1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Psychiatry Grand Rounds. Foundations for an Ontology of Mental Disease. April 1, 2011; 8.00 AM - 9.30 AM BPC - Auditorium, Rehabilitation Building, Buffalo Psychiatric Center Werner CEUSTERS, MD Ontology Research Group, Center of Excellence in Bioinformatics and Life Sciences Department of Psychiatry, University at Buffalo, NY, USA

2. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Abstract. While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as ‘mental disorder’, ‘disease’ and ‘illness’ might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology (BFO) and in the application of BFO in the Ontology of General Medical Science (OGMS). We analyzed statements about what counts as a mental disease provided (1) in the research agenda for the DSM-V, and (2) in Pies’ model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future.

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Structure of this presentation 1.Ontology and fantology 2.Foundations of our work –Methodological –Representational 3.Towards an ontology for mental health 4.Utility of our work

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology In philosophy: –Ontology (no plural) is the study of what entities exist and how they relate to each other; –by some philosophers taken to be synonymous with ‘metaphysics’ while others draw distinctions in many distinct ways (the distinctions being irrelevant for this talk), but almost agreeing on the following classification: metaphysics –general metaphysics »ontology –special metaphysics –distinct from ‘epistemology’ which is the study of how we can come to know about what exists.

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Some MDs got it quite early… ‘We have to thank the metaphysicians for, if not explaining many things, at least giving us useful terms under which discussions may be carried on.’ Although: –‘Why should he, why should man, ever have been born, if to be born simply means to begin with his first breath a struggle against death?’ question in the realm of special metaphysics. Bryce PH. Ontology in relation to preventive medicine. Am J Public Health (N Y). 1912 Jan;2(1):32-3.

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U … and worse ‘If he thinks ontologically at all, he can no longer imagine human life only an accident, flotsam and jetsam on a turbulent and never-resting sea, but rather that "being" is an emanation from the Infinite Consciousness which makes the ego in us the occasion for the realization, by each - even in the smallest degree - that he is a constituent atom in Universal Mind, wherein is the definite idea illustrating not alone a common humanity, but also the manifestation of a universal good’. –here is not an ontological issue, but a psychiatric one. Bryce PH. Ontology in relation to preventive medicine. Am J Public Health (N Y). 1912 Jan;2(1):32-3.

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U A legitimate ontological question Do mental illnesses / disorders / diseases exist? –The answer can, arguably, be ‘no’: if one does not subscribe to the mind-brain dichotomy: –no mind  nothing mental if one does, but also entertains a strong body-related interpretation of what is an illness, disorder, disease: –STEDMAN (27th edition): an interruption, cessation, or disorder of body function, system, or organ. –DORLAND: any deviation from or interruption of the normal structure or function of a part, organ, or system of the body as manifested by characteristic symptoms and signs; –WHO: an interconnected set of one or more dysfunctions in one or more body parts, linking to underling genetic factors and to interacting environmental factors and possibly: to a pattern or patterns of response to interventions. –and under the same conditions: ‘yes’: ‘mental disorder’ would be synonymous with ‘brain disorder’

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U A legitimate ontological question Do mental illnesses / disorders / diseases exist? –The answer can, arguably, be ‘no’: if one does not subscribe to the mind-brain dichotomy: –no mind  nothing mental if one does, but also entertains a strong body-related interpretation of what is an illness, disorder, disease: –STEDMAN (27th edition): an interruption, cessation, or disorder of body function, system, or organ. –DORLAND: any deviation from or interruption of the normal structure or function of a part, organ, or system of the body as manifested by characteristic symptoms and signs; –WHO: an interconnected set of one or more dysfunctions in one or more body parts, linking to underling genetic factors and to interacting environmental factors and possibly: to a pattern or patterns of response to interventions. –and under the same conditions: ‘yes’: ‘mental disorder’ would be synonymous with ‘brain disorder’

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U A better phrased ontological question Do mental illnesses / disorders / diseases exist? What, if anything at all, do the terms ‘mental illness’, ‘mental disorder’, … denote?

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U A better phrased ontological question Do mental illnesses / disorders / diseases exist? What, if anything at all, do the terms ‘mental illness’, ‘mental disorder’, … denote? termsfirst-order reality ‘mental disorder’ ‘person’ ‘UB’

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U This is distinct from terminological questions Terminological question: –What does ‘mental disorder’ mean ?

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U This is distinct from terminological questions Terminological question: –What does ‘mental disorder’ mean ? ‘mental disorder’ meaning of ‘mental disorder’

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Terminological approaches raise further questions Terminological question: –What does ‘mental disorder’ mean ? ‘mental disorder’ meaning of ‘mental disorder’ What are meanings? Do meanings denote? How are these related?

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The half-baked semantic/semiotic triangle does not provide any good answers despite its overwhelming popularity ‘mental disorder’ meaning of ‘mental disorder’ Concept Symbol / Sign / TermThing / Referent

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The semantic triangle works sometimes fine term concept referent ‘Beethoven’ Ludwig van Beethoven that great German composer that became deaf …

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The semantic triangle works sometimes fine term concept referent ‘Beethoven's Symphony No. 3’ Beethoven’s symphony dedicated to Bonaparte the symphony played after the Munich Olympics massacre … ‘Beethoven's Opus 55’ ‘Eroica’

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Sometimes the semantic triangle fails term concept referent ‘Beethoven's Symphony No. 11’ the symphony Beethoven wrote after the tenth …

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Sometimes the semantic triangle fails term concept referent ‘Beethoven's Symphony No. 11’ the symphony Beethoven wrote after the tenth … some hold this term has meaning

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Sometimes the semantic triangle fails term concept referent ‘Beethoven's Symphony No. 10’ the one assembled by Barry Cooper from fragmentary sketches Beethoven’s hypothetical symphony …

20. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Prehistoric ‘psychiatry’: drapetomania term concept referent ‘drapetomania’ disease which causes slaves to suffer from an unexplainable propensity to run away … painting by Eastman Johnson. A Ride for Liberty: The Fugitive Slaves. 1860.

21. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Drapetomania

22. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Some etiologic and diagnostic reflections

23. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The North’s ‘Effugium Discipulorum’

24. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The questions the triangle raises become trickier Is … –Beethoven’s 10 th symphony a symphony ? –Beethoven’s 10 th symphony a hypothetical symphony ? –a hypothetical symphony a symphony ? In medicine, is … –a prevented abortion an abortion ? –an absent nipple a nipple ?

25. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology should give the answer In philosophy: –Ontology (no plural) is the study of what entities exist and how they relate to each other;

26. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Unfortunately, ‘ontology’ denotes ambiguously In philosophy: –Ontology (no plural) is the study of what entities exist and how they relate to each other; In computer science and many biomedical informatics applications: –An ontology (plural: ontologies) is a shared and agreed upon conceptualization of a domain;

27. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Semantic Applications use Ontologies and Software 27 Domain ‘Philosophical’ approach to ontology Ontologies Ontology Authoring Tools Reasoners create Computer Science approach to ‘ontology’

28. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology in CS: relates concepts drapetomania slavemental disorderrunning awaypropensity How concepts are / can be related

29. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The green highlights of before logical accuracy literary efforts the inventor (of a disease) language nor concept structures are without additional measures robust enough to represent reality adequately.

30. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Three, thus far unrelated, ways of relating drapetomania slavemental disorderrunning awaypropensity How concepts are / can be related How referents are related How terms are related

31. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U We want to prevent mistakes ‘drapetomania’: –the term clearly denotes, it has an existing first-order referent: the irrestrainable propensity to run away inhering in slaves. –‘mental illness’ should not be defined in such a way that this propensity satisfies the definition of ‘mental illness’.

32. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The modern focus of (philosophy in) psychiatry The philosophical debate over mental illness is not about its existence, but rather over –how to define it, and –whether it can be given a scientific or objective definition, or –whether normative and subjective elements are essential to our concept of mental illness.

33. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Foundations for an ontology of mental disease Methodological foundations: –Ontological Realism –Open Biomedical Ontologies Foundry Representational foundations: –Basic Formal Ontology –Relation Ontology –Ontology of General Medical Science

34. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology as it should be done In philosophy: –Ontology (no plural) is the study of what entities exist and how they relate to each other; In computer science and many biomedical informatics applications: –An ontology (plural: ontologies) is a shared and agreed upon conceptualization of a domain; The realist view within the Ontology Research Group combines the two: –We use Ontological Realism, a specific methodology that uses ontology as the basis for building high quality ontologies, using reality as benchmark.

35. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U

36. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 1.There is an external reality which is ‘objectively’ the way it is; 2.That reality is accessible to us; 3.We build in our brains cognitive representations of reality; 4.We communicate with others about what is there, and what we believe there is there. The basis of Ontological Realism Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA

37. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontological Realism makes three crucial distinctions 1.Between data and what data are about; 2.Between continuants and occurrents; 3.Between what is generic and what is specific. 37 Smith B, Ceusters W. Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies. Applied Ontology, 2010. (forthcoming)

38. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U 38

39. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U L1 - L2 L3 39 Linguistic representations about (1), (2) or (3) Clinicians’ beliefs about (1) Entities (particular or generic) with objective existence which are not about anything Representations First Order Reality

40. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontological Realism makes crucial distinctions Between data and what data are about; Between continuants and occurrents: –obvious differences: a person versus his life a disease versus its course space versus time –more subtle differences: observation (data-element) versus observing diagnosis versus making a diagnosis message versus transmitting a message 40

41. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Is depression considered a continuant or occurrent? What do we mean by ‘depression’ ? –The name of some disease ?  continuant –A bout of feelings of being worth nothing, sobbing, appearance of suicidal thoughts, …  occurrent

42. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The representational square L1. First-order reality L2. Beliefs (knowledge) GenericSpecific DIAGNOSIS INDICATION my doctor’s work plan my doctor’s diagnosis MOLECULE PERSON DISEASE PATHOLOGICAL STRUCTURE PORTION OF INSULIN DRUG me my blood glucose level my NIDDM my doctor my doctor’s computer L3. Representation ‘person’‘drug’‘insulin’‘W. Ceusters’‘my sugar’ Referent TrackingBasic Formal Ontology GenericSpecific 42

43. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U tt t instanceOf The essential pieces material object spacetime region me some temporal region my life my 4D STR some spatial region history spatial region temporal region dependent continuant some quality located-in at t … at t participantOf at toccupies projectsOn projectsOn at t

44. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U OBO Foundry L1 L2 L3 44

45. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U

46. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology of General Medical Science First ontology in which the L1/L2/L3 distinction is used Scheuermann R, Ceusters W, Smith B. Toward an Ontological Treatment of Disease and Diagnosis. 2009 AMIA Summit on Translational Bioinformatics, San Francisco, California, March 15-17, 2009;: 116-120. Omnipress ISBN:0-9647743-7-22009 AMIA Summit on Translational Bioinformatics

47. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Motivation Clarity about: –disease etiology and progression –disease and the diagnostic process –phenotype and signs/symptoms

48. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Big Picture

49. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U a disease is a disposition rooted in a physical disorder in the organism and realized in pathological processes. Approach

50. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Disposition A disposition is a realizable entity which is such that (1) if it ceases to exist, then its bearer is physically changed, (2) whose realization occurs, in virtue of the bearer’s physical make-up, when this bearer is in some special physical circumstances.

51. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U a disease is a disposition rooted in a physical disorder in the organism and realized in pathological processes. etiological processdisorderdispositionpathological process abnormal bodily featuressigns & symptomsinterpretive processdiagnosis producesbearsrealized_in producesparticipates_inrecognized_as produces Approach

52. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Disorder =def. – –A causally linked combination of physical components that is (a) clinically abnormal and (b) maximal, in the sense that it is not a part of some larger such combination. Pathological Process =def. – –A bodily process that is a manifestation of a disorder and is clinically abnormal. Foundational Terms (1)

53. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Clinically abnormal - something is clinically abnormal if: –(1) is not part of the life plan for an organism of the relevant type (unlike aging or pregnancy), –(2) is causally linked to an elevated risk either of pain or other feelings of illness, or of death or dysfunction, and –(3) is such that the elevated risk exceeds a certain threshold level.

54. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Disorder =def. – A causally linked combination of physical components that is (a) clinically abnormal and (b) maximal, in the sense that it is not a part of some larger such combination. Pathological Process =def. – A bodily process that is a manifestation of a disorder and is clinically abnormal. Disease =def. – –A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. Foundational Terms (2)

55. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Disease course the totality of all P ROCESSES through which a given D ISEASE instance is realized. multiple D ISEASE C OURSES will be associated with the same D ISORDER type, for example in reflection of the presence or absence of pharmaceutical or other interventions, of differences in environmental influence, and so forth.

56. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Clinical Picture =def. – A representation of a clinical phenotype that is inferred from the combination of laboratory, image and clinical findings about a given patient. Diagnosis =def. – –A conclusion of an interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease of such and such a type. Diagnosis

57. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U In a nut shell The disorder is thereThe diagnosis is here The disease is there

58. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Relevance of OGMS: Pies’ model Introduces a 5-stage account of how our scientific understanding of a mental disease condition might evolve over time. The goal is a framework that is designed to allow us to determine: whether a condition represents, in the first place, dis-ease and, secondarily, whether it constitutes a specific disease, on a par with, say, bipolar I disorder. For example, how do we decide whether to consider “pathological bigotry” and “internet addiction” as specific mental disorders? Pies R: What should count as a mental disorder in DSM-V. Psychiatric Times 2009, 26.

59. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The basics: existence (in a patient) criterion ‘prolonged and severe suffering and incapacity in the affective, cognitive, or interpersonal- behavioral realms’ –Pies R: What should count as a mental disorder in DSM-V. Psychiatric Times 2009, 26. based on: –Kendell RE: The concept of disease and its implications for psychiatry. British Journal of Psychiatry 1975, 127:305-315.

60. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Pies’ 5-stage model (1) Stage 1: patient’s acknowledgement of daily substantial and prolonged suffering and incapacity that is ‘specified in terms of social and vocational impairment, impaired vital functions, and distortions in the phenomenological realm (feeling “totally worthless,” “like I’m nothing”)’. –This must be acknowledged as an intrinsic element of the condition and not simply as a consequence of society’s punitive responses to the person’s behavior.

61. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Pies’ 5-stage model (2) Stage 2: –availability of a general syndromal description of the condition supported by evidence that the constituent signs and symptoms reliably ‘hang together’ over long periods and in geographically distant populations.

62. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Pies’ 5-stage model (3) Stage 3: –the syndrome has been characterized by authoritive sources in terms of usual course, outcome, comorbidity, familial pattern, and response to treatment; –there may also be preliminary data on pathophysiology and biomarkers, and a more specific understanding of the afflicted person’s phenomenology

63. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Pies’ 5-stage model (4) Stage 4: –known pathophysiology, cause, a specific set of biomarkers, and –in some cases an inheritance pattern for the condition (or for multiple conditions that become identified as separate entities only after Stage 2).

64. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Pies’ 5-stage model (5) Stage 5: –availability of a precise chromosomal and biomolecular etiology, and –a specification of the phenomenology, for all disease subtypes.

65. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology for Mental Health

66. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ontology for Mental Health V0.0001 Legend representation process continuant disjunction MHOBFO/OGMS

67. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Core elements

68. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U M ENTAL P ROCESS (L1,U) =def. B ODILY P ROCESS which brings into being, sustains or modifies a C OGNITIVE R EPRESENTATION or a B EHAVIOR I NDUCING S TATE

69. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U B EHAVIOR I NDUCING S TATE (L1,U) =def. B ODILY Q UALITY inhering in a M ENTAL F UNCTIONING R ELATED A NATOMICAL S TRUCTURE which leads to B EHAVIOR of some specific sort

70. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U B EHAVIOR (L1,U) =def. a P ROCESS having P ROCESSES as parts in which an O RGANISM participates as agent in response to external or internal stimuli and following some pattern which is dependent upon some combination of that O RGANISM ’s internal state and external conditions. (Derived from the Gene Ontology)

71. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U M ENTAL F UNCTIONING R ELATED A NATOMICAL S TRUCTURE (L1,U) =def. A NATOMICAL S TRUCTURE in which there inheres the D ISPOSITION to be the agent of a M ENTAL P ROCESS

72. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Disorder related definitions M ENTAL D ISORDER =def. D ISORDER in a M ENTAL F UNCTIONING R ELATED A NATOMICAL S TRUCTURE P ATHOLOGICAL M ENTAL P ROCESS =def. P ATHOLOGICAL P ROCESS which is the manifestation of a M ENTAL D ISORDER M ENTAL D ISEASE =def. a D ISEASE which is a D ISPOSITION to undergo P ATHOLOGICAL M ENTAL P ROCESSES

73. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Diagnosis related entities D IAGNOSIS OF M ENTAL D ISEASE =def. –D IAGNOSIS asserting the presence of an instance of M ENTAL D ISEASE in a given O RGANISM M ARKER F EATURES FOR D ISEASE X =def. –R EPRESENTATION which is a collection of D ISEASE P ICTURE C OMPONENTS which are characteristic for D ISEASE X (where ‘X’ serves as placeholder for some disease name)

74. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Utility and future work

75. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Emotion Ontology Janna Hastings, Werner Ceusters, Barry Smith, and Kevin Mulligan. Dispositions and processes in the Emotion Ontology

76. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U An ontology for pain and related disability, mental health and quality of life. 1R01DE021917-01A1 The goal of this project is to obtain better insight into the complexity of pain disorders, specifically concerning the assessment of different pain types as well as pain-related disablement and its association with mental health and quality of life. This will be achieved by developing an ontology which will then be used to integrate five existing datasets that broadly encompass the major types of pain (orofacial pains, temporomandibular disorder pain, headache) recognized to occur in the oral and associated regions and incorporating a broad array of measures consistent with a biopsychosocial perspective regarding pain.

77. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Easy access to, for instance, NESARC National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) Example data elements: –BIOLOGICAL FATHER EVER LIVE IN HOUSEHOLD BEFORE RESPONDENT WAS 18 (36862 Yes; 4750 No; 67 Unknown; 1414 did not live or unknown if lived with biological parent(s) before age 18) –RAISED BY ADOPTIVE PARENTS BEFORE AGE 18 (378 Yes; 824 No; 212 Unknown; 41679 lived with biological parent(s) before age 18.