It is argued, on the basis of ideas derived from Wittgenstein's Tractatus and Husserl's Logical Investigations, that the formal comprehends more than the logical. More specifically: that there exist certain formal-ontological constants (part, whole, overlapping, etc.) which do not fall within the province of logic. A two-dimensional directly depicting language is developed for the representation of the constants of formal ontology, and means are provided for the extension of this language to enable the representation of certain materially necessary relations. The (...) paper concludes with a discussion of the relationship between formal logic, formal ontology, and mathematics. (shrink)

How, as Caldwell puts it, does one choose between rival systems all of which claim to rest on a priori foundations? On the nonfallibilistic conception it is difficult to make sense even of the possibility of rival systems of this sort. On the conception here defended, in contrast, the existence of such rival systems can be seen to be a perfectly natural and acceptable consequence of the just-mentioned difficulties we will often fact in coming to know even the intelligible traits (...) of reality: one adjudicates between such systems in the same way in which one adjudicates between all rival scientific hypotheses, namely via a complex mixture of empirical and a priori considerations. (shrink)

Bence Nanay, in Aesthetics as Philosophy of Perception, and Murray Smith, in Film, Art, and the Third Culture, have given us a pair of rich and interesting works about the relationships between aesthetics and the sciences of mind. Nanay’s work focuses on perception and attention, while Smith’s addresses the relations among experiential, psychological, and neuroscientific understandings of a wide range of aesthetically relevant phenomena, particularly as they occur in film. These books make a valuable contribution to a (...) project that remains fledgling: that of taking seriously the relevance of the sciences to our conceptions and explanations of experiential phenomena in aesthetics and the philosophy of art. I will focus on a specific issue from each of these works. Nanay offers an account of aesthetic experience that ties it closely to the concepts of focused and distributed attention that are invoked in the sciences of perception. While I agree with Nanay that attention should play a central role in accounts of aesthetic experience, I raise questions about his specific account of the relationship. With Smith, we zoom out to a broader issue, that of the mutual explanatory relationships among phenomenological, functional/cognitive, and neurophysiological observations in our aesthetic theorizing. Smith makes a strong claim that all three of these levels are essential and irreducible, and none is subsidiary to the others. I argue that given the current state of the science, we should not regard neurophysiological observations as being on a par with observations at the other two levels. I also raise some doubts about the prospect of neurophysiological data making an independent contribution to aesthetic theorizing, even once the science is far more advanced. (shrink)

In Film, Art and the Third Culture, Murray Smith articulates and defends a naturalized aesthetics of film that exemplifies a “third culture,” integrating the insights and methods of the natural sciences with those of the arts and humanities. By contrast with skeptics who reject the relevance of psychology or neuroscience to the study of film and art, I agree with Smith that we should embrace the third-cultural project. However, I argue that Smith does not go far (...) enough in in developing this project. In defending the contribution of the natural sciences to film aesthetics as traditionally conceived in the arts and humanities, Smith focuses on only one side of the equation, unduly limiting the potential contribution of the arts and humanities to the scientific study of film. Using the example of emotional responses to fiction film, I propose that we adopt a more genuinely integrative approach. (shrink)

Philosophy has long either dismissed or paid only minimal attention to creativity, and even with the rise of research on imagination, the creative imagination has largely been ignored as well. The aim of this volume is to correct this neglect. By bringing together existing research in various sub-disciplines, we also aim to open up new avenues of research. The chapters in Part I provide some framing and history on the philosophical study of imagination and creativity, along with an overview of (...) the empirical literature. Part II explores imagination and creativity as they manifest in, and in turn shape, the individual. Part III surveys the role of imagination and creativity across a wide variety of artistic domains, and the chapters of Part IV turn to societal domains. Part V focuses on the interplay of imagination and creativity with regard to particular features of creative subjects and different kinds of creative subjects. *** -/- Part I: Theories and Approaches 1. Theories of Imagination (Peter Kung) 2. Theories of Creativity (Julia Langkau) 3. Historical Treatments of Imagination in the Western Tradition (Lucia Oliveri) 4. Historical Treatments of Creativity in the Western Tradition (Elliot Paul) 5. Non-Western Treatments of Imagination (Reza Hadisi and Jing Iris Hu) 6. Non-Western Treatments of Creativity (Nicolas B. Verger and Vlad Glăveanu) 7. Empirical Treatments of Imagination and Creativity (Dustin Stokes) 8. Experimental Philosophy of Imagination and Creativity (Michael T. Stuart) 9. The Relationship between Imagination and Creativity (Margherita Arcangeli) -/- Part II: Imagination and Creativity in Mind and Action 10. Imagination, Creativity, and Skill (Amy Kind) 11. Imagination, Creativity, and Attention (Bence Nanay) 12. Imagination, Creativity, and Agency (Caterina Moruzzi) 13. Imagination, Creativity, and Emotion (Julien Deonna and Fabrice Teroni) 14. Imagination, Creativity, and Embodiment (Adriana Clavel-Vázquez and María Jimena Clavel Vázquez) 15. Imagination, Creativity, and Gender (Luke Roelofs) 16. Imagination, Creativity, and Race (Nicholas Whittaker) 17. Imagination, Creativity, and Child Development (Thalia Goldstein, Anna Sofia Caruso, Darian Stapleton, and Lamin Fatty) -/- Part III: Imagination and Creativity in the Arts 18. Imagination, Creativity, and the Visual Arts (Claire Anscomb) 19. Imagination, Creativity, and Music (Matteo Ravasio) 20. Imagination, Creativity, and Fiction (Hannah H. Kim) 21. Imagination, Creativity, and Dance (David Davies and Anna Pakes) 22. Imagination, Creativity, and the Culinary Arts (Patrik Engisch) 23. Imagination, Creativity, and Film (Murray Smith) 24. Imagination, Creativity, and Acting (Tzachi Zamir) 25. Imagination, creativity, and fashion (Laura T. Di Summa) -/- Part IV: Imagination and Creativity in Society 26. Imagination and Creativity in the Scientific Realm (Alice Murphy) 27. Imagination and Creativity in the Moral Realm (Tim Mulgan) 28. Imagination and Creativity in the Political Realm (Avshalom Schwartz) 29. Imagination and Creativity in the Law (Maksymilian Del Mar) 30. Imagination and Creativity in the Religious Realm (Neil Van Leeuwen) 31. Imagination and Creativity in Business (Eric Peterson) 32. Imagination and Creativity in Times of Crisis (Jennifer Fraser and Noah Stemeroff) Part V: Emerging Issues in Imagination and Creativity Research 33. Imagination, Creativity, and Aphantasia (Andrea Blomkvist) 34. Imagination, Creativity, and Neurodivergence (Sofia Ortiz-Hinojosa) 35. Imagination, Creativity, and Non-Human Animals (Henry Shevlin) 36. Imagination, Creativity, and Artificial Intelligence (Peter Langland-Hassan) 37. Collective Imagination and Collective Creativity (Nick Wiltsher) . (shrink)

My primary target in this paper is a puzzle that emerges from the conjunction of several seemingly innocent assumptions in action theory and the metaphysics of moral responsibility. The puzzle I have in mind is this. On one widely held account of moral responsibility, an agent is morally responsible only for those actions or outcomes over which that agent exercises control. Recently, however, some have cited cases where agents appear to be morally responsible without exercising any control. This leads some (...) to abandon the control-based account of responsibility and replace it with an alternative account. It leads others to deny the intuition that agents are responsible in these troublesome cases. After outlining the account of moral responsibility I have in mind, I look at some of the arguments made against the viability of this theory. I show that there are conceptual resources for salvaging the control account, focusing in particular on the nature of vigilance. I also argue that there is empirical data that supports the control account so conceived. (shrink)

Loyalty is considered central to people’s moral life, yet little is known about how people think about what it means to be loyal. We used a prototype approach to understand how loyalty is represented in Colombia and the United States and how these representations mediate attributions of loyalty and moral judgments of loyalty violations. Across 7 studies (N = 1,984), we found cross-cultural similarities in the associative meaning of loyalty (Study 1) but found differences in the centrality of features associated (...) with loyalty (Study 2) and the latent structure of loyalty representations (Study 3). Colombians represent loyalty in terms of more general moral characteristics, while US participants represent loyalty in terms of interpersonal commitment, both in contrast with current approaches to loyalty. By comparing representations of loyalty and honesty, we establish that difference in loyalty conceptualizations reflect a different way of thinking about loyalty rather than morality more generally (Study 4). Further, Colombians attributed greater loyalty to individuals with general moral characteristics compared to participants from the United States sample (Study 5) and were more likely to classify non-loyal values as loyalty-related (Study 6). While the centrality of prototypical features predicts categorizing norm violations as loyalty-related, differences in prototypical structure account for differences in the severity of moral judgment for such violations (Study 7), which suggests that loyalty representations have similar functions even though these representations differ in structural characteristics. (shrink)

We sometimes fail unwittingly to do things that we ought to do. And we are, from time to time, culpable for these unwitting omissions. We provide an outline of a theory of responsibility for unwitting omissions. We emphasize two distinctive ideas: (i) many unwitting omissions can be understood as failures of appropriate vigilance, and; (ii) the sort of self-control implicated in these failures of appropriate vigilance is valuable. We argue that the norms that govern vigilance and the value of self-control (...) explain culpability for unwitting omissions. (shrink)

Some research suggests that moral behavior can be strongly influenced by trivial features of the environment of which we are completely unaware. Philosophers, psychologists, and neuroscientists have argued that these findings undermine our commonsense notions of agency and responsibility, both of which emphasize the role of practical reasoning and conscious deliberation in action. We present the results of four vignette-based studies (N = 1,437) designed to investigate how people think about the metaphysical and moral implications of scientific findings that reveal (...) our susceptibility to automaticity and situational influences. When presented with lightly fictionalized narratives about these findings, participants exhibit no tendency toward changing judgments of freedom and responsibility compared to control groups. This suggests that people seem unwilling to adopt skeptical attitudes about agency on the basis of these scientific findings. (shrink)

In this paper, we focus on whether and to what extent we judge that people are responsible for the consequences of their forgetfulness. We ran a series of behavioral studies to measure judgments of responsibility for the consequences of forgetfulness. Our results show that we are disposed to hold others responsible for some of their forgetfulness. The level of stress that the forgetful agent is under modulates judgments of responsibility, though the level of care that the agent exhibits toward performing (...) the forgotten action does not. We argue that this result has important implications for a long-running debate about the nature of responsible agency. (shrink)

The third Meditation is typically understood to contain two a posteriori arguments for the existence of God. The author focuses on the second argument, where Descartes proves the existence of God partly in virtue of proving that Descartes cannot be the cause of himself. To establish this, Descartes argues that if he were the cause of himself, then he would endow himself with any conceivable perfection. The justification for this claim is that bringing about a substance is more difficult than (...) creating an attribute, so anything that can do the former can do the latter. While current explanations of this justification are either implausible or inadequate, the author argues that this principle derives support from a scholastic distinction between being-as-such and determinate being. With this distinction in view, we can make sense of Descartes's argument without appealing to ambiguous or inadequate notions. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Mind wandering is typically operationalized as task-unrelated thought. Some argue for the need to distinguish between unintentional and intentional mind wandering, where an agent voluntarily shifts attention from task-related to task-unrelated thoughts. We reveal an inconsistency between the standard, task-unrelated thought definition of mind wandering and the occurrence of intentional mind wandering (together with plausible assumptions about tasks and intentions). This suggests that either the standard definition of mind wandering should be rejected or that intentional mind wandering is an incoherent (...) category. Solving this puzzle is critical for advancing theoretical frameworks of mind wandering. (shrink)

Judgments of blame for others are typically sensitive to what an agent knows and desires. However, when people act negligently, they do not know what they are doing and do not desire the outcomes of their negligence. How, then, do people attribute blame for negligent wrongdoing? We propose that people attribute blame for negligent wrongdoing based on perceived mental control, or the degree to which an agent guides their thoughts and attention over time. To acquire information about others’ mental control, (...) people self-project their own perceived mental control to anchor third-personal judgments about mental control and concomitant responsibility for negligent wrongdoing. In four experiments (N = 841), we tested whether perceptions of mental control drive third-personal judgments of blame for negligent wrongdoing. Study 1 showed that the ease with which people can counterfactually imagine an individual being non-negligent mediated the relationship between judgments of control and blame. Studies 2a and 2b indicated that perceived mental control has a strong effect on judgments of blame for negligent wrongdoing and that first-personal judgments of mental control are moderately correlated with third-personal judgments of blame for negligent wrongdoing. Finally, we used an autobiographical memory manipulation in Study 3 to make personal episodes of forgetfulness salient. Participants for whom past personal episodes of forgetfulness were made salient judged negligent wrongdoers less harshly compared to a control group for whom past episodes of negligence were not salient. Collectively, these findings suggest that first-personal judgments of mental control drive third-personal judgments of blame for negligent wrongdoing and indicate a novel role for counterfactual thinking in the attribution of responsibility. (shrink)

To manage conflicts between temptation and commitment, people use self-control. The process model of self-control outlines different strategies for managing the onset and experience of temptation. However, little is known about the decision-making factors underlying strategy selection. Across three experiments (N = 317), we tested whether the moral valence of a commitment predicts how people advise attentional self-control strategies. In Experiments 1 and 2, people rated attentional focus strategies as significantly more effective for people tempted to break moral relative to (...) immoral commitments, even when controlling for perceived temptation and trait self-control. Experiment 3 showed that as people perceived commitments to have more positive moral valence, they judged attentional focus strategies to be significantly more effective relative to attentional distraction strategies. Moreover, this effect was partly mediated by perceived differences in motivation. These results indicate that moralization informs decision-making processes related to self-control strategy selection. (shrink)

In recent years, the number of studies examining mind wandering has increased considerably, and research on the topic has spread widely across various domains of psychological research. Although the term “mind wandering” has been used to refer to various cognitive states, researchers typically operationalize mind wandering in terms of “task-unrelated thought” (TUT). Research on TUT has shed light on the various task features that require people’s attention, and on the consequences of task inattention. Important methodological and conceptual complications do persist, (...) however, in current investigations of TUT. As we argue, these complications may be dampening the development of a more nuanced scientific account of TUT. Here, we outline three of the more prominent methodological and conceptual complications in the literature on TUT, and we discuss potential directions for researchers to take as they move forward in their investigations of TUT. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

One popular theory of moral responsibility locates responsible agency in exercises of control. These control-based theories often appeal to tracing to explain responsibility in cases where some agent is intuitively responsible for bringing about some outcome despite lacking direct control over that outcome’s obtaining. Some question whether control-based theories are committed to utilizing tracing to explain responsibility in certain cases. I argue that reflecting on certain kinds of negligence shows that tracing plays an ineliminable role in any adequate control-based theory (...) of responsibility. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

According to the attentional resources account, mind wandering (or “task-unrelated thought”) is thought to compete with a focal task for attentional resources. Here, we tested two key predictions of this account: First, that mind wandering should not interfere with performance on a task that does not require attentional resources; second, that as task requirements become automatized, performance should improve and depth of mind wandering should increase. Here, we used a serial reaction time task with implicit- and explicit-learning groups to test (...) these predictions. Providing novel evidence for the attentional resource account’s first prediction, results indicated that depth of mind wandering was negatively associated with learning in the explicit, but not the implicit, group, indicating that mind wandering is associated with impaired explicit, but not implicit, learning. Corroborating the attention resource account’s second prediction, we also found that, overall, performance improved while at the same time depth of mind wandering increased. From an implicit learning perspective, these results are consistent with the claim that explicit learning is impaired under attentional load, but implicit learning is not. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Experimental work on free will typically relies on deterministic stimuli to elicit judgments of free will. We call this the Vignette-Judgment model. We outline a problem with research based on this model. It seems that people either fail to respond to the deterministic aspects of vignettes when making judgments or that their understanding of determinism differs from researcher expectations. We provide some empirical evidence for this claim. In the end, we argue that people seem to lack facility with the concept (...) of determinism, which calls into question the validity of experimental work operating under the Vignette-Judgment model. We also argue that alternative experimental paradigms are unlikely to elicit judgments that are philosophically relevant to questions about the metaphysics of free will. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

The science of mind wandering has rapidly expanded over the past 20 years. During this boom, mind wandering researchers have relied on self-report methods, where participants rate whether their minds were wandering. This is not an historical quirk. Rather, we argue that self-report is indispensable for researchers who study passive phenomena like mind wandering. We consider purportedly “objective” methods that measure mind wandering with eye tracking and machine learning. These measures are validated in terms of how well they predict self-reports, (...) which means that purportedly objective measures of mind wandering retain a subjective core. Mind wandering science cannot break from the cycle of self-report. Skeptics about self-report might conclude that mind wandering science has methodological foundations of sand. We take a rather more optimistic view. We present empirical and philosophical reasons to be confident in self-reports about mind wandering. Empirically, these self-reports are remarkably consistent in their contents and behavioral and neural correlates. Philosophically, self-reports are consistent with our best theories about the function of mind wandering. We argue that this triangulation gives us reason to trust both theory and method. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

In the graphical representation of ontologies, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations. We focus here on a problem in the graph-based representation of ontologies in complex domains such as biomedical, engineering and manufacturing: lack of mereotopological representation. Based on such limitation, we proposed a diagrammatic way to represent an entity’s structure and various forms of mereotopological relationships between the entities.

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

There have long been calls from industry for guidance in implementing strategies for sustainable development. The Circular Economy represents the most recent attempt to conceptualize the integration of economic activity and environmental wellbeing in a sustainable way. This set of ideas has been adopted by China as the basis of their economic development, escalating the concept in minds of western policymakers and NGOs. This paper traces the conceptualisations and origins of the Circular Economy, tracing its meanings, and exploring its antecedents (...) in economics and ecology, and discusses how the Circular Economy has been operationalized in business and policy. The paper finds that while the Circular Economy places emphasis on the redesign of processes and cycling of materials, which may contribute to more sustainable business models, it also encapsulates tensions and limitations. These include an absence of the social dimension inherent in sustainable development that limits its ethical dimensions, and some unintended consequences. This leads us to propose a revised definition of the Circular Economy as “an economic model wherein planning, resourcing, procurement, production and reprocessing are designed and managed, as both process and output, to maximize ecosystem functioning and human well-being”. (shrink)

In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant to the (...) Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some (...) of its anticipated uses. (shrink)

Does self-control require willpower? The question cuts to the heart of a debate about whether self-control is identical with some psychological process internal to the agents or not. Noticeably absent from these debates is systematic evidence about the folk-psychological category of self-control. Here, we present the results of two behavioral studies (N = 296) that indicate the structure of everyday use of the concept. In Study 1, participants rated the degree to which different strategies to respond to motivational conflict exemplify (...) self-control. Participants distinguished between intra-psychic and externally-scaffolded strategies and judged that the former exemplified self-control more than the latter. In Study 2, participants provided various solutions to manage motivational conflict and rated their proposals on effectiveness. Participants produced substantially more intra-psychic strategies, rated them as more effective, and advised them at a higher rate than externally-scaffolded strategies. Taken together, these results suggest that while people recognize a plurality of strategies as genuine instances of self-control, purely internal exercises of self-control are considered more prototypical than their externally-scaffolded counterparts. This implies a hierarchical structure for the folk psychological category of self-control. The concept encompasses a variety of regulatory strategies and organizes these strategies along a hierarchical continuum, with purely intra-psychic strategies at the center and scaffolded strategies in the periphery. (shrink)

We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude with a description of how the (...) body fluids ontology initiative may provide support to basic and translational science. (shrink)

In the management of biomedical data, vocabularies such as ontologies and terminologies (O/Ts) are used for (i) domain knowledge representation and (ii) interoperability. The knowledge representation role supports the automated reasoning on, and analysis of, data annotated with O/Ts. At an interoperability level, the use of a communal vocabulary standard for a particular domain is essential for large data repositories and information management systems to communicate consistently with one other. Consequently, the interoperability benefit of selecting a particular O/T as a (...) standard for data exchange purposes is often seen by the end-user as a function of the number of applications using that vocabulary (and, by extension, the size of the user base). Furthermore, the adoption of an O/T as an interoperability standard requires confidence in its stability and guaranteed continuity as a resource. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Electronic health records (EHRs) serve as repositories of documented data collected in a health care encounter. An EHR records information about who receives, who provides the health care and about the place where the encounter happens. We also observe additional elements relating to social relations in which the healthcare consumer is involved. To provide a consensus representation of common data and to enhance interoperability between different EHR repositories we have created a solution grounded in formal ontology. Here, we present how (...) an ontology for the obstetric and neonatal domain deals with these general elements documented in health care encounters. Our goal is to promote the interoperability of information among EHRs created in different specialties. To develop our ontology, we used two main approaches: one based on ontological realism, the other based on the principles of the OBO Foundry, including reuse of reference ontologies. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)