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Re: Summary of HL7 RDF / W3C COI call: FHIR Ontology Requirements

From: David Booth <david@dbooth.org>
Date: Mon, 09 Feb 2015 15:18:37 -0500
Message-ID: <54D9161D.9000809@dbooth.org>
To: Lloyd McKenzie <lloyd@lmckenzie.com>, Anthony Mallia <amallia@edmondsci.com>
CC: Robert Hausam <rrhausam@gmail.com>, Sajjad Hussain <hussain@cs.dal.ca>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <its@lists.hl7.org>
Okay, I've added another option:
[[
Option F: '''(MUST)''' The FHIR ontology must support inference, both in 
use cases based on the open world assumption and in use cases based on 
the closed world assumption.<br>
]]

David

On 02/09/2015 02:44 PM, Lloyd McKenzie wrote:
> Well, interoperability is defined by the base specification, not by any
> particular technology representation (schema, schematron, OWL, etc.)
>   What really matters for interoperability is the RDF format, not the
> OWL.  We have two use-cases for the OWL representation - instance
> validation and reasoning.  The first requires closed world.  The latter
> could use open or closed world depending on the type of reasoning desired.
>
> I'm ok with asserting SHALL for both.  I think both are doable and both
> are useful, so we may as well get them both done.
>
> *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 /*
>
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>
> On Mon, Feb 9, 2015 at 12:11 PM, Anthony Mallia <amallia@edmondsci.com
> <mailto:amallia@edmondsci.com>> wrote:
>
>     David,
>     I believe this question brings into play the definition of
>     interoperability.
>     With current technology it seems that we can get interoperability
>     only with a closed world assumption. It all depends on the
>     definition of interoperability (which has not been formally defined)
>     but the expectation is that the structure and semantics of an
>     exchange are understood computationally at run time.
>
>     I would invert Option C to MUST for closed and MAY for open. Or we
>     can choose another option.
>
>     Tony
>
>     -----Original Message-----
>     From: David Booth [mailto:david@dbooth.org <mailto:david@dbooth.org>]
>     Sent: Monday, February 09, 2015 1:50 PM
>     To: Lloyd McKenzie; Robert Hausam
>     Cc: Anthony Mallia; Sajjad Hussain; w3c semweb HCLS;
>     its@lists.hl7.org <mailto:its@lists.hl7.org>
>     Subject: Re: Summary of HL7 RDF / W3C COI call: FHIR Ontology
>     Requirements
>
>     I have listed the proposed wordings for requirement #11 that I have
>     seen so far:
>     http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements#11._Enable_Inference
>     [[
>     #11. Enable Inference
>     Option A: (MUST) The FHIR ontology must enable OWL/RDFS inference.
>     Option B: (MUST) The FHIR ontology must enable OWL/RDFS inference
>     with monotonicity and open world assumption.
>     Option C: (MUST) The FHIR ontology must enable OWL/RDFS inference
>     under the open world assumption. However, some uses of the ontology
>     may require use of the closed world assumption.
>     Option D: (SHOULD) The FHIR ontology should allow expressions
>     enforcing both closed world and open-world reasoning against instances.
>     Option E: (MUST) The FHIR ontology must allow expressions enforcing
>     either closed world or open-world reasoning against instances.
>     Option F: Drop this requirement
>     ]]
>
>     This includes option C that I just added.
>
>     If anyone has any other suggested wording changes for this or any
>     other requirement, please propose them now so that we can finalize
>     them on tomorrow's teleconference.
>
>     Thanks,
>     David
>
>     On 02/07/2015 03:00 PM, Lloyd McKenzie wrote:
>      > Hi Rob,
>      >
>      > It was working just fine for minimum cardinality.  If you have a rule
>      > that says "must have at least one" and your instances says "I'm a
>      > subclass of the things that have exactly zero", the validator will
>      > detect the error.  And we can do that because we know exactly what
>      > elements can potentially be allowed and can thus assert what has a
>      > cardinality of zero if they're missing from the instance.
>      >
>      > *Lloyd McKenzie
>      > *Consultant, Information Technology Services Gevity Consulting Inc.
>      >
>      > E: lmckenzie@gevityinc.com <mailto:lmckenzie@gevityinc.com>
>     <mailto:lmckenzie@gevityinc.com <mailto:lmckenzie@gevityinc.com>>
>      > M: +1 587-334-1110 <tel:%2B1%20587-334-1110> <tel:1-587-334-1110
>     <tel:1-587-334-1110>>
>      > W: gevityinc.com <http://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 Sat, Feb 7, 2015 at 10:03 AM, Robert Hausam
>     <rrhausam@gmail.com <mailto:rrhausam@gmail.com>
>      > <mailto:rrhausam@gmail.com <mailto:rrhausam@gmail.com>>> wrote:
>      >
>      >     Lloyd, that's certainly correct with the "upper bound", given the
>      >     conditions that you describe.  If an instance has 5 of
>     "something"
>      >     when it's declared that it should have 4, then the reasoner can
>      >     clearly determine that the instance is invalid.  However,
>     using OWA,
>      >     you can't do this for the "lower bound" of cardinality, as there
>      >     always may be another "something" out there that the reasoner
>     is not
>      >     aware of.  I'm sure that we all know all of this, but it
>     definitely
>      >     makes validating integrity constraints using pure OWL in many
>     cases
>      >     either difficult or impossible.
>      >
>      >     I've found this discussion of the issue from Clark&Parsia to
>     be useful:
>      >
>      > http://clarkparsia.com/pellet/icv/
>      >
>      >     This is obviously referring to a proprietary solution (their
>     Pellet
>      >     reasoner and the ICV extension), and certainly there are other
>      >     techniques and options available.  But I think this does
>     frame the
>      >     issue and some potential solutions for it pretty well.
>      >
>      >     So, getting back to the ontology requirements, I think we clearly
>      >     will need to be able to use *both* the open and closed world
>      >     assumptions, so maybe we should say that we *MUST* be able to do
>      >     both? - something like:
>      >
>      >     MUST: OWL ontology will allow expressions enforcing either closed
>      >     world or open-world reasoning against instances.
>      >
>      >     Rob
>      >
>      >     On Sat, Feb 7, 2015 at 9:07 AM, Lloyd McKenzie
>     <lloyd@lmckenzie.com <mailto:lloyd@lmckenzie.com>
>      >     <mailto:lloyd@lmckenzie.com <mailto:lloyd@lmckenzie.com>>> wrote:
>      >
>      >         Hi Tony,
>      >
>      >         If you declare an instance has 4 of something, that those
>      >         instances are disjoint and that the instance is a subclass of
>      >         those instances that allow only 3 of something, the reasoner
>      >         *should* declare the instance invalid.  Certainly I was
>     able to
>      >         get that happening w/ Protege when I used that approach
>     with the
>      >         RIM.
>      >
>      >
>      >         Lloyd
>      >
>      >         *Lloyd McKenzie
>      >         *Consultant, Information Technology Services
>      >         Gevity Consulting Inc.
>      >
>      >         E: lmckenzie@gevityinc.com
>     <mailto:lmckenzie@gevityinc.com> <mailto:lmckenzie@gevityinc.com
>     <mailto:lmckenzie@gevityinc.com>>
>      >         M: +1 587-334-1110 <tel:%2B1%20587-334-1110>
>     <tel:1-587-334-1110 <tel:1-587-334-1110>>
>      >         W: gevityinc.com <http://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 Sat, Feb 7, 2015 at 9:03 AM, Anthony Mallia
>      >         <amallia@edmondsci.com <mailto:amallia@edmondsci.com>
>     <mailto:amallia@edmondsci.com <mailto:amallia@edmondsci.com>>> wrote:
>      >
>      >             Lloyd,____
>      >
>      >             This is the pattern that is used by TopQuadrant in
>     its XSD
>      >             to OWL conversion and the FHIR generation was shared by
>      >             Cecil. The advantage of this mechanism is that all
>      >             subclasses of Patient also are subclasses of the
>     Anonymous
>      >             Ancestor which is the Class Expression
>     “hasPhoneNumber max 3
>      >             PhoneNumber”.____
>      >
>      >             __ __
>      >
>      >             Having done that however the reasoned does not
>     invalidate if
>      >             there are 4 phone numbers (i.e. Open World).____
>      >
>      >             __ __
>      >
>      >             Tony____
>      >
>      >             __ __
>      >
>      >             *From:*Lloyd McKenzie [mailto:lloyd@lmckenzie.com
>     <mailto:lloyd@lmckenzie.com>
>      >             <mailto:lloyd@lmckenzie.com
>     <mailto:lloyd@lmckenzie.com>>]
>      >             *Sent:* Saturday, February 07, 2015 10:48 AM
>      >             *To:* Sajjad Hussain
>      >             *Cc:* David Booth; w3c semweb HCLS; its@lists.hl7.org
>     <mailto:its@lists.hl7.org>
>      >             <mailto:its@lists.hl7.org <mailto:its@lists.hl7.org>>
>      >             *Subject:* Re: Summary of HL7 RDF / W3C COI call: FHIR
>      >             Ontology Requirements____
>      >
>      >             __ __
>      >
>      >             You can also close the world declaritively.  If I have a
>      >             Patient with 3 phone numbers, the instance can
>     declare it's
>      >             a subclass of Patients with an upper bound of 3 on the
>      >             number of phone numbers. You can do similar things
>     for the
>      >             vocabulary. It's verbose, but it works.____
>      >
>      >
>      >             ____
>      >
>      >             *Lloyd McKenzie
>      >             *Consultant, Information Technology Services
>      >             Gevity Consulting Inc.____
>      >
>      >             E: lmckenzie@gevityinc.com
>     <mailto:lmckenzie@gevityinc.com> <mailto:lmckenzie@gevityinc.com
>     <mailto:lmckenzie@gevityinc.com>>
>      >             M: +1 587-334-1110 <tel:%2B1%20587-334-1110>
>     <tel:1-587-334-1110 <tel:1-587-334-1110>>
>      >             W: gevityinc.com <http://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, Feb 6, 2015 at 10:00 PM, Sajjad Hussain
>      >             <hussain@cs.dal.ca <mailto:hussain@cs.dal.ca>
>     <mailto:hussain@cs.dal.ca <mailto:hussain@cs.dal.ca>>> wrote:____
>      >
>      >             I agree with Lloyd. However, we need to keep in mind that
>      >             semantic web standard languages especially OWL rely
>     on Open
>      >             World Assumption (OWA):
>      >
>      >
>      >
>     http://www.w3.org/TR/2004/REC-owl-guide-20040210/#StructureOfOntologie
>      > s
>      >
>      >             For validation purposes, while respecting OWA, it is
>     still
>      >             possible validate data based on " Scoped Negation as
>     Failure":
>      >
>      >
>      > https://ai.wu.ac.at/~polleres/publications/poll-etal-2006b.pdf
>      >
>      >             Best,
>      >             Sajjad
>      >
>      >             ******************************************____
>      >
>      >
>      >
>      >             On 2/6/15 11:29 PM, Lloyd McKenzie wrote:____
>      >
>      >                 I expect we'll need to be able to handle both
>     open-world
>      >                 and closed-world versions of the ontology.
>     Closed-world
>      >                 is essential to validation.  If a profile says
>     something
>      >                 is 1..1 and the instance doesn't have it, then that
>      >                 needs to be flagged as an error, which open-world
>      >                 wouldn't do.  On the other hand, reasoners may
>     well need
>      >                 to operate with some degree of open-world.  The fact
>      >                 something isn't present in the EHR doesn't
>     necessarily
>      >                 mean it isn't true.  I'd be happy for us to include
>      >                 something like this: ____
>      >
>      >                 __ __
>      >
>      >                 SHOULD: OWL ontology should allow expressions
>     enforcing
>      >                 both closed world and open-world reasoning against
>      >                 instances.____
>      >
>      >
>      >                 ____
>      >
>      >                 *Lloyd McKenzie
>      >                 *Consultant, Information Technology Services
>      >                 Gevity Consulting Inc.____
>      >
>      >                 E: lmckenzie@gevityinc.com
>     <mailto:lmckenzie@gevityinc.com> <mailto:lmckenzie@gevityinc.com
>     <mailto:lmckenzie@gevityinc.com>>
>      >                 M: +1 587-334-1110 <tel:%2B1%20587-334-1110>
>     <tel:1-587-334-1110 <tel:1-587-334-1110>>
>      >                 W: gevityinc.com <http://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, Feb 6, 2015 at 9:20 PM, David Booth
>      >                 <david@dbooth.org <mailto:david@dbooth.org>
>     <mailto:david@dbooth.org <mailto:david@dbooth.org>>>
>      > wrote:____
>      >
>      >                 Hi Sajjad,
>      >
>      >                 On 02/04/2015 07:12 AM, Sajjad Hussain wrote:____
>      >
>      >                 Hi All,
>      >
>      >                 Responding to Action # 2 carried during last call:
>      >
>      > http://www.w3.org/2015/02/03-hcls-minutes.html#action02
>      >
>      > <http://www.w3.org/2015/02/03-hcls-minutes.html#action02>
>      >
>      >                 I would suggest the following wording for FHIR
>     Ontology
>      >                 Requirement # 11
>      >
>       (http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements#11._Enable_Inference
>      >
>      > <http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements>)
>      >
>      >                 11. Enable Inference
>      >                 (MUST) The FHIR ontology must enable OWL/RDFS
>     inference with
>      >                 monotonicity and open world assumption [1]
>      >                 [1]
>      > http://www.cs.man.ac.uk/~drummond/presentations/OWA.pdf
>      >
>       <http://www.cs.man.ac.uk/%7Edrummond/presentations/OWA.pdf>
>      >
>      > <http://www.cs.man.ac.uk/%7Edrummond/presentations/OWA.pdf>____
>      >
>      >
>      >                 I would expect the closed world assumption to be used
>      >                 quite a lot to  in data validation and perhaps other
>      >                 ways, so I would be uncomfortable having that as
>     a MUST
>      >                 requirement.
>      >
>      >                 David Booth____
>      >
>      >                 Best regards,
>      >                 Sajjad
>      >
>      >                 ***************************************************
>      > ____
>      >
>      >
>      >                 On 2/3/15 10:45 PM, David Booth wrote:____
>      >
>      >                 On today's call we almost finished working out
>     our FHIR
>      >                 ontology
>      >                 requirements.  Only two points remain to be resolved:
>      >
>      > http://wiki.hl7.org/index.php?title=FHIR_Ontology_Requirements
>      >
>      >                    - Sajjad suggested that the wording of requirement
>      >                 #11 be changed to
>      >                 be clearer, and agreed to suggest new wording.
>     Current
>      >                 wording:
>      >                 "Enable Inference: The FHIR ontology must enable
>      >                 OWL/RDFS inference."
>      >
>      >                   - Paul Knapp noted that requirement #16 is
>     related to
>      >                 requirement #2,
>      >                 and suggested that they might be merged.
>      >
>      >                 We did not get to other agenda today.
>      >
>      >                 The full meeting log is here:
>      > http://www.w3.org/2015/02/03-hcls-minutes.html
>      >
>      >                 Thanks!
>      >                 David Booth
>      >
>      >                 ____
>      >
>      >                 __ __
>      >
>      >
>      >
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>      >     --
>      >     Robert Hausam, MD
>      >     Hausam Consulting LLC
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Received on Monday, 9 February 2015 20:19:13 UTC

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