1. ECO R European Centre for Ontological Research Realist Ontology for the Semantic Web: Applications in Biomedical Informatics Werner Ceusters European Centre for Ontological Research Universität des Saarlandes Saarbrücken, Germany

2. ECO R European Centre for Ontological Research Lecture overview Credentials The many faces of “ontology” Realist ontology Why is the concept-based approach so wide- spread ? The price you pay if you go for concepts... Can Description Logics save the world ? And then there was OWL Take home messages

3. ECO R European Centre for Ontological Research European Centre for Ontological Research Local members External members Partners Status Dec 2, 2004

4. ECO R European Centre for Ontological Research European Centre for Ontological Research DirectorsMember representatives Advisory Board Management Board Status Dec 2, 2004

5. ECO R European Centre for Ontological Research Institute for Formal Ontology and Medical Information Science an interdisciplinary research group –Philosophy, –Computer and Information Science, –Logic, –Medicine, –Medical Informatics. a center of theoretically grounded research in both formal and applied ontology. Main goal: to develop a formal ontology that will be applied and tested in the domain of medical and biomedical information science.

6. ECO R European Centre for Ontological Research IFOMIS competences Status Dec 2, 2004 Formal Ontology / metaphysics Logics History of philosophy Philosophy of science

7. ECO R European Centre for Ontological Research Our building

8. ECO R European Centre for Ontological Research What philosophers are good for...

9. ECO R European Centre for Ontological Research Short personal history 1959 -... 1977 1989 1992 1998 2002 2004

10. ECO R European Centre for Ontological Research “Ontology”

11. ECO R European Centre for Ontological Research WordNet 2.0 - 2003

12. ECO R European Centre for Ontological Research “Ontology” on the web Status Nov 29, 2004 The most cited definition: Tom Grüber 1993 Inactive since August 7, 2004. W3C Web Ontology initiative Ontology from a philosophical perspective. Important bioinformatics resource Realist ontology in use. Barry Smith Popular ontology editor from Manchester SUO Upper Ontology Initiative John Sowa’s ontology page

13. ECO R European Centre for Ontological Research New search on Nov 30: 10.000 results more 1What is an Ontology? 3Gene Ontology Consortium 4W3C Web Ontology (WebOnt) Working Group (OWL) (Closed) 7Buffalo Ontology Site 15MGED NETWORK :: Ontology Working Group (OWG) 20Laboratory for Applied Ontology (LOA) 21ONTOLOGY WORKS INC. 34John Bateman; ontology portal root 53The Protégé Ontology Editor and Knowledge Acquisition System 59Institute for Formal Ontology and Medical Information Science... 86Autofellatio and Ontology 188EUROREC 2004, Implemantation Guidelines,... 192Foundational Ontology (Leeds) 676Ontology Server research (StarLab) ?????

14. 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 you use the word “ontology”, ALWAYS be specific about what you mean by it.

15. ECO R European Centre for Ontological Research Tom Gruber’s view In the context of knowledge sharing, I use the term ontology to mean a specification of a conceptualization. That is, 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. This definition is consistent with the usage of ontology as set-of-concept-definitions, but more general. And it is certainly a different sense of the word than its use in philosophy. An ontology is a specification of a conceptualization. The word "ontology" seems to generate a lot of controversy in discussions about AI. It has a long history in philosophy, in which it refers to the subject of existence. It is also often confused with epistemology, which is about knowledge and knowing.

16. ECO R European Centre for Ontological Research The O-word in science 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.

17. ECO R European Centre for Ontological Research The O-word in buzz-speak “An ontology is a classification methodology for formalizing a subject's knowledge or belief system in a structured way. Dictionaries and encyclopedias are examples of ontologies.” (X1) “A terminology (or classification) is a kind of ontology by definition and it should preserve (and "understand") the relationships between the 1,000s of terms in it or else it would become a mere dictionary (or at best a thesaurus).” (X2) “Ontologies are Web pages that contain a mystical unifying force that gives differing labels common meaning.” (X3)

18. ECO R European Centre for Ontological Research “Ontology” An ontology defines the terms used to describe and represent an area of knowledge, and are used by people, databases, and applications that need to share domain information (a domain is a specific subject area, such as health or medicine). OWL Web Ontology Language; Use Cases and Requirements W3C Recommendation 10 February 2004 http://www.w3.org/TR/webont-req/ e-Health - making healthcare better for European citizens: An action plan for a European e-Health Area COM (2004) 356 final, 30.4.2004, p17

19. ECO R European Centre for Ontological Research Ontologies need to specify descriptions for the following kinds of concepts: – Classes (general things) in the many domains of interest – The relationships that can exist among things – The properties (or attributes) those things may have OWL Web Ontology Language; Use Cases and Requirements W3C Recommendation 10 February 2004 http://www.w3.org/TR/webont-req/ “Ontology”

20. ECO R European Centre for Ontological Research Realist Ontology

21. ECO R European Centre for Ontological Research A visit 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

22. ECO R European Centre for Ontological Research 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 A visit to the operating theatre

23. ECO R European Centre for Ontological Research “Axiom” 1 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

24. ECO R European Centre for Ontological Research The realist ontological square (Ignacio Angelelli) Substance ParticularsQuality Particulars Substance Universals Quality Universals instance differentia exemplify inheres

25. ECO R European Centre for Ontological Research How to differentiate qualities from substances ? Language may fool us: – Being pale – Being human – Being a person – Being sick Can all be properties of particulars, namely me and you ! But so does logic: – Pale(x) – Human(x) – Person(x) – Sick(x)

26. ECO R European Centre for Ontological Research “Realist ontology” describes what is fundamental in the totality of what exists, defines the most general categories to which we need to refer in constructing a description of reality, tells us how these categories are related. is able to be used to describe reality at any point in time.

27. ECO R European Centre for Ontological Research Basic Ontological Notions Identity – How are particulars distinguished from each other ? Unity – How are all the parts of a particular isolated ? Essence – Can a property change over time ? Dependence – Can an entity exist without some others ?

28. ECO R European Centre for Ontological Research Identity & instanciation childadult caterpillar butterfly t person animal Living creature

29. ECO R European Centre for Ontological Research +I The property carries a common identity criterion for all its instances. −I The property does not carry a common identity criterion for all its instances. +U The property carries a common unity criterion for all its instances. −U The property does not carry a common unity criterion for all its instances. U No instance of the property satisfies a unity criterion. +R The property is essential to all its instances: an instance of a rigid property cannot stop satisfying that property. −R The property is not essential to all its instances: some instances of a non rigid property can stop satisfying that property. R No instance of the property has it essentially: all instances of the property can stop satisfying it. A practical example: OntoClean Guarino & Welty

30. ECO R European Centre for Ontological Research Ontological theories = theories between reality and “the ontology” (“ontology” as a representation) – Granular Partition Theory (T Bittner & B. Smith) – Logic of Classes (B. Smith) – Foundational relations

31. ECO R European Centre for Ontological Research Theory of granular partitions (B. Smith) Think of it as Alberti’s grid

32. ECO R European Centre for Ontological Research Granular partitions: main principles a partition is the drawing of a (typically complex) fiat boundary over a certain domain a partition typically comes with labels and/or an address system partitions are artefacts of our cognition a partition is transparent (veridical) bona fide objects exist independently of our partitions, fiat objects are determined by partitions different partitions may represent cuts through the same reality which are skew to each other entities (existing in reality) located in the same cell of a partition share common characteristics

33. 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 particulars are not instances; e.g. some mereological sums subsumption defined resorting to instances:

34. ECO R European Centre for Ontological Research Reference Ontology a theory of a domain of entities in the world based on realizing the goals of maximal expressiveness and adequacy to reality sacrificing computational tractability for the sake of representational adequacy

35. 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: continuants –SpanBFO a single videoscopic ontology (O v ): occurants. 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.

36. ECO R European Centre for Ontological Research Occurants and continuants Picture by Vladimir Brajic

37. ECO R European Centre for Ontological Research

38. ECO R European Centre for Ontological Research SpanBFO

39. ECO R European Centre for Ontological Research a for a computer understable 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. “A” Realist 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” 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

40. ECO R European Centre for Ontological Research Why is the concept-based approach so wide-spread ?

41. ECO R European Centre for Ontological Research Back to the operating theatre Haydom Lutheran Hospital, Tanzania I must get rid of that blood Suction, please ! He wants me to remove that blood Fluid being removed

42. ECO R European Centre for Ontological Research = ? This is communication ! kocher Give me a kocher, please.

43. 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

44. 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.

45. ECO R European Centre for Ontological Research An interesting sidestep: “understanding” “understanding”  Latin “substare” – literally: “to stand under” Websters Dictionary (1961) understanding = the power to render experience intelligible by bringing perceived particulars under appropriate concepts. “particulars” = what is NOT SAID of a subject (Aristotle) – substances: this patient, that tumor,... – qualities: the red of that patient’s skin, his body temperature, blood pressure,... – processes: that incision made by that surgeon, the rise of that patient’s temperature,... “concepts”: may be taken in the above definition as Aristotle’s “universals” = what is SAID OF a subject – Substantial concepts: patient, tumor,... – Quality concepts: white, temperature –...

46. 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

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

48. 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

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

50. 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 (mst/ist) 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

51. ECO R European Centre for Ontological Research Ontology and the semantic triangle 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.” concept termreferent

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

53. ECO R European Centre for Ontological Research Before the introduction of “concepts”, it was even worse... Characteristics of an ideal medical knowledge system a unique code for each term (word, phrase) each code-term being defined each term independent, not defined as the result of other terms in the system synonyms recognisable through the codes to each codes could be attached codes of related terms the system would encompass all of medicine the system would be in the public domain the format of the KB should be functionally described, independent from hard- or software (C. Bishop, 1989)

54. ECO R European Centre for Ontological Research With “concepts”, it became: Characteristics of an ideal medical knowledge system a unique code for each term (word, phrase) and concept each code-term concept being defined each term concept independent, not defined as the result of other terms in the system??? synonyms recognisable through the codes concepts to each code concept could be attached codes concepts of related terms the system would encompass all of medicine the system would be in the public domain the format of the KB should be functionally described, independent from hard- or software

55. ECO R European Centre for Ontological Research Requirements for clinical vocabularies (1) Domain completeness: coverage of all possible terms that lie within a vocabulary’s domain Non-vagueness: the term should represent the concept behind it as close as possible Non-ambiguity: the same term cannot refer to more than one concept Non-redundancy: each concept must be represented by one unique identifier (Cimino, 1989)

56. ECO R European Centre for Ontological Research Requirements for clinical vocabularies (2) Synonomy: multiple ways for expressing a word (or concept) must be allowed Multiple classification: concepts must be allowed to be classified in multiple hierarchies Consistency of view: concepts must have the same relationships in all views Explicit relationships: all relationships (e.g. class, synonymy,…) must be explicitly labelled.

57. ECO R European Centre for Ontological Research The price you pay if you go for concepts...

58. ECO R European Centre for Ontological Research Border’s classification of medicine Medicine – Mental health – Internal medicine Endocrinology – Oversized endocrinology Gastro-enterology... – Pediatrics –... – Oversized medicine

59. ECO R European Centre for Ontological Research MeSH: Medical Subject Headings Designed for bibliographic indexing, eg Index Medicus Basis for MedLINE focuses on biomedicine and other basic healthcare sciences clinically very impoverished Consistency amongst indexers: – 60% for headings – 30% for sub-headings

60. ECO R European Centre for Ontological Research MeSH Tree Structures - 2004 1. Anatomy [A] 2. Organisms [B] 3. Diseases [C] 4. Chemicals and Drugs [D] 5. Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] 6. Psychiatry and Psychology [F] 7. Biological Sciences [G] 8. Physical Sciences [H] 9. Anthropology, Education, Sociology and Social Phenomena [I] 10. Technology and Food and Beverages [J] 11. Humanities [K] 12. Information Science [L] 13. Persons [M] 14. Health Care [N] 15. Geographic Locations [Z] What about this as a top ontology ???

61. ECO R European Centre for Ontological Research Cardiovascular Diseases [C14] – Heart Diseases [C14.280] Arrhythmia [C14.280.067] + Carcinoid Heart Disease [C14.280.129] Cardiomegaly [C14.280.195] + Endocarditis [C14.280.282] + Heart Aneurysm [C14.280.358] Heart Arrest [C14.280.383] + Heart Defects, Congenital [C14.280.400] – Aortic Coarctation [C14.280.400.090] – Arrhythmogenic Right Ventricular Dysplasia [C14.280.400.145] – Cor Triatriatum [C14.280.400.200] – Coronary Vessel Anomalies [C14.280.400.210] – Crisscross Heart [C14.280.400.220] – Dextrocardia [C14.280.400.280] + MeSH Tree Structures - 2004

62. ECO R European Centre for Ontological Research Body Regions [A01] – Extremities [A01.378] Lower Extremity [A01.378.610] – Buttocks [A01.378.610.100] – Foot [A01.378.610.250] » Ankle [A01.378.610.250.149] » Forefoot, Human [A01.378.610.250.300] + » Heel [A01.378.610.250.510] – Hip [A01.378.610.400] – Knee [A01.378.610.450] – Leg [A01.378.610.500] – Thigh [A01.378.610.750] MeSH Tree Structures - 2004 The most abundant sort of mistakes !

63. ECO R European Centre for Ontological Research Body Regions [A01] – Abdomen [A01.047] + – Back [A01.176] + – Breast [A01.236] + – Extremities [A01.378] Amputation Stumps [A01.378.100] Lower Extremity [A01.378.610] + Upper Extremity [A01.378.800] + – Head [A01.456] + – Neck [A01.598] – Pelvis [A01.673] + – Perineum [A01.719] – Thorax [A01.911] + – Viscera [A01.960] MeSH Tree Structures - 2004 And here ?

64. ECO R European Centre for Ontological Research SNOMED International (1995) Multi-axial coding system: – morphology, disease, function, procedure,... Each axis has an hierarchical structure Translations in other languages than English only for older versions Informal internal structuring Being translated in CG formalism, but with only internal consistency Possibility to generate meaningless concepts Mixing of hierarchies: – Bone Long Bone Periosteum Shaft

65. ECO R European Centre for Ontological Research Snomed International (1995) Number of records (V3.1) TTopography12,385 MMorphology 4,991 FFunction16,352 LLiving Organisms24,265 CDrugs &Biological Products14,075 APhysical Agents, Forces and Activities 1,355 DDisease/ Diagnosis28,623 PProcedures27,033 SSocial Context 433 JOccupations 1,886 GGeneral Modifiers 1,176 TOTAL RECORDS 132,641

66. ECO R European Centre for Ontological Research Snomed International (1995): knowledge in the codes. posterior anatomic leaflet mitral cardiac valve cardiovascular T-23532 Why was this not a good idea ?

67. ECO R European Centre for Ontological Research Snomed International : multiple ways to express the same thing D5-46210Acute appendicitis, NOS D5-46100Appendicitis, NOS G-A231Acute M-41000Acute inflammation, NOS G-C006In T-59200Appendix, NOS G-A231Acute M-40000Inflammation, NOS G-C006In T-59200Appendix, NOS

68. 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 :... D50.1... D51Vit B12 deficiency anaemia Haemolytic Anemias (D55-D59)... Chapter IV:...

69. ECO R European Centre for Ontological Research UMLS: Unified Medical Language System (NLM) Tool for information retrieval of 4 components: – Metathesaurus contains information about biomedical concepts and how they are represented in diverse terminological systems. – Semantic Network contains information about concept categories and the permissible relationships among them – Information Sources Map contains both human- readable and machine-processable information about all kinds of biomedical terminological systems – Specialist lexicon: english words with POS “The” tool from and for the U.S. :-)

70. ECO R European Centre for Ontological Research UMLS Semantic Network

71. ECO R European Centre for Ontological Research Semantic Network Relationships Is_a physically related to spatially related to temporally related to functionally related to conceptually related to

72. ECO R European Centre for Ontological Research Semantic Network “Biologic Function” Hierarchy

73. ECO R European Centre for Ontological Research Semantic Network "affects" Hierarchy

74. ECO R European Centre for Ontological Research “Axiom” 2 Concept-based terminology (and standardisation thereof) is there as a mechanism to improve understanding of messages by humans. 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 communication), – to reason about reality, – to make machines understand what is real, – to integrate across different views, languages, conceptualisations,...

75. ECO R European Centre for Ontological Research Why not ? Does not take care of universals and particulars appropriately 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”...

76. ECO R European Centre for Ontological Research Ok, then Description Logics will save us... ?

77. ECO R European Centre for Ontological Research Description Logics A decidable fragment of FOL A propositional modal logic A classes and properties (concepts and roles) oriented KR language Subsumption and satisfiability (consistency) are the key inferences Most DLs are supersets of ALC – Boolean operators on concepts – Existential and Universal quantifiers OWL-DL is a large superset (SHOIN): – Property hierarchies & Transitive roles (SH) – Inverse (I) – Nominals (O) (hasValue and one of) – Number restrictions (counting quantifiers)

78. ECO R European Centre for Ontological Research Snomed and DL SNOMED-RT (2000) SNOMED-CT (2003) DL don’t guarantee you to get parthood right !

79. ECO R European Centre for Ontological Research Use of description logics does not guarantee correct representations !

80. ECO R European Centre for Ontological Research Sloppiness in definitions new-1 new-2

81. ECO R European Centre for Ontological Research NCI Thesaurus a biomedical thesaurus created specifically to meet the needs of the National Cancer Institute. semantically modeled cancer-related terminology built using description logics

82. ECO R European Centre for Ontological Research NCI Thesaurus Root concepts Anatomic Structure, Anatomic System, or Anatomic Substance ? Or ? Does the NCI not know to which category Any item classified there belongs ? Anatomic Substance ? If yes, why is gene product not subsumed by it ? If no, why are drugs and chemicals not subsumed by it ?

83. ECO R European Centre for Ontological Research Conceptual entity Definition: none Semantic type: – Conceptual entity – Classification Subconcepts: – Action: definition: action; a thing done – And: Definition: an article which expresses the relation of connection or addition, used to conjoin a word with a word,... – Classification Definition: the grouping of things into classes or categories

84. ECO R European Centre for Ontological Research Definition of “cancer gene”

85. ECO R European Centre for Ontological Research NCI Thesaurus architecture Disease BreastBreast neoplasm Disease-has-associated-anatomy ISA Findings-And- Disorders-Kind Anatomy-Kind “Formal subsumption” or “inheritance” “Associative” relationships providing “differentiae” “Kinds” restrict the domain and range of associative relationships What diseases have a diameter of over 3 cm ?

86. ECO R European Centre for Ontological Research Ontology versus Description Logics In the Description Logic world – terms and definitions come first, – the job is to validate them and reason with them by means of a model – but whether the model correspond to reality is not its problem ( Workshop on DL, Saarbrücken, 22-23/11/2004 ) In the realist ontology world – robust ontology (with all its reasoning power) comes first – terms, term-hierarchies and record architectures must be subjected to the constraints of ontological coherence

87. ECO R European Centre for Ontological Research Thanks x there is OWL ? Where x  { },,,,

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

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

90. ECO R European Centre for Ontological Research Understanding content (3) John Doe 17372009 76505004 7771000

91. ECO R European Centre for Ontological Research XML OWL XML – Pure syntax – Simulated semantics OWL: – Very precise semantics – But is the semantics of the right sort to faithfully describe simple medical facts ?

92. ECO R European Centre for Ontological Research NCIT’s “Lung” in OWL Lung C12468 primitive <owl:onProperty rdf:resource="#rAnatomic_Structure_Has_Location"/>... “All instances of lung must be located in at least one instance of thoracic cavity” Hence: total lung excision is impossible.

93. ECO R European Centre for Ontological Research NCIT’s “Lung” in OWL Lung C12468 primitive <owl:onProperty rdf:resource="#rAnatomic_Structure_Has_Location"/>... “every assigned location of pleura must be an instance of the class Thoracic Cavity” Allows lungs not to be located at all.

94. ECO R European Centre for Ontological Research Take home messages Very few “ontologies” are ontologies. Realist ontology offers a good methodology for building consistent representations. DLs are helpful, but only if you know how to use them properly. OWL is inadequate to represent even the most obvious facts. Please... be critical when buzz words are used.