eco r european centre for ontological research practical implementations of realism-based...

ECOREuropean Centre forOntological Research

Practical implementations of realism-based ontologies:

Referent Tracking in Electronic Health Records

MIE 2005 tutorial #35 on Ontology Design (part 4)Geneva, Switzerland, August 28, 2005

Dr. W. CeustersEuropean Centre for Ontological Research

Saarland University

Saarbrücken - Germany


Three models for a Comprehensive Patient Care

Information System *

Information model of the medical record: What can be said ?

Process model of clinical care: What

ought to occur ?

Inferred model of the state of the patient:

What actually occurs.

* Rector AL, Nolan WA, and Kay S. Foundations for an Electronic Medical Record. Methods of Information in Medicine 30: 179-86, 1991. (Figure 1)

requirements inferences

modification

Inferred model of the state of the patient:

What actually occurs.

?


What ‘event’ occurred in my left hand being a part of my left arm ?

Is ‘saying that an event has occurred’ a requirement for the event to have occurred ?

An event model of medicalinformation representation *

• ‘The real world consist of objects (or entities)’ • ‘Objects interact with other objects and can be associated with

other objects by relationships’ • ‘When two or more objects interact in the real world, an ‘event’

is said to have occurred’

* Huff SM, Rocha RA, Bray BE, Warner HR, and Haug PJ. An Event Model of Medical Information Representation. J Am Med Informatics Assoc. 1995;2:116-134.

?


Observation Event Instance Created from the Statement

‘Surgical clips are again seen along the right mediastinum’ *

* Huff SM, Rocha RA, Bray BE, Warner HR, and Haug PJ. An Event Model of Medical Information Representation. J Am Med Informatics Assoc. 1995;2:116-134.

?Are the clips there because they have been observed ?

Is the observation located in the mediastinum ?


What is wrong in both cases(and so many others) ?

• Further clues to the answer:– Huff SM, Rocha RA, Bray BE, Warner HR, and Haug

PJ. An Event Model of Medical Information Representation. J Am Med Informatics Assoc. 1995;2:116-134.

– Rector et al.’s paper: Many of the difficulties experienced in attempting to generalize existing [patient record] systems stem from the fact that they have pre-selected and distorted information in order to fit into particular applications, usually clinical research and epidemiology. The models emit much of the information actually used in clinical care and do not accurately reflect the real status of the data they record.

• Further clues to the answer:– Huff SM, Rocha RA, Bray BE, Warner HR, and Haug

PJ. An Event Model of Medical Information Representation. J Am Med Informatics Assoc. 1995;2:116-134.

– Rector et al.’s paper: Many of the difficulties experienced in attempting to generalize existing [patient record] systems stem from the fact that they have pre-selected and distorted information in order to fit into particular applications, usually clinical research and epidemiology. The models emit much of the information actually used in clinical care and do not accurately reflect the real status of the data they record.


What is wrong (continued) ?

• An overemphasis on data and information and too little attention to reality:

– “data modelling”– “information modelling”

• Is the “Object Oriented” model approach any better, since, after all, objects are said to be those things that exist in reality ?

– The object-oriented model is based on a collection of objects

– An object contains values stored in instance variables within the object.

– Unlike the record-oriented models, these values are themselves objects.


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

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.


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.”


Note:Mixing statements and entities

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


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

A look at the database:Use of SNOMED codes for ‘unambiguous’

understanding

*

*

*

* cause, not disorder

How many disorders have patients 5572, 2309 and 298 each had thus far in their lifetime ?

How many numerically different disorders are listed here ?

How many different types of disorders are listed here ?


















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 ?

Would the terms help ?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

• ‘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 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 Assertion of assignments

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

• IUId IUI of the registering agent

• Ai the assertion of the assignment < IUIp, IUIa, tap>

» IUIa IUI of the author of the assertion

» IUIp IUI of the particular

» tap time of the assignment

• td time of registering Ai in the IUI-repository

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

started to exist ! That might be asserted in statements

providing information about # IUIp .


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 PtoP statements -

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

IUIa 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.


PtoU statements – particular to universal

Ui = <IUIa, ta, inst, o, IUIp, u, 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 u are taken,

IUIp the IUI referring to the particular whose inst

relationship with u is asserted,u the universal in o to which p enjoys the inst relationship, and,tr a reference to the time at which the relationship obtains.


PtoCO statements particular to concept code

Coi = <IUIa, ta, cbs, IUIp, co, tr>



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

IUIp 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 ofPtoCO 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

















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


A case study

• Double goal:– Application of referent tracking to a concrete

patient story– Ontological analysis of what is involved

• The latter is NOT to be performed to the same extent when referent tracking is used as an alternative to coding using concept-based systems.

• So, don’t go home with the idea: “that’s all too cumbersome and time cosuming”


Jim Cimino’s Woods Hole caseJane Smith is a 30 year old, Native American female who presents to the emergency room with the chief complaint of cough and chest pain.The patient reports that she has had a productive cough for three days but that chest pain developed one hour ago. She gives a history of hypertension. She also reports that she was treated in the past for tuberculosis while she was pregnant. The patient reports an allergy to Bufferin.Physical examination revealed a well-developed, well-nourished female in moderate respiratory distress. Vital signs showed a pulse of 90, a respiratory rate of 22, an oral temperature of 100.3, and a blood pressure of 150/100. Examination revealed rales and rhonchi in the left upper chest. Abdominal exam revealed a tender, palpable liver edge.Labs:Chem7 (serum): Glucose 100 (70-105) Chem7 (plasma): Glucose 150 (75-110)CBC: Hgb 15 (12.0-15.8), Hct 45 (42.4-48.0), WBC 11,000 (3,540-9,060), Platelets 145,000 (165,000-415,000)A fingerstick blood sugar was 80Urinalysis showed protein of 1+ and glucose of 0.A blood culture was positive for methicillin-resistant Staphylococcusaureus (MRSA)

ECOREuropean Centre forOntological Research case study continued ...

• ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST segment 2mm elevated andT-waves down in leads I, L, V5 and V6

Chest X-ray Left upper lobe infiltrate, left ventricular hypertrophy

The patients nurse reported that the patient seemed depressed about her condition. On questioning, the nurse found that the patient was caringfor her elderly father and was concerned that she would no longer be able to manage caring for herself and him. The nurse asked the patients physician to consider an antidepressant and a social work consult.

A medical student reviewing the case is concerned about the risk of MRSA in patients with pneumonia and a recent myocardial infarction. She decides to do a literature search.


Step 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.

Question:What if the patient is not tellingthe truth ?







Step 2: indentify to what particulars these phrases refer

Jane Smith Jane Smith’s age

Jane Smith’s race Jane SmithJane Smith’s gender Jane Smith’s showing up at ...

A specific emergency room of health facility XYZ

Jane Smith’s complaining primarily about ...

A temporal part of Jane Smith’slife marked by happenings of coughs

Jane Smith’s chest

A specific pain experienced by Jane Smith


Compare with simple clinical coding in juxtaposition






“Jane Smith” CS1-age

CS1-native-americanCS1-female-gender

CS1-emergency room

CS1-chief-complaint

CS1-coughing CS1-chest-pain

CS2-woman

CS2-painCS2-chest


Compare with the output of the perfect semantic analyser we all would dream of

CS3-50 years oldHas-Age

CS3-woman

Is-A

CS3-native american

Is-ACS3-complaining

“Jane Smith”

Has-Sayer

CS3-chest pain

Has-Saying

CS3-coughing

Has-Saying

CS3-consultation

Has-happening-during

CS3-Em.RoomHas-Loc

Has-participant

Compare with the output of the NAIVE !!! semantic analyser we all would dream of


What it (more or less) should be

CS3-complaining

CS3-chest pain

Has-Saying

CS3-coughing

Has-Saying

“chest-pain”

Has-’referent’

“coughing”

Has-’referent’

ECOREuropean Centre forOntological Research Most important difference:

Use of generic terms

Use of concrete particulars











Jane Smith Jane Smith’s age

Jane Smith’s race Jane SmithJane Smith’s gender Jane Smith’sshowing up at ...

A specific emergency room of health facility XYZ

Jane Smith’s complaining primarily about ...

A temporal part of Jane Smith’slife marked by happenings of coughs

Jane Smith’s chest

A specific pain experienced by JaneSmith








CS1-emergency room

CS1-chief-complaint














CS1-emergency room

CS1-chief-complaint


CS2-woman

CS2-painCS2-chest

CS2-womanCS2-woman

CS2-painCS2-painCS2-chestCS2-chest



CS3-woman

Is-A

CS3-woman

Is-A

CS3-native american

Is-A

CS3-native american

Is-ACS3-complaining

“Jane Smith”

Has-Sayer

“Jane Smith”

Has-Sayer

CS3-chest pain

Has-Saying

CS3-chest pain

Has-Saying

CS3-coughing

Has-Saying

CS3-coughing

Has-Saying

CS3-consultation


CS3-consultation


CS3-Em.RoomHas-Loc CS3-Em.RoomHas-Loc

Has-participantHas-participant

ECOREuropean Centre forOntological Research Step 3: are relevant and

necessary particulars missing ?• 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)


Step 4: IUI assignment

• 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 Coi = <IUIa, ta, CS1, IUI-1.2, cherokee, tr>

Ri = <IUIa, ta, depends-on, BFO, {IUI-1.2, IUI-1}, tr>

• IUI-1.3 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)


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

eco r european centre for ontological research practical implementations of realism-based...

Documents

information model

distorted information

clinical research

methods of information

eco r european centre

inferred model

process model of clinical

electronic medical record