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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: Vipul Kashyap <kashyap.vipul@gmail.com>
Date: Sat, 20 Dec 2014 18:35:55 -0500
To: "'Lloyd McKenzie'" <lloyd@lmckenzie.com>
Cc: "'David Booth'" <david@dbooth.org>, "'w3c semweb HCLS'" <public-semweb-lifesci@w3.org>, "'HL7 ITS'" <its@lists.hl7.org>, "'Vipul Kashyap'" <kashyap.vipul@gmail.com>
Message-ID: <03f301d01cad$b4230be0$1c6923a0$@gmail.com>
Thanks for the feedback and clarification  – Looks like we will have to work at two different layers:

 

1.       The syntactic translation from FHIR XML/JSON to RDF/OWL – 

2.       Enrichment of the RDF/OWL representation via ontologies and OWL axioms.. which is where I believe would provide the value due to inferencing in a wide variety of applications –e.g., CDS, Clinical Documentation, Quality Metrics, etc.

 

Am I correct in assuming that we are focusing on (1) in this group – Shouldn’t we try to do (2) as well?

 

Thanks,

 

---Vipul

 

From: Lloyd McKenzie [mailto:lloyd@lmckenzie.com] 
Sent: Saturday, December 20, 2014 6:15 PM
To: Vipul Kashyap
Cc: David Booth; w3c semweb HCLS; HL7 ITS
Subject: Re: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

 

Well, for FHIR at a minimum, you must be able to round-trip instances.  And what will appear in the JSON and XML instances is the code + code system (and often multiple code-code system pairs).   Often, the code + code system won't even link to an ontology that's known by the receiver.  And if we want to be able to convert v2 or v3 instances, what appears over the wire there is the code + code system too.  All knowledge of what the binding is for an element is carried outside the instance. 




--------------------------------------
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 Sat, Dec 20, 2014 at 4:07 PM, Vipul Kashyap <kashyap.vipul@gmail.com> wrote:

Not clear about the reason for this design decision – Has it been discussed and agreed upon by the members of this group?

Or is it the case that if we adopt a different approach – it will not be accorded official status by the FHIR folks?

 

BTW – It might turn out that code system + code approach is indeed better – but I would love to see use cases and examples illustrating this… 

 

Thanks,

 

---Vipul

 

From: Lloyd McKenzie [mailto:lloyd@lmckenzie.com] 
Sent: Saturday, December 20, 2014 6:00 PM
To: Vipul Kashyap
Cc: David Booth; w3c semweb HCLS; HL7 ITS


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

 

>From a FHIR (or v2 or v3) perspective, the linkage will *have* to be by code + code system.  That's what appears in the instance and the RDF representations will need to be driven purely based on what appears in the instances.  The code + code system can be used to infer the concept represented by the code - with all of its associated properties and relationships.  Essentially "all v2/v3/FHIR elements with a code = [SNOMED Code X] and a code system of SNOMED_CT are specializations of the SNOMED Concept X".




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

+1-780-993-9501 <tel:%2B1-780-993-9501> 

 

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 Sat, Dec 20, 2014 at 3:33 PM, Vipul Kashyap <kashyap.vipul@gmail.com> wrote:

 

VK> Partially agree with you. Another reason for taking up RDF/OWL representation is to make these descriptions (business, clinical) user friendly. I have added this requirement to the wiki page.

Then we have a different notion of "user friendly" :>  The RDF syntax will almost certainly be less friendly for consumption than the XML syntax.  And in the end, the users shouldn't be consuming any of the syntaxes directly - they'll be consuming interfaces that systems use to expose the content, not the syntax directly. 

 

VK> I think one of the key goals of a semantic representation is to make the content user friendly and also “executable” at the same time. Whereas it definitely doesn’t make sense to expose the underlying RDF/XML serializations to the business/clinical users, there has been work e.g., triples, Manchester OWL syntax which can be leveraged to make the OWL expressions understandable to informatics users.

 

I don't expect we'll see broad uptake of the RDF syntax.  It will remain a specialized syntax for those wishing to use SPARQL, make inferences, etc.  That's a small fraction of the overall community.  However, if we build it into the reference implementations, it'll be straightforward for most servers to expose the RDF to those clients that actually need it.

 

So, we should definitely enumerate some of the use cases and perhaps flesh them out – so that they can be used to motivate the requirements – e.g., Clinical Decision Support, Quality Metrics, Clinical Trial Protocols, etc.

Especially for folks who are not familiar with FHIR – the requirements focusing on the RDF syntax are rather opaque and the value for the broader community is not evident.

VK> I am in agreement with your first approach. One approach is to model both FHIR Resources and Terminology Concepts as classes. For e.g.., we could model “Condition” as a class with “Diabetes” as a subclass with some kind of relationship (sameAs, subClassOf) between FHIR:Diabetes and Snomed:Diabetes, MedDRA:Diabetes, ICD11:Diabetes

The relationship would be that the concept represented by Condition.code was a specialization of Snomed:Diabetes, etc. (though it's unlikely the name would be that user-friendly).  It certainly wouldn't be a link to the overall class.

 

VK> I think one of the design choices we have to make is whether Snomed is a collection of codes or whether it’s better modeled as a set of classes with properties and relationships and perhaps instances as well.

I understand that the HL7 efforts have historically looked at the Information Model and Terminology as two different artifacts that can be “bound” together – but viewing both Terminological concepts and Information Model

Entities as classes provdes a common meta-model to facilitate the merge.

 

Just my 2 cents.

 

Thanks,

 

---Vipul

 

 

---Vipul

 

(Feel free to add your thoughts to the wiki page.)

 

 

Lloyd

 




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

+1-780-993-9501 <tel:%2B1-780-993-9501> 

 

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 Wed, Dec 10, 2014 at 2:59 PM, Vipul Kashyap <kashyap.vipul@gmail.com> wrote:

Good list, Lloyd. Would like to suggest some more additions (apologies if these have already been suggested).

 

·         Clearly articulate the value of the new RDF/RDFS/OWL representation over the current XML/JSON representation

·         Enablement of OWL/RDFS inference – so we could identify use cases that cannot be easily done based on the XML/JSON representation

·         A common OWL/RDFS representation for information model elements and medical terminology concepts.

 

Thoughts. Suggestions?

 

---Vipul

 

From: Lloyd McKenzie [mailto:lloyd@lmckenzie.com] 
Sent: Monday, December 08, 2014 1:36 PM
To: David Booth
Cc: w3c semweb HCLS; its@lists.hl7.org
Subject: Re: Minutes of last week's (Dec 2) HL7 ITS RDF Subgroup / W3C HCLS COI call -- Review of FHIR ontology approaches (cont.)

 

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 <tel:%2B1-780-993-9501> 

 

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/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

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Guessing input format: RRSAgent_Text_Format (score 1.00)

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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 Saturday, 20 December 2014 23:36:27 UTC

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