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

Hi Tony,

I don't think I'm following.  There should be no need for
custodian-specific ontologies.  The sender never needs to identify a
profile in the instance.  Some senders may choose to specify a profile in
the instance (or even 20 different profiles in the instance), but the
sender isn't required to pay any attention to any of them.

I'm not sure how any FHIR-based ontology would help to support
de-duplication.

Profiles aren't just created by WGs.  Profiles are any statement of
restrictions and extensions that can be associated with a resource or data
type - they can be created by anyone.

The FHIR RDF message will have to contain *exactly* the same information
that is in the JSON and XML instances - no more, no less.  Otherwise we
can't properly round-trip.  If you want to use the SNOMED ontology with an
instance, then you can import it yourself - it doesn't need to be imported
by the instance.


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 Sun, Dec 21, 2014 at 11:19 AM, Anthony Mallia <amallia@edmondsci.com>
wrote:
>
>  Hi Lloyd,
>
>
>
> It will be worth more discussion on the ontology structures.
>
>
>
> At the profile instance level (the FHIR RDF message) the ontologies are
> probably associated with the custodian of the record – they assigned the
> identities (unique within their ontology). When you query and aggregate
> FHIR RDF records from multiple custodians you know where the record came
> from and may have the same subject due to equivalence of the patients in
> the different ontologies (patient matching). A custodian based ontology
> allows the recipient to perform efficient de-duplication if they are
> caching the records.
>
>
>
> The Profile ontology has been negotiated in a WG (the custodian) and has
> its own ontology (and version). I am not sure if this needs to be single
> FHIR Resource or can be across many Resources.
>
>
>
> The Terminology ontologies come from the terminology custodians. E.g.
> IHTSDO and WHO
>
>
>
> If you don’t use the ontologies outside the FHIR RDF message then
> redundant information needs to be put into the FHIR RDF message to be able
> to round trip with the XML. If you are using OWL tools then importing the
> other ontologies makes a more comprehensive view and graph aggregation is
> natural.
>
>
>
> I don’t see why we can’t have it both ways.
>
>
>
> Tony
>
>
>
> *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com]
> *Sent:* Sunday, December 21, 2014 12:31 PM
> *To:* Anthony Mallia
> *Cc:* Vipul Kashyap; 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.)
>
>
>
> Hi Tony,
>
>
>
> Every profile instance will be its own ontology and will import the "base"
> ontology it's built on top of.  All instances will be bound to the base
> resource profile, but I think we should be cautious about importing
> referenced profiles.
>
>
>
> In FHIR you don't need to reference a profile in order to understand
> meaning (unlike with something like CDA).  If you stripped out all profile
> references from an instance, you'd be able to reconstitute them (though in
> some cases, doing so might be computationally intensive).  Certainly in the
> instance you would generally indicate what terminologies were used for
> coded elements, but that doesn't mean you want the ontologies for all of
> those terminologies to be present when you're trying to reason about an
> instance.  As Peter pointed, out, some ontologies are rather large, so you
> should only bring them in if you need them.  And there will certainly be
> terminologies referenced in instances for which the receiver doesn't have
> an ontology at all, so presuming to include an import just because the code
> system was referenced would actually often break things.
>
>
>
>
>
> 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 Sun, Dec 21, 2014 at 10:09 AM, Anthony Mallia <amallia@edmondsci.com>
> wrote:
>
> Lloyd,
>
> Each Profile ( or group of profiles) would be in its own ontology which
> might import the raw FHIR type ontology and restrict/extend it. This means
> that when we bind from the instance to the type, the type is in the named
> profile ontology (unambiguous).
>
> All importing in my approach is done by off the shelf OWL tools which are
> an additional layer I guess.
>
> I don’t understand how you can be interoperable if you don’t know the
> profile being used and the terminology terms referenced.
>
>
>
> Tony
>
>
>
> *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com]
> *Sent:* Sunday, December 21, 2014 12:00 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.)
>
>
>
> Hi Vipul,
>
>
>
> Yes, we'll be creating two different forms.  Instances will be expressed
> in RDF - and round-trippable between the JSON and XML syntaxes.  At that
> level, all you'll have is data - no "knowledge".  Profiles we will also
> convert to RDFS/OWL/something which will reflect things such as constraints
> on instances, vocabulary bindings, etc.  We may even define extensions on
> Profile which allow us to capture additional information (e.g. hierarchy)
> and represent that in our semantic web expressions as well.  (We should
> never include anything in our OWL expressions that isn't derivable from a
> Profile instance because it's the Profile that is the source of truth.)
>
>
>
> @Tony: Definitely agree they'll be separate ontologies.  The instance
> ontology might import the profile ontology if the instance happens to be
> tagged with a given profile, but my recommendation would be to leave the
> importing to be done by an additional layer - one that  knows what profiles
> and code systems you actually care (and have access to).  Relevant profiles
> may not be referenced and not all referenced code systems will be known.
>
>
>
>
>
> 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 Sat, Dec 20, 2014 at 4:35 PM, Vipul Kashyap <kashyap.vipul@gmail.com>
> wrote:
>
> 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
>
>
>
> 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
>
>
>
> 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
>
>
>
> 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
>
>    [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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