Strategies for Referent Tracking in Electronic Health Records

ECOREuropean Centre forOntological Research

Strategies for Referent Tracking in Electronic

Health Records

Dr. W. CeustersEuropean Centre for Ontological Research

Saarland University

Saarbrücken - Germany


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


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.

ECOREuropean Centre forOntological Research City HC’s EHR model



CityHC’s representation formalism(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

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.”


Mixing statements and entities

• “Every occurrence level statement concerning the Jane Smith’s Fracture of the Femur is an observation of the corresponding individual.”

• “The existence of the individual Jane Smith’s Fracture of Femur does not imply that Jane Smith has, or has ever had, a fracture of the femur, but merely that some observation has been made about Jane Smith regarding a fracture of the femur.”

• “(The only observation recorded about Jane Smith’s Fracture of the Femur might be that she did not have it.)”


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 ?

But, there are some problems ...Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ?Or different supermarkets, but always in the freezer sections ?

Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?

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.


Architecture of aReferent 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


IUI generation

• Universally Unique IDs: – recently standardized through ISO/IEC 9834-

8:2004, – 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)


IUI asignment

• = 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, one out of 2 electrons in a György’s box

– 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 Assertion of assignments

• IUI assignment is an act of which the execution has to be asserted in the IUI-repository:– <da, Ai, td>

• da IUI of the registering agent

• Ai the assertion of the assignment <pa, pp, tap, c>

» pa IUI of the author of the assertion

» pp IUI of the particular

» tap time of the assignment

» c optional description for identification

• td time of registering Ai in the IUI-repository

• Neither td or tap give any information about when #pp

started to exist ! That might be asserted in statements

providing information about #pp .


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.

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 PTP statements -

particular to particular • ordered sextuples of the form <sa, ta, r, o, P, tr>

sa 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.


PTCL statements – particular to class

<sa, ta, inst, o, p, cl, tr>



inst a reference to an instance relationship available in o obtaining between p and cl,

o a reference to the ontology from which inst and cl are taken,

p the IUI referring to the particular whose inst relationship with cl is asserted,

cl the class in o to which p enjoys the inst relationship, and,

tr a reference to the time at which the relationship obtains.


PTCO statements particular to concept code

<sa, ta, cbs, p, co, tr>



cbs a reference to the concept-based system from which co is taken,

p the IUI referring to the particular which the author associates with co,

co the concept-code in cbs which the author associates with p, and,tr a reference to the time at which the author considers the

association appropriate,


Interpretation ofPTCO 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.

ECOREuropean Centre forOntological Research A SNOMED-CT example

• <IUI-0945, 18/04/2005, SNOMED-CT v0301, IUI-1921, 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

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 tranfert 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 cbs– 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 (cbs) can play an interesting 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

Documents

Strategies for Referent Tracking in Electronic Health Records