Transcript PowerPoint-presentatie

R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Referent Tracking:
The New Paradigm
Dagstuhl May 23th, 2006
Werner Ceusters, MD
Ontology Research Group
Center of Excellence in Bioinformatics & Life Sciences
SUNY at Buffalo, NY
R T U New York State
Center of Excellence in
Bioinformatics
& Life
Sciences
Three
models for
a Comprehensive
Patient Care
Information System *
Information model of
the medical record:
What can be said ?
requirements
Process model of
clinical care: What
ought to occur ?
?
inferences
Inferred model of the
state of the patient:
modification What actually occurs.
* Rector AL, Nolan WA, and Kay S. Foundations for an Electronic Medical Record.
Methods of Information in Medicine 30: 179-86, 1991. (Figure 1)
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
An event model of medical
information representation *
• ‘The real world consist of objects (or entities)’
• ‘Objects interact with other objects and can be associated with
other objects by relationships’
• ‘When two or more objects interact in the real world, an ‘event’ is
said to have occurred’
Is ‘saying that an event has occurred’ a requirement
for the event to have occurred ?
What ‘event’ occurred in my left hand being a part
of my left arm ?
* Huff SM, Rocha RA, Bray BE, Warner HR, and Haug PJ. An Event Model of Medical
Information Representation. J Am Med Informatics Assoc. 1995;2:116-134.
?
R T U New York State
Center
of Excellence
in Created from the Statement
Observation
Event Instance
Bioinformatics
& Life
‘Surgical clips are
againSciences
seen along the right mediastinum’ *
?
Are the clips there
because they have
been observed ?
Is the observation
located in the
mediastinum ?
* Huff SM, Rocha RA, Bray BE, Warner HR, and Haug PJ. An Event Model of Medical
Information Representation. J Am Med Informatics Assoc. 1995;2:116-134.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
What is wrong in both cases
(and so many others) ?
• Further clues to the answer:
– Huff SM, Rocha RA, Bray BE, Warner HR, and Haug PJ.
An Event Model of Medical Information Representation. J Am
Med Informatics Assoc. 1995;2:116-134.
– Rector et al.’s paper: Many of the difficulties experienced in
attempting to generalize existing [patient record] systems stem
from the fact that they have pre-selected and distorted
information in order to fit into particular applications, usually
clinical research and epidemiology. The models emit much of the
information actually used in clinical care and do not accurately
reflect the real status of the data they record.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
What is wrong (continued) ?
• An overemphasis on data and information and too little
attention to reality:
– “data modelling”
– “information modelling”
• Is the “Object Oriented” model approach any better, since,
after all, objects are said to be those things that exist in
reality ?
– The object-oriented model is based on a collection of objects
– An object contains values stored in instance variables within the object.
– Unlike the record-oriented models, these values are themselves objects.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Current mainstream thinking
wisdom (- representation)
knowledge - representation
information - representation
data - representation
Questions not often enough asked:
•
•
What part of our data corresponds with
something out there in reality ?
What part of reality is not captured by our
data, but should because it is relevant ?
Reality
What is there on the side of the patient
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The story of Jane
Smith
an old case, well known in the
literature ...
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
July 4th, 1990:
Jane goes shopping:
Jane’s favourite supermarket
The freezer section of
Jane’s favourite
supermarket
The only available
warning sign used
outside
A very suspiciously
shaped upper leg
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
A visit to the hospital
City Health Centre Dr. Peters
(City HC)
Dr. Longley
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Diagnosis: a severe spiral fracture of the femur
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
The City HC’s medical record
• Main principles:
– a faithful record of the clinicians’ observations: what
they have heard, seen, thought and done.
– captures in a structured form all of the ‘clinically
significant’ information in the narrative notes, where
by clinically significant they mean the information
which is within the medical domain rather than the
domain of everyday life.
Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ. A framework for modelling the
electronic medical record. Methods Inf Med. 1993 Apr;32(2):109-19.
R T U New York State
Center CityHC’s
of Excellence
in
representation
formalism
Bioinformatics & Life Sciences
(for statements in records)
Categories: “represent
concepts and are analogous to
classes in other formalisms”
Individuals:
“concrete instances
of categories which
persist in space and
time”
Occurrences: “are
Rector AL, Nowlan WA, Kay S, Goble CA,
Howkins TJ.
A framework for modelling the electronic
medical record.
Methods Inf Med. 1993 Apr;32(2):109-19.
specific occurrences of
individuals and must be
situated in space and time.
The most important
group of occurrences are
observations — i.e. agents’
observations of individuals.”
R T U New York State
A look at
Center of Excellence in
the
database:
of SNOMED
Bioinformatics
& Lifeuse
Sciences
codes for
‘unambiguous’ understanding
PtID
Date
ObsCode
Narrative
How
many
closed
fracture
of shaft numerically
of femur
different
disorders are
Fracture,
closed, spiral
closed
fracture
of shaft?of femur
listed
here
5572
04/07/1990
26442006
5572
04/07/1990
81134009
5572
12/07/1990
26442006
5572
12/07/1990
9001224
5572
04/07/1990
79001
0939
24/12/1991
255174002
2309
21/03/1992
26442006
2309
21/03/1992
9001224
47804
03/04/1993
58298795
Other lesion on other specified region
5572
17/05/1993
79001
Essential hypertension
298
22/08/1993
2909872
298
22/08/1993
9001224
5572
01/04/1997
26442006
How many disorders
have
patients
5572, 2309
Closed
fracture
of radial head
and in298
thus
Accident
publiceach
buildinghad
(supermarket)
closed
of shaftlifetime
of femur
farfracture
in their
?
5572
01/04/1997
79001
Essential hypertension
0939
20/12/1998
255087006
malignant polyp of biliary tract
*
Accident in public building (supermarket)
How many different
benign
polypof
of biliary
tract
types
disorders
are
closed fracture of shaft of femur
listed here ?
Essential hypertension
*
*
Accident in public building (supermarket)
* cause, not disorder
R T U New York State
Center of Excellence in
Bioinformatics & Life
Sciences
Different
patients. Same supermarket?
Does seeing the labels help you ?
PtID
Date
Maybe the same (irrelevant ?) freezer
section ?
ObsCode
Narrative
Or different
supermarkets,
but always
26442006
closed
fracture of shaft of femur
Same patient,
same
hypertension
code:
81134009
Fracture,
closed, spiral
in the freezer
sections
?
Same (numerically
identical)
hypertension
?
5572
04/07/1990
5572
04/07/1990
5572
12/07/1990
26442006
closed fracture of shaft of femur
5572
12/07/1990
9001224
Accident in public building (supermarket)
5572
04/07/1990
79001
Essential hypertension
0939
24/12/1991
255174002
benign polyp of biliary tract
298
Same patient, different
21/03/1992
26442006
closed fracturedates,
of shaft ofsame
femur fracture
Same
patient,
21/03/1992
9001224
Accident
in publicsame
buildingdate,
(supermarket)
codes:
same
03/04/1993patient,
58298795
Other lesion
on other specified
region
2patients,
different
fracture
codes:
Same
different
Differentdates,
same
fracture
codes:
(numerically
identical)
17/05/1993
79001
Essential
hypertension
same (numerically
Different codes.Same
Same(numerically
(numerically
identical)headfracture
? ?
22/08/1993
2909872
Closed fracture of radialfracture
identical) fracture ?
identical)
polyp
?
22/08/1993
9001224
Accident in public building (supermarket)
5572
01/04/1997
26442006
closed fracture of shaft of femur
5572
01/04/1997
79001
Essential hypertension
0939
20/12/1998
255087006
malignant polyp of biliary tract
2309
2309
47804
5572
298
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Main problem areas for CityHC’s EHR
• Statements refer only very implicitly to the concrete
entities about which they give information.
• Idiosyncracies of concept-based terminologies
– tell us only that some instance of the class the codes refer to, is
refered to in the statement, but not what instance precisely.
– Are usually confused about classes and individuals.
• “Country” and “Belgium”.
• Mixing up the act of observation and the thing observed.
• Mixing up statements and the entities these statements
refer to.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Consequences
• Very difficult to:
– Count the number of (numerically) different diseases
• Bad statistics on incidence, prevalence, ...
• Bad basis for health cost containment
– Relate (numerically same or different) causal factors to
disorders:
–
–
–
–
Dangerous public places (specific work floors, swimming pools),
dogs with rabies,
HIV contaminated blood from donors,
food from unhygienic source, ...
• Hampers prevention
– ...
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Proposed solution:
• Purpose:
Referent Tracking
– explicit reference to the concrete individual entities relevant to
the accurate description of each patient’s condition, therapies,
outcomes, ...
• Method:
– Introduce an Instance Unique Identifier (IUI) for each relevant
individual (= particular, = instance).
– Distinguish between
• IUI assignment: for instances that do exist
• IUI reservation: for entities expected to come into existence in the future
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Ontology
• ‘Ontology’: the study of being as a science
• ‘An ontology’ is a representation of some pre-existing
domain of reality which
– (1) reflects the properties of the objects within its domain in such a way
that there obtains a systematic correlation between reality and the
representation itself,
– (2) is intelligible to a domain expert
– (3) is formalized in a way that allows it to support automatic information
processing
• ‘ontological’ (as adjective):
– Within an ontology.
– Derived by applying the methodology of ontology
R T U New York State
Center An
of Excellence
in
ontological
analysis
Bioinformatics & Life Sciences
Universals
EHR system
HC
Freezer section
continuants
City HC’s EHR system
City HC
The freezer section of Jane’s favourite supermarket
Jane Smith
Person
Dr. Peters
Dr. Longley
Femur
Jane’s left femur
Jane’s left femur
Jane’s left femur fracture
Fracture
Jane’s fracture’s image
Image
t
occurrents
Jane’s fracture as seen by Dr. Peters
Jane’s fracture as seen by Dr. Longley
Jane’s falling
Jane’s femur breaking
Dr. Peter’s examination of Jane’s fracture
Dr. Peter’s ordering of an X-ray
Shooting the pictures of Jane’s leg
Jane’s fracture’s healing
Dr. Peter’s diagnosis making
Dr. Longley’s examination of Jane’ s fracture
Freezer section dismantled
Jane dies
Instances of
Jane’s fracture
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Ontological recategorisation
Fracture
Of Femur
CityHC
Dr. Peters
City HC
exists on
4th July
1990
Dr. Peters
located at
City HC on
4th July
1990
Jane
Smith
Jane Smith’s
consultation
with
Dr. Peters at
City HC on
4th July
1990
Jane
Smith’s
Fracture
Of Femur
Dr. Peters’
assessment of
Jane Smith’s
fracture of
femur
at
City HC on
4th July
1990
Severe
Jane
Smith’s
Fracture
Of Femur’s
severity
Spiral
Jane
Smith’s
Fracture
Of Femur’s
shape
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Essentials of Referent Tracking
• Generation of universally unique identifiers;
• deciding what particulars should receive a IUI;
• finding out whether or not a particular has already been
assigned a IUI (each particular should receive maximally
one IUI);
• using IUIs in the EHR, i.e. issues concerning the syntax
and semantics of statements containing IUIs;
• determining the truth values of statements in which IUIs
are used;
• correcting errors in the assignment of IUIs.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Architecture of a
Referent Tracking System (RTS)
• RTS: system in which all statements referring to particulars
contain the IUIs for those particulars judged to be relevant.
• Ideally set up as broad as possible:
– some metrics:
• % of particulars referred to by means of IUI
• % of HCs active in a region
– Geographic region
– functional region: defined by contacts amongst patients
• % of patients referred to within a region
• Services:
– IUI generator
– IUI repository: statements about assignments and reservations
– Referent Tracking ‘Database’ (RTDB): index (LSID) to statements relating
instances to instances and classes
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
IUI generation
• Universally Unique IDs:
– recently standardized through ISO/IEC 98348:2004,
– specifies format and generation rules enabling users
to produce 128-bit identifiers that are either
guaranteed or have a high probability of being
globally unique
– Meaningless strings
– Central management or certification not needed to
guarantee uniqueness
• (But use as IUI requires this)
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
IUI assignment
• = an act carried out by the first ‘cognitive agent’
feeling the need to acknowledge the existence of a
particular it has information about by labelling it
with a UUID.
• ‘cognitive agent’:
– A person;
– An organisation;
– A device or software agent, e.g.
• Bank note printer,
• Image analysis software.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Criteria for IUI assignment (1)
1. The particular’s existence must be determined:
–
–
Easy for persons in front of you, body parts, ...
Easy for ‘planned acts’: they do not exist before the plan is
executed !
•
–
More difficult: subjective symptoms
•
–
Only the plan exists and possibly the statements made about the
future execution of the plan
But the statements the patient makes about them do exist !
However:
•
•
no need to know what the particular exactly is, i.e. which universal
it instantiates
No need to be able to point to it precisely
–
–
One bee out of a particular swarm that stung the patient, one pain out
of a series of pain attacks that made the patient worried
But: this is not a matter of choice, not ‘any’ out of ...
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Criteria for IUI assignment (2)
2. The particular’s existence ‘may not already have
been determined as the existence of something else’:
•
•
•
Morning star and evening star
Himalaya
Multiple sclerosis
3. May not have already been assigned a IUI.
4. It must be relevant to do so:
•
•
•
Personal decision, (scientific) community guideline, ...
Possibilities offered by the EHR system
If a IUI has been assigned by somebody, everybody else making
statements about the particular should use it
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Assertion of assignments
• IUI assignment is an act of which the execution has to
be asserted in the IUI-repository:
– Di = <IUId, Ai, td>
• IUId IUI of the registering agent
• Ai
the assertion of the assignment < IUIp, IUIa, tap>
» IUIa IUI of the author of the assertion
» IUIp IUI of the particular
» tap
• td
time of the assignment
time of registering Ai in the IUI-repository
• Neither td or tap give any information about when #
IUIp started to exist ! That might be asserted in
statements providing information about # IUIp .
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Management of the IUI-repository
• Adequate safety and security provisions
– Access authorisation, control, read/write, ...
– Pseudonymisation
• Deletionless but facilities for correcting
mistakes.
• Registration of assertion ASAP after IUI
assignment
• (virtual, e.g. LSID) central management with
adequate search facilities.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Representation in the EHR
Fracture
Of Femur
Severe
CityHC
Dr. Peters
Jane
Smith
Jane Smith’s
consultation
with
Dr. Peters at
City HC on
4th July
1990
4th July 1990
Jane
Smith’s
Fracture
Of Femur
Dr. Peters’
assessment of
Jane Smith’s
fracture of
femur
at
City HC on
4th July
1990
Jane
Smith’s
Fracture
Of Femur’s
severity
Spiral
Jane
Smith’s
Fracture
Of Femur’s
shape
particulars referred to
• Relevant particulars
using IUIs
• Relationships that obtain
between particulars at time t
expressed using relations from
an ontology (type OBO)
• Statements describing for each
particular, at time t:
– Of what universal from an ontology
it is an instance of
– AND/OR (if one insists):
– By means of what concept from a
concept-based system it can
sensibly be described
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
PtoP statements - particular to particular
•
ordered sextuples of the form
Ri = <IUIa, ta, r, o, P, tr>
IUIa is the IUI of the author of the statement,
ta
a reference to the time when the statement is made,
r
a reference to a relationship (available in o) obtaining between the
particulars referred to in P,
o
a reference to the ontology from which r is taken,
P
an ordered list of IUIs referring to the particulars between which
r obtains, and,
tr
a reference to the time at which the relationship obtains.
• P contains as much IUIs as required by the arity of r. In most cases, P will
be an ordered pair such that r obtains between the particular represented by the
first IUI and the one referred to by the second IUI.
• As with A statements, these statements must also be accompanied by a
meta-statement capturing when the sextuple became available to the referent
tracking system.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
PtoU statements – particular to universal
Ui = <IUIa, ta, inst, o, IUIp, u, tr>
IUIa
ta
inst
o
IUIp
u
tr
is the IUI of the author of the statement,
a reference to the time when the statement is made,
a reference to an instance relationship available in o
obtaining between p and cl,
a reference to the ontology from which inst and u are
taken,
the IUI referring to the particular whose inst
relationship with u is asserted,
the universal in o to which p enjoys the inst relationship,
and,
a reference to the time at which the relationship obtains.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
U--tuples: “negative findings”
Relation
type
Type of Negative Finding
Examples
%
C1
<p, u> *
he denies abdominal pain; no alcohol abuse;
A particular is not related in a
specific way to any instance of a no hepatosplenomegaly; he has no children,
without any cyanosis
universal at some given time
85.4
C2
<p, u>
A par
ticular is not the instance of which ruled out primary hyperaldosteronism,
a given class at some given time nontender, in no apparent distress, Romberg
sign was absent , no palpable lymph nodes
12.4
C3
<p, p>
A particular is not related to
another partic
ular in a specific
way at some given time
this record is not available to me; it is not
the intense edema she had before; he has not
identified any association with meals.
2.2
* ‘p’ ranges over particulars, ‘u’ over universals
Ui = <IUIa, ta, r, o, IUIp, u, tr>
The particular referred to by IUIa asserts at time ta that the relation r
of ontology o does not obtain at time tr between the particular
referred to by IUIp and any of the instances of the universal u at
time tr
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
PtoCO statements
particular to concept code
Coi = <IUIa, ta, cbs, IUIp, co, tr>
IUIa
ta
cbs
IUIp
co
tr
is the IUI of the author of the statement,
a reference to the time when the statement is made,
a reference to the concept-based system from which co
is taken,
the IUI referring to the particular which the author
associates with co,
the concept-code in cbs which the author associates with
p, and,
a reference to the time at which the author considers the
association appropriate,
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Interpretation of
PtoCO statements
• must be interpreted as simple indexes to terms in a
dictionary.
• All that such a statement tells us, is that within the
linguistic and scientific community in which cbs is
used, the terms associated with co may - i.e. are
acceptable to - be used to denote p in their
determinative version.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
A SNOMED-CT example
• <IUI-0945, 18/04/2005, SNOMED-CT v0301, IUI1921, 367720001, forever>
• #IUI-0945: author of the statement
• #IUI-1921: the left testicle of patient #IUI-78127
• 367720001: the SNOMED concept-code to which “left testis” is (in
SNOMED) attached as term
• So we can denote #IUI-1921 by means of
• that left testis
• that entire left testis
• that testicle, that male gonad, that testis
•
that genital structure
•
that physical anatomical entity
• BUT NOT: that SNOMED-CT concept
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Pragmatics of IUIs in EHRs
• IUI assignment requires an additional effort
• In principle no difference qua (or just a little bit more)
effort compared to using directly codes from conceptbased systems
– A search for concept-codes is replaced by a search for the
appropriate IUI using exactly the same mechanisms
• Browsing
• Code-finder software
• Auto-coding software (CLEF NLP software Andrea Setzer)
– With that IUI comes a wealth of already registered information
– If for the same patient different IUIs apply, the user must make
the decision which one is the one under scrutiny, or whether it is
again a new instance
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
PtoN-statements
Ni=< IUIa, ta, ntj, ni, IUIp, tr>
• The person referred to by IUIa asserts at time ta
that ni is the name of the nametype ntj that
designates in the real world the particular referred
to by IUIp at tr. This template will further be
referred to as PtoN template.
• Would assert that “Werner” is my first name, and
“Ceusters” is my last name.
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Advantage: better reality representation
PtID
Date
ObsCode
Narrative
5572
04/07/1990
26442006
IUI-001
closed fracture of shaft of femur
5572
04/07/1990
81134009
IUI-001
Fracture, closed, spiral
5572
12/07/1990
26442006
IUI-001
closed fracture of shaft of femur
5572
12/07/1990
9001224
5572
04/07/1990
79001
IUI-005
Essential hypertension
0939
24/12/1991
255174002
IUI-004
benign polyp of biliary tract
2309
21/03/1992
26442006
IUI-002
closed fracture of shaft of femur
2309
21/03/1992
9001224
IUI-007
Accident in public building (supermarket)
47804
03/04/1993
58298795
Other lesion on other specified region
5572
17/05/1993
79001
IUI-005
Essential hypertension
298
22/08/1993
2909872
IUI-003
Closed fracture of radial head
298
22/08/1993
9001224
5572
01/04/1997
26442006
IUI-012
closed fracture of shaft of femur
5572
01/04/1997
79001
IUI-005
Essential hypertension
0939
20/12/1998
255087006
IUI-004
malignant polyp of biliary tract
IUI-007
Accident in public building (supermarket)
IUI-007
Accident in public building (supermarket)
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Other Advantages
• mapping as by-product of tracking
– Descriptions about the same particular using different
ontologies/concept-based systems
• Quality control of ontologies and concept-based
systems
– Systematic “inconsistent” descriptions in or cross
terminologies may indicate poor definition of the
respective terms
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
A case study
• Double goal:
– Application of referent tracking to a concrete patient
story
– Ontological analysis of what is involved
• The latter is NOT to be performed to the same
extent when referent tracking is used as an
alternative to coding using concept-based systems.
• So, don’t go home with the idea: “that’s all too
cumbersome and time cosuming”
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Jim Cimino’s Woods Hole case
• Jane Smith is a 30 year old, Native American female who
presents to the emergency room with the chief complaint
of cough and chest pain.
• The patient reports that she has had a productive cough
for three days but that chest pain developed one hour
ago. She gives a history of hypertension. She also
reports that she was treated in the past for tuberculosis
while she was pregnant. The patient reports an allergy to
Bufferin.
• Physical examination revealed a well-developed, …
R T U New York State
Center
of Excellence
in phrases referring to
Step
1: identify
the
Bioinformatics & Life Sciences
particulars
Jane Smith
is
a
50
year
Native American female who
to
with
of
the
the
cough
old ,
presents
Question:
What if the
patient is not telling
emergency
room
the truth ?
chief
and
complaint
chest
pain.
R T U New York State
of Excellence
StepCenter
2: indentify
toinwhat particulars these
Bioinformatics & Life Sciences
phrases refer
Jane Smith
is
a
50
old ,
Jane Smith’s age
Jane Smith
Native American
Jane Smith’s race
to
year
the
female
Jane Smith’s gender
who
Jane Smith
emergency
room
presents
Jane Smith’s
showing up at ...
A specific emergency room of health facility XYZ
with
the
chief
complaint
Jane Smith’s complaining primarily about ...
of
cough
and
A temporal part of Jane Smith’s
life marked by happenings of coughs
chest
Jane Smith’s chest
pain.
A specific
pain
experienced
by Jane
Smith
R T U New York State
Center of Excellence in
CompareBioinformatics
with simple
clinical
coding
& Life
Sciences
Jane Smith
is
a
50
“Jane Smith”
old ,
female
who
presents
CS1-femaleCS2-woman
gender
CS1-native-american
the
year
CS1-age
Native American
to
in juxtaposition
emergency
room
CS1-emergency room
with
the
chief
complaint
CS1-chief-complaint
of
cough
CS1-coughing
and
chest
pain.
CS2-chest
CS1-chest-pain CS2-pain
R T U New York State
Center
of with
Excellence
Compare
the
output
of the
NAIVE
Compare
with the
output
of
thein
perfect semantic
analyser
we all!!!
would
Bioinformatics
& Lifedream
Sciences
semantic
analyser
we ofall would dream of
“Jane Smith”
Has-Age
CS3-50 years old
Is-A
Has-Sayer
CS3-woman
CS3-complaining
Hasparticipant
Is-A
Has-Saying CS3-native american
CS3-chest pain
Hashappeningduring
CS3-consultation
Has-Saying
CS3-coughing
Has-Loc
CS3-Em.Room
R T U New York State
Center of Excellence in
Bioinformatics
& Lifeor
Sciences
What
it (more
less)
CS3-complaining
Has-Saying
should be
“chest-pain”
Has-’referent’
Has-Saying
CS3-chest pain
“coughing”
Has-’referent’
CS3-coughing
R T U New York State
Center of Excellence in
Bioinformatics & Life Sciences
Conclusion
• Referent tracking can solve a number of problems in an
elegant way.
• Existing (or emerging) technologies can be used for the
implementation.
• Old technologies (concept-based systems) can play an
interesting, but different role.
• Big Brother feeling is to be expected but with adequate
measures easy to fight.
• The proof of the pudding is in the eating
– Pilote is going to be set up