Re: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

Well, FHIR brings in a mixture of things.  It defines structures (with
relationships) but it also defines coded terms (with subsumption
hierarchies and in theory other kinds of relationships, though none of
those yet).  I think the initial focus is an owl representation for the
structures.  On the terminology side, I don't think there's anything
particularly different in FHIR terminology than there was in v3
terminology, so it would just be a question of translation from the
ValueSet resource format to something more amenable to logic processing.

--------------------------------------
Lloyd McKenzie

+1-780-993-9501



Note: Unless explicitly stated otherwise, the opinions and positions
expressed in this e-mail do not necessarily reflect those of my clients nor
those of the organizations with whom I hold governance positions.

On Tue, Dec 9, 2014 at 9:41 AM, <snachimuthu@mmm.com> wrote:

> Question - are we talking about a structual ontology (analogous to various
> structural codesystems/tables like ActStatus or Acknowledgment in v2/v3),
> or a domain ontology such as Administrative Sex or one derived from
> domain-specific codesystems such as RxNorm/LOINC/SNOMED CT?
>
> If it's a structural terminology, it's easy to see how it can be
> automatically derived from FHIR artifacts. If it's a domain terminology, it
> would be rather uncontrolled if it's derived from any inline definitions in
> FHIR artifacts. Note that I refrain from the word ontology here, because I
> use "ontology" to mean one with formal computable definitions (like FMA or
> SNOMED CT) and amenable to description logics, not one with just a
> collection of terms/concepts.
>
> If it's a formal ontology, OWL would be useful. If it's a (controlled)
> terminology, we can use SKOS. RDF/RDFS are more generic than SKOS and OWL,
> and so would be applicable in both cases.
> Thanks,
>
> Senthil.
>
> PS. cross posting to vocab list for comments.
>
>  ------------------------------
>
>  *Senthil K. Nachimuthu, MD, PhD* | Medical Informaticist
> 3M Health Information Systems, Inc.
> 575 W Murray Blvd, Murray, UT 84123, USA
> Office: +1 801 265 4636
> *snachimuthu@mmm.com* <snachimuthu@mmm.com> | *www.3mtcs.com*
> <http://www.3mtcs.com/>
>
>
>
>
> From:        Lloyd McKenzie <lloyd@lmckenzie.com>
> To:        David Booth <david@dbooth.org>
> Cc:        Grahame Grieve <grahame@healthintersections.com.au>, w3c
> semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <
> its@lists.hl7.org>
> Date:        12/08/2014 04:13 PM
> Subject:        Re: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup /
> W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)
> Sent by:        owner-its@lists.hl7.org
> ------------------------------
>
>
>
> I think that any ontology we create will have to be produceable in an
> automated fashion from the FHIR artifacts.  Any introduction of
> hand-editing would be unacceptable from a maintainability and consistency
> perspective.  So we're looking at mechanical, no matter what.  The question
> is what the mechanical outputs would be.
>
> --------------------------------------
> Lloyd McKenzie
>
> +1-780-993-9501
>
>
>
> Note: Unless explicitly stated otherwise, the opinions and positions
> expressed in this e-mail do not necessarily reflect those of my clients nor
> those of the organizations with whom I hold governance positions.
>
> On Mon, Dec 8, 2014 at 1:51 PM, David Booth <*david@dbooth.org*
> <david@dbooth.org>> wrote:
> Possibly a dream ontology would link to more other ontologies, such as
> upper level ontologies, but other than that I view it as more of a
> stylistic difference: more oriented toward a human conceptualization that
> is natural to express in RDF (i.e., reflecting RDF's natural style).
>
> But one problem is that the whole notion of a dream ontology is very
> subjective, and this means that it is apt to take a lot more work to reach
> convergence on it.  That is why I think it is important to prioritize a
> mechanical ontology first, so that we can progress as rapidly.  If at some
> later point we wish -- and we are able -- to converge on a dream ontology
> then that's great, and it could complement the mechanical ontology for
> those who wish to use it.  But I think it would be a big mistake to try for
> that at the outset.
>
> Again, the distinction between mechanical ontology and dream ontology is
> qualitative, fuzzy and subjective: to the extent that we can make a
> mechanical ontology that is human friendly and natural to RDF, that would
> of course be ideal.   I just want to guard against going down a potential
> rat hole from the start.  :)
>
> David
>
> On 12/08/2014 02:24 PM, Grahame Grieve wrote:
> can you explain your dream ontology more? what sort of things does it do?
>
> Grahame
>
>
> On Tue, Dec 9, 2014 at 6:01 AM, David Booth <*david@dbooth.org*
> <david@dbooth.org>
> <mailto:*david@dbooth.org* <david@dbooth.org>>> wrote:
>
>     Hi Lloyd,
>
>     On 12/08/2014 01:35 PM, Lloyd McKenzie wrote:
>
>         I think we need to define our objectives for the RDF
> representation.
>         Mine are as follows:
>
>
>     Great list!  My comments . . .
>
>
>         1. It must be possible to round-trip from XML/JSON through RDF
>         representation
>
>
>     +1
>
>         * This includes retaining information about order of repeating
>         elements
>
>
>     Is the order of repeating elements semantically significant in FHIR?
>     I.e., would it affect or use of the interpretation of the
>     information?  If not, then why do you view this as important?
>     (Playing devil's advocate here, to elicit the rationale.)
>
>         * Needs to allow for extensions where-ever they can appear,
>         including
>         simple types (date, boolean, etc.)
>
>
>     +1
>
>         2. We want to be able to represent instances as RDF
>
>
>     +1
>
>     and Profiles as OWL/RDFS
>
>     +0.9.  I think the profiles MUST be represented in some form of RDF,
>     but whether it is done using OWL, RDFS or some combination of OWL,
>     RDFS and something else (SKOS?) I think should be a judgement call
>     that is made as we go along.
>
>         3. Syntax needs to be "safe" when dealing with modifier extensions
>         4. Syntax should support vocabulary bindings to code, Coding and
>         CodeableConcept - including dealing with extensible value sets and
>         multi-code system value sets
>         5. Syntax should enforce constraints that are representable in
>         RDF (i.e.
>         schema constraints, regular expressions, etc.)
>
>
>     Can you explain what you mean by syntax in the above?  For example,
>     if Turtle is used to serialize the RDF, what would the above points
>     mean?
>
>         6. In the RDFS/OWL, should expose at least minimal annotation
>         information for display
>
>
>     +1
>
>     BTW, there's another distinction that Eric Prud'hommeaux used to
>     distinguish between different ontology styles or goals.  I think he
>     referred to one style as a "mechanical" ontology, which might be
>     fairly directly derived from the FHIR spec and is oriented mainly
>     toward ease of round tripping between RDF and XML or JSON.  The
>     other style is a "dream" ontology, which is friendlier and more
>     natural for humans to view and may take more work to converge upon.
>       The two are not mutually exclusive, of course, but in prioritizing
>     our work effort I'm of the opinion that we should FIRST go for the
>     mechanical ontology, and once we've got that sufficiently nailed
>     down, we could try to figure out a dream ontology, with the ability
>     to automatically translate instance data between the two.
>
>     Thanks,
>     David Booth
>
>
> ******************************__******************************__***********************
>     Manage subscriptions - *http://www.HL7.org/listservice*
> <http://www.hl7.org/listservice>
>     View archives - *http://lists.HL7.org/read/?__forum=its*
> <http://lists.hl7.org/read/?__forum=its>
>     <*http://lists.HL7.org/read/?forum=its*
> <http://lists.hl7.org/read/?forum=its>>
>     Unsubscribe -
>
> *http://www.HL7.org/tools/__unsubscribe.cfm?email=grahame@__healthintersections.com.au&__list=its*
> <http://www.hl7.org/tools/__unsubscribe.cfm?email=grahame@__healthintersections.com.au&__list=its>
>     <
> *http://www.HL7.org/tools/unsubscribe.cfm?email=grahame@healthintersections.com.au&list=its*
> <http://www.hl7.org/tools/unsubscribe.cfm?email=grahame@healthintersections.com.au&list=its>
> >
>
>     Terms of use -
>     *http://www.HL7.org/myhl7/__managelistservs.cfm?ref=nav#__listrules*
> <http://www.hl7.org/myhl7/__managelistservs.cfm?ref=nav#__listrules>
>     <*http://www.HL7.org/myhl7/managelistservs.cfm?ref=nav#listrules*
> <http://www.hl7.org/myhl7/managelistservs.cfm?ref=nav#listrules>>
>
>
>
>
> --
> -----
> *http://www.healthintersections.com.au*
> <http://www.healthintersections.com.au/> /
> *grahame@healthintersections.com.au* <grahame@healthintersections.com.au>
> <mailto:*grahame@healthintersections.com.au*
> <grahame@healthintersections.com.au>> / *+61 411 867 065*
> <%2B61%20411%20867%20065>
>
>
> ***********************************************************************************
> Manage your subscriptions <*http://www.HL7.org/listservice*
> <http://www.hl7.org/listservice>> | View the
> archives <*http://lists.HL7.org/read/?forum=its*
> <http://lists.hl7.org/read/?forum=its>> | Unsubscribe
> <
> *http://www.HL7.org/tools/unsubscribe.cfm?email=david@dbooth.org&list=its*
> <http://www.hl7.org/tools/unsubscribe.cfm?email=david@dbooth.org&list=its>
> >
> | Terms of use
> <*http://www.HL7.org/myhl7/managelistservs.cfm?ref=nav#listrules*
> <http://www.hl7.org/myhl7/managelistservs.cfm?ref=nav#listrules>>
>
>
> ***********************************************************************************
> *Manage your subscriptions* <http://www.hl7.org/listservice> | *View the
> archives* <http://lists.hl7.org/read/?forum=its> | *Unsubscribe*
> <http://www.hl7.org/tools/unsubscribe.cfm?email=snachimuthu@mmm.com&list=its>
> | *Terms of use*
> <http://www.hl7.org/myhl7/managelistservs.cfm?ref=nav#listrules>
>
>
> ***********************************************************************************
> Manage your subscriptions <http://www.HL7.org/listservice> | View the
> archives <http://lists.HL7.org/read/?forum=its> | Unsubscribe
> <http://www.HL7.org/tools/unsubscribe.cfm?email=lloyd@lmckenzie.com&list=its>
> | Terms of use
> <http://www.HL7.org/myhl7/managelistservs.cfm?ref=nav#listrules>
>
>