code system is a prefix (?)
15:10:06 <rhausam> rob: code system is a "namespace" generally - not specific to FHIR
15:10:41 <rhausam> tony: code system would be a named individual
15:10:52 <rhausam> tony: that is consistent with O-RIM
15:11:45 <rhausam> tony: concept may be a single class in RDF
15:12:47 <rhausam> rob: code system is a class
15:12:51 <rhausam> tony: agree
15:14:51 <rhausam> tony: something missing - may be part of the problem - systemconcept class
15:15:16 <rhausam> david: can you run through that again?
15:15:52 <rhausam> tony: concept "red" - system concept would say that this is "red" as defined by SNOMED CT (for example)
15:18:40 <rhausam> david: think you are referring to in an observation when there is more than one code indicated - this observation is both of those system concepts
15:19:57 <rhausam> tony: intersection of both types
15:20:18 <rhausam> rob: but the two types are not necessarily equivalent
15:20:22 <rhausam> tony: correct
15:20:44 <dbooth> david: When an FHIR observation says that it is SNOMED code 123 and LOINC code 456, it is saying that the observation is both of those concepts -- a subclass of both of those concept classes.
15:21:56 <rhausam> rob: but "red" generally doesn't actually exist (outside of the code systems)
15:22:35 <rhausam> tony: do we declare the abstract concept? we might or might not
15:23:25 <rhausam> david: unless we tie into an upper ontology, there may not be any of these high-level declarations
15:24:31 <rhausam> tony: 3M NCID does this
15:24:53 <rhausam> rob: any number of choices could be made for the "upper" concepts - including SNOMED CT
15:25:58 <rhausam> david: I'm fundamentally skeptical about having any concepts that are not tied to system
15:26:36 <rhausam> tony: value set binds to system concepts, not to the "abstract" concept
15:27:27 <rhausam> tony: relationships are brought to the object property level - this is where the problem is, since object properties relate individuals
15:29:15 <rhausam> tony: fundamentally different from FHIR and O-RIM - declare the values to be a set of individuals
15:29:39 <rhausam> rob: choice of modeling - has consequences
15:30:19 <rhausam> tony: the question has been are concepts classes or instances?
15:30:28 <rhausam> rob: the answer is yes :)
15:30:49 <rhausam> tony: probably need both
15:31:09 <rhausam> david: discuss with Barry Smith in September
15:31:23 <rhausam> tony: don't know his position on this issue
15:31:50 <dbooth> david: You are modeling a valueset as a union of concept classes, because each concept is a class rather than an individual.
15:32:19 <dbooth> david: Whereas ORIM models a valueset as a set of individuals.
15:32:23 <rhausam> tony: need grounding and consensus in how to express concepts in RDF/OWL
15:33:01 <rhausam> tony; CTS deals with instances
15:33:03 <dbooth> david: Maybe we should discuss this question with Barry Smith at the CTS ontology workshop in September http://ncorwiki.buffalo.edu/index.php/CTS_Ontology_Workshop_2015
15:33:20 <rhausam> rob: not specified whether instances or classes in CTS
15:33:43 <dbooth> ISSUE: Should a ValueSet be modeled as a union of concept classes, or as a set of concept individuals?
15:33:43 <trackbot> Created ISSUE-15 - Should a valueset be modeled as a union of concept classes, or as a set of concept individuals?.  Please complete additional details at <http://www.w3.org/2014/HCLS/track/issues/15/edit>.
15:34:02 <rhausam> tony: need to decide this
15:35:30 <rhausam> tony: SNOMED concept is an identity - label tells what it means - is an OWL class
15:36:14 <rhausam> tony: FHIR value set definitions - object of the "include" is an individual
15:36:43 <rhausam> david: tony, can you show an example?
15:38:57 <rhausam> tony: show SNOMED example
15:39:18 <rhausam> rob: SKOS represents as individuals
15:40:04 <rhausam> tony: SKOS fits at metamodel - individuals can be puns of classes
15:40:14 <rhausam> rob: have done this with SKOS
15:41:36 <rhausam> david: what other relationships and properties do you want to define?
15:41:38 <dbooth> rob: if you have the concept Red in two terminologies, it isn't safe to say that they are exactly the owl:sameAs, but with SKOS you can say narrower/broader.
15:42:36 <rhausam> tony: can also say things similar to narrower, broader in OWL by subclassing
15:43:05 <rhausam> tony: mapping is "comfort food" - doesn't necessarily mean anything
15:43:47 <rhausam> tony: "equivalent" concepts may break systems when substituted - can be a dangerous thing
15:45:24 <rhausam> tony: if you find something that needs to be expressed beyond equivalence, disjoint and subclass, can use SKOS
15:45:58 <dbooth> s/SKOS/SKOS and punning/
15:46:09 <rhausam> tony: proposing that concepts and value sets would all be declared as classes
15:46:46 <rhausam> tony: instances of concepts are artifacts in the medical record
15:47:32 <rhausam> tony: would be happy to do a paper on this (could be multiple authors) - how to define code systems, value sets and concepts
15:48:17 <rhausam> david: should discuss this with Barry Smith in September
15:48:34 <rhausam> rob: want concrete material to discuss with him
15:49:48 <rhausam> david: OWL full allows something to be both an individual and a class - while still keeping classes and individuals as distinct
15:50:44 <rhausam> david: sort of an artificial distinction between classes and individuals - tooling issue
15:51:07 <rhausam> rob: nothing
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15:52:32 <rhausam> tony: was getting confused on how O-RIM and FHIR were doing this, and what we want to do in RDF/OWL
15:53:57 <dbooth> s/while still keeping/non-OWL-full likes to keep/
15:57:35 <dbooth> eric: Cecil wrote programs to swap between forms of expressing valueset concepts (as classes or as values).
15:58:06 <dbooth> eric: Tony
15:59:41 <dbooth> eric: Tony's suggestion (to model valueset concepts as classes) is consistent with other things we have done so far, but we should look at the expressivity that we'll need, and consider whether we'll need them, versus modeling them as individuals
16:03:08 <dbooth> david: Downside of concepts as classes?
16:03:59 <dbooth> eric: The system has to work harder.  You're adding more inferences.  It's gotten in Cecil's way in the past.  Should ask Cecil where/when it got him into trouble.
16:05:51 <dbooth> eric: I took apart gender in the ORIM and it took me ages.
16:06:05 <dbooth> tony: ORIM is very difficult to understand.
16:06:59 <dbooth> eric: another thing that would simplify ORIM a ton would be to change 'act' relationships with a type code, to that type property directly.
16:07:57 <dbooth> ... E.g., if the type is 'severs', then use a 'severs' property directly.
16:09:53 <dbooth> ACTION: Tony to draft a paper describing how valuesets and values in a valueset are represented
16:09:53 <trackbot> Error finding 'Tony'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.
16:15:14 <dbooth> i/swap between/Scribe: dbooth
16:16:58 <dbooth> Chair: David Booth
16:18:27 <dbooth> Present: David Booth, Tony Mallia, Calvin Beebe, Darrell Woelk, Rob Hausam, EricP (last 15 minutes)
16:18:37 <dbooth> rrsagent, draft minutes
16:18:37 <RRSAgent> I have made the request to generate http://www.w3.org/2015/08/25-hcls-minutes.html dbooth
16:29:40 <dbooth> david: recap discussion for Eric who just joined
16:29:41 <dbooth> eric: two different patterns affect what inferences you want to support, and how much "coal" you need to supply
16:29:41 <dbooth> eric: what tony is proposing is more consistent with the other decisions that we have been making, but we should (a) determine if we need that expressivity and (b) what do we lose if we turn that expressivity down?
16:29:41 <dbooth> tony: value set would be a union of the concepts - not a superclass - that's different
16:29:41 <dbooth> tony: could declare the coding to be the value set
16:29:43 <dbooth> rob: don't think that's right
16:29:45 <dbooth> tony: that's unspecified
16:29:47 <dbooth> rob: right
16:29:52 <dbooth> tony: focus on what code systems, value sets and concepts are
16:29:53 <dbooth> david: write this up as a separate write up - discuss with Barry in Charleston in September
16:29:55 <dbooth> david: downside of going with concepts as classes?
16:29:57 <dbooth> eric: makes the system work harder
16:30:01 <dbooth> eric: ask Cecil at what level he ran into difficulty with this? what use cases needed this expressivity?
16:30:03 <dbooth> tony: O-RIM is very complex to understand - wanted to try to simplify it - that's a major "no-no" for what we want to do here
16:30:06 <dbooth> eric: would really simplify the O-RIM to remodel ActRelationship objects - replace them with arcs
16:30:08 <dbooth> eric: effectively a reification
16:30:10 <dbooth> david: Google doc?
16:30:12 <dbooth> tony: prefer to send emails - Word doc
16:30:14 <dbooth> tony: prefer to go with smaller group at first while draft, then make public
16:30:16 <dbooth> tony: will try to have draft by this weekend
16:30:22 <dbooth> rrsagent, draft minutes
16:30:22 <RRSAgent> I have made the request to generate http://www.w3.org/2015/08/25-hcls-minutes.html dbooth
16:31:04 <dbooth> ADJOURNED
16:31:10 <dbooth> rrsagent, draft minutes
16:31:10 <RRSAgent> I have made the request to generate http://www.w3.org/2015/08/25-hcls-minutes.html dbooth
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