- From: Dan Russler <dan.russler@oracle.com>
- Date: Mon, 02 Jun 2008 13:15:07 -0400
- To: Adrian Walker <adriandwalker@gmail.com>
- CC: "Kashyap, Vipul" <VKASHYAP1@partners.org>, Samson Tu <swt@stanford.edu>, public-semweb-lifesci@w3.org, public-hcls-coi@w3.org, Elkin.Peter@mayo.edu
- Message-ID: <48442A9B.4040305@oracle.com>
Hi Adrian, I like your use case...we need better tools for CQI of ontologies...Dan Adrian Walker wrote: > Hi Dan -- > > Thanks for your thoughts about this. > > You wrote... > > If you used a modifier as you suggest below, you would need to modify > many of the hundreds of thousands of assertions represented in an > ontology like SNOMED. > > Actually, it seems that reasoning in executable English over SNOMED > and other ontologies could be a useful way of addressing your point that > > ...it is impossible to create an ontology where everyone agrees with > every belief stated. > > The executable English can be used to say things like > > "according to SNOMED this-type1 and this-type2 are closely related > but not everyone agrees" > > Users can then get English explanations showing the pertinent entries > in SNOMED, and showing who disagrees and why and for what purposes. > > How does that sound? > > If it's of interest, we can put up an example at [1] that folks can > run using browsers. Scalability comes from automatically generating > and running SQL from the executable English. The results are still > explained in English. > > Cheers, -- Adrian > > [1] Internet Business Logic > A Wiki and SOA Endpoint for Executable Open Vocabulary English > over SQL and RDF > Online at www.reengineeringllc.com > <http://www.reengineeringllc.com> Shared use is free > > Adrian Walker > Reengineering > > > > > > On Mon, Jun 2, 2008 at 9:25 AM, Dan Russler <dan.russler@oracle.com > <mailto:dan.russler@oracle.com>> wrote: > > Hi Adrian, > > Belief is at the core of an ontology, not at the perphery as you > suggest. > > For example, the belief that "Type 1 Diabetes" and "Type 2 > Diabetes" both have a parent called "Diabetes" is a belief > instantiated in the SNOMED hierarchy. Of course, this > representation is frought with physiologic heresy (Type 1 and Type > 2 Diabetes are only related physiologically through a symptom, > i.e. hyperglycemia, not through common causal phisiologic > pathways). However, many people will argue that the belief is "true." > > Like most beliefs, one can argue that if the belief is traditional > or pragmatic instead of strictly valid, it belongs in the ontology > because it is accepted as "true" by many. However, it is > impossible to create an ontology where everyone agrees with every > belief stated. This situation isn't "wrong;" it is simply a fact > of life in ontology development. > > If you used a modifier as you suggest below, you would need to > modify many of the hundreds of thousands of assertions represented > in an ontology like SNOMED. > > Dan > > > Adrian Walker wrote: > >> Dan -- >> >> You wrote >> >> How does one bring belief into a model, e.g. realism, >> creationism, etc? >> >> One way of doing this is to write a layer of knowledge as rules >> in executable English. The rules can conclude things like >> >> "it is currently the view of US health professionals that..." >> >> "a possibly useful hypothesis is that...." >> >> Then, English explanations can show the data and inferential >> evidence for the conclusions. >> >> There's a kind of Wiki for executable English that supports >> this. It's online at the site below, and shared use is free. >> The English vocabulary is open, and so to a large extent is the >> syntax. Some background is in [1,2]. >> >> Apologies to folks who have seen this before, and thanks for >> comments. >> >> -- Adrian >> >> >> [1] www.reengineeringllc.com/ibldrugdbdemo1.htm >> <http://www.reengineeringllc.com/ibldrugdbdemo1.htm> (Flash >> video with audio) >> >> [2] >> www.reengineeringllc.com/A_Wiki_for_Business_Rules_in_Open_Vocabulary_Executable_English.pdf >> <http://www.reengineeringllc.com/A_Wiki_for_Business_Rules_in_Open_Vocabulary_Executable_English.pdf> >> >> Internet Business Logic >> A Wiki and SOA Endpoint for Executable Open Vocabulary English >> over SQL >> Online at www.reengineeringllc.com >> <http://www.reengineeringllc.com> Shared use is free >> >> Adrian Walker >> Reengineering >> >> On Tue, Apr 22, 2008 at 5:25 PM, Dan Russler >> <dan.russler@oracle.com <mailto:dan.russler@oracle.com>> wrote: >> >> Hi Vipul, >> >> Peter is right that the term "EAV" is a data schema >> implementation model, even though it maps directly to a >> classic proposition model with subject, predicate, and object >> of the predicate. >> >> Layer 0 then would be the most abstract layer consisting >> purely of formal propositions. In this layer, some >> propositions may express relationships between one or two >> other propositions, but otherwise, no grouping of >> propositions (classes) nor inheritance are characteristic of >> this layer. >> >> Peter brings up a good point about the need to deal with >> belief and values in the model. After all, an ontology is >> really a belief system asserted by one or more people. How >> does one bring belief into a model, e.g. realism, >> creationism, etc? >> >> Regarding your note below on Layer 2...The question is >> whether there are finer layers of distinction between level 1 >> and layer 2 (before one actually creates instances that apply >> to individual patients)? >> >> Dan >> >> >> Kashyap, Vipul wrote: >> >>> Dan and Peter, >>> >>> Based on conversations on this topic, there appears to be >>> consensus of the need for multi-layered knowledge >>> representation schemes >>> for heatlhcare. Will be great if we could brainstorm and >>> come to some sort of consensus on these "layers". Would like >>> to propose a >>> strawman as enumerated below. >>> >>> Layer 0 = Entity - Attribute - Value or RDF triple based >>> rerpesentations. >>> Layer 1 = MetaClasses, e.g., Observation as in HL7/RIM >>> Layer 2 = Classes in a Patient Model, Document Models, etc, >>> e.g., the class of HbA1c results for a class of Patients. >>> Layer 3 = Data that are instances of Classes, e.g., a >>> particular HbA1c result for a patient John... >>> >>> As per your e-mail, you seem to be suggesting that there is >>> something in between Layer 1 and Layer 2. However, please >>> note that Layer 2 consists >>> of classes of assertions in the patient record and not >>> instances. >>> >>> More reespnses are embedded in the e-mail below. >>> >>> <dan> With apologies to Peter in case I misrepresented your >>> SOA presentation...Last week, Peter Elkin of Mayo Clinic >>> delivered a presentation where he called the HL7 RIM a >>> "first order ontology" because of the abstraction level of >>> the RIM. He called the models derived from the RIM, e.g. >>> analytic models, patient care document models like CDA, etc, >>> "second order ontology" because they add a layer of >>> concreteness to the abstractions of the RIM, i.e. an object >>> with classCode of observation and moodCode of order becomes >>> an "observation order object" with neither a classCode nor a >>> moodCode. >>> >>> [VK] Are there mathematical ways of describing these >>> "derivations" for e.g., by using operations such as >>> instantiations and generalizations/specializations. >>> >>> Also, in the above, it's not clear what the semantics of an >>> "observation order" object is? >>> For e.g., observations and orders are semantically distinct >>> concepts, so in some sense an observation order class is >>> likely to be unsatisfiable? >>> >>> The semantics of "moodCode" is not clear in Knowledge >>> Representation terms. For instance, do various mood codes >>> partition the instances of a class >>> into subclasses that are possbily mutually disjoint? >>> >>> Finally, the coding systems themselves support the >>> concreteness of a "third order ontology." For example, the >>> SNOMED concept becomes an object itself without a code >>> attribute, moodCode attribute, or classCode attribute, e.g. >>> a WBC order. /> >>> [VK] One way of looking at a Snomed code is that it defines >>> a class (e.g., blood pressure) of all the instances of blood >>> pressure readings which would imply that it belongs to Layer >>> 2 as defined above? >>> >>>> <dan> see above for the "first order to third order >>>> model." Your metaclass looks like Peter's "first >>>> order ontology." However, your "instances" get >>>> introduced too early...your "instances" point to >>>> actual medical record assertions, and Peter's model >>>> suggests that there is more "in between." In >>>> Peter's model, the actual medical record assertion >>>> would be an instance of his "third order ontology." /> >>>> [VK] Agree. As per the layering introduced above, >>>> Layer 2 would correspond to classes of assetions >>>> and Layer 3 would correspond to actual instances or >>>> assertions. >>>> >>>> <dan> I completely agree that the HL7 RIM is one >>>> level more "concrete" than the earlier EAV models. >>>> The EAV model represents the ultimate in >>>> abstraction, similar to RDF triples. Perhaps Peter >>>> would be more correct to say that EAV is a "first >>>> order ontology" and that the HL7 RIM is a "second >>>> order ontology." /> >>>> >>>> [VK] Agree: As per layering introduced abiove, >>>> The EAV/RDF triples layer could be layer 0, and >>>> the HL7/RIM layer could be layer 1 >>>> >>>> >>>> Look forward to further brainstorming and feedback >>>> on this. >>>> >>>> Cheers, >>>> >>>> ---Vipul >>>> >>>The information transmitted in this electronic communication is intended only >>>for the person or entity to whom it is addressed and may contain confidential >>>and/or privileged material. Any review, retransmission, dissemination or other >>>use of or taking of any action in reliance upon this information by persons or >>>entities other than the intended recipient is prohibited. If you received this >>>information in error, please contact the Compliance HelpLine at 800-856-1983 and >>>properly dispose of this information. >>> >>> >>> >>> >> >
Received on Monday, 2 June 2008 17:17:19 UTC