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RE: exchanging OWL through RIF --> oncology example

From: Vincent, Paul D <PaulVincent@fairisaac.com>
Date: Mon, 6 Mar 2006 00:56:31 -0800
Message-ID: <B3636F07C8359844A9A2370C5EA08CCBD07337@SRFMSGMB00.corp.fairisaac.com>
To: "Jim Hendler" <hendler@cs.umd.edu>, <edbark@nist.gov>, "Michael Kifer" <kifer@cs.sunysb.edu>
Cc: "RIF WG" <public-rif-wg@w3.org>

Jim - thanks for the added detail. Can I expand some more on this as it seems to be an important use case (ie for OWL and RIF)... 

Let me try and express your oncology use case slightly differently (for my benefit at a software system level)...
1. Location 1: defines (an) oncology ontology
2. Location 2: has an internal IT system (eg DB) and requires to check its vocabulary (terms and/or term relationships) against the Location 1 ontology.
3. ?

Option A for 3 (proposed RIF use case):
i. Location 1 publishes the term relationships it defines in OWL as RIF
ii. Location 2 reads the RIF and maps this to rules (eg via SQL expressions) that analyzes its IT (eg DB) system

Option B for 3 (current scenario):
i. Location 2 reads the OWL and maps this to rules (eg via SQL expressions) to analyze its IT (eg DB) system.

My questions:
a. Is the above interpretation correct / oversimplified / etc?
b. Presumably there is some advantage (eg reduction in complexity) in A vs B, per your para2 below. 
c. Out of interest, how does this case relate to Arden / HL7, if at all? Are bio/medical ontologies being used for HL7 today? 

Thanks,

Paul Vincent
Fair Isaac Blaze Advisor --- Business Rule Management
OMG Standards for Business Rules, PRR & BPMI
-----Original Message-----
From: Jim Hendler [mailto:hendler@cs.umd.edu] 
Sent: Friday, March 03, 2006 3:50 PM
To: Vincent, Paul D; edbark@nist.gov; Michael Kifer
Cc: RIF WG
Subject: RE: exchanging OWL through RIF
Importance: Low

Paul - there's a lot more to this, and some of it is in the 
vocabulary -- let me start simple - in this case when I say "OWL" I 
don't mean the theoretical content of some ontology, I mean a 
document somewhere on the Web which contains RDF/OWL description - 
for example, if you point your browser at 
www.mindswap.org/2003/CancerOntology/nciOncology.owl (be careful, it 
is big) then you would see a particvular version of this ontology 
(the definitive version lives in NIH space and I don't have the link 
at the moment, it's considerably bigger than this 25M one).

  Enter RIF (phase 2) - we want to take the stuff in that NCI 
ontology, take that document to our cancer research center, and check 
to see whether the data gathered in our datatbase corresponds to the 
expectations of the OWL model.  So, for example, if we see that an 
ONCOGENE is defined as any GENE which is ASSOCIATED with a DISEASE 
that is of type CANCER - we could go to the database and pull out all 
the things that are ONCOGENEs by this definition,  This couldn't be 
done by OWL itself - it's a variant  of the famous "uncle" thing- 
essentially we need a chaining rule in here (from Gene to disease and 
disease to cancer)

So, right now, if you wanted to use the info in the cancer ontology 
to do actual identification of instances in a database using a rule 
langauge, you would need to either reduplicate the information in the 
cancer ontology in the rules by hand (good luck, call me when you are 
done) or write a program to do it -- in the latter case, if the 
target langauge were known (RIF phase2) and the mapping was known 
(RIF Owl Deliverable) then you'd be able to use some sort of off the 
shelf mapper.

by the way, I agree with Francois and Uli that this is only one of 
three caases (Owl to RIF, RIF to OWL, OWL and RIF bi-directional). 
In [1] (member only) I proposed 3 cases, the first was this one, the 
other two were (I'm making these public, but not the context from [1] 
whcih should remain member only)
<snip>

Hope that helps
  Jim H.


[1] http://lists.w3.org/Archives/Member/w3c-semweb-cg/2005Jun/0014.html

At 1:06 -0800 3/3/06, Vincent, Paul D wrote:
>Jim - thanks. My apologies in advance for my lack of understanding 
>on the use of OWL...
>
>>...  They or some other org decide they'd
>>like to use it on databases and datasets for datacleansing or other
>>"rule based" operation.
>>     Recoding the whole into a new rules language would be
>>prohibitively expensive unless there is some sort of automagic
>>translator of some or all of the RDFS/OWL they use.
>
>It would seem to me that this would be a case for exchange of OWL 
>ontologies and/or interchange of different ontology representations 
>(eg different varieties of OWL?).
>
>Or: are we talking about, say, some hospital publishing some rules 
>for interpreting OWL (eg mapping OWL to a DB schema), which can then 
>be interchanged / shared amongst other users of this ontology? And 
>if so, what rule languages are typically applied to OWL vocabularies?
>
>Paul Vincent
>Fair Isaac Blaze Advisor --- Business Rule Management
>OMG Standards for Business Rules, PRR & BPMI
>mobile: +44 (0)781 493 7229 ... office: +44 (0)20 7871 7229 
>
>-----Original Message-----
>From: Jim Hendler [mailto:hendler@cs.umd.edu]
>Sent: Thursday, March 02, 2006 11:16 PM
>To: Vincent, Paul D; edbark@nist.gov; Michael Kifer
>Cc: RIF WG
>Subject: RE: exchanging OWL through RIF
>Importance: Low
>
>Back before the group was chartered, I had shared some use cases for
>OWL meets Rules in various member lists.  One of the examples was:
>
>At 19:52 -0400 6/5/05, Jim Hendler wrote:
>>1 - Consider an organization like the  Natl Cancer Inst which has a
>>big OWL ontology (i.e. has a number of full time people working on
>>curation, versioning, etc).  They or some other org decide they'd
>>like to use it on databases and datasets for datacleansing or other
>>"rule based" operation.
>>     Recoding the whole into a new rules language would be
>>prohibitively expensive unless there is some sort of automagic
>>translator of some or all of the RDFS/OWL they use.
>
>This, I think, is more like what Ed was proposing.  I am afraid I'm
>not familiar enough with some of the things Paul says in this thread,
>but I think this pushes it a little further.   I can give more
>details of a cancer example, but it's a lot like what Ed talked
>about, but I don't need to postulate multiple organizations - all I
>need is one group doing "modeling" and another trying to use those
>models for "data related" ops (i.e. open world OWL meets Closed World
>rules)
>   -JH
>
>
>At 14:59 -0800 3/2/06, Vincent, Paul D wrote:
>>I may be a little off base here, but: design-time model interchange
>>from say OWL to a (production) rules engine, where the (vocabulary)
>>"rules" would map to the object (/data) model the rules engine works
>>with, could in theory be covered by the ODM --> class diagram + PRR
>>mapping using MDA.
>>
>>[Caveat: The role of OWL in rule interchange seems (to me) to be
>>around describing the context (ie vocabulary) that the rules are
>>specified in. The target *must* already have its own ontology/data
>>to be mapped - after all, sending rules + data is not very useful
>>outside of verification tasks (as indicated in Harold Boley's F2F1
>>use case showing rules + data = results etc)].
>>
>>Another transformation that could possibly be done in RIF would be
>>OWL <-- --> SBVR, although again this is more likely to be a
>>design-time issue when in the context of conventional IT systems
>>(and again could also be done via an ODM <-- --> SBVR "model"). But
>>for ontologists / business consultants sharing vocabularies across
>>the semantic web, maybe this would be interesting.
>>
>>I await the OWL experts' views on this with interest!
>>
>>Paul Vincent
>>Fair Isaac Blaze Advisor --- Business Rule Management
>>mobile: +44 (0)781 493 7229 ... office: +44 (0)20 7871 7229
>>-----Original Message-----
>>From: public-rif-wg-request@w3.org
>>[mailto:public-rif-wg-request@w3.org] On Behalf Of Ed Barkmeyer
>>Sent: Thursday, March 02, 2006 9:33 PM
>>To: Michael Kifer
>>Cc: RIF WG
>>Subject: Re: exchanging OWL through RIF
>>
>>
>>Michael Kifer wrote:
>>
>>>   I am having a second thought about the requirement that OWL should be
>>>   exchangeable through RIF by encoding it in FOL (which I am 
>>>guilty of voting
>>>   for also and now attribute it to sleep deprivation :-).
>>>
>>>   I think this requirement is completely misguided.
>>
>>I think the above statement of the requirement can be misunderstood, but I
>>don't think the intent is at all misguided.
>>
>>It is not a matter of "exchanging an OWL ontology"; the requirement is to
>>deliver the semantic content of an OWL ontology as a ruleset, so that a rules
>>engine can incorporate that content into its rulebase.
>>
>>A pseudo use-case: A given site "Uhu" using OWL ontologies and an OWL engine
>>may find it necessary to communicate with a site "Rex" that has only
>>"rulesets" and "rule engines" for some task in which Uhu needs the support of
>>Rex.  In this case, it is important that Uhu be able to convert the relevant
>>OWL ontology to a "rules" (RIF) form, so that it can be used by Rex in
>>performing its supporting task.  And the requirement for RIF is that its "FOL
>>subset" be able to capture the semantics of the OWL ontology.
>>
>>The alternative view of this scenario is that Uhu simply sends the OWL
>>ontology, and it is incumbent on Rex to convert the OWL ontology to its
>>internal "rules" form.  There is nothing wrong with this view, except that it
>>has no role for RIF -- it makes the OWL->rules conversion a software project
>>for the Rex engine, and another project for the ILOG engine, and another for
>>the Jena engine, etc., creating lots of work for the engine 
>>providers and many
>>third parties who are familiar with the proprietary rules forms.  By
>>comparison, any tool that can convert OWL to RIF without loss (standard form
>>to standard form) gives Uhu what is need to work with Rex, and also Rudi and
>>Regina, no matter what rules engines they have.
>>
>>>   For interoperability, we will need to be able to send queries to OWL
>>>   engines. Representation of those queries will need to be hashed out later.
>>
>>This is, of course, exactly the inverse use case.  Here the Rex 
>>site needs the
>>assistance of the Uhu site in making some inference.  But Rex does not need
>>RIF for this at all, only something like SPARQL.  But suppose that Rex needs
>>to send this ruleset to Regina, so that Regina can use its local KB to assist
>>Rex in making some inferences.  Then when Rex sends the RIF ruleset 
>>to Regina,
>>the SPARQL queries to Uhu that appear in some of the antecedents must have a
>>RIF representation.  (And I think this is in some sense the degenerate case.
>>It is entirely possible that Regina is a 'hybrid' site, combining both DL and
>>Rules reasoning capabilities, with the consequence that Regina wants to
>>"understand" the SPARQL query, not just blindly send it to Uhu.)
>>
>>It seems to me that "Web-based Rules exchange" demands that we 
>>support BOTH of
>>these two use cases, not just the latter.
>>
>>-Ed
>>
>>--
>>Edward J. Barkmeyer                        Email: edbark@nist.gov
>>National Institute of Standards & Technology
>>Manufacturing Systems Integration Division
>>100 Bureau Drive, Stop 8263                Tel: +1 301-975-3528
>>Gaithersburg, MD 20899-8263                FAX: +1 301-975-4482
>>
>>"The opinions expressed above do not reflect consensus of NIST,
>>    and have not been reviewed by any Government authority."
>
>--
>Professor James Hendler			  Director
>Joint Institute for Knowledge Discovery	  	  301-405-2696
>UMIACS, Univ of Maryland			  301-314-9734 (Fax)
>College Park, MD 20742	 		  http://www.cs.umd.edu/~hendler
>Web Log: http://www.mindswap.org/blog/author/hendler

-- 
Professor James Hendler			  Director
Joint Institute for Knowledge Discovery	  	  301-405-2696
UMIACS, Univ of Maryland			  301-314-9734 (Fax)
College Park, MD 20742	 		  http://www.cs.umd.edu/~hendler
Web Log: http://www.mindswap.org/blog/author/hendler
Received on Monday, 6 March 2006 08:57:29 GMT

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