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VT 1 Medical Ontology Barry Smith http://ifomis.de 2 IFOMIS Institute for Formal Ontology and Medical Information Science Faculty of Medicine University of Leipzig 3 Reference Ontology An ontology is a theory of a domain of entities in the world Ontology is outside the computer seeks maximal expressiveness and adequacy to reality and sacrifices computational tractability for the sake of representational adequacy 4 Reference Ontology a theory of the tertium quid – called reality – needed to hand-callibrate database/terminology systems 5 Methodology Get ontology right first (realism; descriptive adequacy; rather powerful logic); solve tractability problems later 6 The Reference Ontology Community IFOMIS (Leipzig) Laboratories for Applied Ontology (Trento/Rome, Turin) Foundational Ontology Project (Leeds) Ontology Works (Baltimore) Ontek Corporation (Buffalo/Leeds) Language and Computing (L&C) (Belgium/Philadelphia) 7 Domains of Current Work IFOMIS Leipzig: Medicine, Bioinformatics Laboratories for Applied Ontology Trento/Rome: Ontology of Cognition/Language Turin: Law Foundational Ontology Project: Space, Physics Ontology Works: Genetics, Molecular Biology Ontek Corporation: Biological Systematics Language and Computing: Natural Language Understanding 8 Ontologie als Zweig der Philosophie die Wissenschaft von den Arten und Strukturen von Objekten, Qualitäten, Prozessen, Ereignissen, Funktionen und Relationen in allen Bereichen der Wirklichkeit 9 Aristotle Der erste Ontologe 10 Eine biologische Ontologie 11 Linné 1763: Genera Morborum (Nosologie oder Ontologie der Krankheitsarten) 12 Q: Warum “Ontologie” in der medizinischen Informatik? A: Das Turm von Babel-Problem der Informationssysteme 13 Turm von Babel Jedes Informationssystem basiert auf einer eigenen Terminologie Wie können wir die Inkompatibilitäten lösen, die entstehen, wenn Daten aus verschiedenen Quellen kombiniert werden? Vgl. Wie können wir Anatomie und Physiologie integrieren? 14 Wie lösen Medizinstudenten dieses Problem? Vielfach erst durch die Begegnung mit dem Patienten Der Patient und die in ihm ablaufenden Prozesse dienen als Kristallisationspunkt für eine sinnvolle Ordnung sonst isoliert stehender (gelernter) Fakten. (Aus Wissen-dass wird Wissen-wie) 15 Dem Computer fehlt praktisches Wissen Wie können in Medizininformationssystemen isolierte Datenartefakte zu konsistentem und anwendbarem Wissen integriert werden? 16 Ursprünglicher Traum der Ontologie in der Informatik Eine einzige allumfassende Taxonomie aller Gegenstandsarten, die als zentrales integrierendes Kategoriensystem für alle Informationssysteme dient. Dieser Traum ist ausgeträumt ... 17 Gegenwärtige Lösungen Standardisierte Terminologien UMLS SNOMED ICD-10 Gene Ontology Digital Anatomist usw. 18 Standardisierte Terminologien sollen Zugriff auf biomedizinische Literatur und Faktendatenbanken erleichtern Beispielsweise um Verbindungen zwischen spezifischen Genen und spezifischen Körperreaktionen auffindbar zu machen Eine neue Art medizinischer Forschung soll dadurch ermöglicht werden 19 Database and terminology standardization is desparately needed in medical and bioinformatics to enable the huge amounts of existing data to be fused together automatically 20 To reap the benefits of standardization we need to make ONE SYSTEM out of many different terminologies But how? Through government edict? (Scandinavia) Through efforts of international standards bodies (ISO, CEN …)? Through UMLS Metathesaurus? 21 Zentrale Schaltstelle UMLS Universal Medical Language System National Library of Medicine Bethesda, MD 22 UMLS Metathesaurus eine riesige Kombination verschiedener maschinenlesbarer Quellterminologien 800,000 Begriffe 10 Mio. Beziehungen 23 Beispiele für Quell-Terminologien SNOMED-RT Systematized Nomenclature of Medicine MeSH Medical Subject Headings 24 is_a trees hormone peptide hormone adrenocorticotropin digestive hormone glycopeptide hormone follicle-stimulating hormone 25 is_a = ist ein / ist von der Art Diabetes Melletus is_a Disease 26 Bad Coding deriving from over-simplification and from failure to pay attention to ontological principles Z.B. SNOMED both_testes is_a testis (beide_Hoden ist_ein Hoden) 27 Terminological Incompatibilities 28 Representation of Blood in SNOMED Blood is_a Tissue 29 Representation of Blood in MeSH Blood is_a Bodily Fluid 30 Bad Coding Incompatibilities Context-Dependence Standardized Terminologies must be used properly 31 people are lazy and idiosyncratic Sie machen Schreibfehler Jeder pflegt seine eigene Terminologie, die sich mehr oder weniger von der anderer Akteure unterscheidet Sie verwenden verschiedene natürlichsprachliche Darstellungen der gleichen medizinischen Phänomena 32 The codes are not formulated on the basis of clear principles Therefore inconsistent Unintuitive Difficult to train people to use them Application often depends on contextdependent knowledge 33 The IFOMIS Contribution help to improve standardizations through constructive criticism based on robust ontological principles 34 UMLS Metathesaurus eine riesige Kombination verschiedener maschinenlesbarer Quellterminologien UMLS Semantic Network bestehend aus 134 Semantic Types soll Ordnung in diesem Wust schaffen 35 UMLS Semantic Network entity physical entity event conceptual entity 36 conceptual entity Organism Attribute Finding Idea or Concept Occupation or Discipline Organization Group Group Attribute Intellectual Product Language 37 conceptual entity Organism Attribute Finding Idea or Concept Occupation or Discipline Organization Group Group Attribute Intellectual Product Language 38 Idea or Concept Functional Concept Qualitative Concept Quantitative Concept Spatial Concept Body Location or Region Body Space or Junction Geographic Area Molecular Sequence Amino Acid Sequence Carbohydrate Sequence Nucleotide Sequence 39 INNSBRUCK is an Idea or Concept 40 Idea or Concept Functional Concept Qualitative Concept Quantitative Concept Spatial Concept Body Location or Region Body Space or Junction Geographic Area Molecular Sequence Amino Acid Sequence Carbohydrate Sequence Nucleotide Sequence 41 Confusion of Ontology and Epistemology Physical Entity Chemical Entity Chemical Viewed Structurally Chemical Viewed Functionally 42 Confusion of Ontology and Epistemology the hydraulic equation: BP = CO*PVR arterial blood pressure is directly proportional to the product of blood flow (cardiac output, CO) and peripheral vascular resistance (PVR). Cardiac Output in UMLS = A Finding 43 UMLS-Semantic Types: blood pressure is an Organism Function, cardiac output is a Laboratory or Test Result or Diagnostic Procedure BP = CO*PVR thus asserts that blood pressure is proportional either to a laboratory or test result or to a diagnostic procedure 44 The goal Formulate clear principles for building ontologies Reconstitute the UMLS Semantic Types on the basis of these principles 45 Zusammenarbeit mit der National Library of Medicine Revision der UMLS Semantic Types und der Gene Ontology 46 GO: the Gene Ontology 3 large telephone directories of standardized designations for gene functions and products organized into hierarchies via is_a and part_of 47 GO can in practice be used only by trained biologists (with know how) whether a GO-term truly stands in the is_a relation depends e.g. on the type of organism involved glycosome is part-of cytoplasm only for Kinetoplastidae Computers have no counterpart of such context-dependent know-how 48 GO divided into three disjoint term hierarchies the cellular component ontology, e.g. flagellum, chromosome, cell the molecular function ontology, e.g. ice nucleation, binding, protein stabilization the biological process ontology, e.g. glycolysis, death 49 Definition of Molecular Function “the action characteristic of a gene product.” On March 2003 all nodes in the Molecular Function ontology (except the root) had ‘activity’ added to their names -- confusion of function with functioning (how deal with dormant/suppressed functions?) 50 Definition of Biological Process “A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products” 51 How are the 3 ontologies related? Function = “the action characteristic of a gene product.” Process = “phenomenon marked by changes that lead to a particular result, mediated by one or more gene products” No part-whole relations across ontologies? 52 The GO isa relation in its intended meaning indicates a necessary relationship. That is, when we say “eukaryotic cell isa cell”, we mean that every eukaryotic cell is a cell. Confusion of necessarily, universally, and permanently (No time in GO) 53 part_of The Relation part-of: The intended meaning of part-of as explained in the GO Usage Guide is: “can be a part of, not is always a part of” 54 Uses of part_of – membrane part-of cell, intended to mean “a membrane is a part-of any cell” – flagellum part-of cell, intended to mean “a flagellum is part-of some cells” – replication fork part-of cell cycle, intended to mean: “a replication fork is part-of the nucleoplasm only during certain times of the cell cycle” – regulation of sleep part-of sleep, should be corrected to: “regulation of sleep is co-located with and is causally involved with the sleep process”. 55 Need to find ways to deal with time in medical informatics Functions vs. Realizations of Functions Function is still there even when not being realized need to be clear about the distinction between continuants and occurrents 56 SNAP and SPAN 57 SNAP and SPAN Substances and processes Continuants and occurrents In preparing an inventory of reality we keep track of these two different categories of entities in two different ways 58 Substances and processes exist in time in different ways process substance 59 Need for different perspectives Not one ontology, but a multiplicity of complementary ontologies Cf. Quantum mechanics: particle vs. wave ontologies 60 SNAPshot ontology Video (SPAN) ontology process substance 61 SNAP and SPAN stocks and flows commodities and services product and process anatomy and physiology synchrony and diachrony 62 SNAP and SPAN SNAP entities - have continuous existence in time - preserve their identity through change - exist in toto if they exist at all SPAN entities - have temporal parts - unfold themselves phase by phase - exist only in their phases/stages 63 SNAP: Entities existing in toto at a time MedO Draft 0.0004 Enduring Entity [Exists in space and time, has no temporal parts] Dependent Entity [±Relational] Spatial Entity Occupied Spatial region of 3 dimensions occupied by organism Spatial region of 2 dimensions * occupied by burn, bruise SNAP Unoccupied Quality [Sometimes form qualityregions or scales] Tunnel Alimentary Canal Hollow Nostril Cavity Interior of Lung Requisite [Have determinable/ determinate structure] Temperature. height Optional Diabetes State Being pregnant, being thirsty Independent Entity Role, Function, Power, Disposition [Have realizations, called processes] To circulate blood, to secrete hormones Substance Organism, organ Fiat part of substance * Extremity, upper body Boundary of substance * Surface of skin or hide Aggregate of substances * Family, mother and fetus 64 Three kinds of SNAP entities • • • Substances Dependent SNAP entities (qualities, functions, roles, powers …) Spatial regions, Contexts, Niches 65 0.0004 Enduring Entity [Exists in space and time, has no temporal parts] SNAP Dependent Entity [±Relational] Quality [Sometimes form qualityregions or scales] Requisite [Have determinable/ determinate structure] Temperature. height State Being pregnant, being thirsty Role, Function, Power, Disposition [Have realizations, called processes] To circulate blood, to secrete hormones Functions The function of the heart is to pump blood Optional Diabetes 66 Spatial Entity Occupied Spatial region of 3 dimensions occupied by organism Spatial region of 2 dimensions * occupied by burn, bruise Unoccupied Qu [Sometimes regions Tunnel Alimentary Canal Hollow Nostril Requisite [Have determinable/ determinate structure] Temperature. height Cavity Interior of Lung 67 NAP Independent Entity Role, Function, Power, Disposition [Have realizations, called processes] To circulate blood, to secrete hormones SNAP Substance Organism, organ Fiat part of substance * Extremity, upper body Fiat part of substance Extremity (hand, arm) Bodily System Boundary of substance * Surface of skin or hide Aggregate of substances * Family, mother and fetus 68 SPAN: Entities extended in time Entity extended in time Processual Entity [Exists in space and time, unfolds in time phase by phase] Portion of Spacetime Spacetime worm of 3 + T dimensions occupied by life of organism Temporal interval * projection of organism’s life onto temporal dimension SPAN Process [±Relational] Circulation of blood, secretion of hormones, course of disease, life Fiat part of process * First phase of a clinical trial Aggregate of processes * Clinical trial Temporal boundary of process * onset of disease, death 69 SPAN: Entities extended in time Entity extende Portion of Spacetime Proce Spacetime worm of 3 + T dimensions occupied by life of organism Temporal interval * projection of organism’s life onto temporal dimension [±Relatio Circulation o secretion of h course of dis 70 SPAN: Entities extended in time Entity extended in time SPAN Processual Entity [Exists in space and time, unfolds in time phase by phase] Process [±Relational] Circulation of blood, secretion of hormones, course of disease, life Fiat part of process * First phase of a clinical trial Aggregate of processes * Clinical trial Functioning The heart’s pumping of blood Temporal boundary of process * onset of disease, death 71 Granularity spatial region substance parts of substances are always substances 72 Granularity spatial region substance parts of spatial regions are always spatial regions 73 Granularity process parts of processes are always processes 74 MORAL Relations crossing the SNAP/SPAN border are never part-relations 75 Relations crossing the SNAP/SPAN border are never part-relations substance John John’s life physiological processes 76 DIGESTIVE SYSTEM 77 RESPIRATORY SYSTEM 78 URINARY SYSTEM 79 IMMUNE SYSTEM 80 CIRCULATORY SYSTEM 81 CIRCULATORY SYSTEM (Principal Organs) 82 The autonomous part of the nervous system (regulatory links to other systems) 83 ENDOCRINE SYSTEM 84 Bodily Systems are Component Parts of Bodies digestive respiratory skeletal musculatory circulatory 85 immune 86 A system for keeping your jewels safe 87 Bodily Systems interconnect 88 Systems are SNAP entities They are dependent continuants We can take photographs of them 89 The Monarchic System of Government 90