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

From: Lloyd McKenzie <lloyd@lmckenzie.com>
Date: Mon, 8 Dec 2014 11:35:43 -0700
Message-ID: <CAJ860J+kAA9rF4JFP3b5cpShE_krXrBzzFndvqevGULPRROVfQ@mail.gmail.com>
To: David Booth <david@dbooth.org>
Cc: w3c semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <its@lists.hl7.org>
I think we need to define our objectives for the RDF representation.  Mine
are as follows:

1. It must be possible to round-trip from XML/JSON through RDF
representation
* This includes retaining information about order of repeating elements
* Needs to allow for extensions where-ever they can appear, including
simple types (date, boolean, etc.)
2. We want to be able to represent instances as RDF and Profiles as OWL/RDFS
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.)
6. In the RDFS/OWL, should expose at least minimal annotation information
for display


Lloyd

--------------------------------------
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 11:11 AM, David Booth <david@dbooth.org> wrote:

> I'm so sorry I forgot to send these out last Tuesday, but here are draft
> minutes from our call, with Eric Prud'hommeaux reviewing his FHIR ontology
> approach:
> http://www.w3.org/2014/12/02-hcls-minutes.html
> and below in plain text.
>
> Also, as a reminder, tomorrow's call (Tuesday) will continue with Claude
> Nanjo reviewing his FHIR ontology approach.
>
> Thanks,
> David Booth
>    --------------------------------------------------------
>    [1]W3C
>
>       [1] http://www.w3.org/
>
>                                - DRAFT -
>
> Semantic Web Health Care and Life Sciences Interest Group Teleconference
>
> 02 Dec 2014
>
>    See also: [2]IRC log
>
>       [2] http://www.w3.org/2014/12/02-hcls-irc
>
> Attendees
>
>    Present
>           Bryn_Rhodes, Cati, Claude_Nanjo, David_Booth, EricP,
>           Guoqian, Hans_Cools, Ingeborg, Joshua_Phillips,
>           Kerstin_Forsberg, Marc_Twagirumukiza, Neda, Paul_Knapp,
>           TimW, Tony_Mallia, Charlie_Mead, egonw_(IRC_only?),
>           Scott_Marshall, Patricia, Rob_Hausam, Vassil_(IRC_only?)
>
>    Regrets
>    Chair
>           David Booth (and Paul Knapp)
>
>    Scribe
>           dbooth
>
> Contents
>
>      * [3]Topics
>          1. [4]Approve Minutes of previous meetings
>          2. [5]Action Review
>          3. [6]FHIR Ontology Review
>      * [7]Summary of Action Items
>      __________________________________________________________
>
>    <trackbot> Date: 02 December 2014
>
>    <ericP> trackbot, start meeting
>
>    <trackbot> Meeting: Semantic Web Health Care and Life Sciences
>    Interest Group Teleconference
>
>    <trackbot> Date: 02 December 2014
>
>    <ericP> oops
>
>    <TimW> TimW is from +1.919.767...
>
>    <RHausam> RHausam is 801.949.1556
>
>    <Claude> [8]https://global.gotomeeting.com/join/157514853
>
>       [8] https://global.gotomeeting.com/join/157514853
>
>    <Claude> Please join our GoToMeeting
>
> Approve Minutes of previous meetings
>
>    Nov 18:
>    [9]http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_
>    20141118
>
>       [9] http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_
> 20141118
>
>    Nov 25:
>    [10]http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes
>    _20141125
>
>      [10] http://wiki.hl7.org/index.php?title=ITS_RDF_Concall_Minutes_
> 20141125
>
>    Nov 18 minutes unanimously approved.
>
>    Nov 25 minutes unanimously approved.
>
> Action Review
>
>    <scribe> ACTION: ericP to set up tracker [recorded in
>    [11]http://www.w3.org/2014/11/25-hcls-minutes.html#action01 --
>    PENDING
>
>      [11] http://www.w3.org/2014/11/25-hcls-minutes.html#action01
>
>    <trackbot> Created ACTION-2 - Set up tracker [recorded in
>    [12]http://www.w3.org/2014/11/25-hcls-minutes.html#action01 --
>    pending [on Eric Prud'hommeaux - due 2014-12-09].
>
>      [12] http://www.w3.org/2014/11/25-hcls-minutes.html#action01
>
>    <scribe> ACTION: Tony to find out more details about how iCat
>    handles ICD-11 ont and report back [recorded in
>    [13]http://www.w3.org/2014/11/18-hcls-minutes.html#action01 --
>    PENDING
>
>      [13] http://www.w3.org/2014/11/18-hcls-minutes.html#action01
>
>    <trackbot> Error finding 'Tony'. You can review and register
>    nicknames at <[14]http://www.w3.org/2014/HCLS/track/users>.
>
>      [14] http://www.w3.org/2014/HCLS/track/users
>
>    <scribe> ACTION: Guoqian to figure out whether he can share URI
>    conventions for ICD-11 [recorded in
>    [15]http://www.w3.org/2014/11/25-hcls-minutes.html#action07 --
>    PENDING
>
>      [15] http://www.w3.org/2014/11/25-hcls-minutes.html#action07
>
>    <trackbot> Created ACTION-3 - Figure out whether he can share
>    uri conventions for icd-11 [recorded in
>    [16]http://www.w3.org/2014/11/25-hcls-minutes.html#action07 --
>    pending [on Guoqian Jiang - due 2014-12-09].
>
>      [16] http://www.w3.org/2014/11/25-hcls-minutes.html#action07
>
>    <Claude> For those who just joined IRC, we also have a
>    GoToMeeting at:
>
>    <Claude> [17]https://global.gotomeeting.com/join/157514853
>
>      [17] https://global.gotomeeting.com/join/157514853
>
>    <scribe> ACTION: Kerstin and Ingeborg to prepare a status and
>    future state ideas for PhUSE-FDA work [recorded in
>    [18]http://www.w3.org/2014/11/18-hcls-minutes.html#action05 --
>    PENDING
>
>      [18] http://www.w3.org/2014/11/18-hcls-minutes.html#action05
>
>    <trackbot> Error finding 'Kerstin'. You can review and register
>    nicknames at <[19]http://www.w3.org/2014/HCLS/track/users>.
>
>      [19] http://www.w3.org/2014/HCLS/track/users
>
>    <scribe> ACTION: Eric to establish/make a wiki page for C-CDA
>    RDF representations work [recorded in
>    [20]http://www.w3.org/2014/11/18-hcls-minutes.html#action06 --
>    PENDING
>
>      [20] http://www.w3.org/2014/11/18-hcls-minutes.html#action06
>
>    <trackbot> Created ACTION-4 - Establish/make a wiki page for
>    c-cda rdf representations work [recorded in
>    [21]http://www.w3.org/2014/11/18-hcls-minutes.html#action06 --
>    pending [on Eric Prud'hommeaux - due 2014-12-09].
>
>      [21] http://www.w3.org/2014/11/18-hcls-minutes.html#action06
>
>    <scribe> ACTION: Eric and Joshua to report on C-CDA RDF
>    representations work plan [recorded in
>    [22]http://www.w3.org/2014/11/18-hcls-minutes.html#action07 --
>    PENDING
>
>      [22] http://www.w3.org/2014/11/18-hcls-minutes.html#action07
>
>    <trackbot> Created ACTION-5 - And joshua to report on c-cda rdf
>    representations work plan [recorded in
>    [23]http://www.w3.org/2014/11/18-hcls-minutes.html#action07 --
>    pending [on Eric Prud'hommeaux - due 2014-12-09].
>
>      [23] http://www.w3.org/2014/11/18-hcls-minutes.html#action07
>
>    Joshua: Sent email describing a use case. Will add to wiki
>    page.
>
>    <scribe> ACTION: Tony and Rob to report their plan on
>    High-level concept mapping to RDF work [recorded in
>    [24]http://www.w3.org/2014/11/18-hcls-minutes.html#action08 --
>    PENDING
>
>      [24] http://www.w3.org/2014/11/18-hcls-minutes.html#action08
>
>    <trackbot> Error finding 'Tony'. You can review and register
>    nicknames at <[25]http://www.w3.org/2014/HCLS/track/users>.
>
>      [25] http://www.w3.org/2014/HCLS/track/users
>
>    <scribe> ACTION: Tony and all to decide on a wiki for Term Info
>    work [recorded in
>    [26]http://www.w3.org/2014/11/18-hcls-minutes.html#action09] --
>    PENDING
>
>      [26] http://www.w3.org/2014/11/18-hcls-minutes.html#action09]
>
>    <trackbot> Error finding 'Tony'. You can review and register
>    nicknames at <[27]http://www.w3.org/2014/HCLS/track/users>.
>
>      [27] http://www.w3.org/2014/HCLS/track/users
>
>    <scribe> ACTION: Guoqian to figure out whether he can share URI
>    conventions for ICD-11 [recorded in
>    [28]http://www.w3.org/2014/11/25-hcls-minutes.html#action07]
>
>      [28] http://www.w3.org/2014/11/25-hcls-minutes.html#action07]
>
>    <trackbot> Created ACTION-6 - Figure out whether he can share
>    uri conventions for icd-11 [recorded in
>    [29]http://www.w3.org/2014/11/25-hcls-minutes.html#action07]
>    [on Guoqian Jiang - due 2014-12-09].
>
>      [29] http://www.w3.org/2014/11/25-hcls-minutes.html#action07]
>
>    <scribe> [PENDING]
>
> FHIR Ontology Review
>
>    <Claude> Please use GoToMeeting only for video
>
>    [30]https://global.gotomeeting.com/join/157514853
>
>      [30] https://global.gotomeeting.com/join/157514853
>
>    Access Code: 157-514-853
>
>    Eric's slides: ->
>    [31]http://www.w3.org/2014/Talks/1125-fhir-rdf-egp/ FHIR-RDF
>
>      [31] http://www.w3.org/2014/Talks/1125-fhir-rdf-egp/
>
>    Eric: Our goal was to let anything in FHIR XML be translated
>    into RDF.
>    ... We wrote something that read the XML definition files and
>    produced something that maps the XML to RDF.
>    ... Python code reads the json definition files and spits out
>    XML, being the parts that we need of the FHIR spec.
>    ... "subs" is what is allowed inside a FHIR resource.
>    ... effectively the attributes of a resource.
>    ... Then we embedded that in an XSLT script, and hand edited
>    the foot of it.
>    ... The stuff we wrote into the footer of the XSLT says that
>    for a particular construct in the XML instance data, there's
>    special handling, such as URLs for identifiers.
>
>    David: How does the fact that it is an atom feed affect the
>    interpretatinon of the XML?
>
>    Eric: It leaves some other graph stuff superimposed on it.
>
>    Marc: Re datatypes, you used FHIR value, but the value itself
>    looks like it is a string.
>    ... If it is a string, then reasoners cannot do much with it.
>
>    Eric: Datatype values are showing up as literals.
>
>    Marc: Another is that a date is just a string, not an xsd:date.
>    ... On slide 2
>
>    Eric: Ideally it should have the datatype stuck on the end of
>    it. There's a tension between having the datatype on the
>    fhir:value and having it on a blank node.
>    ... The natural RDF-ish way to do it would be using
>    xsd:datetime.
>    ... Need to decide which of these ways will be most palatable
>    to RDF folks versus native FHIR folks.
>    ... Sometimes these things are not just datetimes in FHIR. Need
>    to make it as simple as possible and no simpler.
>
>    Guoqian: Is a different URI being used for the namespaces? Will
>    it cause problems when you use SPARQL across different models?
>
>    Eric: I tested some of this. I stuck a bunch of these
>    namespaces together, and I believe we've addressed your
>    concern.
>
>    David: Is the datatype issue due to the fact that datatypes are
>    extensible in FHIR?
>
>    Eric: Maybe. RDF needs to be monotonic.
>
>    Paul: Modifying extensions can appear only in the roots of
>    classes (considering the complex type as a class)
>
>    Eric: The XSLT footer has the custom code for extensions.
>
>    Paul: We did that to limit what you need to examine, to find
>    out if there is a modifying extension.
>
>    Claude: I think you can have modifying extensions on the root
>    type and anything that is defined from the root type.
>
>    ISSUE: FHIR Modifying extensions and monotonicity
>
>    <trackbot> Created ISSUE-1 - Fhir modifying extensions and
>    monotonicity. Please complete additional details at
>    <[32]http://www.w3.org/2014/HCLS/track/issues/1/edit>.
>
>      [32] http://www.w3.org/2014/HCLS/track/issues/1/edit
>
>    Eric: Example here may not be up to date. Anyone know?
>
>    Paul: the dev site has DSTU 2.
>
>    Eric: Another script generates the ShEx definitions from the
>    FHIR spec.
>    ... and the ShEx is used to generate FHIR XML back again from
>    FHIR RDF.
>    ... Slide 7 is showing how to take C-CDA in RDF and producing
>    FHIR RDF.
>
>    Guoqian: The result prefix is fhir but should be patient.
>
>    Eric: Yes, you're right. That can be fixed in the ShEx.
>
>    Tony: Sort of verbatim translation. The difference is maybe
>    target audience style -- a style that is good for the general
>    tools used in RDF. Only difference is the end style of RDF.
>    ... Establishing closure between FHIR ontology and SNOMED-CT
>    would need to happen. Main difference is in the final RDF
>    style.
>
>    <pknapp> Zakim: Have to leave for another meeting, thx, great
>    work.
>
>    Eric: Will need to need to be a balance.
>    ... Once we have transliterated, what we map to our dream
>    ontology. May want to balance how much is wedged into the XSLT
>    and how much into the interpretive dance later.
>
>    Claude: Might want a low level FHIR ont and a higher level FHIR
>    ont both.
>
>    David: I kind of like the auto-generated aspect of this
>    approach.
>
>    <vassil> чуит
>
>    ADJOURNED
>
>    <vassil> quit
>
>    <ericP> [33]coding mapping example
>
>      [33] https://www.w3.org/wiki/HCLS/ClinicalObservationsInteropera
> bility/FDATherapeuticAreaOntologies#codeAndSystemToIRI
>
>    <ericP> (for next week)
>
>    <vassil> exit
>
> Summary of Action Items
>
>    [PENDING] ACTION: Eric and Joshua to report on C-CDA RDF
>    representations work plan [recorded in
>    [34]http://www.w3.org/2014/11/18-hcls-minutes.html#action07]
>    [PENDING] ACTION: Eric to establish/make a wiki page for C-CDA
>    RDF representations work [recorded in
>    [35]http://www.w3.org/2014/11/18-hcls-minutes.html#action06]
>    [PENDING] ACTION: ericP to set up tracker [recorded in
>    [36]http://www.w3.org/2014/11/25-hcls-minutes.html#action01]
>    [PENDING] ACTION: Guoqian to figure out whether he can share
>    URI conventions for ICD-11 [recorded in
>    [37]http://www.w3.org/2014/11/25-hcls-minutes.html#action07]
>    [PENDING] ACTION: Kerstin and Ingeborg to prepare a status and
>    future state ideas for PhUSE-FDA work [recorded in
>    [38]http://www.w3.org/2014/11/18-hcls-minutes.html#action05]
>    [PENDING] ACTION: Tony and all to decide on a wiki for Term
>    Info work [recorded in
>    [39]http://www.w3.org/2014/11/18-hcls-minutes.html#action09]
>    [PENDING] ACTION: Tony and Rob to report their plan on
>    High-level concept mapping to RDF work [recorded in
>    [40]http://www.w3.org/2014/11/18-hcls-minutes.html#action08]
>    [PENDING] ACTION: Tony to find out more details about how iCat
>    handles ICD-11 ont and report back [recorded in
>    [41]http://www.w3.org/2014/11/18-hcls-minutes.html#action01]
>
>      [34] http://www.w3.org/2014/11/18-hcls-minutes.html#action07
>      [35] http://www.w3.org/2014/11/18-hcls-minutes.html#action06
>      [36] http://www.w3.org/2014/11/25-hcls-minutes.html#action01
>      [37] http://www.w3.org/2014/11/25-hcls-minutes.html#action07
>      [38] http://www.w3.org/2014/11/18-hcls-minutes.html#action05
>      [39] http://www.w3.org/2014/11/18-hcls-minutes.html#action09
>      [40] http://www.w3.org/2014/11/18-hcls-minutes.html#action08
>      [41] http://www.w3.org/2014/11/18-hcls-minutes.html#action01
>
>    [End of minutes]
>      __________________________________________________________
>
>
>     Minutes formatted by David Booth's [42]scribe.perl version
>     1.140 ([43]CVS log)
>     $Date: 2014-12-02 17:30:25 $
>      __________________________________________________________
>
>      [42] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
>      [43] http://dev.w3.org/cvsweb/2002/scribe/
>
> Scribe.perl diagnostic output
>
>    [Delete this section before finalizing the minutes.]
> This is scribe.perl Revision: 1.140  of Date: 2014-11-06 18:16:30
> Check for newer version at [44]http://dev.w3.org/cvsweb/~checkout~/2002/
> scribe/
>
>      [44] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/
>
> Guessing input format: RRSAgent_Text_Format (score 1.00)
>
> No ScribeNick specified.  Guessing ScribeNick: dbooth
> Inferring Scribes: dbooth
> Default Present: DBooth, +1.919.767.aaaa, ericP, rhausam, TimW, Joshua_P
> hillips, +1.202.528.aabb, charlie, +1.469.226.aacc, Tony, Neda, patricia
> , Mark_Twagirumukiza, Kerstin_Forsberg, Cati, Kerstin, +1.801.368.aadd,
> +1.604.250.aaee, Bryn_Rhodes, +31.62.427.aaff, mscottm, Guoqian, +1.608.
> 310.aagg, vassil, +41.78.847.aahh, [IPcaller]
>
> WARNING: Replacing previous Present list. (Old list: Bryn_Rhodes, Cati,
> Claude_Nanjo, David_Booth, EricP, Guoqian, Hans_Cools, Ingeborg, Joshua_
> Phillips, Kerstin_Forsberg, Marc_Twagirumukiza, Neda, Paul_Knapp, TimW,
> Tony_Mallia, Charlie_Mead, egonw, (IRC, only?), Scott_Marshall, Patricia
> , Rob_Hausam, Vassil, (IRC, only?))
> Use 'Present+ ... ' if you meant to add people without replacing the lis
> t,
> such as: <dbooth> Present+ Bryn_Rhodes, Cati, Claude_Nanjo, David_Booth,
>  EricP, Guoqian, Hans_Cools, Ingeborg, Joshua_Phillips, Kerstin_Forsberg
> , Marc_Twagirumukiza, Neda, Paul_Knapp, TimW, Tony_Mallia, Charlie_Mead,
>  egonw_(IRC_only?), Scott_Marshall, Patricia, Rob_Hausam, Vassil_(IRC_on
> ly?)
>
> Present: Bryn_Rhodes Cati Claude_Nanjo David_Booth EricP Guoqian Hans_Co
> ols Ingeborg Joshua_Phillips Kerstin_Forsberg Marc_Twagirumukiza Neda Pa
> ul_Knapp TimW Tony_Mallia Charlie_Mead egonw_(IRC_only?) Scott_Marshall
> Patricia Rob_Hausam Vassil_(IRC_only?)
> Found Date: 02 Dec 2014
> Guessing minutes URL: [45]http://www.w3.org/2014/12/02-hcls-minutes.html
> People with action items: all eric ericp guoqian ingeborg joshua kerstin
>  rob tony
>
>      [45] http://www.w3.org/2014/12/02-hcls-minutes.html
>
>
>    [End of [46]scribe.perl diagnostic output]
>
>      [46] http://dev.w3.org/cvsweb/~checkout~/2002/scribe/scribedoc.htm
>
>
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Received on Monday, 8 December 2014 18:36:33 UTC

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