ECO R European Centre for Ontological Research Strategies

ECO R European Centre for Ontological Research Strategies for Referent Tracking in Electronic Health Records Dr. W. Ceusters European Centre for Ontological Research Saarland University Saarbrücken - Germany

ECO R European Centre for Ontological Research The story of Jane Smith an old case, well known in the literature. . .

ECO R European Centre for Ontological Research July 4 th, 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

ECO R European Centre for Ontological Research A visit to the hospital City Health Centre (City HC) Dr. Peters Dr. Longley

ECO R European Centre for Ontological Research Diagnosis: a severe spiral fracture of the femur

ECO R The City HC’s medical record European Centre for Ontological Research • 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.

ECO R European Centre for Ontological 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.

ECO R European Centre for Ontological Research City. HC’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 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. 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. ”

ECO R Mixing statements and entities European Centre for Ontological Research • “Every occurrence level statement concerning the Jane Smith’s Fracture of the Femur is an observation of the corresponding individual. ” • “The existence of the individual Jane Smith’s Fracture of Femur does not imply that Jane Smith has, or has ever had, a fracture of the femur, but merely that some observation has been made about Jane Smith regarding a fracture of the femur. ” • “(The only observation recorded about Jane Smith’s Fracture of the Femur might be that she did not have it. )”

ECO R But, there are Different patients. Same supermarket? some problems. . . European Centre for Ontological Research Pt. ID Date Maybe the same (irrelevant ? ) freezer section ? Obs. Code Narrative Or different supermarkets, but always 26442006 closed fracture of shaft of femur Same patient, same hypertension code: 81134009 Fracture, closed, spiral in the freezer sections ? Same (numerically identical) hypertension ? 5572 04/07/1990 5572 12/07/1990 26442006 closed fracture of shaft of femur 5572 12/07/1990 9001224 Accident in public building (supermarket) 5572 04/07/1990 79001 Essential hypertension 24/12/1991 255174002 benign polyp of biliary tract 298 Same patient, different 21/03/1992 26442006 closed fracturedates, of shaft ofsame femur fracture Same patient, 21/03/1992 9001224 Accident in publicsame buildingdate, (supermarket) codes: same 03/04/1993 patient, 58298795 Other lesionfracture on other specified region 2 patients, different codes: Same different Differentdates, same fracture codes: (numerically identical) 17/05/1993 79001 Essential hypertension same (numerically Different codes. Same(numerically identical)headfracture ? ? 22/08/1993 2909872 Closed fracture of radialfracture identical) fracture ? identical) polyp ? 22/08/1993 9001224 Accident in public building (supermarket) 5572 01/04/1997 26442006 closed fracture of shaft of femur 5572 01/04/1997 79001 Essential hypertension 0939 20/12/1998 255087006 malignant polyp of biliary tract 0939 2309 47804 5572 298

ECO R European Centre for Ontological Research Main problem areas for City. HC’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.

ECO R European Centre for Ontological Research 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 –. . .

ECO R Proposed solution: European Centre for Ontological Research 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

ECO R European Centre for Ontological Research Ontology • ‘Ontology’: the study of being as a science • ‘An ontology’ is a representation of some preexisting 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 –. . .

ECO An ontological analysis R Universals European Centre for Ontological Research EHR system HC Freezer section continuants City HC’s EHR system City HC The freezer section of Jane’s favourite supermarket Jane Smith Person Dr. Peters Dr. Longley Femur Jane’s left femur Fracture Jane’s left femur fracture Image t Jane’s fracture’s image occurrents Jane’s fracture as seen by Dr. Peters Jane’s fracture as seen by Dr. Longley 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 Jane’s fracture’s healing Dr. Peter’s diagnosis making Dr. Longley’s examination of Jane’ s fracture Freezer section dismantled Jane dies Instances of Jane’s fracture

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

ECO R Essentials of Referent Tracking European Centre for Ontological Research • 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.

ECO R European Centre for Ontological Research 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

ECO R European Centre for Ontological Research IUI generation • Universally Unique IDs: – recently standardized through ISO/IEC 98348: 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)

ECO R European Centre for Ontological Research IUI asignment • = 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.

ECO R Criteria for IUI assignment (1) European Centre for Ontological Research 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 ! • – More difficult: subjective symptoms • – Only the plan exists and possibly the statements made about the future execution of the plan 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, one out of 2 electrons in a György’s box But: this is not a matter of choice, not ‘any’ out of. . .

ECO R Criteria for IUI assignment (2) European Centre for Ontological Research 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

ECO R Assertion of assignments European Centre for Ontological Research • IUI assignment is an act of which the execution has to be asserted in the IUI-repository: – <da, Ai, td> • da • Ai • td IUI of the registering agent the assertion of the assignment <pa, pp, tap, c> » pa » pp IUI of the author of the assertion IUI of the particular » tap time of the assignment » c optional description for identification time of registering Ai in the IUI-repository • Neither td or tap give any information about when #pp started to exist ! That might be asserted in statements providing information about #pp.

ECO R Management of the IUI-repository European Centre for Ontological Research • 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.

ECO Representation in the EHR R European Centre for Ontological Research Fracture Of Femur Severe City. HC Dr. Peters Jane Smith’s consultation with Dr. Peters at City HC on 4 th July 1990 Jane Smith’s Fracture Of Femur Dr. Peters’ assessment of Jane Smith’s fracture of femur at City HC on 4 th July 1990 Jane Smith’s Fracture Of Femur’s severity Spiral Jane Smith’s Fracture Of Femur’s shape 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

ECO R European Centre for Ontological Research PTP statements particular to particular • ordered sextuples of the form an <sa, ta, r, o, P, tr> sa is the IUI of the author of the statement, ta a reference to the time when the statement is made, r reference a relationship ato (available o) obtaining in between the particulars referred to in P, o a reference to the ontology from which r is taken, P 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.

ECO R European Centre for Ontological Research PTCL statements – particular to class <sa, ta, inst, o, p, cl, tr> sa is the IUI of the author of the statement, ta a reference to the time when the statement is made, inst obtaining between p and cl, a reference o to the ontology frominst clwhich are and taken, the p IUI referring to the particular whose inst relationship with cl is asserted, nst othe enjoys torelationship, class which the cl in and, tr a reference to the time at which the relationship obtains.

ECO PTCO statements R particular to concept code European Centre for Ontological Research ce a <sa, ta, cbs, p, co, tr> sa is the IUI of the author of the statement, ta a reference to the time when the statement is made, cbs is taken, p the IUI referring to the particular which the author associates with co, co p, and,

ECO R European Centre for Ontological Research Interpretation of PTCO 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.

ECO R European Centre for Ontological Research A SNOMED-CT example • <IUI-0945, 18/04/2005, SNOMED-CT v 0301, 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

ECO Pragmatics of IUIs in EHRs R European Centre for Ontological Research • 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

ECO R European Centre for Ontological Research Pt. ID Advantage: better reality representation Date Obs. Code Narrative 5572 04/07/1990 26442006 IUI-001 closed fracture of shaft of femur 5572 04/07/1990 81134009 IUI-001 Fracture, closed, spiral 5572 12/07/1990 26442006 IUI-001 closed fracture of shaft of femur 5572 12/07/1990 9001224 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 2309 21/03/1992 9001224 IUI-007 Accident in public building (supermarket) 47804 03/04/1993 58298795 Other lesion on other specified region 5572 17/05/1993 79001 IUI-005 Essential hypertension 298 22/08/1993 2909872 IUI-003 Closed fracture of radial head 298 22/08/1993 9001224 5572 01/04/1997 26442006 IUI-012 closed fracture of shaft of femur 5572 01/04/1997 79001 IUI-005 Essential hypertension 0939 20/12/1998 255087006 IUI-004 malignant polyp of biliary tract IUI-007 Accident in public building (supermarket)

ECO R European Centre for Ontological Research 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

ECO R European Centre for Ontological Research 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