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

From: David Booth <david@dbooth.org>
Date: Mon, 08 Dec 2014 13:11:42 -0500
Message-ID: <5485E9DE.3060300@dbooth.org>
To: w3c semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <its@lists.HL7.org>
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/ClinicalObservationsInteroperability/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
Received on Monday, 8 December 2014 18:12:16 UTC

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