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

From: Robert Hausam <rrhausam@gmail.com>
Date: Sat, 7 Feb 2015 10:45:43 -0700
Message-ID: <CA+KThc_jWr-OKzWrQBXj5p5wkgpk=F+bmZZcq_S2LRW9+emyZQ@mail.gmail.com>
To: Anthony Mallia <amallia@edmondsci.com>
Cc: Lloyd McKenzie <lloyd@lmckenzie.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>
Tony, Pellet 2.2.0 is available for Protege 5.0.0-beta-15 (I just
checked).  I'm not sure what's happened or will be happening (if anything)
with Pellet 3, as I don't see a further reference to it anywhere on their
Web site (and I hadn't been checking on it for a while).  As I recall, the
Pellet ICV preview had to be used outside of Protege (I think that's
correct?).  Pellet ICV is apparently no longer available for download, but
I expect that I should have a copy of it somewhere (I'll need to do a
little looking).

Rob

On Sat, Feb 7, 2015 at 10:13 AM, Anthony Mallia <amallia@edmondsci.com>
wrote:

>  Rob,
>
> Thanks for the great reference. Do you know whether Pellet and the ICV
> extension is available for Protégé 5?
>
>
>
> Tony
>
>
>
>
>
> *From:* Robert Hausam [mailto:rrhausam@gmail.com]
> *Sent:* Saturday, February 07, 2015 12:06 PM
> *To:* Lloyd McKenzie
> *Cc:* Anthony Mallia; Sajjad Hussain; David Booth; w3c semweb HCLS;
> its@lists.hl7.org
>
> *Subject:* Re: Summary of HL7 RDF / W3C COI call: FHIR Ontology
> Requirements
>
>
>
> 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 *
>
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>
> NOTE: Unless explicitly stated otherwise, the opinions and positions
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> 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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> --
>
> 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 Monday, 9 February 2015 11:01:33 UTC

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