1. Werner CEUSTERS a, Peter ELKIN b and Barry SMITH a, c
MIE 2006 Presentation Referent Tracking: The Problem of Negative Findings Maastricht, The Netherlands, Tuesday August 29th, 2006
Werner CEUSTERS a, Peter ELKIN b and Barry SMITH a, c
a Center of Excellence in Bioinformatics and Life Sciences, and
National Center for Biomedical Ontology, University at Buffalo, NY, USA
b Department of Medicine, Mayo Foundation, Rochester, MN, USA
c IFOMIS, Saarbrücken, Germany, and
Department of Philosophy, University at Buffalo, NY, USA

2. Using codes does not prevent ambiguities as to what is described
The same type of location code used
in relation to three different events might or might not refer to the same
location.
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
Three references of hypertension for the same
patient denote three times the same disease.
If two different fracture codes are used in relation to observations made on the same day for the same patient, they might refer to the same fracture
If the same fracture code is used for the same patient on different dates, then these codes might or might not refer to the same fracture.
If two different tumor codes are used
in relation to observations made on different
dates for the same patient,
they may still refer to the same tumor.
The same fracture code used in relation
to two different patients can not refer to
the same fracure.

3. 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
...

4. 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 particular (individual) entity

5. 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-006
IUI-003

6. Referent Tracking is based on Basic Formal Ontology (BFO), a theory of ontology that …
Accepts the existence of
a real world outside mind and language
a structure in that world prior to mind and language (universals / particulars)
Rejects ontology as a matter of agreement on ‘conceptualizations’
Uses reality as a benchmark for testing the quality of ontologies as artifacts by building appropriate logics with referential semantics (rather than model-theoretic)

7. It differentiates radically between …
Two basic types of entities:
Particulars versus universals
Werner Ceusters person
Werner Ceusters’ nose nose
Three types of relationships:
<p, p>: Werner Ceusters’ nose part_of Werner Ceusters
<p, u>: Werner Ceusters instance_of person
<u, u>: nose isa anatomical structure

8. RT’s formal machinery is based on BFO’s relationship types
Ai = < IUIp, IUIa, tap>
Act of assignment of IUIp to a particular at time tap by the particular referred to by IUIa *
Ri = <IUIa, ta, r, o, P, tr>
It is asserted by the particular referred to by IUIa at time ta that the relationship r from ontology o obtains between the particulars referred to in the set of IUIs P at time tr
Ui = <IUIa, ta, inst, o, IUIp, u, tr>
It is asserted by the particular referred to by IUIa at time ta that the instantiation relation as defined in ontology o obtains between the particular referred to by IUIp and the universal u at time tr
Tuple type
Phenomenon described

9. 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.

10. Criteria for IUI assignment
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
The particular’s existence ‘may not already have been determined as the existence of something else’:
The particular may not have already been assigned a IUI.
It must be relevant to do so.

11. ‘negative findings’: a challenge for RT
Some examples:
“no history of diabetes”
“hypertension ruled out”
“absence of metastases in the lung”
“prevented abortion”
“cancelled X-Ray”
RT does NOT allow a IUI to be assigned to what does not exist !

12. Negative findings are important in care
Occur relatively frequent:
Elkin et al found SNOMED-CT to provide coverage for 14,792 concepts in 41 health records from Johns Hopkins University, of which 12.3% were identified as negative.
Mutalik et al report the presence of 8,358 instances of UMLS concepts in 60 documents of which 6.8% were negative.
Medico-legal issues:
In 1998, an NHS Independent Review panel judged the record-keeping in a specific case to fall below the level of good practice because ‘the notes make no reference to any other findings, nor of any negative ones which would be relevant when considering problems specific to diabetes. Thus no reference is made to the absence of a smell of ketones on Miss J’s breath, nor any other negative indications’
In the US, Medicare and Medicaid compliance requires that the patient record should document ‘specific abnormal and relevant negative findings of the examination of the affected or symptomatic body area(s) or organ system(s)’

13. NOT to introduce in the referential machinery
Our strategy
NOT to introduce in the referential machinery
Possibilia
Non-existent objects
Absences
But to find the relationships that do obtain in reality between the entities involved

14. Negative findings under a BFO perspective
Relation type
Type of Negative Finding
Examples % C1
<p, u> *
A particular is not related in a specific way to any instance of a universal at some given time
he denies abdominal pain; no alcohol abuse; no hepatosplenomegaly; he has no children, without any cyanosis
85.4 C2
<p, u>
A particular is not the instance of a given class at some given time
which ruled out primary hyperaldosteronism, nontender, in no apparent distress, Romberg sign was absent , no palpable lymph nodes
12.4 C3
<p, p>
A particular is not related to another particular in a specific way at some given time
this record is not available to me; it is not the intense edema she had before; he has not identified any association with meals.
2.2

15. Solution For C1 and C2: For C3: simple logical negation
Introduce a family of relations called ‘lacks’ such that for
C1-type of negative findings (for example concerning ‘part’):
p lacks u at t with respect to part =def. there is no x such that: x part_of p at t and x instance_of u
C2-type of negative findings:
p lacks u at t with respect to identity =def. there is no x such that: x identical_to p at t and x instance_of u
Introduce a new tuple-type in the RT-formalism
Ui = <IUIa, ta, r, o, IUIp, u, tr>
The particular referred to by IUIa asserts at time ta that the relation r of ontology o does not obtain at time tr between the particular referred to by IUIp and any of the instances of the universal u at time tr
For C3: simple logical negation

16. Testing the approach
Our study sample: 396 negative findings encountered in 250 sentences out of 18 patient charts from Johns Hopkins University
We excluded (8.3%) :
Misjudged negations:
The patient actually answers yes, no, and sir to all questions’
Negative formulation of positive phenomenon
‘He has no idea why he is here’
Her workup showed that she had an MRI of the brain that was negative in 03/02’
We ignored certain modalities:
‘He has no family history of GI malignancies that I know of’

17. Failures only because of phenomena RT can’t (yet?) deal with:
Results
We were able to represent 99,9% of the negative findings using the lacks relation or logical negation of relationships between existing entities
Failures only because of phenomena RT can’t (yet?) deal with:
‘no other complications of gastroesophageal reflux disease were noted’.

18. Conclusion
With the introduction of the lacks family of relations, we have been able to
Provide additional support for the thesis that negation is outside the realm of ontology but belongs rather to the domains of logic, language and epistemology.
Stay away from ‘fantology’, i.e. the false belief that the structures of logic, language and information are mirrors of the structure of reality.
In reality, there is only what there is. Language and logic allow us to talk and reason about what there is by using negation. But the corresponding negative expressions do not mirror anything in reality.