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

From: Lloyd McKenzie <lloyd@lmckenzie.com>
Date: Sat, 7 Feb 2015 13:00:26 -0700
Message-ID: <CAJ860J+XOSynp-vQoHEcKS8WRTPnjEe=XsA-abpcOk-pffwn5Q@mail.gmail.com>
To: Robert Hausam <rrhausam@gmail.com>
Cc: Anthony Mallia <amallia@edmondsci.com>, Sajjad Hussain <hussain@cs.dal.ca>, David Booth <david@dbooth.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, "its@lists.hl7.org" <its@lists.hl7.org>
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
M: +1 587-334-1110 <1-587-334-1110>
W: gevityinc.com


*GEVITY**Informatics for a healthier world *

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On Sat, Feb 7, 2015 at 10:03 AM, Robert Hausam <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>
> 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
>> 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 Sat, Feb 7, 2015 at 9:03 AM, Anthony Mallia <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]
>>> *Sent:* Saturday, February 07, 2015 10:48 AM
>>> *To:* Sajjad Hussain
>>> *Cc:* David Booth; w3c semweb HCLS; 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
>>> 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, Feb 6, 2015 at 10:00 PM, Sajjad Hussain <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/#StructureOfOntologies
>>>
>>> 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
>>> 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, Feb 6, 2015 at 9:20 PM, David Booth <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>
>>>
>>>
>>> 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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>>>
>>
>>
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>
>
>
> --
> Robert Hausam, MD
> Hausam Consulting LLC
> +1 (801) 949-1556
> rrhausam@gmail.com
>
>
Received on Saturday, 7 February 2015 20:01:19 UTC

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