RE: Proposed RDF FHIR syntax feedback

Lloyd,
RDF, RDFS and OWL can all be expressed in RDF/XML. I am using it all the time out of Protégé.

Tony


From: Lloyd McKenzie [mailto:lloyd@lmckenzie.com]
Sent: Friday, March 06, 2015 2:17 PM
To: Jim McCusker
Cc: Anthony Mallia; Marc Twagirumukiza; David Booth; HL7 ITS; owner-its@lists.hl7.org; w3c semweb HCLS
Subject: 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<mailto:lmckenzie@gevityinc.com>
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GEVITY
Informatics for a healthier world

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On Fri, Mar 6, 2015 at 10:59 AM, Jim McCusker <mccusj@rpi.edu<mailto: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<mailto: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<mailto:lmckenzie@gevityinc.com>
M: +1 587-334-1110<tel:1-587-334-1110>
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Informatics for a healthier world

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On Fri, Mar 6, 2015 at 8:36 AM, Anthony Mallia <amallia@edmondsci.com<mailto: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<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<mailto: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<mailto:lmckenzie@gevityinc.com>
M: +1 587-334-1110<tel:1-587-334-1110>
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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.

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On Fri, Mar 6, 2015 at 7:25 AM, Anthony Mallia <amallia@edmondsci.com<mailto: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<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<mailto: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<mailto:lmckenzie@gevityinc.com>
M: +1 587-334-1110<tel:1-587-334-1110>
W: gevityinc.com<http://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<mailto: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<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<mailto: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<mailto:lmckenzie@gevityinc.com>
M: +1 587-334-1110<tel:1-587-334-1110>
W: gevityinc.com<http://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<mailto: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
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From:        Anthony Mallia <amallia@edmondsci.com<mailto:amallia@edmondsci.com>>
To:        Lloyd McKenzie <lloyd@lmckenzie.com<mailto:lloyd@lmckenzie.com>>
Cc:        Marc Twagirumukiza/AXPZC/AGFA@AGFA, David Booth <david@dbooth.org<mailto:david@dbooth.org>>, HL7 ITS <its@lists.hl7.org<mailto:its@lists.hl7.org>>, "owner-its@lists.hl7.org<mailto:owner-its@lists.hl7.org>" <owner-its@lists.hl7.org<mailto:owner-its@lists.hl7.org>>, w3c semweb HCLS <public-semweb-lifesci@w3.org<mailto: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]
Sent: Thursday, March 05, 2015 12:25 PM
To: Anthony Mallia
Cc: Marc Twagirumukiza; David Booth; HL7 ITS; owner-its@lists.hl7.org<mailto: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<mailto:lmckenzie@gevityinc.com>
M: +1 587-334-1110<tel:1-587-334-1110>
W: gevityinc.com<http://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<mailto: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<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<mailto: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://www.agfahealthcare.com/>
http://blog.agfahealthcare.com<http://blog.agfahealthcare.com/>

________________________________

Click on link to read important disclaimer: http://www.agfahealthcare.com/maildisclaimer




From:        Lloyd McKenzie <lloyd@lmckenzie.com<mailto:lloyd@lmckenzie.com>>
To:        David Booth <david@dbooth.org<mailto:david@dbooth.org>>
Cc:        w3c semweb HCLS <public-semweb-lifesci@w3.org<mailto:public-semweb-lifesci@w3.org>>, HL7 ITS <its@lists.hl7.org<mailto:its@lists.hl7.org>>
Date:        04/03/2015 19:33
Subject:        Proposed RDF FHIR syntax feedback
Sent by:        owner-its@lists.hl7.org<mailto: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<mailto:lmckenzie@gevityinc.com>
M: +1 587-334-1110<tel:1-587-334-1110>
W: gevityinc.com<http://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<mailto:david@dbooth.org>> wrote:
David Booth <david@dbooth.org<mailto:david@dbooth.org>> has invited you to HL7/W3C FHIR RDF & Validation/Translation Task Force


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