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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

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Werner CEUSTERS a , Peter ELKIN b and Barry SMITH a, c

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  1. MIE 2006 PresentationReferent Tracking: The Problem of Negative FindingsMaastricht, 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. The same type of location code used in relation to three different events might or might not refer to the same location. PtID Date ObsCode Narrative Three references of hypertension for the same patient denote three times the same disease. 5572 5572 5572 5572 2309 5572 298 5572 298 5572 47804 03/04/1993 12/07/1990 01/04/1997 04/07/1990 22/08/1993 01/04/1997 21/03/1992 12/07/1990 04/07/1990 22/08/1993 17/05/1993 26442006 2909872 9001224 26442006 9001224 79001 9001224 81134009 58298795 79001 26442006 Essential hypertension Accident in public building (supermarket) closed fracture of shaft of femur closed fracture of shaft of femur Accident in public building (supermarket) Closed fracture of radial head Other lesion on other specified region Essential hypertension closed fracture of shaft of femur Accident in public building (supermarket) Fracture, closed, spiral 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 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. 2309 21/03/1992 26442006 closed fracture of shaft of femur 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 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. 0939 20/12/1998 255087006 malignant polyp of biliary tract Using codes does not prevent ambiguities as to what is described

  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: • explicitreference 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. PtID Date ObsCode Narrative IUI-001 5572 5572 5572 2309 5572 5572 298 5572 298 5572 47804 17/05/1993 01/04/1997 04/07/1990 04/07/1990 12/07/1990 12/07/1990 21/03/1992 01/04/1997 22/08/1993 03/04/1993 22/08/1993 9001224 26442006 81134009 26442006 9001224 79001 58298795 79001 2909872 26442006 9001224 Essential hypertension Closed fracture of radial head closed fracture of shaft of femur Accident in public building (supermarket) Accident in public building (supermarket) closed fracture of shaft of femur closed fracture of shaft of femur Essential hypertension Fracture, closed, spiral Accident in public building (supermarket) Other lesion on other specified region IUI-001 IUI-001 IUI-007 5572 04/07/1990 79001 IUI-005 Essential hypertension 0939 24/12/1991 255174002 IUI-004 benign polyp of biliary tract 2309 21/03/1992 26442006 IUI-002 closed fracture of shaft of femur IUI-007 IUI-005 IUI-007 IUI-012 IUI-005 0939 20/12/1998 255087006 IUI-004 malignant polyp of biliary tract Advantage: better reality representation 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. Tuple type Phenomenon described 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 RT’s formal machinery is based on BFO’s relationship types

  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. 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. C1 Relation type <p, u> * Type of Negative Finding 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 Examples 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 Negative findings under a BFO perspective

  15. Solution • For C1 and C2: • 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 topart =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 toidentity =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. 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.

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