Re: Proposed RDF FHIR syntax feedback

Both OWL and RDFS are abstract models with no particular serialization.
Ontologies are usually serialized as RDF/XML (that's what's in a .owl file,
usually), but can just as easily be serialized to JSON-LD, Turtle, OWL
Abstract Syntax, Manchester Notation, or many others. Generally, RDF/XML
and Turtle are the easiest for existing toolkits to use, although many of
them are starting to support JSON-LD too.

Jim

On Fri, Mar 6, 2015 at 12:42 PM Lloyd McKenzie <lloyd@lmckenzie.com> wrote:

> XML, JSON, RDF or OWL, I expect, but yes based on the http accept header.
> The OWL representation would only exist for resources that are
> infrastructure (StructureDefinition, ValueSet, ConceptMap, etc.)  This
> might be one reason to push us towards OWL rather than RDFS, as I'm not
> sure whether RDFS has a distinct mime type that could be used in the Accept
> header.
>
>
> *Lloyd McKenzie*Consultant, Information Technology Services
> Gevity Consulting Inc.
>
>  E: lmckenzie@gevityinc.com
> M: +1 587-334-1110 <1-587-334-1110>
> W: gevityinc.com
>
>
> *GEVITY**Informatics for a healthier world *
>
> CONFIDENTIALITY – This communication is confidential and for the exclusive
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>
> NOTE: Unless explicitly stated otherwise, the opinions and positions
> expressed in this e-mail do not necessarily reflect those of my employer,
> my clients nor the organizations with whom I hold governance positions
>
> On Fri, Mar 6, 2015 at 8:36 AM, Anthony Mallia <amallia@edmondsci.com>
> wrote:
>
>>  Yes. A FHIR Resource instance will have a URL and the type that will be
>> returned is XML, JSON or RDF based on accept in the http (I assume).
>>
>>
>>
>> From the RDF viewpoint it must always points to an RDF individual. That
>> individual can be within the loaded ontologies (as a cache) or closure is
>> not achieved (which is OK).
>>
>> There are probably some nice tool plug in possibilities for pulling and
>> importing a resource which cannot be found in the loaded ontologies (the
>> wider definition of ontology which includes instances).
>>
>>
>>
>> The FHIR Resource type maybe has the same mechanism? RDF always requires
>> a Class – possibly a Class in an Ontology which contains the other classes
>> in that Resource.
>>
>> If the FHIR Resource Class is not available locally it might be retrieved
>> and imported by the same mechanism – the URI of the Resource type with
>> “accept RDF” retrieves the Ontology for the Resource.
>>
>>
>>
>> Some thoughts to try to move this along.
>>
>>
>>
>> Tony
>>
>>
>>
>>
>>
>> *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com]
>> *Sent:* Friday, March 06, 2015 10:10 AM
>>
>> *To:* Anthony Mallia
>> *Cc:* Marc Twagirumukiza; David Booth; HL7 ITS; owner-its@lists.hl7.org;
>> w3c semweb HCLS
>> *Subject:* Re: Proposed RDF FHIR syntax feedback
>>
>>
>>
>> Well, the situation we're in is that there is an official URL for each
>> resource and that's the only place you can be guaranteed to receive either
>> the instance (RDF) or type (OWL).  And that will be true for both
>> HL7-defined artifacts as well as those defined by anyone else.
>>
>>
>>
>> *Lloyd McKenzie *Consultant, Information Technology Services
>> Gevity Consulting Inc.
>>
>>  E: lmckenzie@gevityinc.com
>> M: +1 587-334-1110 <1-587-334-1110>
>> W: gevityinc.com
>>
>>
>> *GEVITY **Informatics for a healthier world *
>>
>> CONFIDENTIALITY – This communication is confidential and for the
>> exclusive use of its intended recipients. If you have received this
>> communication by error, please notify the sender and delete the message
>> without copying or disclosing it*.*
>>
>> NOTE: Unless explicitly stated otherwise, the opinions and positions
>> expressed in this e-mail do not necessarily reflect those of my employer,
>> my clients nor the organizations with whom I hold governance positions
>>
>>
>>
>> On Fri, Mar 6, 2015 at 7:25 AM, Anthony Mallia <amallia@edmondsci.com>
>> wrote:
>>
>> Lloyd – that is called a pun and is possible in that the same IRI for
>> both an individual and a class. The impact on reasoners may be complex.
>>
>>
>>
>> Tony
>>
>>
>>
>>
>>
>> *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com]
>> *Sent:* Friday, March 06, 2015 9:06 AM
>>
>>
>> *To:* Anthony Mallia
>> *Cc:* Marc Twagirumukiza; David Booth; HL7 ITS; owner-its@lists.hl7.org;
>> w3c semweb HCLS
>> *Subject:* Re: Proposed RDF FHIR syntax feedback
>>
>>
>>
>> Hi Tony,
>>
>>
>>
>> I thought it was possible to have both instance definitions and class
>> definitions at the same IRI?
>>
>>
>>
>> *Lloyd McKenzie *Consultant, Information Technology Services
>> Gevity Consulting Inc.
>>
>>  E: lmckenzie@gevityinc.com
>> M: +1 587-334-1110 <1-587-334-1110>
>> W: gevityinc.com
>>
>>
>> *GEVITY **Informatics for a healthier world *
>>
>> CONFIDENTIALITY – This communication is confidential and for the
>> exclusive use of its intended recipients. If you have received this
>> communication by error, please notify the sender and delete the message
>> without copying or disclosing it*.*
>>
>> NOTE: Unless explicitly stated otherwise, the opinions and positions
>> expressed in this e-mail do not necessarily reflect those of my employer,
>> my clients nor the organizations with whom I hold governance positions
>>
>>
>>
>> On Fri, Mar 6, 2015 at 6:59 AM, Anthony Mallia <amallia@edmondsci.com>
>> wrote:
>>
>> Lloyd,
>>
>>
>>
>> I think the thread has mutated from the prefix discussion which seems to
>> be closed to the IRI discussion which needs a lot more thought.
>>
>>
>>
>> In RDF the IRI points to the RDF individual or entity that is being
>> referenced not its FHIR structural definition. However the FHIR URIs should
>> give us identity uniqueness.
>>
>> If we were to get distributed RDF Ontology support where the IRI’s might
>> be network dereferenceable we would have a conflict.
>>
>>
>>
>> Tony
>>
>>
>>
>>
>>
>> *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com]
>> *Sent:* Friday, March 06, 2015 8:46 AM
>> *To:* Marc Twagirumukiza
>> *Cc:* Anthony Mallia; David Booth; HL7 ITS; owner-its@lists.hl7.org; w3c
>> semweb HCLS
>>
>>
>> *Subject:* Re: Proposed RDF FHIR syntax feedback
>>
>>
>>
>> The URIs are already defined.  We use a base of ..../fhir/ for code
>> systems and ..../fhir/vs/ for value sets.  And it's entirely possible to
>> have both reactionSeverity and conditionSeverity and numerous other
>> orthogonal severity value sets.
>>
>>
>>
>> This discussion is purely about what prefixes we define for our
>> "standard" representation created by automatic transformation of XML or
>> JSON to RDF.  And my leaning is to define only one - "fhir" = "
>> http://hl7.org/fhir/".  In terms of consuming source data, we would be
>> able to consume RDF regardless of what prefixes it chose to declare, but we
>> wouldn't round-trip any of them.
>>
>>
>>
>> *Lloyd McKenzie *Consultant, Information Technology Services
>> Gevity Consulting Inc.
>>
>>  E: lmckenzie@gevityinc.com
>> M: +1 587-334-1110 <1-587-334-1110>
>> W: gevityinc.com
>>
>>
>> *GEVITY **Informatics for a healthier world *
>>
>> CONFIDENTIALITY – This communication is confidential and for the
>> exclusive use of its intended recipients. If you have received this
>> communication by error, please notify the sender and delete the message
>> without copying or disclosing it*.*
>>
>> NOTE: Unless explicitly stated otherwise, the opinions and positions
>> expressed in this e-mail do not necessarily reflect those of my employer,
>> my clients nor the organizations with whom I hold governance positions
>>
>>
>>
>> On Fri, Mar 6, 2015 at 1:51 AM, Marc Twagirumukiza <
>> marc.twagirumukiza@agfa.com> wrote:
>>
>> Tony,
>> +1  to declare http://hl7.org/fhir/ as FHIR:
>> For IRI:
>> I would use  "http://hl7.org/fhir/severity/ <http://hl7.org/fhir/>"
>> rather than  http://hl7.org/fhir/vs/reactionSeverity
>> To disambiguate from a ValueSet to another will be done with the pattern
>> model.
>>
>> Otherwise we may end up with multiple
>> http://hl7.org/fhir/vs/reactionSeverity ,
>> http://hl7.org/fhir/vs/conditionSeverity
>> <http://hl7.org/fhir/vs/reactionSeverity> , etc.
>>
>> Kind Regards,
>>
>> * Marc *
>>  ------------------------------
>>
>> Click on link to read important disclaimer:
>> http://www.agfahealthcare.com/maildisclaimer
>>
>>
>>
>> From:        Anthony Mallia <amallia@edmondsci.com>
>> To:        Lloyd McKenzie <lloyd@lmckenzie.com>
>> Cc:        Marc Twagirumukiza/AXPZC/AGFA@AGFA, David Booth <
>> david@dbooth.org>, HL7 ITS <its@lists.hl7.org>, "owner-its@lists.hl7.org"
>> <owner-its@lists.hl7.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
>> Date:        05/03/2015 19:14
>> Subject:        RE: Proposed RDF FHIR syntax feedback
>>  ------------------------------
>>
>>
>>
>>
>> Lloyd,
>> I agree. The use of prefix is a presentation issue and does not change
>> the behavior of reasoners etc.
>> If a user wants to add prefixes it can be done locally based on the IRI
>> structure which is what we need to focus on.
>> However we do want to use the dereferenceable URIs that FHIR designates
>> so we can get at the semantic definition if needed.
>>
>> So a proposed position will be to declare http://hl7.org/fhir/ as FHIR:
>> but the dereferenceable URI probably has
>> http://hl7.org/fhir/structuredefinition/ so we should use this maybe in
>> an annotation not the name IRI.
>> I was just working on reactionSeverity ValueSet which would have an IRI
>> of http://hl7.org/fhir/vs/reactionSeverity and its display will be
>> determined by rdfs:label value derived from ValueSet.name.
>>
>> Tony
>>
>> *From:* Lloyd McKenzie [mailto:lloyd@lmckenzie.com <lloyd@lmckenzie.com>]
>>
>> * Sent:* Thursday, March 05, 2015 12:25 PM
>> * To:* Anthony Mallia
>> * Cc:* Marc Twagirumukiza; David Booth; HL7 ITS; owner-its@lists.hl7.org;
>> w3c semweb HCLS
>> * Subject:* Re: Proposed RDF FHIR syntax feedback
>>
>> Hi Tony,
>>
>> I wouldn't treat structure definitions as distinct from any other.  The
>> "vs" namespace is just for FHIR-defined valuesets.  There will be 100s of
>> value set namespaces out in the real world once more people start
>> profiling, so I wouldn't necessarily recommend giving prefixes to any of
>> them.  They don't mean anything special.
>>
>> *Lloyd McKenzie*
>> Consultant, Information Technology Services
>> Gevity Consulting Inc.
>>
>>  E: lmckenzie@gevityinc.com
>> M: +1 587-334-1110 <1-587-334-1110>
>> W: gevityinc.com
>>
>> *GEVITY*
>> * Informatics for a healthier world *
>>
>> CONFIDENTIALITY – This communication is confidential and for the
>> exclusive use of its intended recipients. If you have received this
>> communication by error, please notify the sender and delete the message
>> without copying or disclosing it*.*
>>
>> NOTE: Unless explicitly stated otherwise, the opinions and positions
>> expressed in this e-mail do not necessarily reflect those of my employer,
>> my clients nor the organizations with whom I hold governance positions
>>
>> On Thu, Mar 5, 2015 at 9:25 AM, Anthony Mallia <amallia@edmondsci.com>
>> wrote:
>> Marc,
>> There is probably some right balance between having the prefix state the
>> namespace or to have the dot notation as in FHIR.
>> However there are some base FHIR URIs which might deserve prefixes:
>>
>> http://hl7.org/fhir/structuredefinition/ (when the FHIR website moves
>> there)
>> http://hl7.org/fhir/vs/ which supports the valuesets
>>
>> There may be more in FHIR that I have not yet discovered and Lloyd will
>> know what they are.
>>
>> Regards,
>>
>> Tony
>>
>>
>> *From:* Marc Twagirumukiza [mailto:marc.twagirumukiza@agfa.com]
>> * Sent:* Thursday, March 05, 2015 3:42 AM
>> * To:* Lloyd McKenzie
>> * Cc:* David Booth; HL7 ITS; owner-its@lists.hl7.org; w3c semweb HCLS
>> * Subject:* Re: Proposed RDF FHIR syntax feedback
>>
>> I fully support having a single "fhir" prefix. This will help at 'FHIR
>> ontology' development level with making reusable predicates.
>> Also at instance level it would help to include something that identifies
>> order for array elements
>> Kind Regards,
>>
>> * Marc Twagirumukiza | Agfa HealthCare*
>> Senior Clinical Researcher | HE/Advanced Clinical Applications Research
>> T  +32 3444 8188 | M  +32 499 713 300
>>
>> http://www.agfahealthcare.com
>> http://blog.agfahealthcare.com
>>
>>
>>  ------------------------------
>>
>>
>> Click on link to read important disclaimer:
>> http://www.agfahealthcare.com/maildisclaimer
>>
>>
>>
>> From:        Lloyd McKenzie <lloyd@lmckenzie.com>
>> To:        David Booth <david@dbooth.org>
>> Cc:        w3c semweb HCLS <public-semweb-lifesci@w3.org>, HL7 ITS <
>> its@lists.hl7.org>
>> Date:        04/03/2015 19:33
>> Subject:        Proposed RDF FHIR syntax feedback
>> Sent by:        owner-its@lists.hl7.org
>>
>>
>>  ------------------------------
>>
>>
>>
>>
>>
>> Several comments:
>> 1. I'm not clear on the benefit of defining prefixes for every resource
>> and type.  The alternative is a single "fhir" prefix
>> 2. We need to include something in the instances that identifies order
>> for array elements
>> 3. Do we need to declare type everywhere?  Quite often, the type can be
>> inferred from the context and the property name by consulting the
>> resource/data type definition ontology.  Explicitly listing types
>> everywhere adds verbosity to the instances and also adds complexity to the
>> conversion process
>> 4. Not sure why we have nodes underneath "div".  Can't we just have "div"
>> be of type string for our purposes?
>>
>> Additional things to add to our example:
>> - a nested structure (e.g. DiagnosticReport.image)
>> - a reference to an external resource (outside the bundle) and reference
>> to something within the bundle (local, full reference-version independent,
>> full reference-version dependent)
>> - a codeable concept with multiple codings
>> - a coding with version declared
>> - a coding with valueset declared
>> - a coding with code but no system
>> - an instance of identifier
>> - an "id" attribute on an element
>> - a reference to the same id attribute (likely from an extension)
>> - an extension with a simple type
>> - an extension with a complex type
>> - an extension that repeats and has multiple values
>> - an element that is an instance a choice (element name is something[x])
>> - a reference to Questionnaire or one of the other resources that has
>> recursion.  Could just be added to the bundle
>>
>> *Lloyd McKenzie*
>> Consultant, Information Technology Services
>> Gevity Consulting Inc.
>>
>>  E: lmckenzie@gevityinc.com
>> M: +1 587-334-1110 <1-587-334-1110>
>> W: gevityinc.com
>>
>> *GEVITY*
>> * Informatics for a healthier world *
>>
>> CONFIDENTIALITY – This communication is confidential and for the
>> exclusive use of its intended recipients. If you have received this
>> communication by error, please notify the sender and delete the message
>> without copying or disclosing it*.*
>>
>> NOTE: Unless explicitly stated otherwise, the opinions and positions
>> expressed in this e-mail do not necessarily reflect those of my employer,
>> my clients nor the organizations with whom I hold governance positions
>>
>>
>> On Tue, Mar 3, 2015 at 12:05 PM, <david@dbooth.org> wrote:
>> David Booth <david@dbooth.org> has invited you to HL7/W3C FHIR RDF &
>> Validation/Translation Task Force
>>
>>
>>
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