Semantic Web Health Care and Life Sciences Interest Group Teleconference

25 Aug 2015

See also: IRC log


David_Booth, Tony_Mallia, Calvin_Beebe, Darrell_Woelk, Rob_Hausam, EricP_(last_15_minutes)
David Booth
rhausam, dbooth


<trackbot> Date: 25 August 2015


<dbooth> Scribe: rhausam

<ericP> en route

david: defer minutes until we have quorum - no chair yet

tony: presented to ARB last Thursday on FHIR mapping to O-RIM
... issues with value set bindings - how do we declare the code system and concepts?
... divergenge with FHIR
... in RDF/OWL code system is a namespace where a code is unique
... code is a fragment of a URI - code system is a prefix (?)

rob: code system is a "namespace" generally - not specific to FHIR

tony: code system would be a named individual
... that is consistent with O-RIM
... concept may be a single class in RDF

rob: code system is a class

tony: agree
... something missing - may be part of the problem - systemconcept class

david: can you run through that again?

tony: concept "red" - system concept would say that this is "red" as defined by SNOMED CT (for example)

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

tony: intersection of both types

rob: but the two types are not necessarily equivalent

tony: correct

<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.

rob: but "red" generally doesn't actually exist (outside of the code systems)

tony: do we declare the abstract concept? we might or might not

david: unless we tie into an upper ontology, there may not be any of these high-level declarations

tony: 3M NCID does this

rob: any number of choices could be made for the "upper" concepts - including SNOMED CT

david: I'm fundamentally skeptical about having any concepts that are not tied to system

tony: value set binds to system concepts, not to the "abstract" concept
... relationships are brought to the object property level - this is where the problem is, since object properties relate individuals
... fundamentally different from FHIR and O-RIM - declare the values to be a set of individuals

rob: choice of modeling - has consequences

tony: the question has been are concepts classes or instances?

rob: the answer is yes :)

tony: probably need both

david: discuss with Barry Smith in September

tony: don't know his position on this issue

<dbooth> david: You are modeling a valueset as a union of concept classes, because each concept is a class rather than an individual.

<dbooth> david: Whereas ORIM models a valueset as a set of individuals.

tony: need grounding and consensus in how to express concepts in RDF/OWL

tony; CTS deals with instances

<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

rob: not specified whether instances or classes in CTS

<dbooth> ISSUE: Should a ValueSet be modeled as a union of concept classes, or as a set of concept individuals?

<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>.

tony: need to decide this
... SNOMED concept is an identity - label tells what it means - is an OWL class
... FHIR value set definitions - object of the "include" is an individual

david: tony, can you show an example?

tony: show SNOMED example

rob: SKOS represents as individuals

tony: SKOS fits at metamodel - individuals can be puns of classes

rob: have done this with SKOS

david: what other relationships and properties do you want to define?

<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.

tony: can also say things similar to narrower, broader in OWL by subclassing
... mapping is "comfort food" - doesn't necessarily mean anything
... "equivalent" concepts may break systems when substituted - can be a dangerous thing
... if you find something that needs to be expressed beyond equivalence, disjoint and subclass, can use SKOS and punning
... proposing that concepts and value sets would all be declared as classes
... instances of concepts are artifacts in the medical record
... would be happy to do a paper on this (could be multiple authors) - how to define code systems, value sets and concepts

david: should discuss this with Barry Smith in September

rob: want concrete material to discuss with him

david: OWL full allows something to be both an individual and a class - non-OWL-full likes to keep classes and individuals as distinct
... sort of an artificial distinction between classes and individuals - tooling issue

rob: nothing

tony: was getting confused on how O-RIM and FHIR were doing this, and what we want to do in RDF/OWL

<inserted> Scribe: dbooth

eric: Cecil wrote programs to swap between forms of expressing valueset concepts (as classes or as values).
... Tony
... 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

david: Downside of concepts as classes?

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.
... I took apart gender in the ORIM and it took me ages.

tony: ORIM is very difficult to understand.

eric: another thing that would simplify ORIM a ton would be to change 'act' relationships with a type code, to that type property directly.
... E.g., if the type is 'severs', then use a 'severs' property directly.

<scribe> ACTION: Tony to draft a paper describing how valuesets and values in a valueset are represented [recorded in http://www.w3.org/2015/08/25-hcls-minutes.html#action01]

<trackbot> Error finding 'Tony'. You can review and register nicknames at <http://www.w3.org/2014/HCLS/track/users>.

david: recap discussion for Eric who just joined

eric: two different patterns affect what inferences you want to support, and how much "coal" you need to supply
... 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?

tony: value set would be a union of the concepts - not a superclass - that's different
... could declare the coding to be the value set

rob: don't think that's right

tony: that's unspecified

rob: right

tony: focus on what code systems, value sets and concepts are

david: write this up as a separate write up - discuss with Barry in Charleston in September
... downside of going with concepts as classes?

eric: makes the system work harder
... ask Cecil at what level he ran into difficulty with this? what use cases needed this expressivity?

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

eric: would really simplify the O-RIM to remodel ActRelationship objects - replace them with arcs
... effectively a reification

david: Google doc?

tony: prefer to send emails - Word doc
... prefer to go with smaller group at first while draft, then make public
... will try to have draft by this weekend


Summary of Action Items

[NEW] ACTION: Tony to draft a paper describing how valuesets and values in a valueset are represented [recorded in http://www.w3.org/2015/08/25-hcls-minutes.html#action01]
[End of minutes]

Minutes formatted by David Booth's scribe.perl version 1.140 (CVS log)
$Date: 2015/08/25 16:31:16 $

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Guessing input format: RRSAgent_Text_Format (score 1.00)

Succeeded: s/SKOS/SKOS and punning/
Succeeded: s/while still keeping/non-OWL-full likes to keep/
Succeeded: i/swap between/Scribe: dbooth
Found Scribe: rhausam
Inferring ScribeNick: rhausam
Found Scribe: dbooth
Inferring ScribeNick: dbooth
Scribes: rhausam, dbooth
ScribeNicks: rhausam, dbooth
Present: David_Booth Tony_Mallia Calvin_Beebe Darrell_Woelk Rob_Hausam EricP_(last_15_minutes)
Found Date: 25 Aug 2015
Guessing minutes URL: http://www.w3.org/2015/08/25-hcls-minutes.html
People with action items: tony

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