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 is a review article on Franz Brentano’s Descriptive Psychology published in 1982. We provide a detailed exposition of Brentano’s work on this topic, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based (...) multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration. (shrink)

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

The topic of fake news has received increased attention from philosophers since the term became a favorite of politicians (Habgood-Coote 2016; Dentith 2016). Notably missing from the conversation, however, is a discussion of fake news and conspiracy theory media as a market. This paper will take as its starting point the account of noxious markets put forward by Debra Satz (2010), and will argue that there is a pro tanto moral reason to restrict the market for fake news. Specifically, we (...) begin with Satz’s argument that restricting a market may be required when i) that market inhibits citizens from being able to stand in an equal relationship with one another, and ii) this problem cannot be solved without such direct restrictions. Our own argument then proceeds in three parts: first, we argue that the market for fake news fits Satz’s description of a noxious market; second, we argue against explanations of the proliferation of fake news that are couched in terms of “epistemic vice”, and likewise argue against prescribing critical thinking education as a solution to the problem; finally, we conclude that, in the absence of other solutions to mitigate the noxious effects of the fake news market, we have a pro tanto moral reason to impose restrictions on this market. At the end of the paper, we consider one proposal to regulate the fake news market, which involves making social media outlets potentially liable in civil court for damages caused by the fake news hosted on their websites. (shrink)

A number of logicians and philosophers have turned their attention in recent years to the problem of developing a logic of interrogatives. Their work has thrown a great deal of light on the formal properties of questions and question-sentences and has led also to interesting innovations in our understanding of the structures of performatives in general and, for example, in the theory of presuppositions. When, however, we examine the attempts of logicians such as Belnap or Åqvist to specify what, precisely, (...) a question is, or what it is to ask or raise a question, then what we are offered is somewhat less illuminating. Two alternative reductionist accounts seem in particular to have gained most favor: questions are identified either as special sorts of statements, or as special sorts of requests. As we hope will become clear in what follows, neither of these accounts is even nearly adequate; and matters are not improved if questions are identified, by force majeure, as combinations of statements and requests. (shrink)

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

I argue that propaganda does not characteristically interfere with individual rationality, but instead with group agency. Whereas it is often claimed that propaganda involves some sort of incitement to irrationality, I show that this is neither necessary nor sufficient for a case’s being one or propaganda. For instance, some propaganda constitutes evidence of the speaker’s power, or else of the risk and futility of opposing them, and there is nothing irrational about taking such evidence seriously. I outline an alternative account (...) of propaganda inspired by Hannah Arendt, on which propaganda characteristically creates or destroys group agency. One aspiring to control the public should have an interest in both creating and suppressing group agency, I argue, both because groups have capacities that individuals don’t, and because participation in group action can have a transformative effect upon the individual. Finally, I suggest that my characterization of propaganda suggests a vision of resistance to propaganda quite unlike the one that emerges from irrational-belief accounts, on which propaganda cannot be resisted by oneself. (shrink)

The philosophical “problem of evil” goes back at least as far as Epicurus and has remained a powerful argument against the existence of God in contemporary philosophy. The argument is rooted in apparent contradictions between God’s divine attributes and various conditions of human existence. But these contradictions arise only given certain assumptions of what we should expect both God and the world to be like given God’s existence. In this paper, I argue that we can utilize the work of the (...) 20th century French philosopher Simone Weil to craft a coherent metaphysical picture of God, creation, and suffering which rejects these common assumptions. Further, I contend that this picture very plausibly follows from commonly-accepted tenets of traditional monotheism. Given this, I argue that this Weil-inspired framework provides serious reasons for reframing the problem of evil and its corresponding theodicies by presenting a radically different view of how God must relate to creation. Yet, this picture does not necessarily vindicate the theist. I argue that this picture may leave us with a new question about creation in the face of evil. Namely, is it possible to understand God’s initial creative act as Weil describes it—as an act of love? (shrink)

In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.

According to a recent survey by the HR Research Institute, as the presence of artificial intelligence (AI) becomes increasingly common in the workplace, HR professionals are worried that the use of recruitment algorithms will lead to a “dehumanization” of the hiring process. Our main goals in this paper are threefold: i) to bring attention to this neglected issue, ii) to clarify what exactly this concern about dehumanization might amount to, and iii) to sketch an argument for why dehumanizing the hiring (...) process is ethically suspect. After distinguishing the use of the term “dehumanization” in this context (i.e., removing the human presence) from its more common meaning in the interdisciplinary field of dehumanization studies (i.e., conceiving of other humans as subhuman), we argue that the use of hiring algorithms may negatively impact the employee-employer relationship. We argue that there are good independent reasons to accept a substantive employee-employer relationship, as well as an applicant-employer relationship, both of which are consistent with a stakeholder theory of corporate obligations. We further argue that dehumanizing the hiring process may negatively impact these relationships because of the difference between the values of human recruiters and the values embedded in recruitment algorithms. Drawing on Nguyen’s (2021) critique of how Twitter “gamifies communication”, we argue that replacing human recruiters with algorithms imports artificial values into the hiring process. We close by briefly considering some ways to potentially mitigate the problems posed by recruitment algorithms, along with the possibility that some difficult trade-offs will need to be made. (shrink)

Recent scholarship in intellectual humility (IH) has attempted to provide deeper understanding of the virtue as personality trait and its impact on an individual's thoughts, beliefs, and actions. A limitations-owning perspective of IH focuses on a proper recognition of the impact of intellectual limitations and a motivation to overcome them, placing it as the mean between intellectual arrogance and intellectual servility. We developed the Limitations-Owning Intellectual Humility Scale to assess this conception of IH with related personality constructs. In Studies 1 (...) (n= 386) and 2 (n = 296), principal factor and confirmatory factor analyses revealed a three-factor model – owning one's intellectual limitations, appropriate discomfort with intellectual limitations, and love of learning. Study 3 (n = 322) demonstrated strong test-retest reliability of the measure over 5 months, while Study 4 (n = 612) revealed limitations-owning IH correlated negatively with dogmatism, closed-mindedness, and hubristic pride and positively with openness, assertiveness, authentic pride. It also predicted openness and closed-mindedness over and above education, social desirability, and other measures of IH. The limitations-owning understanding of IH and scale allow for a more nuanced, spectrum interpretation and measurement of the virtue, which directs future study inside and outside of psychology. (shrink)

Johannes Daubert he was an acknowledged leader, and in some respects the founder, of the early phenomenological movement, and was considered – as much by its members as by Husserl himself – the most brilliant member of the group. In Daubert’s unpublished writings we find a series of reflections on Lask, and on Neo-Kantianism, which form the subject-matter of this paper. They range over topics such as the ontology of the ‘Sachverhalt’ or state of affairs, truthvalues (Wahrheitswerte) and the value (...) of truth, negative judgments and the copula, and the relation between perception and judgment. (shrink)

Digital Rights Management (DRM) covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of entities involved in this domain. Although the system has been very well designed to manage object identifiers, some important questions relating to the creation and assignment of identifiers are left open. The paradigm of a Referent Tracking System (RTS) recently advanced in the (...) healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the existing DOI models and by showing how they can be corrected using an RTS. (shrink)

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

Non-causal accounts of action explanation have long been criticized for lacking a positive thesis, relying primarily on negative arguments to undercut the standard Causal Theory of Action The Stanford Encyclopedia of Philosophy, 2016). Additionally, it is commonly thought that non-causal accounts fail to provide an answer to Donald Davidson’s challenge for theories of reasons explanations of actions. According to Davidson’s challenge, a plausible non-causal account of reasons explanations must provide a way of connecting an agent’s reasons, not only to what (...) she ought to do, but to what she actually does. That is, such explanations must be truth-apt, not mere rationalizations. My aim in this paper is to show how a non-causal account of action can provide explanations that are truth-apt and genuinely explanatory. To make this argument, I take as a given an account of the practical syllogism discussed by Michael Thompson and Eric Wiland, according to which the practical syllogism is truly practical rather than propositional in nature. Next, I present my primary positive thesis: reasons for actions have explanatory power in virtue of being parts of a structure—the practical syllogism—that contains the action being explained. I then argue that structural action explanations can meet Davidson’s challenge and that they genuinely explain actions. Finally, I conclude by addressing some objections to my argument. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

Contemporary action theory is generally concerned with giving theories of action ontology. In this paper, we make the novel proposal that the standard view in action theory—the Causal Theory of Action—should be recast as a “model”, akin to the models constructed and investigated by scientists. Such models often consist in fictional, hypothetical, or idealized structures, which are used to represent a target system indirectly via some resemblance relation. We argue that recasting the Causal Theory as a model can not only (...) accomplish the goals of causal theorists, but also give the theory greater flexibility in responding to common objections. (shrink)

Ingarden distinguishes four strata making up the structure of the literary work of art: the stratum of word sounds and sound-complexes; the stratum of meaning units; the stratum of represented objectivities (characters, actions, settings, and so forth); and the stratum of schematized aspects (perspectives under which the represented objectivities are given to the reader). It is not only works of literature which manifest this four-fold structure but also certain borderline cases such as newspaper articles, scientific works, biographies, and so forth. (...) Ingarden specifies what is characteristic of a work of literature by asserting that all declarative sentences appearing in the stratum of meaning units of such work possess what he calls a quasi-judgmental character. We discuss here Ingarden’s theory of quasi-judgments and draw out its implication that all works of literature are works of fiction through and through. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

According to many accounts, propaganda is a variety of politically significant signal with a distinctive connection to irrationality. This irrationality may be theoretical, or practical; it may be supposed that propaganda characteristically elicits this irrationality anew, or else that it exploits its prior existence. The view that encompasses such accounts we will call irrationalism. This essay presents two classes of propaganda that do not bear the sort of connection to irrationality posited by the irrationalist: hard propaganda and propaganda by the (...) deed. Faced with these counterexamples, some irrationalists will offer their account of propaganda as a refinement of the folk concept rather than as an attempt to capture all of its applications. The author argues that any refinement of the concept of propaganda must allow the concept to remain essentially political, and that the irrationalist refinement fails to meet this condition. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

In this paper, we examine how the availability of massive quantities of data i.e., the “Big Data” phenomenon, contributes to the creation, spread, and harms of online misinformation. Specifically, we argue that a factor in the problem of online misinformation is the evolved human instinct to recognize patterns. While the pattern-recognition instinct is a crucial evolutionary adaptation, we argue that in the age of Big Data, these capacities have, unfortunately, rendered us vulnerable. Given the ways in which online media outlets (...) profit from the spread of misinformation by preying on this pattern-finding instinct, we conceptualize the problem that we identify as a morally objectionable form of “epistemic exploitation.” As we argue, the consumer of digital misinformation is often exploited by having her pattern-recognition instinct used against her. This exploitation is morally objectionable because it deprives her of an epistemic good to which she has a right. This epistemic good is the integrity of the pattern-recognition instinct itself which, we argue, is a capacity that allows us to participate in uniquely human goods. While our primary goal is to bring attention to this form of epistemic exploitation, we conclude by briefly evaluating some general solutions to the growing problem of online misinformation. (shrink)

This paper takes up the question of how videographic public announcements (VPAs)---i.e. videos that a wide swath of the public sees and knows that everyone else can see too--- have functioned to mobilize people politically, and how the presence of deepfakes in our information environment stands to change the dynamics of this mobilization. Existing work by Regina Rini, Don Fallis and others has focused on the ways that deepfakes might interrupt our acquisition of first-order knowledge through videos. But I point (...) out that even where every audience member takes a video to be veridical, where first-order knowledge acquisition is secure, an audience aware of deepfakes in their environment will not acquire higher order knowledge in the way that has erstwhile been characteristic for audiences of VPAs. Engaging with ideas from the literatures on public announcement logic, common knowledge, and convention, I enumerate a variety of ways in which we should expect this absence of higher order knowledge to throw up barriers to political mobilization. I go on to apply my analysis of VPAs to the mechanisms by which an uptick in publicly available videos of police brutality over the last decade, mediated by camera phones and social media, was responsible for the largest mass protests in US history in summer 2020. This makes vivid the stakes of the transformation in our mobilizing environment that I've claimed deepfakes effect: where we lose the common-knowledge-generating effects of VPAs, there are fresh obstacles to this sort of mass mobilization. (shrink)

Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

There is a common misconception across the lntelligence Community (IC) to the effect that information trapped within multiple heterogeneous data silos can be semantically integrated by the sorts of meaning-blind statistical methods employed in much of artificial intelligence (Al) and natural language processlng (NLP). This leads to the misconception that incoming data can be analysed coherently by relying exclusively on the use of statistical algorithms and thus without any shared framework for classifying what the data are about. Unfortunately, such approaches (...) do not yield sustainable results where we are dealing with widely distributed, highly heterogeneous and often changing bodies of data. We argue here that the needed integration requires the use of what we call an lntegrating Semantic Framework (ISF), which provldes a consistent set of categories and relationships that can be reused over and over again to tag successive bodies of data in ways which foster more coherent representation and reasoning. (shrink)

The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and that applying (...) the theory to the IPAP schizophrenia algorithm results in a representation that can be used by software agents to perform monitoring and control in a referent tracking environment. (shrink)

In this paper we offer an argument against supererogation and in favour of moral perfectionism. We argue three primary points: 1) That the putative moral category is not generated by any of the main normative ethical systems, and it is difficult to find space for it in these systems at all; 2) That the primary support for supererogation is based on intuitions, which can be undercut by various other pieces of evidence; and 3) That there are better reasons to favour (...) perfectionism, including competing intuitions about the good-ought tie-up, and the epistemic preference for theoretical simplicity. (shrink)

One famous scene in The Wolf of Wall Street (2013) is the dialogue between the young Jordan Belfort (Leonardo DiCaprio) and the expert trader Mark Hanna (Matthew McConaughey). Hanna is complaining that the stock market is unpredictable; it’s “fugazi … it’s fairy dust. It doesn’t exist. It’s never landed. It is not matter. It’s not on the element chart. It’s not real”. But the fact that something is unpredictable and non-physical does not imply that it does not exist. On the (...) other hand, its unpredictability, non-physicality, and the fact that the stock market trend is largely determined by investors’ beliefs, do make its nature difficult to grasp. -/- This special issue of Rivista di Estetica aims to explore the financial sector from an ontological point of view. While the ontology of money has been extensively studied, few scholars have focused on the stock market and, more generally, on those entities belonging to the investment landscape. Matters are made more complicated by the fact that the financial sector is characterized by an ever-increasing use of digital technology, including software elements that trade in the market themselves. We believe that a careful study of this phenomenon may help us better to understand the role of artificial agents in the social world. (shrink)

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based (...) approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy. (shrink)

Affective science conducts interdisciplinary research into the emotions and other affective phenomena. Currently, such research is hampered by the lack of common definitions of terms used to describe, categorise and report both individual emotional experiences and the results of scientific investigations of such experiences. High quality ontologies provide formal definitions for types of entities in reality and for the relationships between such entities, definitions which can be used to disambiguate and unify data across different disciplines. Heretofore, there has been little (...) effort directed towards such formal representation for affective phenomena, in part because of widespread debates within the affective science community on matters of definition and categorization. To address this requirement, we are developing an Emotion Ontology (EMO). (shrink)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (ETA). We describe (...) here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (shrink)

Generative artificial intelligence has given us synthetic media that are increasingly easy to create and increasingly hard to distinguish from photographs and videos. Whereas an existing literature has been concerned with how these new media might make a difference for would-be knowers—the viewers of photographs and videos—I advance a thesis about how they will make a difference for would-be communicators—those who embed photos and videos in their speech acts. I claim that the presence of these media in our information environment (...) reduces our ability to show one another things, even as it may increase our resources for telling. And I argue that this has consequences beyond the disruption of knowledge acquisition; showing is a way that we preserve relational equality through superficial asymmetries in political communication, and thereby express respect for our audiences. If synthetic media reduce our options for showing, they then interfere in the way that we manage our relationships in the context of collective political action. (shrink)

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)

Neo-Kantianism is common conceived as a philosophy ‘from above’, excelling in speculative constructions – as opposed to the attitude of patient description which is exemplified by the phenomenological turn ‘to the things themselves’. When we study the work of Emil Lask in its relation to that of Husserl and the phenomenologists, however, and when we examine the influences moving in both directions, then we discover that this idea of a radical opposition is misconceived. Lask himself was influenced especially by Husserl’s (...) Logical Investigations, and Husserl, especially in his later writings, was in some respects closer to Kant than were the Neo-Kantians. The contrast between the two philosophers can be illustrated by looking at their view of the objects of judgment; for Lask, as for Kant, judgment can relate to the thing as such only in an indirect way. The world of judgment is a collection of ‘imitations holding a secondary position’. It is cut apart from the plain world of real things by what Lask calls a ‘chasm of artificiality and imagery’. For Husserl, in contrast, the object of judgment is a ‘Sachverhalt’ or state of affairs, something ontologically ‘positive’ in the sense that it is an entity in its own right and does not point beyond itself in the manner of a mere sign or proxy for something else. (shrink)

In discussions about responsibility for climate change, it is often suggested that the historical use of natural resources is in some way relevant to our current attempts to address this problem fairly. In particular, both theorists and actors in the public realm have argued that historical high-emitters of greenhouse gases (GHGs) – or the beneficiaries of those emissions – are in possession of some form of debt, deriving from their overuse of a natural resource that should have been shared more (...) equitably. These accounts of what might be termed ‘natural debt’ generally focus on one particular natural resource (global GHG sink capacity); invoke a principle of justice by which rights to consume this resource should have been allocated (most commonly, equal per capita shares); and then argue that historical violations of this principle give rise to certain rectificatory duties in the present (generally, duties on the part of those who have historically consumed an excessive amount of the world’s GHG sink capacity, or who have benefitted from such excess consumption, to offer some form of compensation to those who have not – such compensation usually taking the form of emission credits or cash). Though many seem to find it intuitively plausible that historical high-emissions have incurred some form of debt, significant challenges arise in rendering the concept of natural debt both coherent and defensible. Such problems are not, however, my focus in this piece. Instead, I here suggest that discussions about historical responsibility for climate change commonly fail to recognise certain other past injustices concerning natural resources that appear to hold contemporary relevance. In particular, I argue that it is not just the unequal consumption of global GHG sink capacity that may be of moral significance here; but also the way in which the world’s resources have more generally been governed. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...) medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

Philosophers sometimes wonder whether academic work can ever be truly interdisciplinary. Whether true interdisciplinarity is possible is an open question, but given current trends in higher education, it seems that at least gesturing toward such work is increasingly important. This volume serves as a testament to the fact that such work can be done. Of course, while it is the case that high-level theoretical work can flourish at the intersection of dance and philosophy, it remains to be seen how we (...) might share this with undergraduate students. For many of us in philosophy and dance, a large number of the students we teach are neither philosophy nor dance majors. As such, we are familiar with the challenge of convincing our students to care about our fields. Both philosophy and dance, qua disciplines on a college campus, face similar challenges. These disciplines are often deeply misunderstood, frequently presumed to be “impractical” (a powerful, but confused objection), intimidating, and frivolous. In this chapter, we offer an account of the course we co-taught at Southern Utah University in the Spring of 2016 titled “Movement and Space” as a rough framework for how to introduce the intersection between philosophy and dance to students. We simultaneously attempted to break students of their misconceptions about philosophy and dance, and worked to engage students and professors alike in a truly interdisciplinary educational experience. Treating philosophy as an embodied endeavor, and employing philosophical concepts through the act of dance encouraged students and faculty alike to rethink the fundamental nature of aesthetics. (shrink)

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...) For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (shrink)

When does a human being begin to exist? We argue that it is possible, through a combination of biological fact and philosophical analysis, to provide a definitive answer to this question. We lay down a set of conditions for being a human being, and we determine when, in the course of normal fetal development, these conditions are first satisfied. Issues dealt with along the way include: modes of substance-formation, twinning, the nature of the intra-uterine environment, and the nature of the (...) relation between fetus and mother. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

In The Epistemology of Groups, Jennifer Lackey investigates the conditions for the possibility of groups telling lies. Central to this project is the goal of holding groups, and individuals within groups, accountable for their actions. I show that Lackey’s total account of group phenomena, however, may open up a means by which groups can evade accusations of having lied, thus allowing them to evade responsibility in precisely the way Lackey set out to avoid. Along the way, I also take note (...) of some interesting implications of Lackey’s view: that it makes groups uniquely susceptible to a lack of self-knowledge and that it creates an interesting mechanism by which groups can lie to themselves. (shrink)

Those in the Gricean tradition take it that successful human communication features an audience who not only arrives at the intended content of the signal, but also recognizes the speaker’s intention that they do so. Some in this tradition have also argued that there are yet further conditions on communicative success, which rule out the possibility of communicating by luck. Supposing that both intention-recognition and some sort of anti-luck condition are correctly included in an analysis of human communication, this article (...) asks what the value of events satisfying these conditions is. I present a puzzle concerning the value of intention-recognition which is analogous to the Meno Problem in epistemology, but ultimately argue that this puzzle is solveable: the signaling-relevant value of intention recognition can be vindicated. However, I argue that the version of this puzzle that concerns the further proposed luck-proofing conditions on communication can not be answered. I argue therefore that communication, as analyzed by many, is no more valuable qua signal than a proper subset of its conditions. Human communication is thennot a uniquely valuable signaling event. (shrink)