1. European Centre for Ontological 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. Ceusters
European Centre for Ontological Research
Saarland University
Saarbrücken - Germany

2. Three models for a Comprehensive Patient Care Information System *?
Information model of the medical record: What can be said ?
inferences
requirements
Process model of clinical care: What ought to occur ?
Inferred model of the state of the patient: What actually occurs.
Inferred model of the state of the patient: What actually occurs.
modification
* Rector AL, Nolan WA, and Kay S. Foundations for an Electronic Medical Record. Methods of Information in Medicine 30: , (Figure 1)

3. An event model of medical information 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’
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 ? ?
* 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:

4. Observation Event Instance Created from the Statement ‘Surgical clips are again seen along the right mediastinum’ * ?
Are the clips there because they have been observed ?
Is the observation located in the 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:

5. 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:
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:
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.

6. 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.

7. The story of Jane Smith an old case, well known in the literature ...

8. July 4th, 1990: Jane goes shopping:
Jane’s favourite supermarket
The freezer section of Jane’s favourite supermarket
The only available warning sign used outside
A very suspiciously shaped upper leg

9. A visit to the hospital City Health Centre Dr. Peters
(City HC) Dr. Longley

10. Diagnosis: a severe spiral fracture of the femur

11. 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 Apr;32(2):

12. 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 Apr;32(2):

13. 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 important
group of occurrences are observations — i.e. agents’ observations of individuals.”
Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ.
A framework for modelling the electronic medical record.
Methods Inf Med Apr;32(2):

14. 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.”

15. Use of SNOMED codes for ‘unambiguous’ understanding
A look at the database:
Use of SNOMED codes for ‘unambiguous’ understanding
5572
04/07/1990
closed fracture of shaft of femur
Fracture, closed, spiral
12/07/1990
Accident in public building (supermarket)
79001
Essential hypertension
0939
24/12/1991
benign polyp of biliary tract
2309
21/03/1992
47804
03/04/1993
Other lesion on other specified region
17/05/1993
298
22/08/1993
Closed fracture of radial head
01/04/1997
PtID
Date
ObsCode
Narrative
20/12/1998
malignant polyp of biliary tract
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

16. 2 different fracture codes: same (numerically identical) fracture ?
Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ?
Or different supermarkets, but always in the freezer sections ?
Would the terms help ?
5572
04/07/1990
closed fracture of shaft of femur
Fracture, closed, spiral
12/07/1990
Accident in public building (supermarket)
79001
Essential hypertension
0939
24/12/1991
benign polyp of biliary tract
2309
21/03/1992
47804
03/04/1993
Other lesion on other specified region
17/05/1993
298
22/08/1993
Closed fracture of radial head
01/04/1997
PtID
Date
ObsCode
Narrative
20/12/1998
malignant polyp of biliary tract
Same patient, same hypertension code:
Same (numerically identical) hypertension ?
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 (numerically
identical) polyp ?
Different patients, same fracture codes:
Same (numerically identical) fracture ?

17. 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.

18. 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
...

19. 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

20. 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
...

21. An ontological analysis
Universals
EHR system HC
Freezer section
Person
Femur
Fracture
Image
continuants
City HC
The freezer section of Jane’s favourite supermarket
Jane’s left femur
Jane’s left femur fracture
Jane Smith
Dr. Peters
Jane’s fracture’s image
Dr. Longley
City HC’s EHR system
Jane’s falling
Jane’s femur breaking
Dr. Peter’s examination of Jane’s fracture
Dr. Peter’s ordering of an X-ray
Shooting the pictures of Jane’s leg
occurrents
Jane’s fracture’s healing
Dr. Peter’s diagnosis making
Jane dies
Freezer section dismantled
Dr. Longley’s examination of Jane’ s fracture t
Jane’s fracture as seen by Dr. Peters
Jane’s fracture as seen by Dr. Longley
Instances of
Jane’s fracture

22. Ontological recategorisation
Fracture
Of Femur
Severe
Spiral
Jane
Smith’s
Fracture
Of Femur’s
severity
shape
CityHC
Dr. Peters
Jane
Smith
Smith’s
Fracture
Of Femur
Jane Smith’s
consultation
with
Dr. Peters at
City HC on
4th July
1990
City HC
exists on
4th July
1990
Dr. Peters
located at
City HC on
Dr. Peters’
assessment of
Jane Smith’s
fracture of
femur at
City HC on
4th July
1990

23. 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.

24. Architecture of a Referent 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

25. IUI generation Universally Unique IDs:
recently standardized through ISO/IEC :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)

26. 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.

27. Criteria for IUI assignment (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 ...

28. Criteria for IUI assignment (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
May not have already been assigned a IUI.
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

29. 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 .

30. 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.

31. Representation in the EHR
CityHC
Dr. Peters
Jane
Smith
Smith’s
Fracture
Of Femur
Severe
Spiral
Jane Smith’s
consultation
with
Dr. Peters at
City HC on
4th July
1990
Dr. Peters’
assessment of
fracture of
femur at
Of Femur’s
severity
shape
4th July 1990
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
particulars

32. 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.

33. PtoU statements – particular to universal
Ui = <IUIa, ta, inst, o, IUIp, u, tr>
IUIa is the IUI of the author of the statement,
ta a reference to the time when the statement is made,
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.

34. PtoCO statements particular to concept code
Coi = <IUIa, ta, cbs, IUIp, co, tr>
IUIa is the IUI of the author of the statement,
ta a reference to the time when the statement is made,
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,

35. Interpretation of PtoCO 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.

36. A SNOMED-CT example
<IUI-0945, 18/04/2005, SNOMED-CT v0301, IUI-1921, , forever>
#IUI-0945: author of the statement
#IUI-1921: the left testicle of patient #IUI-78127
: 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

37. 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

38. Advantage: better reality representation
5572
04/07/1990
closed fracture of shaft of femur
Fracture, closed, spiral
12/07/1990
Accident in public building (supermarket)
79001
Essential hypertension
0939
24/12/1991
benign polyp of biliary tract
2309
21/03/1992
47804
03/04/1993
Other lesion on other specified region
17/05/1993
298
22/08/1993
Closed fracture of radial head
01/04/1997
PtID
Date
ObsCode
Narrative
20/12/1998
malignant polyp of biliary tract
IUI-001
IUI-007
IUI-005
IUI-004
IUI-002
IUI-012
IUI-003

39. 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

40. 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”

41. Jim Cimino’s Woods Hole case
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.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 ( ), Hct 45 ( ), WBC 11,000 (3,540-9,060), Platelets 145,000 (165, ,000) A fingerstick blood sugar was 80 Urinalysis showed protein of 1+ and glucose of 0. A blood culture was positive for methicillin-resistant Staphylococcus aureus (MRSA)

42. 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.

43. Step 1: identify the phrases referring to particulars
Jane Smith is a 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 telling
the truth ?

44. Step 2: indentify to what particulars these phrases refer
Jane Smith is a year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
Jane Smith
Jane Smith’s age
Jane Smith’s race
Jane Smith’s gender
Jane Smith
Jane Smith’s showing up at ...
A specific emergency room of health facility XYZ
A specific pain experienced by Jane Smith
Jane Smith’s complaining primarily about ...
A temporal part of Jane Smith’s
life marked by happenings of coughs
Jane Smith’s chest

45. Compare with simple clinical coding in juxtaposition
Jane Smith is a year old ,
Native American female who presents
to the emergency room
with the chief complaint
of cough and chest pain.
“Jane Smith”
CS1-age
CS1-native-american
CS1-female-
gender
CS1-emergency room
CS1-chief-complaint
CS1-coughing
CS1-chest-pain
CS2-woman
CS2-pain
CS2-chest

46. Compare 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
CS3-50 years old
Has-Age
“Jane Smith”
Has-Sayer
Has-participant
CS3-woman
Is-A
CS3-native american
Is-A
CS3-complaining
CS3-consultation
Has-happening-during
CS3-coughing
Has-Saying
CS3-chest pain
Has-Saying
CS3-Em.Room
Has-Loc

47. What it (more or less) should be
“chest-pain”
CS3-complaining
Has-Saying
Has-’referent’
CS3-chest pain
Has-Saying
“coughing”
Has-’referent’
CS3-coughing

48. Most important difference:
Use of generic terms
Use of concrete particulars

49. 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)

50. Step 4: IUI assignment Assumptions: the RTS contains already:
IUI-1 Jane Smith
Coi = <IUIa, ta, CS3, IUI-1, woman, tr>
IUI Ri = <IUIa, ta, depends-on, BFO, {IUI-1.1, IUI-1}, tr>
Coi = <IUIa, ta, CS1, IUI-1.1, age, tr>
IUI Coi = <IUIa, ta, CS1, IUI-1.2, cherokee, tr>
Ri = <IUIa, ta, depends-on, BFO, {IUI-1.2, IUI-1}, tr>
IUI 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)

51. 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