ECO R European Centre for Ontological Research Realist Ontology for Electronic Healthcare Records Dr. Werner Ceusters, MD European Centre for Ontological Research Universität des Saarlandes Saarbrücken, Germany

ECO R European Centre for Ontological Research Electronic Healthcare Record A collection of electronic data about a single patient relevant for his health. Exists in many forms with various degrees of automation: – Scanned documents – “Machine readable” documents (text, XML,...) – Personal (GP), departmental, hospital wide,... Multiple challenges: – Deontological: safety, security, confidentiality – Technical: structure and architecture, communication – Pragmatic: getting them used – Machine interpretable: triggering and allerts

ECO R European Centre for Ontological Research Focus of this presentation Role of ontology in maximizing the potential uses of the EHCR... : – For the patient’s own benefit – For the advance of science – Hence, for the health of the population... by making the contents understandable both for humans and machines.

ECO R European Centre for Ontological Research Understanding content (1) “John Doe has a pyogenic granuloma of the left thumb”    

ECO R European Centre for Ontological Research Understanding content (2) John Doe pyogenic granuloma of the left thumb   

ECO R European Centre for Ontological Research Understanding content (3) John Doe

ECO R European Centre for Ontological Research Current “state of the art” on meaning in healthcare informatics A pervasive bias towards “concepts” – Content wise: Work based on ISO/TC37 that advocates the Ogden-Richards theory of meaning Corresponds with a linguistic reading of “concept” – Architecture wise: In Europe: work based on CEN/TC251 WG1 & WG2 that follow ISO/TC37 In the US: HL7, inspired by Speech Act Theory “Concepts” used as elements of information models, hence mixing a linguistic and engineering reading.

ECO R European Centre for Ontological Research Topics Meaning and understanding Biomedical terminologies and concept systems EHCR architecture Problems of the concept-based approach Ontology as part of the solution

ECO R European Centre for Ontological Research Dyadic models of “meaning” Saussure ( language philosopher ): – signe / signifiant(sign/concept) Ron Stamper ( information scientist ): – thing-A STANDS-FOR thing-B Major drawback: – excludes the “referent” from the model, i.e. that what the sign/symbol/word/... denotes

ECO R European Centre for Ontological Research Triadic models of meaning: The Semiotic/Semantic triangle Sign: Language/ Term/ Symbol Referent: Reality/ Object Reference: Concept / Sense / Model / View / Partition

ECO R European Centre for Ontological Research Aristotle’s triadic meaning model semeia gramma/ phoné pragma pathema Words spoken are signs or symbols (symbola) of affections or impressions (pathemata) of the soul (psyche); written words (graphomena) are the signs of words spoken (phoné). As writing (grammatta), so also is speech not the same for all races of men. But the mental affections themselves, of which these words are primarily signs (semeia), are the same for the whole of mankind, as are also the objects (pragmata) of which those affections are representations or likenesses, images, copies (homoiomata). Aristotle, 'On Interpretation', 1.16.a.4-9, Translated by Cooke & Tredennick, Loeb Classical Library, William Heinemann, London, UK, 1938.

ECO R European Centre for Ontological Research Richards’ semantic triangle Reference (“concept”): “indicates the realm of memory where recollections of past experiences and contexts occur”. Hence: as with Aristotle, the reference is “mind- related”: thought. But: not “the same for all”, rather individual mind-related symbolreferent reference understandingmy your understanding

ECO R European Centre for Ontological Research Don’t confuse with homonymy ! “mole” mole (animal) R1 mole (unit) R2 mole (skin lesion) R3

ECO R European Centre for Ontological Research Different thoughts Homonymy “ mole ” mole “ animal ” R1 mole “ unit ” R2 mole “ skin lesion ” R3 symbol referent understanding One concept of x understanding of y

ECO R European Centre for Ontological Research And by the way, synonymy... the Aristotelian viewRichards’ view “perspiration” “sweat” “perspiration”

ECO R European Centre for Ontological Research Frege’s view “sense” is an objective feature of how words are used and not a thought or concept in somebody’s head 2 names with the same reference can have different senses 2 names with the same sense have the same reference (synonyms) a name with a sense does not need to have a reference (“Beethoven’s 10 th symphony”) reference (=referent) sense name

ECO R European Centre for Ontological Research Tetrahedric extensions conception actor representationreferent concept termreferent definition FRISCO model (information science) CEN/TC251 ENV 12264

ECO R European Centre for Ontological Research The theory in practice Haydom Lutheran Hospital, Tanzania Oops, this is too slippery to hold any longer Take this, please ! He wants me to hold that kocher Nurse reaches for the clamp

ECO R European Centre for Ontological Research = ? Issues in communication Take the kocher, please.

ECO R European Centre for Ontological Research Concept-based Terminology kocher

ECO R European Centre for Ontological Research Kocher clamp in SNOMED-CT

ECO R European Centre for Ontological Research From Speech Acts to Information Model HL7-RIM Entity Language Communication Function Role Participation Act Context Structure Role Link ActLink Living subject person nonPersonLS Place Organisation Material ManufacteredM Device Container Employee Patient LicensedEntity Access Managed Participation PatientEncounter ControlAct Supply Diet WorkingList Procedure Observation PublicHealthcare DiagnosticImage DeviceTask SubstanceAdministration FinancialContract Account FinancialTransaction InvoiceElement

ECO R European Centre for Ontological Research CEN’s view on reality and the healthcare record CEN ENV “The real world of health and health care is made up of individual clinical situations (of which the participants are called “associate topics”), that are described by an EHCR author as clinical statements. Within an EHCR system each clinical statement will be expressed as an elementary healthcare record entry.”

ECO R European Centre for Ontological Research EHR Extended Architecture Architectural Component Root Architectural Component Record Component Original Component Complex Selected Component Complex Data Item Link Item Folder Headed Section Composition Cluster Data Item Specialisation Data Item Specialisation Data Item Specialisation Data Item Specialisation Elementary healthcare record entries CEN ENV 13606

ECO R European Centre for Ontological Research Types of Original Component Complexes OCC specialisation DescriptionExamples of Component Names FolderHigh-level subdivisions of the entire EHCR for a patient, usually grouping entries over long time-spans within one organisation or department, or for a particular health problem GP Record Inpatient Stay Diabetes Care Record CompositionA set of record entries relating to one time and place of care delivery; grouped contributions to an aspect of health care activity; composed reports and overviews of clinical progress Consultation Operation Notes Discharge Summary Vital Signs Chart Headed Section Sub-divisions used to group entries with a common theme or derived through a common healthcare process Past Medical History Presenting Symptoms Examination Findings Treatment Plan ClusterLow-level aggregations of elementary entries (Record Items) to represent a compound clinical concept Heart Sounds Differential White Cell Count Insulin Schedule CEN ENV 13606

ECO R European Centre for Ontological Research Architectural Component Attributes CEN ENV Architectural Component unique identifier Originating Healthcare agent Originating date and time Related healthcare agent Related date and time Component name structure Subject of care identifier Component Status information Distribution Rule Reference Language n Refer to situations and statements and rely on terminology

ECO R European Centre for Ontological Research “Archetypes” clinical situation –pertains tobody component, product, environment –has context facet subject of information, process status, role for dates –has information qualifierknowing mode has information sourceactor has qualifiercommunication modality –has qualifierrelevance –has role role for clinical situation Is stated by actor, healthcare organisation has temporal marker timing marker CEN ENV To be used to build terminologies that may be used for the EHR

ECO R European Centre for Ontological Research Structure of concept-based terminologies gall gallbladder urinary bladder urine urinary bladder inflammation gallbladder inflammation gall gall bladder bladder inflammation urine cystitis biliary cystitis gallbladder inflammation urinary bladder

ECO R European Centre for Ontological Research “Axiom” Concept-based terminology (and standardisation thereof) is there as a mechanism to improve understanding of messages, originally by humans, now also by machines. It is NOT the right device to explain why reality is what it is, how it is organised, etc., (although it is needed to allow us to communicate on insights thereof).

ECO R European Centre for Ontological Research Why not ? Ad hoc readings of statements of the type C1-relationship- C2 – Human has-part head // Human has-part finger – California is-part-of United States // California isa name – labial vein isa vein of head // labial vein isa vulval vein Concepts not necessarily correspond to something that (will) exist(ed) – Sorcerer, unicorn, leprechaun,... Definitions set the conditions under which terms may be used, and may not be abused as conditions an entity must satisfy to be what it is Language can make strings of words look as if it were terms – “Middle lobe of left lung”

ECO R European Centre for Ontological Research What is then the right way ? Realist Ontology !

ECO R European Centre for Ontological Research If, later, you can remember just one thing of this presentation, then make sure it is this one: If somebody uses the word “ontology”, ALWAYS let him be specific about what he understands by it.

ECO R European Centre for Ontological Research The O-word N. Guarino, P. Giaretta, "Ontologies and Knowledge Bases: Towards a Terminological Clarification". In Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing, N. Mars (ed.), pp IOS Press, Amsterdam, 1995.

ECO R European Centre for Ontological Research “Ontology” In Information Science: – “An ontology is a description (like a formal specification of a program) of the concepts and relationships that can exist for an agent or a community of agents.” In Philosophy: – “Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality.”

ECO R European Centre for Ontological Research a for a computer understandable representation of some pre-existing domain of REALITY, reflecting the properties of the objects within its domain in such a way that there obtain substantial and systematic correlations between reality and the ontology itself. modified from Barry Smith My use of the word ontology to be used by software (agents) in a machine, and NOT by humans does not rely on what people know or think, hence no “concepts”, not just epistemology instance driven, although it accepts universals that are not instanciated does not “create” or “constrain” reality The T-Box has no meaning without the A-Box

ECO R European Centre for Ontological Research Back to to the operating theatre Haydom Lutheran Hospital, Tanzania This surgeon This amputatio n stump A lot of objects present This mask This hand with some relations Part of

ECO R European Centre for Ontological Research Back to to the operating theatre Haydom Lutheran Hospital, Tanzania This wound being closed by holding... That wound fluid drained A lot of processes going on This kocher being held in that hand of that surgeon with some relations Part of

ECO R European Centre for Ontological Research “Axiom” If the picture is not a fake, we (i.e., me and this audience) KNOW that that hand, that surgeon,... EXIST(ed), i.e. ARE (were) REAL. But importantly: that hand, surgeon, kocher, mask,... EXIST(ed) independent of our knowledge about them and also the part- relationship between that hand and that surgeon, and the processes going on, are (were) equally real. epistemology ontology

ECO R European Centre for Ontological Research (Simplified) Logic of classes primitive: – entities: particulars versus universals – relation inst such that: all classes are universals; all instances are particulars some universals are not classes, hence have no instances: pet, adult, physician some particulars are not instances; e.g. some mereological sums subsumption defined resorting to instances:

ECO R European Centre for Ontological Research Basic Formal Ontology Basic Formal Ontology consists in a series of sub-ontologies (most properly conceived as a series of perspectives on reality), the most important of which are: –SnapBFO, a series of snapshot ontologies (O ti ), indexed by times –SpanBFO a single videoscopic ontology (O v ). Each O ti is an inventory of all entities existing at a time. O v is an inventory (processory) of all processes unfolding through time.

ECO R European Centre for Ontological Research

ECO R European Centre for Ontological Research Take home message: a need for a clean separation of knowledge AND ontology Conceptual knowledge: the knowledge of sensible domain concepts Knowledge of definitions and criteria: how to determine if a concept applies to a particular instance Surface linguistic knowledge: how to express the concepts in any given language Knowledge of classification and coding systems: how an expression has been classified by such a system Pragmatic knowledge: what users usually say or think, what they consider important, how to integrate in software Alan Rector Ontology: what exists and how what exists relates to each other