Representing dispositions

Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious disease ontology, but also as part of a general strategy for modelling knowledge about molecular interactions. But the task of representing dispositions in some formal ontological systems is fraught with several problems, which are partly due to the fact that Description Logics can only deal well with binary relations. The paper will discuss some of the results of the philosophical debate about dispositions, in order to see whether the formal relations needed to represent dispositions can be broken down to binary relations. Finally, we will discuss problems arising from the possibility of the absence of realizations, of multi-track or multi-trigger dispositions and offer suggestions on how to deal with them

OBML - Ontologies in Biomedicine and Life Sciences

The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2(nd) in a series of meetings organized by the Working Group “Ontologies in Biomedicine and Life Sciences” of the German Society of Computer Science (GI) and the German Society of Medical Informatics, Biometry and Epidemiology (GMDS). Integrating, processing and applying the rapidly expanding information generated in the life sciences — from public health to clinical care and molecular biology — is one of the most challenging problems that research in these fields is facing today. As the amounts of experimental data, clinical information and scientific knowledge increase, there is a growing need to promote interoperability of these resources, support formal analyses, and to pre-process knowledge for further use in problem solving and hypothesis formulation. The OBML workshop series pursues the aim of gathering scientists who research topics related to life science ontologies, to exchange ideas, discuss new results and establish relationships. The OBML group promotes the collaboration between ontologists, computer scientists, bio-informaticians and applied logicians, as well as the cooperation with physicians, biologists, biochemists and biometricians, and supports the establishment of this new discipline in research and teaching. Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies to science and medicine. A total of 14 papers were presented, and from these we selected four manuscripts for inclusion in this special issue. An interdisciplinary audience from all areas related to biomedical ontologies attended OBML 2010. In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences. The next event emphasizes the special topic of the ontology of phenotypes, in Berlin, Germany on October 6-7, 2011

Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.

BackgroundUsing knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. We showed that embedding the knowledge representation and question-answering abilities in an electronic textbook helped to engage student interest and improve learning. A natural question that arises from this success, and this paper's primary focus, is whether a similar approach is applicable across a range of life science textbooks. To answer that question, we considered four different textbooks, ranging from a below-introductory college biology text to an advanced, graduate-level neuroscience textbook. For these textbooks, we investigated the following questions: (1) To what extent is knowledge shared between the different textbooks? (2) To what extent can the same upper ontology be used to represent the knowledge found in different textbooks? (3) To what extent can the questions of interest for a range of textbooks be answered by using the same reasoning mechanisms?ResultsOur existing modeling and reasoning methods apply especially well both to a textbook that is comparable in level to the text studied in our previous work (i.e., an introductory-level text) and to a textbook at a lower level, suggesting potential for a high degree of portability. Even for the overlapping knowledge found across the textbooks, the level of detail covered in each textbook was different, which requires that the representations must be customized for each textbook. We also found that for advanced textbooks, representing models and scientific reasoning processes was particularly important.ConclusionsWith some additional work, our representation methodology would be applicable to a range of textbooks. The requirements for knowledge representation are common across textbooks, suggesting that a shared semantic infrastructure for the life sciences is feasible. Because our representation overlaps heavily with those already being used for biomedical ontologies, this work suggests a natural pathway to include such representations as part of the life sciences curriculum at different grade levels

Analytic Metaphysics versus Naturalized Metaphysics: The Relevance of Applied Ontology

The relevance of analytic metaphysics has come under criticism: Ladyman & Ross, for instance, have suggested do discontinue the field. French & McKenzie have argued in defense of analytic metaphysics that it develops tools that could turn out to be useful for philosophy of physics. In this article, we show first that this heuristic defense of metaphysics can be extended to the scientific field of applied ontology, which uses constructs from analytic metaphysics. Second, we elaborate on a parallel by French & McKenzie between mathematics and metaphysics to show that the whole field of analytic metaphysics, being useful not only for philosophy but also for science, should continue to exist as a largely autonomous field

From Affective Science to Psychiatric Disorder: Ontology as Semantic Bridge

Advances in emotion and affective science have yet to translate routinely into psychiatric research and practice. This is unfortunate since emotion and affect are fundamental components of many psychiatric conditions. Rectifying this lack of interdisciplinary integration could thus be a potential avenue for improving psychiatric diagnosis and treatment. In this contribution, we propose and discuss an ontological framework for explicitly capturing the complex interrelations between affective entities and psychiatric disorders, in order to facilitate mapping and integration between affective science and psychiatric diagnostics. We build on and enhance the categorisation of emotion, affect and mood within the previously developed Emotion Ontology, and that of psychiatric disorders in the Mental Disease Ontology. This effort further draws on developments in formal ontology regarding the distinction between normal and abnormal in order to formalize the interconnections. This operational semantic framework is relevant for applications including clarifying psychiatric diagnostic categories, clinical information systems, and the integration and translation of research results across disciplines

Two Approaches to the Identity of Processes in BFO

This paper aims to explore processes and their identity with a focus on the upper ontology Basic Formal Ontology (BFO). We begin with a classification based on two basic classes of changes of independent continuants: changes with respect to a single specifically dependent continuant thereof or with respect to the spatial region that its parts occupy. We accordingly distinguish two kinds of simple processes: specifically dependent continuant changes and spatial changes. Next, we investigate a compositional approach to the identity of processes: the identity of any process is determined by the identity of the simple processes that compose them. Then, we consider a causal approach to the identity of processes with recourse to a dispositional view of processes according to which any process is a realization of some disposition. We also examine assumptions on which these two approaches to the identity of processes are based

Broadening Humor: Comic Styles Differentially Tap into Temperament, Character, and Ability

The present study introduces eight comic styles (i.e., fun, humor, nonsense, wit, irony, satire, sarcasm, and cynicism) and examines the validity of a set of 48 marker items for their assessment, the Comic Style Markers (CSM). These styles were originally developed to describe literary work and are used here to describe individual differences. Study 1 examines whether the eight styles can be distinguished empirically, in self- and other-reports, and in two languages. In different samples of altogether more than 1500 adult participants, the CSM was developed and evaluated with respect to internal consistency, homogeneity, test–retest reliability, factorial validity, and construct and criterion validity. Internal consistency was sufficiently high, and the median test-retest reliability over a period of 1–2 weeks was 0.86 (N = 148). Exploratory and confirmatory factor analyses showed that the eight styles could be distinguished in both English- (N = 303) and German-speaking samples (N = 1018 and 368). Comparing self- and other-reports (N = 210) supported both convergent and discriminant validity. The intercorrelations among the eight scales ranged from close to zero (between humor and sarcasm/cynicism) to large and positive (between sarcasm and cynicism). Consequently, second-order factor analyses revealed either two bipolar factors (based on ipsative data) or three unipolar factors (based on normative data). Study 2 related the CSM to instruments measuring personality (N = 999), intelligence (N = 214), and character strengths (N = 252), showing that (a) wit was the only style correlated with (verbal) intelligence, (b) fun was related to indicators of vitality and extraversion, (c) humor was related to character strengths of the heart, and (d) comic styles related to mock/ridicule (i.e., sarcasm, cynicism, but also irony) correlated negatively with character strengths of the virtues temperance, transcendence, and humanity. By contrast, satire had a moral goodness that was lacking in sarcasm and cynicism. Most importantly, the two studies revealed that humor might be related to a variety of character strengths depending on the comic style utilized, and that more styles may be distinguished than has been done in the past. The CSM is recommended for future explorations and refinements of comic styles

Broadening humor: comic styles differentially tap into temperament, character, and ability

The present study introduces eight comic styles (i.e., fun, humor, nonsense, wit, irony, satire, sarcasm, and cynicism) and examines the validity of a set of 48 marker items for their assessment, the Comic Style Markers (CSM). These styles were originally developed to describe literary work and are used here to describe individual differences. Study 1 examines whether the eight styles can be distinguished empirically, in self- and other-reports, and in two languages. In different samples of altogether more than 1500 adult participants, the CSM was developed and evaluated with respect to internal consistency, homogeneity, test–retest reliability, factorial validity, and construct and criterion validity. Internal consistency was sufficiently high, and the median test-retest reliability over a period of 1–2 weeks was 0.86 (N = 148). Exploratory and confirmatory factor analyses showed that the eight styles could be distinguished in both English- (N = 303) and German-speaking samples (N = 1018 and 368). Comparing self- and other-reports (N = 210) supported both convergent and discriminant validity. The intercorrelations among the eight scales ranged from close to zero (between humor and sarcasm/cynicism) to large and positive (between sarcasm and cynicism). Consequently, second-order factor analyses revealed either two bipolar factors (based on ipsative data) or three unipolar factors (based on normative data). Study 2 related the CSM to instruments measuring personality (N = 999), intelligence (N = 214), and character strengths (N = 252), showing that (a) wit was the only style correlated with (verbal) intelligence, (b) fun was related to indicators of vitality and extraversion, (c) humor was related to character strengths of the heart, and (d) comic styles related to mock/ridicule (i.e., sarcasm, cynicism, but also irony) correlated negatively with character strengths of the virtues temperance, transcendence, and humanity. By contrast, satire had a moral goodness that was lacking in sarcasm and cynicism. Most importantly, the two studies revealed that humor might be related to a variety of character strengths depending on the comic style utilized, and that more styles may be distinguished than has been done in the past. The CSM is recommended for future explorations and refinements of comic styles

Hope as a Mediator between Professor-Student Rapport and Student Achievement

The United States experiences unfavorable outcomes in undergraduate academic achievement despite years of research, especially for historically marginalized students. Accepting that student achievement is the result of the complex interplay between individual and environmental characteristics, tertiary institutions seek useful levers by which to raise academic achievement. Previous research has established that the relationship between a teacher and student can affect student achievement, making professor-student rapport one of the aforementioned levers. However, the mechanism through which professor-student rapport acts remains unclear. The current study explores the mediating effect of hope on the relationship between professor-student rapport and achievement. Utilizing a quantitative correlational design, the researcher conducts a mediation analysis to determine if student hope has a significant mediating effect in a sample of 218 undergraduate students at a mid-sized university in the United States. Participants responded to a survey with demographic data and completed the Adult Dispositional Hope Scale and the Student–Instructor Rapport Scale-9. The total number of points in a specific course out of possible points was paired with participants’ survey data. Analysis of the data did not support the presence of a significant relationship between the mediator hope and the outcome variable achievement and therefore the conditions for mediation were not present. However, the researcher found that hope and rapport were significantly related. This research was completed during a global pandemic which may have confounded the results; therefore, this researcher recommends that it be replicated at another time when social restrictions are not in play