An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

This paper seeks to answer the question: Can contemporary forms of artificial intelligence be creative? To answer this question, I consider three conditions that are commonly taken to be necessary for creativity. These are novelty, value, and agency. I argue that while contemporary AI models may have a claim to novelty and value, they cannot satisfy the kind of agency condition required for creativity. From this discussion, a new condition for creativity emerges. Creativity requires curiosity, a motivation to pursue epistemic (...) goods. I argue that contemporary AI models do not satisfy this new condition. Because they lack both agency and curiosity, it is a mistake to attribute the same sort of creativity to AI that we prize in humans. Finally, I consider the question of whether these AI models stand to make human creativity in the arts and sciences obsolete, despite not being creative themselves. I argue, optimistically, that this is unlikely. (shrink)

I argue for an account of creativity that unifies creative achievements in the arts, sciences, and other domains and identifies its characteristic value. This account draws upon case studies of creative work in both the arts and sciences to identify creativity as a kind of successful exploration. I argue that if creativity is properly understood in this way, then it is fundamentally a property of processes, something only agents can achieve, something that comes in degrees, subjectively novel, and non-formulaic. As (...) I develop the account, I show how it avoids challenges faced by other accounts of creativity, especially concerning creativity’s value. Hills and Bird (2018, 2019) have together argued that creativity is not necessarily valuable. My account challenges this view. If I am right that creativity is a kind of successful exploration, then creativity does have a characteristic value, specifically epistemic value. (shrink)

In this paper I articulate a view of doxastic control that helps defend the legitimacy of our practice of blaming people for their beliefs. I distinguish between three types of doxastic control: intention-based, reason-based, and influence-based. First I argue that, although we lack direct intention-based control over our beliefs, such control is not necessary for legitimate doxastic blame. Second, I suggest that we distinguish two types of reason-responsiveness: sensitivity to reasons and appreciation of reasons. I argue that while both capacities (...) are necessary for satisfying the control condition, neither is sufficient. Finally, I defend an influence-based view of doxastic control according to which we have the capacity to execute intentions to engage in reflection that causally influences our beliefs in positive epistemic ways. This capacity is both necessary and sufficient for satisfying the control condition for legitimate doxastic blame. I end by defending the view from two objections: that reflection is not necessary for meeting the control condition, and that it is not sufficient. (shrink)

There is an underappreciated respect in which the widespread availability of generative artificial intelligence (AI) models poses a threat to human connection. My central contention is that human creativity is especially capable of helping us connect to others in a valuable way, but the widespread availability of generative AI models reduces our incentives to engage in various sorts of creative work in the arts and sciences. I argue that creative endeavors must be motivated by curiosity, and so they must disclose (...) the creative agent’s inquisitive self. It is through self-disclosure, including the disclosure of the inquisitive self, that we put ourselves in a position to be seen by and connect with others through our creative pursuits. Because relying on AI for certain generative tasks is less self-disclosive than the creative work such technologies supplant, this reliance threatens to weaken our connections to one another. (shrink)

In this paper, I solve a puzzle generated by three conflicting claims about the relationship between faith, belief, and control: according to the Identity Thesis, faith is a type of belief, and according to Fideistic Voluntarism, we sometimes have control over whether or not we have faith, but according to Doxastic Involuntarism, we never have control over what we believe. To solve the puzzle, I argue that the Identity Thesis is true, but that either Fideistic Voluntarism or Doxastic Voluntarism is (...) false, depending on how we understand "control." I distinguish two notions of control: direct intention-based control and indirect reflective control. I argue that though we have direct intention-based control over neither belief nor faith, we have indirect reflective control over each of them. Moreover, indirect reflective control helps explain how we can be held accountable for each. (shrink)

What is it for a _belief_ to wrong someone? Views that have largely shaped the recent literature on doxastic wronging maintain that beliefs that wrong do so in virtue of _what_ is believed. This paper offers some criticisms of these views, as well as a contractualist alternative. On the view I defend here, beliefs can wrong when they stem from inferences licensed by principles to which others would have sufficiently weighty objections. Doxastic wronging, on this account, is not (or is (...) not entirely) a matter of having beliefs with certain kinds of objectionable representational content, but rather a matter of our being unable to _morally justify_ our beliefs to others. (shrink)

In this chapter, we explore whether agents have an epistemic duty to eradicate implicit bias. Recent research shows that implicit biases are widespread and they have a wide variety of epistemic effects on our doxastic attitudes. First, we offer some examples and features of implicit biases. Second, we clarify what it means to have an epistemic duty, and discuss the kind of epistemic duties we might have regarding implicit bias. Third, we argue that we have an epistemic duty to eradicate (...) implicit biases that have negative epistemic impact. Finally, we defend this view against the objection that we lack the relevant control over implicit bias that’s required for such a duty. We argue that we have a kind of reflective control over the implicit biases that we are duty-bound to eradicate. And since, as we show, we have this control over a wide variety of implicit biases, there are a lot of implicit biases that we have epistemic duties to eradicate. (shrink)

Eleonore Stump insightfully develops Aquinas’s theodicy to account for a significant source of human suffering, namely the undermining of desires of the heart. Stump argues that what justifies God in allowing such suffering are benefits made available to the sufferer through her suffering that can defeat the suffering by contributing to the fulfillment of her heart’s desires. We summarize Stump’s arguments for why such suffering requires defeat and how it is defeated. We identify three problems with Stump’s account of how (...) such suffering is defeated and offer solutions to each. We defend and strengthen Stump’s response to the hardest cases for her view, and explain what her view demands of God. (shrink)

Numerous studies of the beliefs of people with anorexia nervosa (AN) suggest that a subset of such individuals may experience delusions. We first describe what makes a belief delusional and conclude that such characteristics can be appropriately applied to some beliefs of people with AN. Next, we outline how delusional beliefs may relate to the broader psychopathological process in AN, including: (1) they may be epiphenomenal; (2) they may be an initial partial cause of AN; (3) they may be caused (...) by aspects of AN; or (4) they may be sustaining causes, possibly involved in reciprocal causal relations with aspects of AN. We argue that there is good reason to believe that delusional beliefs of people with AN are not merely epiphenomenal, but rather that they’re causally connected to AN. Because of this, empirical studies can be designed to test for the presence of causal relations. We describe how these studies should be designed. The results of such studies have important implications for understanding the experience of individuals with AN and for the treatment of AN. We outline these implications. (shrink)

In a recent study, we found a negative association between psychopathy and violence against genetic relatives. We interpreted this result as a form of nepotism and argued that it failed to support the hypothesis that psychopathy is a mental disorder, suggesting instead that it supports the hypothesis that psychopathy is an evolved life history strategy. This interpretation and subsequent arguments have been challenged in a number of ways. Here, we identify several misunderstandings regarding the harmful dysfunction definition of mental disorder (...) as it applies to psychopathy and regarding the meaning of nepotism. Furthermore, we examine the evidence provided by our critics that psychopathy is associated with other disorders, and we offer a comment on their alternative model of psychopathy. We conclude that there remains little evidence that psychopathy is the product of dysfunctional mechanisms. (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)

This article seeks to describe in general terms what has become the standard way of conceptualizing moral injury in the clinical psychological and psychiatric literature, which is the key source for applications of the concept in other domains. What we call “the standard model” draws on certain assumptions about beliefs, mental states, and emotions as well as an implicit theory of causation about how various forms of harm arise from certain experiences or “events” that violate persons’ moral beliefs and systems. (...) Our analysis makes these assumptions more explicit and subjects them to critical scrutiny. In so doing, we survey the current literature and identify basic features of how moral injuries are defined, how they are thought to occur, and the forms of treatment or repair that appear to be indicated. We caution that it matters how moral experience is characterized and argue that an alternative understanding of what is the moral in moral injury is important for overcoming critical challenges to the standard model. Moreover, recently evolving approaches to moral repair could be more consistent with an alternative model. Our concluding suggestion is that a more robust account of the nature of moral experience and its relations to self-identity and social experience more generally could advance understanding of the etiology of moral injury and promote rehabilitation. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

The predominant account of the etiology of moral injuries among Veterans and military personnel in the clinical psychological and psychiatric literature construes morality as inherent in belief structures. This supports the conceptualization of moral injuries as intrapsychic phenomena resulting from exposure to high-stakes events in which fixed beliefs are contravened in ways that result in psychological harms, including maladaptive beliefs and distress. We identify several problems with this formulation and offer suggestions for modification, including greater focus on: 1) experiences rather (...) than events in identifying circumstances in which moral injuries occur, and 2) degradation of relevant relationships rather than conflicts with and among moral contents. These shifts in framing could have epidemiological salience, facilitating more robust case characterization and enabling a variety of approaches to reestablishing the moral conditions that support life affirmation. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

This article is about a very important metaphysical concept, macrocosm/microcosm and its appearance in Doric thought which in turn influenced Socrates and Plato. But since this concept has been gainsaid and negated in recent articles and distorted by some ancient thinkers it will be necessary to conduct reconstructive surgery to restore it to its pristine condition. Hopefully, this paper will illustrate how metaphysics is done with the use of the Mind's eye, in the reading of reality that was part and (...) parcel of the Greek mind but also in understanding the ancient Greeks themselves and their culture especially in the creation of the classical republican form of government. This account will discuss what macrocosm/microcosm is, its part in the Cosmos and hence its centrality in the Natural Law and in philosophy (wisdom). Second, it will prove the concept thru another natural law principle, righteousness. Third, point out it's provenance in Doric thought. In a corollary, it points to what the impact macrocosm/microcosm has on the true meaning "to be a lover of wisdom" and its importance in the concept of theosis. More than a research/academic article, this paper is also an exposition in which it will attempt to demonstrate the use and the mechanics of this principle by using a saying of Homer and the tripartite paradigm of the family. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Batı’da teorik felsefe; Analitik Felsefe (AF), Kıta Felsefesi (KF) ve Felsefe Tarihi (FT) olmak üzere üçe ayrılır. Fakat üçünde de işler yolunda değildir. AF, felsefenin bir bilim olabileceği iddiasından kuşku duyduğu için gerçek dünyayla ilgilenmiyorken başından beri uygun bir teorik yöntem izlemeyen Kıta Felsefesinin uygulanışı, belirli politik ve etik yargılara hizmet edecek şekilde özelleştirilmiştir. FT çalışmalarının gidişatı ise eldeki eserin nesnel değerinden daha çok ilgili filozofun ait olduğu ulus veya kültüre göre bölgesel bir temelde gelişmiştir. Felsefede ilerleme sağlanacaksa bu ancak (...) bahsi geçen tuzaklardan kaçınılarak gerçekleşebilir. (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)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are (...) designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (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.

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (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)

There is something puzzling about statistical evidence. One place this manifests is in the law, where courts are reluctant to base affirmative verdicts on evidence that is purely statistical, in spite of the fact that it is perfectly capable of meeting the standards of proof enshrined in legal doctrine. After surveying some proposed explanations for this, I shall outline a new approach – one that makes use of a notion of normalcy that is distinct from the idea of statistical frequency. (...) The puzzle is not, however, merely a legal one. Our unwillingness to base beliefs on statistical evidence is by no means limited to the courtroom, and is at odds with almost every general principle that epistemologists have proposed as to how we ought to manage our beliefs. (shrink)