This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

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

A review of Gary Smith and Jay Cordes: The Phantom Pattern Problem: The Mirage of Big Data. New York: Oxford University Press, 2020.

In this paper we respond to three objections raised by Joshua Harris to our article, “Against a Postmodern Pentecostal Epistemology,” in which we express misgivings about the conjunction of Pentecostalism with James K. A. Smith’s postmodern, story-based epistemolo- gy. According to Harris, our critique: 1) problematically assumes a correspondence theory of truth, 2) invalidly concludes that “Derrida’s Axiom” conflicts with “Peter’s Axiom,” and 3) fails to consider an alternative account of the universality of Christian truth claims. We argue that (...) Harris’s objections either demonstrate a deficient interpretation of the relevant biblical pas- sages or are not directed at us at all. (shrink)

In this paper we explore the idea that Pentecostalism is best supported by conjoining it to a postmodern, narrative epistemology in which everything is a text requiring interpretation. On this view, truth doesn’t consist in a set of uninterpreted facts that make the claims of Christianity true; rather, as James K. A. Smith says, truth emerges when there is a “fit” or proportionality between the Christian story and one’s affective and emotional life. We argue that Pentecostals should reject this (...) account of truth, since it leads to either a self-refuting story-relativism or the equally problematic fallacy of story-ism: favoring one’s own story over others without legitimate reason. In either case, we contend, the gospel itself is placed at risk. (shrink)

Metaethical expressivists claim that we can explain what moral words like ‘wrong’ mean without having to know what they are about – but rather by saying what it is to think that something is wrong – namely, to disapprove of it. Given the close connection between expressivists’ theory of the meaning of moral words and our attitudes of approval and disapproval, expressivists have had a hard time shaking the intuitive charge that theirs is an objectionably subjectivist or mind-dependent view of (...) morality. Expressivism, critics have charged over and again, is committed to the view that what is wrong somehow depends on or at least correlates with the attitudes that we have toward it. Arguments to this effect are sometimes subtle, and sometimes rely on fancy machinery, but they all share a common flaw. They all fail to respect the fundamental idea of expressivism: that ‘stealing is wrong’ bears exactly the same relationship to disapproval of stealing as ‘grass is green’ bears to the belief that grass is green. In this paper I rehearse the motivations for the fundamental idea of expressivism and show how the arguments of Frank Jackson and Philip Pettit [1998], Russ Shafer-Landau [2003], Jussi Suikkanen [2009], and Christopher Peacocke [2004] all fail on this same rock. In part 1 I’ll rehearse the motivation for expressivism – a motivation which directly explains why it does not have subjectivist consequences. Then in each of parts 2-5 I’ll illustrate how each of Jackson and Pettit’s, Peacocke’s, Shafer-Landau’s, and Suikkanen’s arguments work, respectively, and why each of them fails to respect the fundamental parity at the heart of expressivism. Though others have tried before me to explain why expressivism is not committed to any kind of subjectivism or mind-dependence – prominently including Blackburn [1973], [1998], Horgan and Timmons [2006], and, in response to Pettit and Jackson, Dreier [2004] and Smith and Stoljar [2003], the explanation offered in this article is distinguished by its scope and generality.. (shrink)

About the possibility of time traveling based on several specialized works, including those of Nicholas J. J. Smith ("Time Travel"), William Grey (”Troubles with Time Travel”), Ulrich Meyer (”Explaining causal loops”), Simon Keller and Michael Nelson (”Presentists should believe in time-travel”), Frank Arntzenius and Tim Maudlin ("Time Travel and Modern Physics"), and David Lewis (“The Paradoxes of Time Travel”). The article begins with an Introduction in which I make a short presentation of the time travel, and continues with (...) a History of the concept of time travel, main physical aspects of time travel, including backward time travel in the past in general relativity and quantum physics, and time travel in the future, then a presentation of the Grandfather paradox that is approached in almost all specialized works, followed by a section dedicated to the Philosophy of time travel, and a section in which I analyze Causal loops for time travel. I finish my work with Conclusions, in which I sustain my personal opinions on the time travel, and the Bibliography on which the work is based. -/- ISSN 978-606-033-195-7, DOI: 10.58679/TW82554. (shrink)

This book is an anthology with the following themes. Non-European Tradition: Bussanich interprets main themes of Hindu ethics, including its roots in ritual sacrifice, its relationship to religious duty, society, individual human well-being, and psychic liberation. To best assess the truth of Hindu ethics, he argues for dialogue with premodern Western thought. Pfister takes up the question of human nature as a case study in Chinese ethics. Is our nature inherently good (as Mengzi argued) or bad (Xunzi’s view)? Pfister ob- (...) serves their underlying agreement, that human beings are capable of becoming good, and makes precise the disagreement: whether we achieve goodness by cultivating autonomous feelings or by accepting external precepts. There are political consequences: whether government should aim to respect and em- power individual choices or to be a controlling authority. Early Greek Thinking: Collobert examines the bases of Homeric ethics in fame, prudence, and shame, and how these guide the deliberations of heroes. She observes how, by depending upon the poet’s words, the hero gains a quasi- immortality, although in truth there is no consolation for each person’s inevi- table death. Plato: Santas examines Socratic Method and ethics in Republic 1. There Socrates examines definitions of justice and tests them by comparison to the arts and sciences. Santas shows the similarities of Socrates’ method to John Rawls’ method of considered judgments in reflective equilibrium. McPherran interprets Plato’s religious dimension as like that of his teacher Socrates. McPherran shows how Plato appropriates, reshapes, and extends the religious conventions of his own time in the service of establishing the new enterprise of philosophy. Ac- cording to Taylor, Socrates believes that humans in general have the task of helping the gods by making their own souls as good as possible, and Socrates’ unique ability to cross-examine imposes on him the special task of helping others to become as good as possible. This conception of Socrates’ mission is Plato’s own, consisting in an extension of the traditional conception of piety as helping the gods. Brickhouse and Smith propose a new understanding of Socratic moral psychology—one that retains the standard view of Socrates as an intellectualist, but also recognizes roles in human agency for appetites and passions. They compare and contrast the Socratic view to the picture of moral psychology we get in other dialogues of Plato. Hardy also proposes a new, non-reductive understanding of Socratic eudaimonism—he argues that Socrates invokes a very rich and complex notion of the “Knowledge of the Good and Bad”, which is associated with the motivating forces of the virtues. Rudebusch defends Socrates’ argument that knowledge can never be impotent in the face of psychic passions. He considers the standard objections: that knowledge cannot weigh incom- mensurable human values, and that brute desire, all by itself, is capable of moving the soul to action. Aristotle: Anagnostopoulos interprets Aristotle on the nature and acquisition of virtue. Though virtue of character, aiming at human happiness, requires a complex awareness of multiple dimensions of one’s experience, it is not properly a cognitive capacity. Thus it requires habituation, not education, according to Aristotle, in order to align the unruly elements of the soul with reason’s knowledge of what promotes happiness. Shields explains Aristotle’s doctrine that goodness is meant in many ways as the doctrine that there are different analyses of goodness for different types of circumstance, just as for being. He finds Aristotle to argue for this conclusion, against Plato’s doctrine of the unity of the Good, by applying the tests for homonymy and as an immediate cons- equence of the doctrine of categories. Shields evaluates the issue as unresolved at present. Russell discusses Aristotle’s account of practical deliberation and its virtue, intelligence (phronesis). He relates the account to contemporary philo- sophical controversies surrounding Aristotle’s view that intelligence is neces- sary for moral virtue, including the objections that in some cases it is unnecessary or even impedes human goodness. Frede examines the advantages and disadvantages of Aristotle’s virtue ethics. She explains the general Greek con- ceptions of happiness and virtue, Aristotle’s conception of phronesis and compares the Aristotle’s ethics with modern accounts. Liske discusses the question of whether the Aristotelian account of virtue entails an ethical-psy- chological determinism. He argues that Aristotle’s understanding of hexis allows for free action and ethical responsibility : By making decisions for good actions we are able to stabilize our character (hexis). Hellenistic and Roman: Annas defends an account of stoic ethics, according to which the three parts of Stoicism—logic, physics, and ethics—are integrated as the parts of an egg, not as the parts of a building. Since by this analogy no one part is a foundation for the rest, pedagogical decisions may govern the choice of numerous, equally valid, presentations of Stoic ethics. Piering interprets the Cynic way of life as a distinctive philosophy. In their ethics, Cynics value neither pleasure nor tradition but personal liberty, which they achieve by self-suffi- ciency and display in speech that is frank to the point of insult. Plotinus and Neoplatonism: Gerson outlines the place of ordinary civic virtue as well as philosophically contemplative excellence in Neoplatonism. In doing so he attempts to show how one and the same good can be both action-guiding in human life and be the absolute simple One that grounds the explanation of everything in the universe. Delcomminette follows Plotinus’s path to the Good as the foundation of free will, first in the freedom of Intellect and then in the “more than freedom” of the One. Plotinus postulates these divinities as not outside but within each self, saving him from the contradiction of an external foundation for a truly free will. General Topics: Halbig discusses the thesis on the unity of virtues. He dis- tinguishes the thesis of the identity of virtues and the thesis of a reciprocity of virtues and argues that the various virtues form a unity (in terms of reciprocity) since virtues cannot bring about any bad action. Detel examines Plato’s and Aristotle’s conceptions of normativity : Plato and Aristotle (i) entertained hybrid theories of normativity by distinguishing functional, semantic and ethical normativity, (ii) located the ultimate source of normativity in standards of a good life, and thus (iii) took semantic normativity to be a derived form of normativity. Detel argues that hybrid theories of normativity are—from a mo- dern point of view—still promising. Ho ̈ffe defends the Ancient conception of an art of living against Modern objections. Whereas many Modern philosophers think that we have to replace Ancient eudaimonism by the idea of moral obligation (Pflicht), Ho ̈ffe argues that Eudaimonism and autonomy-based ethics can be reconciled and integrated into a comprehensive and promising theory of a good life, if we enrich the idea of autonomy by the central elements of Ancient eudaimonism. Some common themes: The topics in Chinese and Hindu ethics are perhaps more familiar to modern western sensibilities than Homeric and even Socratic. Anagnostopoulos, Brickhouse and Smith, Frede, Liske, Rudebusch, and Russell all consider in contrasting ways the role of moral character, apart from intellect, in ethics. Brickhouse / Smith, Hardy, and Rudebusch discuss the Socratic con- ception of moral knowledge. Brickhouse / Smith and Hardy retain the standard view of the so called Socratic Intellectualism. Shields and Gerson both consider the question whether there is a single genus of goodness, or if the term is a homonym. Bussanich, McPherran, Taylor, and Delcomminette all consider the relation between religion and ethics. Pfister, Piering, Delcomminette, and Liske all consider what sort of freedom is appropriate to human well-being. Halbig, Detel, and Ho ̈ffe propose interpretations of main themes of Ancient ethics. (shrink)

În această lucrare analizez posibilitatea călătoriei în timp pe baza mai multor lucrări de specialitate, printre care cele ale lui Nicholas J.J. Smith ("Time Travel", The Stanford Encyclopedia of Philosophy”), William Grey (”Troubles with Time Travel”), Ulrich Meyer (”Explaining causal loops”), Simon Keller și Michael Nelson (”Presentists should believe in time-travel”), Frank Arntzenius și Tim Maudlin ("Time Travel and Modern Physics") și David Lewis (“The Paradoxes of Time Travel”). Lucrarea începe cu o Introducere în care fac o scurtă (...) prezentare a călătoriei în timp, și continuă cu o Istoria conceptului de călătorie în timp, prezentarea principalelor Aspecte fizice ale călătoriei în timp, inclusiv călătoria în timp în trecut în relativitatea generală și în fizica cuantică și călătoria în timp în viitor, apoi o prezentare a Paradoxul bunicului care este abordat în aproape toate lucrările de specialitate, urmat de o secțiune dedicată Filosofiei călătoriei în timp, și o secțiune în care analizez Buclele cauzale pentru călătoria în timp. Finalizez lucrarea cu Concluzii, în care expun opiniile personale privind călătoria în timp, și Bibliografia pe care se bazează lucrarea. (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)

À propos de la possibilité de voyager dans le temps sur la base de plusieurs ouvrages spécialisés, notamment ceux de Nicholas J. J. Smith (« Time Travel »), William Grey (« Troubles with Time Travel »), Ulrich Meyer (« Explaining causal loops »), Simon Keller and Michael Nelson (« Presentists should believe in time-travel »), Frank Arntzenius and Tim Maudlin (« Time Travel and Modern Physics »), et David Lewis (« The Paradoxes of Time Travel »). L'article commence (...) par une Introduction dans laquelle je fais une brève présentation du voyage dans le temps et poursuit par une Histoire du concept de voyage dans le temps, les principaux aspects physiques du voyage dans le temps, y compris les voyages dans le temps dans le passé dans la relativité générale et la physique quantique , et les voyages dans le temps dans le futur, puis une présentation du Paradoxe du grand-père abordé dans presque toutes les œuvres spécialisées, suivie d’une section consacrée à la Philosophie du voyage dans le temps et d’une section dans laquelle j’analyse les Boucles causales pour le voyage dans le temps. Je termine mon travail avec Conclusions, dans laquelle je maintiens mes opinions personnelles sur le voyage dans le temps et la Bibliographie sur laquelle repose le travail. -/- TABLE: -/- Abstract Introducere Istoria conceptului de călătorie în timp Paradoxul bunicului Filosofía călătoriei în timp Buclele cauzale Concluzii Note Bibliografie -/- DOI: 10.13140/RG.2.2.27116.51841. (shrink)

Moral particularism, on some interpretations, is committed to a shapeless thesis: the moral is shapeless with respect to the natural. (Call this version of moral particularism ‘shapeless moral particularism’). In more detail, the shapeless thesis is that the actions a moral concept or predicate can be correctly applied to have no natural commonality (or shape) amongst them. Jackson et al. (Ethical particularism and patterns, Oxford University Press, Oxford, 2000) argue, however, that the shapeless thesis violates the platitude ‘predication supervenes on (...) nature’—predicates or concepts apply because of how things are, and therefore ought to be rejected. I defend shapeless moral particularism by arguing that Jackson et al’s contention is less compelling than it firstly appears. My defense is limited in the sense that it does not prove shapeless moral particularism to be right and it leaves open the possibility that shapeless moral particularism might attract criticisms different from the ones advanced by Jackson et al. But at the very least, I hope to say enough to undermine Jackson et al’s powerful attack against it. The plan of this paper is as follows. Section 1 glosses the view of moral particularism and why it is taken to be essentially committed to the shapeless thesis. Section 2 examines a Wittgensteinian argument for the shapeless thesis. I shall argue that the Canberrans’ counter-arguments against it on grounds of disjunctive commonality and conceptual competence do not succeed. Section 3 explicates Canberrans’ predication supervenience argument against the shapeless thesis. Section 4 offers my criticisms of the Canberrans’ predication supervenience argument. In view of the above discussions, in Sect. 5, I conclude that there is no compelling argument (from the Canberrans) to believe that the shapeless thesis fails (as I have argued in Sect. 4). In fact, there is some good reason for us to believe it (as I have argued in Sect. 2). If so, I contend that moral particularism, when construed as essentially committed to the shapeless thesis, still remains as a live option. (shrink)

This chapter proposed a novel design methodology called Value-Sensitive Design and its potential application to the field of artificial intelligence research and design. It discusses the imperatives in adopting a design philosophy that embeds values into the design of artificial agents at the early stages of AI development. Because of the high risk stakes in the unmitigated design of artificial agents, this chapter proposes that even though VSD may turn out to be a less-than-optimal design methodology, it currently provides a (...) framework that has the potential to embed stakeholder values and incorporate current design methods. The reader should begin to take away the importance of a proactive design approach to intelligent agents. (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)

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)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

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 goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (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 Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

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

Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...) Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries. (shrink)

In this paper, I offer an analysis of the radical disagreement over the adequacy of string theory. The prominence of string theory despite its notorious lack of empirical support is sometimes explained as a troubling case of science gone awry, driven largely by sociological mechanisms such as groupthink (e.g. Smolin 2006). Others, such as Dawid (2013), explain the controversy by positing a methodological revolution of sorts, according to which string theorists have quietly turned to nonempirical methods of theory assessment given (...) the technological inability to directly test the theory. The appropriate response, according to Dawid, is to acknowledge this development and widen the canons of acceptable scientific methods. As I’ll argue, however, the current situation in fundamental physics does not require either of these responses. Rather, as I’ll suggest, much of the controversy stems from a failure to properly distinguish the “context of justification” from the “context of pursuit”. Both those who accuse string theorists of betraying the scientific method and those who advocate an enlarged conception of scientific methodology objectionably conflate epistemic justification with judgements of pursuit-worthiness. Once we get clear about this distinction and about the different norms governing the two contexts, the current situation in fundamental physics becomes much less puzzling. After defending this diagnosis of the controversy, I’ll show how the argument patterns that have been posited by Dawid as constituting an emergent methodological revolution in science are better off if reworked as arguments belonging to the context of pursuit. (shrink)

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

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

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

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

O livro reúne textos apresentados no II Workshop de Filosofia e Ensino, realizado na UFRGS em 2015, com a temática "Epistemologia e Currículo" -/- .

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

Does ?ought? imply ?can? for collectives' obligations? In this paper I want to establish two things. The first, what a collective obligation means for members of the collective. The second, how collective ability can be ascertained. I argue that there are four general kinds of obligation, which devolve from collectives to members in different ways, and I give an account of the distribution of obligation from collectives to members for each of these kinds. One implication of understanding collective obligation and (...) ability in the proposed way is that a group can be blameworthy for failing to realize its obligation even when no member of the group is blameworthy for failing to realize her obligation. (shrink)

Durch genomweite Analysen werden vielfältige gesundheitsrelevante Informationen über eine Person gewonnen. Solche Informationen können die Behandlung von Krankheiten verbessern. Sie ermöglichen aber auch Vorhersagen, ob eine Person und deren Verwandte in Zukunft möglicherweise erkranken werden. Der neuartige Charakter des Informationseingriffs und sein prädiktive Potential bedürfen der ethischen, juristischen und ökonomischen Reflexion, damit diese Technologie zum Wohl der Patienten, der Familienangehörigen und der Solidargemeinschaft eingesetzt werden kann. Die vorliegende Schrift leistet mit ihren interdisziplinären, vom BMBF finanzierten Analysen dazu einen Beitrag. Grundlagen (...) für einen ethisch und juristisch verantwortbaren Einsatz der Genomsequenzierung zu medizinischen Zwecken werden erörtert und Eckpunkte für Kostenanalysen sowie Elemente einer “Guten klinischen Praxis” präsentiert. (shrink)

The Preface Paradox is often discussed for its implications for rational belief. Much less discussed is a variant of the Preface Paradox for knowledge. In this paper, I argue that the most plausible closure-friendly resolution to the Preface Paradox for Knowledge is to say that in any given context, we do not know much. I call this view “Socraticism”. I argue that Socraticism is the most plausible view on two accounts—(1) this view is compatible with the claim that most of (...) our knowledge ascriptions are true, and (2) provided that (1) is true, the costs of accepting Socraticism are much less than the costs of accepting any other resolution to the Paradox. I argue for (1) in Section 2 by developing a question-sensitive contextualist model for knowledge that shows how Socraticism is compatible with the claim that most of our knowledge ascriptions are true. I also argue how this contextualist model can achieve this result where other contextualist models fail. I then consider other closure-friendly solutions to the paradox in Section 3 and show how accepting those solutions forces us to give up a number of plausible epistemic principles. (shrink)

In this paper, I examine Cicero’s oft-neglected De Divinatione, a dialogue investigating the legitimacy of the practice of divination. First, I offer a novel analysis of the main arguments for divination given by Quintus, highlighting the fact that he employs two logically distinct argument forms. Next, I turn to the first of the main arguments against divination given by Marcus. Here I show, with the help of modern probabilistic tools, that Marcus’ skeptical response is far from the decisive, proto-naturalistic assault (...) on superstition that it is sometimes portrayed to be. Then, I offer an extended analysis of the second of the main arguments against divination given by Marcus. Inspired by Marcus’ second main argument, I formulate, explicate, and defend a substantive principle of scientific methodology that I call the “Ciceronian Causal-Nomological Requirement” (CCR). Roughly, this principle states that causal knowledge is essential for relying on correlations in predictive inference. Although I go on to argue that Marcus’ application of the CCR in his debate with Quintus is dialectically inadequate, I conclude that De Divinatione deserves its place in Cicero’s philosophical corpus, and that ultimately, its significance for the history and philosophy of science ought to be recognized. (shrink)

Definition of the problem The umbrella term “explicability” refers to the reduction of opacity of artificial intelligence (AI) systems. These efforts are challenging for medical AI applications because higher accuracy often comes at the cost of increased opacity. This entails ethical tensions because physicians and patients desire to trace how results are produced without compromising the performance of AI systems. The centrality of explicability within the informed consent process for medical AI systems compels an ethical reflection on the trade-offs. Which (...) levels of explicability are needed to obtain informed consent when utilizing medical AI? Arguments We proceed in five steps: First, we map the terms commonly associated with explicability as described in the ethics and computer science literature, i.e., disclosure, intelligibility, interpretability, and explainability. Second, we conduct a conceptual analysis of the ethical requirements for explicability when it comes to informed consent. Third, we distinguish hurdles for explicability in terms of epistemic and explanatory opacity. Fourth, this then allows to conclude the level of explicability physicians must reach and what patients can expect. In a final step, we show how the identified levels of explicability can technically be met from the perspective of computer science. Throughout our work, we take diagnostic AI systems in radiology as an example. Conclusion We determined four levels of explicability that need to be distinguished for ethically defensible informed consent processes and showed how developers of medical AI can technically meet these requirements. (shrink)

When national borders in the modern sense first began to be established in early modern Europe, non-contiguous and perforated nations were a commonplace. According to the conception of the shapes of nations that is currently preferred, however, nations must conform to the topological model of circularity; their borders must guarantee contiguity and simple connectedness, and such borders must as far as possible conform to existing topographical features on the ground. The striving to conform to this model can be seen at (...) work today in Quebec and in Ireland, it underpins much of the rhetoric of the P.L.O., and was certainly to some degree involved as a motivating factor in much of the ethnic cleansing which took place in Bosnia in recent times. The question to be addressed in what follows is: to what extent could inter-group disputes be more peacefully resolved, and ethnic cleansing avoided, if political leaders, diplomats and others involved in the resolution of such disputes could be brought to accept weaker geometrical constraints on the shapes of nations? A number of associated questions then present themselves: What sorts of administrative and logistical problems have been encountered by existing non contiguous nations and by perforated nations, and by other nations deviating in different ways from the received geometrical ideal? To what degree is the desire for continuity and simple connectedness a rational desire, and to what degree does it rest on species of political rhetoric which might be countered by, for example, philosophical argument? These and a series of related questions will form the subject- matter of the present essay. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.

Purpose: The method of diagnosing diabetic retinopathy (DR) through artificial intelligence (AI)-based systems has been commercially available since 2018. This introduces new ethical challenges with regard to obtaining informed consent from patients. The purpose of this work is to develop a checklist of items to be disclosed when diagnosing DR with AI systems in a primary care setting. -/- Methods: Two systematic literature searches were conducted in PubMed and Web of Science databases: a narrow search focusing on DR and a (...) broad search on general issues of AI-based diagnosis. An ethics content analysis was conducted inductively to extract two features of included publications: (1) novel information content for AI-aided diagnosis and (2) the ethical justification for its disclosure. -/- Results: The narrow search yielded n = 537 records of which n = 4 met the inclusion criteria. The information process was scarcely addressed for primary care setting. The broad search yielded n = 60 records of which n = 11 were included. In total, eight novel elements were identified to be included in the information process for ethical reasons, all of which stem from the technical specifics of medical AI. -/- Conclusions: Implications for the general practitioner are two-fold: First, doctors need to be better informed about the ethical implications of novel technologies and must understand them to properly inform patients. Second, patient's overconfidence or fears can be countered by communicating the risks, limitations, and potential benefits of diagnostic AI systems. If patients accept and are aware of the limitations of AI-aided diagnosis, they increase their chances of being diagnosed and treated in time. (shrink)

Recent years have witnessed intensive efforts to specify which requirements ethical artificial intelligence (AI) must meet. General guidelines for ethical AI consider a varying number of principles important. A frequent novel element in these guidelines, that we have bundled together under the term explicability, aims to reduce the black-box character of machine learning algorithms. The centrality of this element invites reflection on the conceptual relation between explicability and the four bioethical principles. This is important because the application of general ethical (...) frameworks to clinical decision-making entails conceptual questions: Is explicability a free-standing principle? Is it already covered by the well-established four bioethical principles? Or is it an independent value that needs to be recognized as such in medical practice? We discuss these questions in a conceptual-ethical analysis, which builds upon the findings of an empirical document analysis. On the example of the medical specialty of radiology, we analyze the position of radiological associations on the ethical use of medical AI. We address three questions: Are there references to explicability or a similar concept? What are the reasons for such inclusion? Which ethical concepts are referred to? (shrink)

It is very natural to think that if two people, x and y, are qualitatively identical and have committed qualitatively identical actions, then it cannot be the case that one has committed something wrong whereas the other did not. That is to say, if x and y differ in their moral status, then it must be because x and y are qualitatively different, and not simply because x is identical to x and not identical to y. In this fictional dialogue (...) between Socrates and Cantor involving infinitely many qualitatively identical agents, this assumption is challenged. (shrink)

According to the principle of Conjunction Closure, if one has justification for believing each of a set of propositions, one has justification for believing their conjunction. The lottery and preface paradoxes can both be seen as posing challenges for Closure, but leave open familiar strategies for preserving the principle. While this is all relatively well-trodden ground, a new Closure-challenging paradox has recently emerged, in two somewhat different forms, due to Backes :3773–3787, 2019a) and Praolini :715–726, 2019). This paradox synthesises elements (...) of the lottery and the preface and is designed to close off the familiar Closure-preserving strategies. By appealing to a normic theory of justification, I will defend Closure in the face of this new paradox. Along the way I will draw more general conclusions about justification, normalcy and defeat, which bear upon what Backes :2877–2895, 2019b) has dubbed the ‘easy defeat’ problem for the normic theory. (shrink)