ECOREuropean Centre forOntological Research
Referent Tracking in Electronic Health Records
MIE 2005, Geneva
Dr. W. CeustersEuropean Centre for Ontological Research
Saarland University, Saarbrücken - Germany
Barry Smith
Institute for Ontology and Medical Information Science
Saarland University, Saarbrücken - Germany
ECOREuropean Centre forOntological Research
Current mainstream thinking
datainformation
knowledge
wisdom
- representation
- representation
- representation
(- 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 ?
RealityWhat is there on the side of the patient
ECOREuropean Centre forOntological Research
The story of Jane Smith
an old case, well known in the literature ...
ECOREuropean Centre forOntological Research
Jane’s favourite supermarket
July 4th, 1990: Jane goes shopping:
The freezer section of Jane’s favourite supermarket
The only available warning sign used outside
A very suspiciously shaped upper leg
ECOREuropean Centre forOntological Research
A visit to the hospital
City Health Centre Dr. Peters
(City HC) Dr. Longley
ECOREuropean Centre forOntological Research
Diagnosis: a severe spiral fracture of the femur
ECOREuropean Centre forOntological Research
CityHC’s representation formalism(for statements in records)
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.
Categories: “represent concepts and are analogous to classes in other formalisms”
Individuals: “concrete instances of categories which persist in space and time”Occurrences: “are
specific occurrences of individuals and must be situated in space and time. The most importantgroup of occurrences are observations — i.e. agents’ observations of individuals.”
ECOREuropean Centre forOntological Research
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
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
Same patient, same hypertension code:Same (numerically identical) hypertension ?
Different patients, same fracture codes:Same (numerically identical) fracture ?
Same patient, different dates, same fracture
codes: same (numerically identical)
fracture ?
Same patient, same date,2 different fracture codes:
same (numerically identical) fracture ?
Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?
Registration through generic namesBut, there are some problems ...Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ?Or different supermarkets, but always in the freezer sections ?
ECOREuropean Centre forOntological Research 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.
ECOREuropean Centre forOntological 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
– ...
ECOREuropean Centre forOntological Research Proposed solution:
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
ECOREuropean Centre forOntological Research 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– ...
ECOREuropean Centre forOntological Research
An ontological analysis
continuantsCity HC
The freezer section of Jane’s favourite supermarket
Jane’s left femur
Jane’s left femur fracture
Jane Smith
Dr. Peters
Jane’s left femur
Jane’s fracture’s image
Dr. Longley
City HC’s EHR system
t Jane’s fallingJane’s femur breakingDr. Peter’s examination of Jane’s fractureDr. Peter’s ordering of an X-rayShooting the pictures of Jane’s leg
occurrents
Jane’s fracture’s healingDr. Peter’s diagnosis making
Jane diesFreezer section dismantledDr. Longley’s examination of Jane’ s fracture
Jane’s fracture as seen by Dr. PetersJane’s fracture as seen by Dr.
Longley
Instances of
Jane’s fracture
UniversalsEHR system
HC
Freezer section
Person
Femur
Fracture
Image
ECOREuropean Centre forOntological Research Ontological recategorisation
CityHC Dr. PetersJane
Smith
JaneSmith’sFractureOf Femur
FractureOf Femur
Severe Spiral
City HCexists on 4th July1990
Dr. Peterslocated atCity HC on 4th July1990
Jane Smith’sconsultation withDr. Peters atCity HC on 4th July1990
Dr. Peters’assessment ofJane Smith’sfracture offemur atCity HC on 4th July1990
JaneSmith’sFracture
Of Femur’sseverity
JaneSmith’sFracture
Of Femur’sshape
ECOREuropean Centre forOntological Research
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.
ECOREuropean Centre forOntological Research
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.
ECOREuropean Centre forOntological Research
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 !• Only the plan exists and possibly the statements made about
the future execution of the plan
– More difficult: subjective symptoms• 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 ...
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research Representation in the EHR
• Relevant particulars referred to 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
CityHC Dr. PetersJane
Smith
JaneSmith’s
FractureOf Femur
FractureOf Femur
SevereSpiral
Jane Smith’sconsultation withDr. Peters atCity HC on 4th July1990
Dr. Peters’assessment ofJane Smith’sfracture offemur atCity HC on 4th July1990
JaneSmith’s
FractureOf Femur’s
severity
JaneSmith’s
FractureOf Femur’s
shape
4th July 1990
particulars
ECOREuropean Centre forOntological Research 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 concept-based 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
• A transfert or reference mechanism makes the statements visible through the RTDB
ECOREuropean Centre forOntological Research Advantage: better
reality representation
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
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
IUI-001
IUI-001
IUI-001
IUI-003
IUI-004
IUI-004
IUI-005
IUI-005
IUI-005
IUI-007
IUI-007
IUI-007
IUI-002
IUI-012
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
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