ECO R European Centre for Ontological Research Realist

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ECO R European Centre for Ontological Research Realist Ontology for Electronic Healthcare Records Dr.

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 Electronic Healthcare Record European Centre for Ontological Research • A collection of

ECO R Electronic Healthcare Record European Centre for Ontological Research • 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 Focus of this presentation European Centre for Ontological Research • Role of

ECO R Focus of this presentation European Centre for Ontological Research • 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 Understanding content (1) European Centre for Ontological Research “John Doe has a

ECO R Understanding content (1) European Centre for Ontological Research “John Doe has a pyogenic granuloma of the left thumb” John Doe has a pyogenic granuloma of the left thumb

ECO R Understanding content (2) European Centre for Ontological Research <record> <patient>John Doe</patient> <diagnosis>pyogenic

ECO R Understanding content (2) European Centre for Ontological Research <record> <patient>John Doe</patient> <diagnosis>pyogenic granuloma of the left thumb</diagnosis> </record> <subject> John Doe </subject> <diagnosis> pyogenic granuloma of the left thumb </diagnosis> </record>

ECO R Understanding content (3) European Centre for Ontological Research <129465004> <116154003>John Doe</116154003> <

ECO R Understanding content (3) European Centre for Ontological Research <129465004> <116154003>John Doe</116154003> < 8319008 > 17372009 <finding site> 76505004 <laterality>7771000</laterality> </finding site> </ 8319008 > </129465004>

ECO R Current “state of the art” on European Centre for Ontological Research meaning

ECO R Current “state of the art” on European Centre for Ontological Research meaning in healthcare informatics • A pervasive bias towards “concepts” – Content wise: • Work based on ISO/TC 37 that advocates the Ogden -Richards theory of meaning • Corresponds with a linguistic reading of “concept” – Architecture wise: • In Europe: work based on CEN/TC 251 WG 1 & WG 2 that follow ISO/TC 37 • In the US: HL 7, 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

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 Dyadic models of “meaning” European Centre for Ontological Research • Saussure (language

ECO R Dyadic models of “meaning” European Centre for Ontological Research • 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 Triadic models of meaning: European Centre for Ontological Research The Semiotic/Semantic triangle

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

ECO R European Centre for Ontological Research Aristotle’s triadic meaning model pathema semeia gramma/

ECO R European Centre for Ontological Research Aristotle’s triadic meaning model pathema semeia gramma/ phoné 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). pragma Aristotle, 'On Interpretation', 1. 16. a. 4 -9, Translated by Cooke & Tredennick, Loeb Classical Library, William Heinemann, London, UK, 1938.

ECO R Richards’ semantic triangle European Centre for Ontological Research reference my understanding symbol

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

ECO R European Centre for Ontological Research Don’t confuse with homonymy ! R 1

ECO R European Centre for Ontological Research Don’t confuse with homonymy ! R 1 R 2 R 3 mole (skin lesion) mole (unit) “mole” mole (animal)

ECO R European Centre for Ontological Research Different thoughts Homonymy One concept understanding of

ECO R European Centre for Ontological Research Different thoughts Homonymy One concept understanding of x understanding of y R 1 R 2 R 3 mole “skin lesion” mole “unit” symbol referent “mole” mole “animal”

ECO R And by the way, synonymy. . . European Centre for Ontological Research

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

ECO R European Centre for Ontological Research Frege’s view sense name • “sense” is

ECO R European Centre for Ontological Research Frege’s view sense name • “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) reference • a name with a sense does not need to have a (=referent) reference (“Beethoven’s 10 th symphony”)

ECO R European Centre for Ontological Research Tetrahedric extensions CEN/TC 251 ENV 12264 FRISCO

ECO R European Centre for Ontological Research Tetrahedric extensions CEN/TC 251 ENV 12264 FRISCO model (information science) conception concept actor representation definition referent term referent

ECO R European Centre for Ontological Research The theory in practice Oops, this is

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

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

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

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

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

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

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

HL 7 -RIM ECO R From Speech Acts to Information Model European Centre for

HL 7 -RIM ECO R From Speech Acts to Information Model European Centre for Ontological Research Living subject person non. Person. LS Place Organisation Material Manufactered. M Device Container Managed Patient. Encounter Employee Participation Control. Act Patient Licensed. Entity Supply Access Diet Working. List Procedure Observation Entity Public. Healthcare Diagnostic. Image Device. Task Substance. Administration Financial. Contract Account Financial. Transaction Invoice. Element Role Link Language Communication Participation Act. Link Communication Function Act Context Structure

CEN ENV 13606 ECO R CEN’s view on reality and European Centre for Ontological

CEN ENV 13606 ECO R CEN’s view on reality and European Centre for Ontological Research the healthcare record “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. ”

CEN ENV 13606 ECO R EHR Extended Architecture European Centre for Ontological Research Architectural

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

CEN ENV 13606 ECO R Types of Original Component Complexes European Centre for Ontological

CEN ENV 13606 ECO R Types of Original Component Complexes European Centre for Ontological Research OCC specialisation Description Examples of Component Names Folder High-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 Composition A 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 Cluster Low-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 Architectural Component Attributes European Centre for Ontological Research Refer

CEN ENV 13606 ECO R Architectural Component Attributes European Centre for Ontological Research Refer to situations and statements and rely on terminology Language Component unique identifier 0. . 1 1 0. . n Component Status information 1 1 Component name structure Related date and time Architectural Component Related healthcare agent 0. . n 1 Originating Healthcare agent 1 1 Originating date and time 0. . n Distribution Rule Reference Subject of care identifier

ECO R European Centre for Ontological Research CEN ENV 13606 “Archetypes” • clinical situation

ECO R European Centre for Ontological Research CEN ENV 13606 “Archetypes” • clinical situation – pertains to body component, product, environment – has context facet subject of information, process status, role for dates – has information qualifier knowing mode • has information source • has qualifier – has role • Is stated by • has temporal marker actor communication modality relevance role for clinical situation actor, healthcare organisation timing marker To be used to build terminologies that may be used for the EHR

ECO R Structure of concept-based terminologies European Centre for Ontological Research gall bladder gallbladder

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

ECO R European Centre for Ontological Research “Axiom” • Concept-based terminology (and standardisation thereof)

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

ECO R European Centre for Ontological Research Why not ? • Ad hoc readings of statements of the type C 1 -relationship. C 2 – 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 ?

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

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

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 25 -32. IOS Press, Amsterdam, 1995.

ECO R European Centre for Ontological Research “Ontology” • In Information Science: – “An

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 My use of the word ontology European Centre for Ontological Research a

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

ECO R Back to to the operating theatre European Centre for Ontological Research A

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

ECO R Back to to the operating theatre European Centre for Ontological Research A

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

ECO R European Centre for Ontological Research “Axiom” epistemology • If the picture is

ECO R European Centre for Ontological Research “Axiom” epistemology • If the picture is not a fake, we (i. e. , me and this audience) KNOW 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 partrelationship between that hand that surgeon, and the processes going on, are (were) equally real. ontology

ECO R (Simplified) Logic of classes European Centre for Ontological Research • primitive: –

ECO R (Simplified) Logic of classes European Centre for Ontological Research • 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 consists in a series

ECO R European Centre for Ontological Research 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: – Snap. BFO, a series of snapshot ontologies (Oti ), indexed by times – Span. BFO a single videoscopic ontology (Ov). Each Oti is an inventory of all entities existing at a time. Ov is an inventory (processory) of all processes unfolding through time.

ECO R European Centre for Ontological Research

ECO R European Centre for Ontological Research

ECO R Alan Rector European Centre for Ontological Research Take home message: a need

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