Re: Proposed RDF FHIR syntax feedback

Where we'll have a particular challenge is where the RDF and OWL
representations can both be expressed using the same sytnax.  It may be
that the solution there is to return both the instance and class
information.  Is there a distinct mime-type for JSON-LD from regular JSON?


*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 *

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On Fri, Mar 6, 2015 at 10:59 AM, Jim McCusker <mccusj@rpi.edu> wrote:

> 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 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 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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>>