ECO R European Centre for Ontological Research Requirements for natural language understanding in referent-tracking based electronic patient records. CS seminar, Bolzano, Dec 5, 2005 Dr. W. Ceusters European Centre for Ontological Research Saarland University, Saarbrücken - Germany

ECO R European Centre for Ontological Research Presentation overview ECOR and me The Electronic Health Record (EHR) Problems with terminologies and their use in the EHR Realist ontology Referent Tracking Opportunities for narural language understanding

ECO R European Centre for Ontological Research European Centre for Ontological Research

ECO R European Centre for Ontological Research Short personal history

ECO R European Centre for Ontological Research The Electronic Health Record

ECO R European Centre for Ontological Research Electronic Health Record ISO/TS 18308:2003 – Electronic Health Record (EHR): A repository of information regarding the health of a subject of care, in computer processable form. – EHR system: the set of components that form the mechanism by which electronic health records are created, used, stored, and retrieved. It includes people, data, rules and procedures, processing and storage devices, and communication and support facilities. More common meaning of EHR system: – only the “software being executed”

ECO R European Centre for Ontological Research A replacement for This and that

ECO R European Centre for Ontological Research The Medical Informatics dogma To structure or NOT to be Fact: computers can only deal with a structured representation of reality: – structured data: relational databases, spread sheets – structured information: XML simulates context – structured knowledge: rule-based knowledge systems Conclusion: a need for structured data entry(???)

ECO R European Centre for Ontological Research Example of data entry form

ECO R European Centre for Ontological Research Structured EHR data entry Current technical solutions: – Data entry forms provide the structure various paradigms: – Rigid, pre-fixed – Adaptable to user-preferences, but fixed when used – Dynamically adapting to entered data in context – Terminologies, coding and classification systems: provide the language to be used Exchange of information preserving meaning Statistics and epidemiology

ECO R European Centre for Ontological Research The International Classification of diseases (WHO).... Chapter II:Neoplasms (C00-D48) Chapter III:Diseases of the Blood and Blood-forming organs and certain disorders involving the immune mechanism (D50-D89) Excludes : auto-immune disease (systemic) NOS (M35.9).... Nutritional Anemias (D50-D53) D50Iron deficiency anaemia Includes:... D50.0 Iron deficiency anaemia secondary to blood loss (chronic) Excludes :... D D51Vit B12 deficiency anaemia Haemolytic Anemias (D55-D59)... Chapter IV:...

ECO R European Centre for Ontological Research Main problems Internal and external consistency of terminologies. What do the terms in a terminology stand for ?

ECO R European Centre for Ontological Research Problems with terminologies (1) Lack of face value Agrammatical constructions Shift in ontological category (or ambiguous meaning)

ECO R European Centre for Ontological Research Problems with terminologies (2) ‘ventricle’ used in 2 different meanings

ECO R European Centre for Ontological Research Problems with terminologies (3) Mixing of differentiae Ontological nonsense

ECO R European Centre for Ontological Research Problems with terminologies (4) Incomplete classification

ECO R European Centre for Ontological Research What’s wrong with current use of terminologies in the EHR ?

ECO R European Centre for Ontological Research Current mainstream thinking data information knowledge wisdom - representation (- representation) Questions not often enough asked: What part of our data corresponds with something out there in reality ? What part of reality is not captured by our data, but should because it is relevant ? Reality What is there on the side of the patient

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 A look at the database: Use of SNOMED codes for ‘unambiguous’ understanding * * * * cause, not disorder How many disorders have patients 5572, 2309 and 298 each had thus far in their lifetime ? How many numerically different disorders are listed here ? How many different types of disorders are listed here ?

ECO R European Centre for Ontological Research Would it be easier if you could see the code labels ? /07/ closed fracture of shaft of femur557204/07/ Fracture, closed, spiral557212/07/ closed fracture of shaft of femur557212/07/ 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 region557217/05/ Essential hypertension29822/08/ Closed fracture of radial head29822/08/ Accident in public building (supermarket)557201/04/ closed fracture of shaft of femur557201/04/ Essential hypertension PtIDDateObsCodeNarrative /12/ malignant polyp of biliary tract

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 ? Same patient, different dates, Different codes. Same (numerically identical) polyp ? A look at the problems... Different patients. Same supermarket? Maybe the same (irrelevant ?) freezer section ? Or different supermarkets, but always in the freezer sections ?

ECO R European Centre for Ontological Research Main problem areas for current EHRs 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 Foundation: Realist ontology

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 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 An ontological analysis continuants City hospital 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 hospital’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 Universals EHR system HC Freezer section Person Femur Fracture Image

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 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 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 – 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 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

ECO R European Centre for Ontological Research A shift in mind set Not: – ‘this patient has a fracture of the left tibia ’ But: – #12 #234 #876 – #234 is_located_in #876 – #876 is_part_of #12 – #876 is_instance_of left_tibia –... this With Relationships and universals from a realist ontology concepts from a terminology {

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 transfert 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 concept- based systems – Systematic “inconsistent” descriptions in or cross terminologies may indicate poor definition of the respective terms

ECO R European Centre for Ontological Research How to make this practical for the text-based parts of an EHR ? Referent tracking in the linguistic sense !

ECO R European Centre for Ontological Research The problem summarised natural language is the only medium that is able to communicate clinical information about individual patients without loss of necessary detail; (virtual) structured data repositories are required to make subsequent analyses possible; any transformation from free language to coding and classification systems results in information loss that is unacceptable for individual patient care, but at the other hand is a conditio sine qua non for population based studies; today’s graphical user interfaces can deal reasonably well with picking lists build around controlled vocabularies that fulfil a bridging function from free language towards coding and classification systems but are incompatible with referent tracking

ECO R European Centre for Ontological Research The ultimate scenario #IUI-1 ‘affects’ #IUI-2 #IUI-3 ‘affects’ #IUI-2 #IUI-1 ‘causes’ #IUI-3 Referent Tracking Database EHR CAG repeat Juvenile HD person disorder continuant Ontology Natural Language Understanding Technology

ECO R European Centre for Ontological Research Jim Cimino’s Woods Hole case First sentence: 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.

ECO R European Centre for Ontological Research Step 1: identify the phrases referring to particulars Jane Smith is a 50 year old, Native American female who presents to the emergency room with the chief complaint of cough and chest pain.

ECO R European Centre for Ontological Research Jane Smith is 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 SmithJane Smith’s age Jane Smith’s raceJane SmithJane Smith’ s gender Jane Smith ’s showing up at... A specific emergency room of health facility XYZ Jane Smith’s complaining primarily about... A temporal part of Jane Smith’s life marked by happenings of coughs Jane Smith’s chest A specific pain experienced by Jane Smith

ECO R European Centre for Ontological Research Compare with simple clinical coding in juxtaposition Jane Smith is 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-native-american CS1-female- gender CS1-emergency room CS1-chief-complaint CS1-coughingCS1-chest-pain CS2-woman CS2-pain CS2-chest

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

ECO R European Centre for Ontological Research What it (more or less) should be with traditional coding CS3-complaining CS3-chest pain Has-Saying CS3-coughing Has-Saying “chest-pain” Has-’referent’ “coughing” Has-’referent’

ECO R European Centre for Ontological Research What it (more or less) should be with referent tracking CS3-complaining CS3-chest pain Has-Saying CS3-coughing Has-Saying “chest-pain” Has-referent “coughing” Has-referent J.S.’ complaining at t 1 J.S.’ chest pain at t -1 J.S.’ coughing at t -1 Has-code

ECO R European Centre for Ontological Research Most important difference: Use of generic terms Use of concrete particulars

ECO R European Centre for Ontological Research 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 objective truth) – The underlying disorder (under whatever state of affairs)

ECO R European Centre for Ontological Research Step 4: IUI assignment Assumptions: – the RTS contains already: IUI-1 Jane Smith Co i = IUI-1.1 R i = Co i = IUI-1.2 Co i = R i = IUI-1.3 Co i = R i = –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)

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 Collaboration sought for dealing with NLU