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

From: Robert Hausam <rrhausam@gmail.com>
Date: Tue, 10 Feb 2015 09:00:23 -0700
Message-ID: <CA+KThc_tQn-Dhwb_BihNRpAzWx9ehEisBdZx_8Rr48HFYHToOg@mail.gmail.com>
To: Lloyd McKenzie <lloyd@lmckenzie.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>
Lloyd, I do agree that if there is an explicit declaration of the number of
instances of "something", as with the subclass that you suggested, then the
reasoning on minimum cardinality clearly works - and as long as that's done
consistently it would be fine (although maybe cumbersome?).  I was thinking
of the other situation, without an explicit declaration and where the
instances are "counted".

Rob

On Sat, Feb 7, 2015 at 1:00 PM, Lloyd McKenzie <lloyd@lmckenzie.com> 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
> 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
>>
>>
>


-- 
Robert Hausam, MD
Hausam Consulting LLC
+1 (801) 949-1556
rrhausam@gmail.com
Received on Tuesday, 10 February 2015 16:01:40 UTC

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