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

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.

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

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  1. Practical implementations of realism-based ontologies: Referent Tracking in Electronic Health RecordsMIE 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: 179-86, 1991. (Figure 1)

  3. Is ‘saying that an event has occurred’ a requirement for the event to have occurred ? What ‘event’ occurred in my left hand being a part of my left arm ? 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.

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

  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 InformationRepresentation. 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 InformationRepresentation. 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.

  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 Smithan old case, well known in the literature ...

  8. 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 July 4th, 1990: Jane goes shopping:

  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: whatthey have heard, seen, thought and done. • captures in a structured form all of the ‘clinicallysignificant’ information in the narrative notes, where by clinically significant they mean the information which is within the medical domain rather than the domain ofeveryday 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.

  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. 1993 Apr;32(2):109-19.

  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. 1993 Apr;32(2):109-19.

  14. Note:Mixing statements and entities • “Every occurrence level statement concerning the Jane Smith’s Fracture of the Femuris an observation of the corresponding individual.”

  15. PtID Date ObsCode Narrative 5572 5572 298 5572 5572 5572 298 2309 47804 5572 5572 12/07/1990 01/04/1997 22/08/1993 22/08/1993 01/04/1997 12/07/1990 21/03/1992 03/04/1993 04/07/1990 17/05/1993 04/07/1990 26442006 2909872 9001224 26442006 9001224 58298795 26442006 9001224 79001 79001 81134009 Essential hypertension closed fracture of shaft of femur Fracture, closed, spiral closed fracture of shaft of femur Accident in public building (supermarket) Other lesion on other specified region closed fracture of shaft of femur Essential hypertension Accident in public building (supermarket) Closed fracture of radial head Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract 2309 21/03/1992 26442006 closed fracture of shaft of femur 0939 20/12/1998 255087006 malignant polyp of biliary tract A look at the database: Use of SNOMED codes for ‘unambiguous’ understanding 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. Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ? Or different supermarkets, but always in the freezer sections ? PtID Date ObsCode Narrative Same patient, same hypertension code: Same (numerically identical) hypertension ? 5572 298 5572 5572 2309 5572 5572 47804 298 5572 5572 21/03/1992 04/07/1990 17/05/1993 12/07/1990 01/04/1997 22/08/1993 01/04/1997 04/07/1990 22/08/1993 12/07/1990 03/04/1993 9001224 9001224 26442006 81134009 79001 26442006 9001224 26442006 2909872 79001 58298795 Accident in public building (supermarket) Essential hypertension closed fracture of shaft of femur Fracture, closed, spiral closed fracture of shaft of femur closed fracture of shaft of femur Other lesion on other specified region Closed fracture of radial head Essential hypertension Accident in public building (supermarket) Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 0939 24/12/1991 255174002 benign polyp of biliary tract Same patient, different dates, same fracture codes: same (numerically identical) fracture ? 2309 21/03/1992 26442006 closed fracture of shaft of femur 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 ? 0939 20/12/1998 255087006 malignant polyp of biliary tract Would the terms help ?

  17. Main problem areasfor 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: • 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 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 realitywhich • (1) reflects the properties of the objects within its domain in such a waythat there obtains a systematic correlation between realityand 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. Universals EHR system City HC’s EHR system HC City HC Freezer section The freezer section of Jane’s favourite supermarket Jane Smith Person Dr. Peters Dr. Longley Femur Jane’s left femur Jane’s left femur Fracture Jane’s left femur fracture Image Jane’s fracture’s image Jane’s falling occurrents t Jane’s fracture as seen by Dr. Peters Jane’s fracture as seen by Dr. Longley Instances of Jane’s fracture Jane’s femur breaking Dr. Peter’s examination of Jane’s fracture Dr. Peter’s ordering of an X-ray Dr. Peter’s diagnosis making Jane’s fracture’s healing Shooting the pictures of Jane’s leg Dr. Longley’s examination of Jane’ s fracture Freezer section dismantled Jane dies An ontological analysis continuants

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

  25. 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)

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

  32. PtoP statements - particular to particular • ordered sextuples of the formRi = <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, tra 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, tra 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, tra reference to the time at which the author considers the association appropriate,

  35. 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.

  36. 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

  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. PtID Date ObsCode Narrative IUI-001 5572 5572 2309 5572 5572 5572 298 5572 298 5572 47804 03/04/1993 01/04/1997 04/07/1990 04/07/1990 12/07/1990 12/07/1990 21/03/1992 01/04/1997 17/05/1993 22/08/1993 22/08/1993 26442006 81134009 26442006 9001224 9001224 79001 58298795 79001 2909872 26442006 9001224 Accident in public building (supermarket) closed fracture of shaft of femur Other lesion on other specified region closed fracture of shaft of femur Essential hypertension Accident in public building (supermarket) Closed fracture of radial head Essential hypertension closed fracture of shaft of femur Fracture, closed, spiral Accident in public building (supermarket) 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: betterreality representation 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.Thepatient reports that she has had a productive cough for three days but that chest pain developed one hour ago.  She gives a history ofhypertension.  She also reports that she was treated in the past fortuberculosis while she was pregnant.  The patient reports an allergy toBufferin.Physical examination revealed a well-developed, well-nourished female inmoderate respiratory distress.  Vital signs showed a pulse of 90, a respiratory rate of 22, an oral temperature of 100.3, and a blood pressureof 150/100.  Examination revealed rales and rhonchi in the left upperchest.  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)

  42. case study continued ... • ECG - Sinus Rhythm, 74BPM, Axis -30 degrees, ST segment 2mm elevated andT-waves down in leads I, L, V5 and V6Chest X-ray  Left upper lobe infiltrate, left ventricular hypertrophyThe 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 ableto manage caring for herself and him.  The nurse asked the patientsphysician to consider an antidepressant and a social work consult.A medical student reviewing the case is concerned about the risk of MRSAin patients with pneumonia and a recent myocardial infarction.  Shedecides to do a literature search.

  43. Question: What if the patient is not telling the truth ? Step 1: identify the phrases referring to particulars Jane Smithis a 50 year old, Native American female who presents to the emergency room with the chief complaint of cough and chest pain.

  44. Jane Smithis a 50 year old, Native American female who presents to the emergency room with the chief complaint of cough and chest pain. Step 2: indentify to what particulars these phrases refer 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 JaneSmith Jane Smith’s complaining primarily about ... A temporal part of Jane Smith’s life marked by happenings of coughs Jane Smith’s chest

  45. Jane Smithis a 50 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-female- gender CS2-woman CS1-native-american CS1-emergency room CS1-chief-complaint CS2-chest CS1-coughing CS1-chest-pain CS2-pain Compare with simple clinical coding in juxtaposition

  46. Has-Age “Jane Smith” CS3-50 years old Is-A Has-Sayer CS3-woman Is-A CS3-native american Has-participant Has-Saying CS3-chest pain Has-happening-during Has-Saying CS3-coughing CS3-consultation CS3-Em.Room Has-Loc Compare with the output of the NAIVE !!! semantic analyser we all would dream of Compare with the output of the perfect semantic analyser we all would dream of CS3-complaining

  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 objectivetruth) • 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-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, chestpain, 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)

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