lti-layered Knowledge Representations for Healthcare (was RE:
> An argument for bridging information models and ontologies at the syntactic
> level)
>
> At 3:53 PM -0700 7/24/08, Olasov, Ben wrote:
> > > From: [EMAIL PROTECTED] on behalf of Dan Russler
> >>
> >
At 3:53 PM -0700 7/24/08, Olasov, Ben wrote:
> From: [EMAIL PROTECTED] on behalf of Dan Russler
Hi Samson,
If "denote" = "describe" in your sentence, then I withdraw my objection.
But "denote" /= "describe". These two words
were intended to be, and are, used differently.
Consider the
> From: [EMAIL PROTECTED] on behalf of Dan Russler
>
> Hi Samson,
>
> If "denote" = "describe" in your sentence, then I withdraw my objection.
But "denote" /= "describe". These two words were intended to be, and are, used
differently. Consider the sentence, "The matrix P contains the entries
Hi Samson,
If "denote" = "describe" in your sentence, then I withdraw my objection.
My concern is that the term "class" as used in UML doesn't seem to mean
the same thing as you are describing for a class in OWL. For instance, I
don't see the same concept of "resource" in the definition of cla
Dan Russler wrote:
Hi Samson,
We are getting closer.
1) In the reference you site..."A class is the descriptor for a set"...
2) Earlier, you stated that "semantics of a class as denoting a set of
instances."
I believe these two statements represent the "apples" and "orange
I agree with you below, except I think it's peoples' "interpretation" of
the RIM that causes the confusion, e.g. "The focus of the RIM classes had
primarily been structure and not semantics." Since RIM is communicated in UML,
UML semantic rules apply, and one needs to be strict on the UM
See below...Yes let's move on to more examples...Dan
Kashyap, Vipul wrote:
I agree with you below, except I think it's peoples'
"interpretation" of the RIM that causes the confusion, e.g. "The
focus of the RIM classes had primarily been structure and not
semantics." Since RIM
Hi Vipul,
I agree with you below, except I think it's peoples' "interpretation" of
the RIM that causes the confusion, e.g. "The focus of the RIM classes
had primarily been structure and not semantics." Since RIM is
communicated in UML, UML semantic rules apply, and one needs to be
strict on t
1) In the reference you site..."A class is the descriptor for a set"...
2) Earlier, you stated that "semantics of a class as denoting a set of
instances."
I believe these two statements represent the "apples" and "oranges" you
referenced:
Statement 1) is the traditional "a class describes the
Hi Samson,
We are getting closer.
1) In the reference you site..."A class is the descriptor for a set"...
2) Earlier, you stated that "semantics of a class as denoting a set of
instances."
I believe these two statements represent the "apples" and "oranges" you
referenced:
Statement 1) is
Dan,
We are talking apples and oranges.
I am talking about the semantics of "class", of which the Observation
class is an example. [1], for example, says, "A class is the
descriptor for a set of objects with similar structure, behavior, and
relationships." (p. 50)
You are talking about a
Hi Samson,
Sorry for my older-style jargon...
Here is the Wikipedia entry on collection/aggregation. We often called
these classes "collectors" in jargon:
"Aggregation
Class diagram showing Aggregation between two
classes
Aggregation
is a variant of the "has a" or association relationshi
Dan,
You've lost me. What is an ObservationCollectorClass? Googling the term
gives only one hit, namely your message.
The conceptualization of a class as denoting a set of instances is
quite common. It's in UML, frame representation, and OWL. I don't
understand why Observation, as a RIM class
Dear All,
This is meant as a friendly comment, and perhaps a comment on the need
for further work. FWIW, I'm a UK based Oncology Reg. (can't translate to
US terms - sorry) just coming to the end of a PhD in CS. The PhD was
peripherally involved with ontologies, and I have edited OWL files by
Ouch...
A class of Observation does not denote a set of instances of type
Observation...One uses "collector" classes to describe sets. In other
words, an instance of an ObservationCollectorClass contains instances
of an ObservationClass. The ObservationCollectorClass (and instances
thereof) ce
Yes, if we understand the semantics of a class as denoting a set of
instances. Specifying WBC_Count_Observation is equivalent to defining a
subset of all Observations, which is natural to think about. If we see
Observation as a metaclass, then it's the set of sets of
observations.The properties
Hi Samson,
I agree...It is wrong to confuse the process of creating an instance in
the narrow sense (where the structural attributes and other attributes
are constrained to specific values) and creating an incremental
constraint on the structural attributes and code that allow one to
define "m
My understanding of the HL7 RIM is that, when you clone a RIM class,
such as Observation, into a specific domain model class (e.g.,
WBC_Count_Observation), you are placing restrictions on the RIM class,
i.e., constraining the cloned class's properties to have specific
values or to take values f
onday, July 21, 2008 5:02 PM
To: [EMAIL PROTECTED]
Cc: Samson Tu; Elkin, Peter L., M.D.; public-semweb-lifesci@w3.org;
[EMAIL PROTECTED]
Subject: RE: Multi-layered Knowledge Representations for Healthcare (was
RE: An argument for bridging information models and ontologies a
Dan,
Looks like there is increasing convergence in our view points and some minor
divergences.
I'm confused...can you illustrate in UML, perhaps with the blood
pressure example? />
[VK] The UML Diagram illustrating WBC is attached with this e-mail (GIF
format). Look forward to y
sorry for the long delay...see below...Dan
Kashyap, Vipul wrote:
You are correct that classes in HL7 may have sub-classes.
[VK] I think the interesting question is whether these
classes are metaclasses, i.e., whether they belong to layer 1
or whether they are
You are correct that classes in HL7 may have
sub-classes.
[VK] I think the interesting question is whether these
classes are metaclasses, i.e., whether they belong to layer 1 or whether they
are in layer 2.
Classes and subclasses in a UM
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 stu
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
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, -- Ad
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 repres
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
ot
See below...Dan
Kashyap, Vipul wrote:
You are correct that classes in HL7 may have sub-classes.
[VK] I think the interesting question is whether these classes are
metaclasses, i.e., whether they belong to layer 1 or whether they
are in layer 2.
Classes and subclasses in a U
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
physi
Alan,
Thanks for the detailed feedback. Some responses are included below.
My main contention is that the things that we put in medical records
represent statements "ascribing" (or "not ascribing") characteristics and
relationships to patients - i.e.
we are saying that the patie
Healthcare (was
RE: An argument for bridging information models and ontologies at the syntactic
level)
Dear Peter,
Apologies for the delay in responding There'a a lot of stuff going
around right now and I needed some "think" time. Responses to you
: Samson Tu; public-semweb-lifesci@w3.org; [EMAIL PROTECTED]
Subject: RE: Multi-layered Knowledge Representations for Healthcare (was
RE: An argument for bridging information models and ontologies at the syntactic
level)
Dear Vipul,
Attached please
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 possibl
for bridging information models and ontologies at the syntactic level)
Dear Peter,
Apologies for the delay in responding There'a a lot of stuff going around
right now and I needed some "think" time. Responses to your questions are
included inline.
In order to not confu
You are correct that classes in HL7 may have sub-classes.
[VK] I think the interesting question is whether these classes are
metaclasses, i.e., whether they belong to layer 1 or whether they are in layer
2.
To be more specific, by definition, once a class in H
Dear Peter,
Apologies for the delay in responding There'a a lot of stuff going around right
now and I needed some "think" time. Responses to your questions are included
inline.
In order to not confuse the Ontology classification with First Order /
Second Order / Higher Order logics, we
Hi Alan,
Your points are well made regarding the provenance of information and
the information itself.
I captured this "assertion" as a point upon which to comment:
"My main contention is that the things that we put in medical records
represent statements "ascribing" (or "not ascribing") cha
All
I am coming in a bit late on this, but two points
A) I'd like to suggest that there are two, largely orthogonal,
dimensions (at least) being conflated:
i) The evidence trail or "provenance" of information and our
consequent degree of belief/willingness to rely on that information
i
lt;mailto:[EMAIL PROTECTED]>
Cc: Samson Tu; public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>; [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>; Elkin, Peter L., M.D.
Subject: Multi-layered Knowledge Representations for Healthcare (was
RE: An argument for bridging inform
Agreed...Peter already got us to changeOf course, I thought more
people would confuse the term with "first order reaction" or "first
order kinetics" than with "first order logic."
Dan
Pat Hayes wrote:
At 10:46 AM -0400 4/21/08, Dan Russler wrote:
Peter and Vipul...See below...dan
Ka
At 10:46 AM -0400 4/21/08, Dan Russler wrote:
Peter and Vipul...See below...dan
Kashyap, Vipul wrote:
IMHO, codes don't represent classes in some information model. An
information model has classes like Observation, whose instances are
clinical statements made by some entity (person or mac
April 22, 2008 2:48 PM
To: [EMAIL PROTECTED]
Cc: Samson Tu; public-semweb-lifesci@w3.org; [EMAIL PROTECTED];
Elkin, Peter L., M.D.
Subject: Multi-layered Knowledge Representations for Healthcare (was
RE: An argument for bridging information models and ontologies at
the syntactic level)
: [EMAIL PROTECTED]
Cc: Samson Tu; public-semweb-lifesci@w3.org; [EMAIL PROTECTED];
Elkin, Peter L., M.D.
Subject: Multi-layered Knowledge Representations for Healthcare (was RE:
An argument for bridging information models and ontologies at the
syntactic level)
Dan and Peter,
Based on
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 thi
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 enumera
Peter and Vipul...See below...dan
Kashyap, Vipul wrote:
IMHO, codes don't represent classes in some information model. An
information model has classes like Observation, whose instances
are clinical statements made by some entity (person or machine). I
think information model
I agree, Vipul, that individual applications may decide (for reasons of
performance or retrieval or other implementation specific reasons) to
separate the notion of action from the notion of result of the action in
order to reduce the amount of information retrieved.
However, these separations
Ogbuji, Chimezie wrote:
Dan,
I've very familiar with the SOAP model. The primary motivation
for my questions about assessment had more to do with distinguishing an action
from data that is derived from it. This speaks directly
> [[[
> * Clinical care - what we do to the patient based on our
> assessments of the pathophysology of the patient
> * I'm not sure if Alan is deliberately saying that this
> "clinical care" level addresses actions taken *based on*
> assessments/observations, but that assessme
Look forward to your comments.
Tom
____________
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Samson Tu
Sent: Wednesday, April 09, 2008 11:41 PM
IMHO, codes don't represent classes in some information model. An
information model has classes like Observation, whose instances are clinical
statements made by some entity (person or machine). I think information model is
"meta" in the sense that its instances are statements
Hello, Dan. Comments inline below. I'll start with my general
understanding of data and measurements and see if I can't converge on an
answer to your question.
By data, I mean anything that is captured in some (mostly electronic)
medium and typically represents or is a proxy for some phenomenon
Hi Chimezie,
It may be helpful to examine what "data" means and what "measurement" means.
There is a kind of classification system that is used in medicine.
The "process of living" includes many hundreds of thousands of
sub-processes that must work in harmony for the individual to remain alive
A (perhaps) naive question, inline below.
>-Original Message-
>From: Dan Russler [mailto:[EMAIL PROTECTED]
>Hi Dirk,
>Your understanding of "disease" is entirely in synch with mine.
>However, my professors in science felt that all measurements
>were abstractions with a high degree of po
ashyap, Vipul"
<[EMAIL PROTECTED]>, [EMAIL PROTECTED],
public-semweb-lifesci@w3.org, [EMAIL PROTECTED]
Subject
Re: An argument for bridging information models and ontologies at the
syntactic level
Hi Chimezie,
I've been watching this discussion. It parallels a discussion
nt: Fri 4/11/2008 3:20 AM
To: Ogbuji, Chimezie
Cc: Oniki, Tom (GE Healthcare, consultant); Samson Tu; Kashyap, Vipul;
[EMAIL PROTECTED]; public-semweb-lifesci@w3.org; [EMAIL PROTECTED]
Subject: Re: An argument for bridging information models and
ontologies at the syntactic level
Chimezie -
Th
E Healthcare, consultant); Samson Tu; Kashyap, Vipul; [EMAIL
PROTECTED]; public-semweb-lifesci@w3.org; [EMAIL PROTECTED]
Subject: Re: An argument for bridging information models and ontologies at the
syntactic level
Chimezie -
The SOAP pattern is widely used for writing medical charts. As
a
ys are "meta" to the pathophysiology realm
above, i.e., they're data structures that attempt to represent that
realm.
Look forward to your comments.
Tom
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECT
PROTECTED]
Cc: public-semweb-lifesci@w3.org; [EMAIL PROTECTED]
Subject: RE: An argument for bridging information models and
ontologies at the syntactic level
It seems like we're having difficulty getting to a point where
we can see if we agree or not.
______________
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Samson Tu
Sent: Wednesday, April 09, 2008 11:41 PM
To: Kashyap, Vipul
Cc: public-semweb-lifesci@w3.org; [EMAIL PROTECTED]
Subject: Re: An argument for bridging information models and ontologies
at the syntact
On Apr 8, 2008, at 6:50 PM, Kashyap, Vipul wrote:
Fundamentally, the only interpretation that works is to regard codes
as being "meta" to the ontology. I.e. the individuals in the
ontology are things in the conceptualisation of the world - cases of
diabetes, people, livers, etc. - individu
Fundamentally, the only interpretation that works is to regard codes as being
"meta" to the ontology. I.e. the individuals in the ontology are things in the
conceptualisation of the world - cases of diabetes, people, livers, etc. -
individual codes represent classes in the ontology.
[VK] Agree.
Perhaps you can elaborate on your idea of SNOMEDCT the information and what kind
of transformations are involved to get SNOMEDCT the terminology.
[VK] SNOMED-CT the terminology would be a set of codes, but as Alan suggests in
a follow up e-mail, there is an ontology underlying these codes, e.g., th
FYI--this is exactly the approach we take in the caBIG AIM project
(semantic Annotation and Image Markup) wherein we have a domain ontology
containing the biomedical entities, and an information model specifying
the information you can capture when making statements about the
images.
Daniel
At 1
Alan,
I agree completely. The observations and orders we capture in the
information model are clinical statements that are meta to the actual
objects and processes in the world. The codes in the statements are
symbols representing classes in the ontology that is the underpinning
of the te
Samson, Vipul, All
I saw this by accident and have not been involved in the main
discussion - so excuse the intron. However, the issue of the relation
between ontologies and health records is close to my heart. There are
papers about it at both KR-MED 2006 and Medinfo 2007, the KRMed pape
On Apr 3, 2008, at 7:56 PM, Kashyap, Vipul wrote:
OK, we disagree on this point. I'd just point out that, if you are
interested in working with HL7 RIM or BRIDG, you have a conceptual
mismatch with them.
[VK] I do not view it as a conceptual mismatch as I can get Snomed-
CT the terminology
> -Original Message-
> From: Peter Ansell [mailto:[EMAIL PROTECTED]
> Sent: Thursday, April 03, 2008 4:59 PM
> To: Samson Tu
> Cc: Kashyap, Vipul; Ogbuji, Chimezie; [EMAIL PROTECTED];
> public-semweb-lifesci@w3.org
> Subject: Re: An argument for bridging i
OK, we disagree on this point. I'd just point out that, if you are
interested in working with HL7 RIM or BRIDG, you have a conceptual mismatch with
them.
[VK] I do not view it as a conceptual mismatch as I can get Snomed-CT
the terminology by specifying a transformation on Snomed
On 02/04/2008, Samson Tu <[EMAIL PROTECTED]> wrote:
> On Mar 27, 2008, at 3:58 AM, Kashyap, Vipul wrote:
>
> If your Acute MI is a subclass of Observation/Problem, then instances of
> "Acute MI" class are observations of Acute MI, not instances of the disease
> MI. An "observation" does not have s
On Mar 27, 2008, at 3:58 AM, Kashyap, Vipul wrote:
It seems to me that we shouldn't throw out an important distinction
just because SNOMEDCT has terms that should be expressed in
information model.
[VK] I did not mean to throw out the distinction, but to position
the distinction differentl
David (HP Software - Boston)
Cc: Ogbuji, Chimezie; [EMAIL PROTECTED];
public-semweb-lifesci@w3.org
Subject: Re: An argument for bridging information models and
ontologies at the syntactic level
Chimezie, excellent observation. Agree with principals you are
ar
4. Keeping the two (data models and conceptual models) separate allows them to
evolve independently.
[VK] I agree with this principle emphatically, as has been expressed in my
e-mails on the same topic. The semantic web community
needs to articulate in some manner, that SW specifications like RDF/O
Chimezie, excellent observation. Agree with principals you are
articulating.
I would add:
1. Data models like schemas, structures, and data formats are implementation
details.
2. Concept models operate at many levels. As an example, concept models may
represent the entire data model as a concep
It seems to me that we shouldn't throw out an important distinction just because
SNOMEDCT has terms that should be expressed in information model.
[VK] I did not mean to throw out the distinction, but to position the
distinction differently. For instance, I would still differentiate betwe
> Okay, for me, the difference is whether or not the underlying language
> is backed by a some knowledge reprsentation with a formal
> semantics. By
> knowledge representation I primarily mean a language that can
> facilitate
> inference [1].
I agree with the above, though I would probably
Kashyap, Vipul wrote:
An argument for bridging information models and ontologies at
the syntactic level
To get right to the point,
1) I consider approaches that attempt to perform this bridging directly
between information models and ontologies as examples of this
'anti-pattern.' 2)
[[
[VK] I am not sure whether there is merit in the differentiation
between terminologies and information models as they are essentially the
same thing. Take a look at Snomed, and you would know what I mean.
]]
Okay, for me, the difference is whether or not the underlying language
To get right to the point, 1) I consider approaches that attempt to perform this
bridging directly between information models and ontologies as examples of this
'anti-pattern.' 2) I think that performing this bridging at the syntactic level
addresses the important problem of properly separating the
> The main point of emphasis for me is
> that a separation of concerns is maintained so you aren't modeling
> relations such as hasCode, for instance, in OWL. Jim's point
> about this
> being a basic tenant of Engineering principles is absolutely
> correct.
This is a critical separation of
rch 26, 2008 1:22 PM
To: Booth, David (HP Software - Boston)
Cc: Ogbuji, Chimezie; [EMAIL PROTECTED];
public-semweb-lifesci@w3.org
Subject: Re: An argument for bridging information models and
ontologies at the syntactic level
Chimezie, excellent obse
Chimezie,
Ogbuji, Chimezie wrote:
For some time I have had a concern about a theme in the more common
approaches to bridging
information models and ontologies as a path towards bringing the
advantages of the Semantic Web technologies to 'legacy' healthcare
terminology systems.
A good sta
> From: jim herber [mailto:[EMAIL PROTECTED]
> David, do you like "data model to conceptual mapping" better?
Yes, to my eyes that seems more descriptive of the intent, though it is a bit
long. :)
David Booth, Ph.D.
HP Software
+1 617 629 8881 office | [EMAIL PROTECTED]
http://www.hp.com/g
+1. Except I find the term "syntactic mapping" somewhat misleading, because to
my mind, the anti-pattern you are describing involves the encoding of
syntactic-level concerns into the ontology, which as you point out, shouldn't
be there. So pertonally I would have been more inclined to call it
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