Transcript PowerPoint-presentatie

ECO
R
European Centre for
Ontological Research
Ontology for indexing
electronic patient records.
There is only one right way:
Referent Tracking !
STIC-Santé seminar, Paris, Dec 8, 2005
Dr. W. Ceusters
European Centre for Ontological Research
Saarland University, Saarbrücken - Germany
ECO
R
Electronic Health Record
European Centre for
Ontological Research
• ISO/TS 18308:2003
– Electronic Health Record (EHR):
• A repository of information regarding the health of a subject of
care, in computer processable form.
– EHR system:
• the set of components that form the mechanism by which
electronic health records are created, used, stored, and
retrieved. It includes people, data, rules and procedures,
processing and storage devices, and communication and
support facilities.
• More common meaning of EHR system:
– only the “software being executed”
ECO
R
European Centre for
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The Medical
Informatics dogma
To structure or NOT to be
• Fact: computers can only deal with a
structured representation of reality:
– structured data:
• relational databases, spread sheets
– structured information:
• XML simulates context
– structured knowledge:
• rule-based knowledge systems
• Conclusion: a need for structured data
entry
(???)
ECO
Structured EHR data entry
R
European Centre for
Ontological Research
• Current technical solutions:
– Data entry forms
• provide the structure
• various paradigms:
– Rigid, pre-fixed
– Adaptable to user-preferences, but fixed when used
– Dynamically adapting to entered data in context
– Terminologies, coding and classification
systems:
• Provide the language to be used;
• Are claimed
– To allow exchange of information preserving meaning
– To be a good basis for record indexing to allow subsequent
processing for statistics and epidemiology
ECO
R ‘Traditional’ semantic indexing
European Centre for
Ontological Research
• Statement:
– ‘ Joe Smith has a fracture of the left tibia ’
• Becomes indexed as :
–
#12
M-2xg41
A-2t68
– M-2xg41 code in SnowMeat with terms:
– fracture, fractures, fracture NOS, broken, ...
– A-2t68 ibidem associated with:
– left tibia, left tibia NEC, ...
– Additional terms through
– hierarchy: bone, bones, os, ...
– associations: lower leg, limb, body part, ...
ECO
R
At least 2 major drawbacks
European Centre for
Ontological Research
with traditional semantic indexing
1. Bad organisation and structure of
‘traditional’ terminologies and concept
systems
2. Codes from such systems do not capture
‘what they are about’, ‘what was on the
side of the patient’.
ECO
R Problems with terminologies (1)
European Centre for
Ontological Research
Lack of face value
Agrammatical constructions
Shift in ontological category
(or ambiguous meaning)
ECO
R
European Centre for
Ontological Research
Problems with terminologies (2)
‘ventricle’ used in 2 different meanings
ECO
R
European Centre for
Ontological Research
Problems with terminologies (3)
• Mixing of differentiae
• Ontological nonsense
ECO
R
European Centre for
Ontological Research
Problems with terminologies (4)
Incomplete classification
ECO
An index through which the
R
European Centre for
Ontological Research
‘whats’ are lost
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
ECO
Would
it
be
easier
if
you
R could see the code labels ?
European Centre for
Ontological Research
PtID
Date
ObsCode
Narrative
5572
04/07/1990
26442006
closed fracture of shaft of femur
5572
04/07/1990
81134009
Fracture, closed, spiral
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
2309
21/03/1992
26442006
closed fracture of shaft of femur
2309
21/03/1992
9001224
Accident in public building (supermarket)
47804
03/04/1993
58298795
Other lesion on other specified region
5572
17/05/1993
79001
Essential hypertension
298
22/08/1993
2909872
Closed fracture of radial head
298
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
ECO
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European Centre for
Ontological Research
PtID
patients. Same...
supermarket?
A look atDifferent
the problems
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
ECO
R
European Centre for
Ontological Research
Main problem areas
for current EHR indexing
• 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.
ECO
R
European Centre for
Ontological Research
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
– ...
ECO
R
European Centre for
Ontological Research
Proposed solution:
Referent Tracking
• Foundation:
Realist ontology
ECO
R
European Centre for
Ontological Research
Ontology
• ‘Ontology’: the study of being as a science
• ‘An ontology’ is a representation of some preexisting 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
– ...
ECO
R
Proposed solution:
European Centre for
Ontological Research
Referent Tracking
• Purpose:
– 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
ECO
Referent Tracking based
R
semantic indexing
European Centre for
Ontological Research
• Statement:
this
this
– ‘Joe Smith has a fracture of the left tibia ’
• Becomes indexed as :
–
#12
#234
#876
– #234 is_located_in #876
– #876 is_part_of #12
– #876 is_instance_of left_tibia
– ...
concepts from a terminology
{
•With Relationships and
universals from a realist ontology
ECO An ontological analysis
R Universals
European Centre for
Ontological Research
EHR system
HC
Freezer section
continuants
City hospital’s EHR system
City hospital
The freezer section of Jane’s favourite supermarket
Jane Smith
Person
Dr. Peters
Dr. Longley
Femur
Jane’s left femur
Fracture
Image
t
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
Jane’s left femur
Jane’s left femur fracture
Jane’s fracture’s image
occurrents
ECO
R Essentials of Referent Tracking
European Centre for
Ontological Research
• 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.
ECO
R
European Centre for
Ontological Research
PtID
Advantage: better
reality representation
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)
ECO
R
European Centre for
Ontological Research
Steps in referent tracking
based semantic indexing.
ECO
R
European Centre for
Ontological Research
The environment
Ontology
continuant
disorder
person
CAG repeat
EHR
Natural Language
Understanding
Technology
#IUI-1 ‘affects’ #IUI-2
#IUI-3 ‘affects’ #IUI-2
#IUI-1 ‘causes’ #IUI-3
Juvenile HD
Referent Tracking
Database
ECO
R
European Centre for
Ontological Research
Jim Cimino’s
Woods Hole case
First sentence:
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.
ECO Step 1: identify the phrases
R
referring to particulars
European Centre for
Ontological Research
Jane Smith
is
Native American
to
with
of
the
the
cough
a
50
female
who
emergency
chief
and
year
presents
room
complaint
chest
old ,
pain.
ECO Step 2: indentify to what
R particulars these phrases refer
European Centre for
Ontological Research
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
ECO Compare with simple clinical
R
coding in juxtaposition
European Centre for
Ontological Research
Jane Smith
is
a
50
“Jane Smith”
female
who
presents
CS1-femaleCS2-woman
gender
CS1-native-american
the
old ,
CS1-age
Native American
to
year
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
ECO Compare
Comparewith
withthe
theoutput
outputofofthe
theNAIVE
perfect!!!
R
semantic analyser we all would dream of
European Centre for
Ontological Research
“Jane Smith”
Has-Age
CS3-50 years old
Is-A
Has-Sayer
CS3-woman
CS3-complaining
Hasparticipant
Is-A
CS3-native american
Has-Saying
CS3-chest pain
Hashappeningduring
CS3-consultation
Has-Saying
CS3-coughing
Has-Loc
CS3-Em.Room
ECOWhat it (more or less) should be
R
with traditional coding
European Centre for
Ontological Research
CS3-complaining
Has-Saying
“chest-pain”
Has-’referent’
Has-Saying
“coughing”
CS3-chest pain
CS3-coughing
Has-’referent’
ECOWhat it (more or less) should be
R
with referent tracking
European Centre for
Ontological Research
CS3-complaining
Has-code
J.S.’ complaining at t1
Has-Saying
“chest-pain”
Has-referent
Has-Saying
J.S.’ chest pain at t-1
“coughing”
Has-code
Has-referent
J.S.’ coughing at t-1
CS3-chest pain
Has-code
CS3-coughing
ECO
Step 3: are relevant and
R
necessary particulars missing ?
European Centre for
Ontological Research
• Referred to:
–
–
–
–
–
–
–
–
–
–
Jane Smith
Jane Smith’s age
Jane Smith’s race
Jane Smith’s gender
Jane Smith’s showing up at ...
The specific emergency room in the health facility
Jane Smith’s primarily complaining ...
The temporal part ... coughs
Jane Smith’s chest
Jane Smith’s particular pain
• Missing:
–
–
–
–
The health facility
The healthcare worker she consulted
The particular coughs (under the condition she tells the objective truth)
The underlying disorder (under whatever state of affairs)
ECO
R
Step 4: IUI assignment
European Centre for
Ontological Research
• Assumptions:
– the RTS contains already:
• IUI-1
Jane Smith
Coi = <IUIa, ta, CS3, IUI-1, woman, tr>
• IUI-1.1
Ri = <IUIa, ta, depends-on, BFO, {IUI-1.1, IUI-1}, tr>
Coi = <IUIa, ta, CS1, IUI-1.1, age, tr>
• IUI-1.2
• IUI-1.3
Coi = <IUIa, ta, CS1, IUI-1.2, cherokee, tr>
Ri = <IUIa, ta, depends-on, BFO, {IUI-1.2, IUI-1}, tr>
Coi = <IUIa, ta, CS3, IUI-1.3, chest pain, tr>
Ri = <IUIa, ta, is-located-in, BFO, {IUI-1.3, IUI-1}, tr>
– All dates in the statements are 2 years earlier than now
• What to do with:
•
•
•
•
•
Jane Smith
Jane Smith’s race (CS1: native American)
Jane Smith’s gender (CS1: female)
Jane Smith’s chest pain (CS3: chest pain)
Jane Smith’s age (50)
ECO
R
European Centre for
Ontological Research
Conclusion
• Referent tracking can solve a number of
problems in an elegant way, specifically
those related to traditional semantic
indexing.
• Existing (or emerging) technologies can be
used for the implementation.
• Old technologies (cbs) can play an
interesting role.
• The proof of the pudding is in the eating
– Pilote is going to be set up
• Collaboration sought for dealing with NLU