eco r european centre for ontological research referent tracking in electronic health records mie...

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


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


The story of Jane Smith

an old case, well known in the literature ...


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


A visit to the hospital

City Health Centre Dr. Peters

(City HC) Dr. Longley


Diagnosis: a severe spiral fracture of the femur


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.”


5572 04/07/1990 26442006 closed fracture of shaft of femur

5572 04/07/1990 81134009 Fracture, closed, spiral


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



47804 03/04/1993 58298795 Other lesion on other specified region


298 22/08/1993 2909872 Closed fracture of radial head




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.


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– ...


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


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.


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.


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 ...


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 81134009 Fracture, closed, spiral




0939 24/12/1991 255174002 benign polyp of biliary tract



47804 03/04/1993 58298795 Other lesion on other specified region


298 22/08/1993 2909872 Closed fracture of radial head




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


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


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

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