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

From: Anthony Mallia <amallia@edmondsci.com>
Date: Mon, 9 Feb 2015 19:11:27 +0000
To: David Booth <david@dbooth.org>, Lloyd McKenzie <lloyd@lmckenzie.com>, Robert Hausam <rrhausam@gmail.com>
CC: Sajjad Hussain <hussain@cs.dal.ca>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <its@lists.hl7.org>
Message-ID: <D5F9B7889182464788941B4EEDE3E81FFD469D1D@Awacs.esci.com>
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] 
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
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>
> 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 Sat, Feb 7, 2015 at 10:03 AM, Robert Hausam <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>> 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>
>         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 Sat, Feb 7, 2015 at 9:03 AM, Anthony Mallia
>         <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>]
>             *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>
>             *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>
>             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, Feb 6, 2015 at 10:00 PM, Sajjad Hussain
>             <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>
>                 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, Feb 6, 2015 at 9:20 PM, David Booth
>                 <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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>     Hausam Consulting LLC
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Received on Monday, 9 February 2015 19:40:29 UTC

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