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 Jane’s favourite supermarket July 4th, 1990: Jane goes shopping: 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 Dr. Peters (City HC) Dr. Longley

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

ECO R European Centre for Ontological Research 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):

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 Apr;32(2):

ECO R European Centre for Ontological Research CityHC’s representation formalism (for statements in records) Rector AL, Nowlan WA, Kay S, Goble CA, Howkins TJ. A framework for modelling the electronic medical record. Methods Inf Med Apr;32(2): 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. ”

ECO R European Centre for Ontological Research Mixing statements and entities “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 European Centre for Ontological Research /07/ closed fracture of shaft of femur /07/ Fracture, closed, spiral /07/ closed fracture of shaft of femur /07/ Accident in public building (supermarket) /07/ Essential hypertension /12/ benign polyp of biliary tract /03/ closed fracture of shaft of femur /03/ Accident in public building (supermarket) /04/ Other lesion on other specified region /05/ Essential hypertension 29822/08/ Closed fracture of radial head 29822/08/ Accident in public building (supermarket) /04/ closed fracture of shaft of femur /04/ Essential hypertension PtIDDateObsCodeNarrative /12/ malignant polyp of biliary tract Same patient, same hypertension code: Same (numerically identical) hypertension ? Different patients, same fracture codes: Same (numerically identical) fracture ? Same patient, different dates, same fracture codes: same (numerically identical) fracture ? Same patient, same date, 2 different fracture codes: same (numerically identical) fracture ? But, there are some problems... Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ? Or different supermarkets, but always in the freezer sections ? Same patient, different dates, Different codes. Same (numerically identical) polyp ?

ECO R European Centre for Ontological Research 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.

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 European Centre for Ontological Research 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

ECO R European Centre for Ontological Research Ontology ‘Ontology’: the study of being as a science ‘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 –...

ECO R European Centre for Ontological Research An ontological analysis 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 left femur Jane’s fracture’s image Dr. Longley City HC’s EHR system t 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 Jane’s fracture as seen by Dr. Peters Jane’s fracture as seen by Dr. Longley Instances of Jane’s fracture Universals EHR system HC Freezer section Person Femur Fracture Image

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

ECO R European Centre for Ontological Research 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.

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 :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 European Centre for Ontological Research Criteria for IUI assignment (1) 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, one out of 2 electrons in a György’s box – But: this is not a matter of choice, not ‘any’ out of...

ECO R European Centre for Ontological Research Criteria for IUI assignment (2) 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 European Centre for Ontological Research Assertion of assignments IUI assignment is an act of which the execution has to be asserted in the IUI-repository: – d a IUI of the registering agent A i the assertion of the assignment » p a IUI of the author of the assertion » p p IUI of the particular » t ap time of the assignment » coptional description for identification t d time of registering A i in the IUI-repository Neither t d or t ap give any information about when #p p started to exist ! That might be asserted in statements providing information about #p p.

ECO R European Centre for Ontological Research 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.

ECO R European Centre for Ontological Research Representation in the EHR 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 CityHCDr. Peters Jane Smith Jane Smith’s Fracture Of Femur Fracture Of Femur Severe Spiral 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 Jane Smith’s Fracture Of Femur’s severity Jane Smith’s Fracture Of Femur’s shape 4th July 1990 particulars

ECO R European Centre for Ontological Research PTP statements - particular to particular ordered sextuples of the form s a is the IUI of the author of the statement, t a 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, t r 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 s a is the IUI of the author of the statement, t a 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 cl are taken, p the IUI referring to the particular whose inst relationship with cl is asserted, cl the class in o to which p enjoys the inst relationship, and, t r a reference to the time at which the relationship obtains.

ECO R European Centre for Ontological Research PTCO statements particular to concept code s a is the IUI of the author of the statement, t a a reference to the time when the statement is made, cbs a reference to the concept-based system from which co is taken, p 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, t r a reference to the time at which the author considers the association appropriate,

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: author of the statement #IUI-1921: the left testicle of patient #IUI : 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 R European Centre for Ontological Research 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

ECO R European Centre for Ontological Research Advantage: better reality representation /07/ closed fracture of shaft of femur /07/ Fracture, closed, spiral /07/ closed fracture of shaft of femur /07/ Accident in public building (supermarket) /07/ Essential hypertension /12/ benign polyp of biliary tract /03/ closed fracture of shaft of femur /03/ Accident in public building (supermarket) /04/ Other lesion on other specified region /05/ Essential hypertension 29822/08/ Closed fracture of radial head 29822/08/ Accident in public building (supermarket) /04/ closed fracture of shaft of femur /04/ Essential hypertension PtIDDateObsCodeNarrative /12/ malignant polyp of biliary tract IUI-001 IUI-003 IUI-004 IUI-005 IUI-007 IUI-002 IUI-012

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