- From: Dan Russler <dan.russler@oracle.com>
- Date: Tue, 03 Jun 2008 16:39:01 -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: <4845ABE5.7040105@oracle.com>
Hi Adrian, Extending the client stub would be another way to expose a web service. Good thought. Dan Adrian Walker wrote: > Hi Dan -- > > Thanks for your quick reply. You wrote.... > > I'm sure someone would have to write the EJB...for teaching, it would > be nice to expose a web service that a student could incorporate into > a web service orchestration routine over the internet. > > Yes, that would be one approach. > > Another way is to let the IBL system [1] combined with SQL provide the > business logic, and to extend the IBL client stub [2] as needed to > expose a findable web service. > > Slide 17 of [3] illustrates this. > > How does that sound? > > 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 > > [2] www.reengineeringllc.com/iblClient1.java > <http://www.reengineeringllc.com/iblClient1.java> > > [3] www.reengineeringllc.com/WikiSOA.pdf > <http://www.reengineeringllc.com/WikiSOA.pdf> > > > Adrian Walker > Reengineering > > > > > On Tue, Jun 3, 2008 at 2:54 PM, Dan Russler <dan.russler@oracle.com > <mailto:dan.russler@oracle.com>> wrote: > > Looks interesting. I'll keep this in mind. > > Although I'm sure someone woud have to write the EJB...for > teaching, it would be nice to expose a web service that a student > could incorporate into a web service orchestration routine over > the internet. > > Maybe this is a potential student project? > > > Dan > > Adrian Walker wrote: > >> Hi Again Dan -- >> >> You wrote: I like your use case...we need better tools for CQI >> of ontologies.. >> >> Please feel free to use the Internet Business System [1] for this >> and other purposes. >> >> As mentioned, shared use is free. We will be happy to assist. >> >> Best regards, -- 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 >> Phone: USA 860 830 2085 >> >> On Mon, Jun 2, 2008 at 1:15 PM, Dan Russler >> <dan.russler@oracle.com <mailto:dan.russler@oracle.com>> wrote: >> >> 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 Tuesday, 3 June 2008 20:40:16 UTC