Title: Ontology for indexing electronic patient records' There is only one right way: Referent Tracking STI
1Ontology for indexing electronic patient
records.There is only one right wayReferent
Tracking !STIC-Santé seminar, Paris, Dec 8, 2005
- Dr. W. Ceusters
- European Centre for Ontological Research
- Saarland University, Saarbrücken - Germany
2Electronic Health Record
- ISO/TS 183082003
- 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
3The 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 (???)
4Structured EHR data entry
- 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
5Traditional semantic indexing
- Statement
- Joe Smith has a fracture of the left tibia
6At least 2 major drawbackswith traditional
semantic indexing
- Bad organisation and structure of traditional
terminologies and concept systems - Codes from such systems do not capture what they
are about, what was on the side of the patient.
7Problems with terminologies (1)
8Problems with terminologies (2)
- ventricle used in 2 different meanings
9Problems with terminologies (3)
- Mixing of differentiae
- Ontological nonsense
10Problems with terminologies (4)
Incomplete classification
11An index through which the whats are lost
How many numerically different disorders are
listed here ?
How many different types of disorders are listed
here ?
How many disorders have patients 5572, 2309 and
298 each had thus far in their lifetime ?
cause, not disorder
12Would it be easier if youcould see the code
labels ?
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
0939
20/12/1998
255087006
malignant polyp of biliary tract
13A look at the problems ...
14Main problem areasfor 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.
15Consequences
- 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
- ...
16Proposed solutionReferent Tracking
- Foundation
- Realist ontology
17Ontology
- 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
- ...
18Proposed solutionReferent Tracking
- Purpose
- explicit reference to the concrete individual
entities relevant to the accurate description of
each patients 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
19Referent Tracking basedsemantic indexing
- Statement
- Joe Smith has a fracture of the left tibia
20An ontological analysis
continuants
21Essentials 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.
22Advantage betterreality representation
IUI-003
23Steps in referent trackingbased semantic
indexing.
24The environment
Ontology
continuant
disorder
person
CAG repeat
EHR
Juvenile HD
IUI-1 affects IUI-2 IUI-3 affects
IUI-2 IUI-1 causes IUI-3
Referent Tracking Database
25Jim Ciminos 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.
26Step 1 identify the phrases referring to
particulars
- Jane Smith is a 50 year
old , - Native American female who presents
- to the emergency room
- with the chief complaint
- of cough and chest pain.
27Step 2 indentify to what particulars these
phrases refer
28Compare with simple clinical coding in
juxtaposition
29Compare with the output of the perfect semantic
analyser we all would dream of
Compare with the output of the NAIVE !!! semantic
analyser we all would dream of
CS3-complaining
30What it (more or less) should be with traditional
coding
31What it (more or less) should be with referent
tracking
32Step 3 are relevant and necessary particulars
missing ?
- Referred to
- Jane Smith
- Jane Smiths age
- Jane Smiths race
- Jane Smiths gender
- Jane Smiths showing up at ...
- The specific emergency room in the health
facility - Jane Smiths primarily complaining ...
- The temporal part ... coughs
- Jane Smiths chest
- Jane Smiths 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)
33Step 4 IUI assignment
- Assumptions
- the RTS contains already
- IUI-1 Jane Smith
- Coi ltIUIa, ta, CS3, IUI-1, woman, trgt
- IUI-1.1 Ri ltIUIa, ta, depends-on, BFO,
IUI-1.1, IUI-1, trgt - Coi ltIUIa, ta, CS1, IUI-1.1, age, trgt
- IUI-1.2 Coi ltIUIa, ta, CS1, IUI-1.2,
cherokee, trgt - Ri ltIUIa, ta, depends-on, BFO, IUI-1.2,
IUI-1, trgt - IUI-1.3 Coi ltIUIa, ta, CS3, IUI-1.3, chest
pain, trgt - Ri ltIUIa, ta, is-located-in, BFO, IUI-1.3,
IUI-1, trgt - All dates in the statements are 2 years earlier
than now - What to do with
- Jane Smith
- Jane Smiths race (CS1 native American)
- Jane Smiths gender (CS1 female)
- Jane Smiths chest pain (CS3 chest pain)
- Jane Smiths age (50)
34Conclusion
- 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