Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

The current rise of neurodevelopmental disorders poses a critical need to detect risk early in order to rapidly intervene. One of the tools pediatricians use to track development is the standard growth chart. The growth charts are somewhat limited in predicting possible neurodevelopmental issues. They rely on linear models and assumptions of normality for physical growth data – obscuring key statistical information about possible neurodevelopmental risk in growth data that actually has accelerated, non-linear rates-of-change and variability encompassing skewed distributions. Here, (...) we use new analytics to profile growth data from 36 newborn babies that were tracked longitudinally for 5 months. By switching to incremental (velocity-based) growth charts and combining these dynamic changes with underlying fluctuations in motor performance – as the transition from spontaneous random noise to a systematic signal – we demonstrate a method to detect very early stunting in the development of voluntary neuromotor control and to flag risk of neurodevelopmental derail. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

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

This is the first volume to offer a systematic consideration and comprehensive overview of Christianity’s long engagement with the Platonic philosophical tradition. The book offers a detailed consideration of the most fertile sources and concepts in Christian Platonism, a historical contextualization of its development, and a series of constructive engagements with central questions. Bringing together a range of leading scholars, the volume guides readers through each of these dimensions, uniquely investigating and explicating one of the most important, controversial, and often (...) misunderstood elements of Christian intellectual history. (shrink)

The current resurgence of interest in cognition and in the nature of cognitive processing has brought with it also a renewed interest in the early work of Husserl, which contains one of the most sustained attempts to come to grips with the problems of logic from a cognitive point of view. Logic, for Husserl, is a theory of science; but it is a theory which takes seriously the idea that scientific theories are constituted by the mental acts of cognitive subjects. (...) The present essay begins with an exposition of Husserl's act-based conception of what a science is, and goes on to consider his account of the role of linguistic meanings, of the ontology of scientific objects, and of evidence and truth. The essay concentrates almost exclusively on the Logical Investigations of 1900/01. This is not only because this work, which is surely Husserl's single most important masterpiece, has been overshadowed first of all by his Ideas I and then later by the Crisis. It is also because the Investigations contain, in a peculiarly clear and pregnant form, a whole panoply of ideas on logic and cognitive theory which either simply disappeared in Husserl's own later writings or became obfuscated by an admixture of that great mystery which is 'transcendental phenomenology'. (shrink)

This examination considers the influence of the seventeenth century Cambridge Platonist Cudworth upon the thought of the late eighteenth century German thinker Herder. It focuses upon Herder's use of Cudworth's philosophy to create a revised version of Spinoza's metaphysics. Both Cudworth and Herder were concerned with the problem of determinism. Cudworth outlined a number of difficulties relating to this problem in the thought of Spinoza and proposed amendments, particularly the introduction of the middle principle of plastik, which would mediate between (...) the Ideas of transcendent reason and mechanical materialism. We find these amendments to Spinoza's philosophy also employed in Herder's contribution to the Pantheism Controversy, in which he too offers a revised Spinozism and introduces his own middle principle of Kraft. This demonstrates an important but under-explored English contribution to a key development in German intellectual history. The Pantheism Controversy was an epoch-making event, helping to bring an end to the German Enlightenment and to inaugurate the Romantic movement. Herder's version of Spinoza's thought revived the philosopher's fortunes, and Herder's notion of Kraft became central to Romantic aesthetics. Finally, Herder's use of Cudworth demonstrates the important but overlooked source of Platonic realism in German Romantic thought. (shrink)

Largely neglected today, the work of Karl Philipp Moritz was a highly influential source for Early German Romanticism. Moritz considered the form of myth as essential to the absolute nature of the divine subject. This defence was based upon his aesthetic theory, which held that beautiful art was “disinterested”, or complete in itself. For Moritz, Myth, like art, constitutes a totality providing an idiom free from restriction in the imitation of the divine. This examination offers a consideration of Moritz’s aesthetics (...) and mythography, before turning briefly to consider his influence on the authors of Early German Romanticism. An understanding of the role of Moritz’s thought supports a number of recent claims that challenge the conventional reading of Romanticism. At the same time it allows us to see Romanticism’s unconventional realist theological programme, permitting us to overcome the problematic secularising readings of the movement. I would like to thank Kurt Mueller-Vollmer, as well as Fredrick Beiser and Lars Fischer for their help with this project. (shrink)

The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists seek to apply ontological tools (...) to solving practical problems of the sort which arise in various extra-philosophical domains, including law and government administration. (shrink)

This article examines the relationship between the conspicuous and complicated terms of transcendence and immanence, which may equally be defined as essentially connected, or diametrically opposed. Recent developments in two largely unrelated sets of scholarship— the re-evaluation of secularisation, and the relationship between medieval and modern philosophy—provide a helpful means to arrive at a clearer understanding of this challenging problem. Charles Taylor and Jan Aertesn act as foci for these developments, particularly through their respective concerns with epistemic framing in relation (...) to transcendence and immanence, and the role of transcendentals in medieval philosophy. This examination brings these two concepts together, examining the idea of transcendentals offered by both Aquinas, a thinker of the transcendent frame, and Kant, a thinker of the immanent frame. From this juxtaposition we can offer two contrasting understandings of the relationship between transcendence and immanence from within both the transcendent and immanent frames. Finally, two brief literary examples demonstrate how these two ways of reading transcendence and immanence may be employed in the contextual understanding of religious writing. To understand the unity and division between transcendence and immanence is to better comprehend two primary terms in the study of religion, and to appreciate a fundamental development in the history of religion in the West. (shrink)

Herder’s earliest philosophical writing, the essay fragment Versuch über das Sein, explores the concept of Being (Sein) in dialogue with Kant’s pre-critical Der einzig mögliche Beweisgrund zu einer Demonstration des Daseins Gottes. In this often critically omitted work, Herder arrives at a number of insights that would be determinative for the development of his later thought. This examination details Herder’s concept of Being as the transcendent ground of predication, his contention that Being can never be experienced directly, and his consequent (...) conclusion that the shape of philosophical inquiry should not be one of abstract speculation, but instead one of non-foundational, historically aware, empirical observation. This consideration then briefly addresses how the concept of Being informs Herder’s philosophy of science, history, language and religion. (shrink)

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

This examination makes the case that the tradition of Christian Platonism can constitute a valuable resource for addressing the long-running and increasingly-acute environmental crisis that threatens the global ecosystem and all who inhabit it. More than a scientific, technological or political challenge, the crisis requires a fundamental shift in the way humans understand nature and their place within it. Key to implementing this shift is the need to address the problematic anthropocentric conceptualisation of nature characteristic of the contemporary social imaginary (...) that determines a wide range of present day economic, religious and scientific perspectives. The case made here is that Christian Platonism, and in particular its participatory ontology, can offer a radically non-anthropocentric alternative to the present-day understanding of nature, reconceptualising the way we understand the meaning, value, and way we know nature. (shrink)

With the turn of the twenty-first century, a group of writers began rehabilitating British nature writing and the voice of the individual interacting with it, producing what has become collectively known as the new nature writing. This examination considers how this literature represents a post-secular re-conceptualization of our relationship to nature. The new nature writing challenges a key element of the secular social imaginary, namely the subject-centered, immanence-bound, disenchanted representation of nature, which sets the self over and above nature, destabilizing (...) existing dichotomies, and generating a multiplicity of hybridized possibilities that re-conceptualize our relationship to nature. (shrink)

The development of Christian mysticism is deeply bound to poetics. This examination first considers Platonic poetry, Hebrew creation, and Christian kenosis as sources of poetic mysticism, before turning to an elaboration of the role of rhythm, language, and the poetic imagination. The appraisal then considers the historical development of mystical poetry, beginning with early Christian reflection on the figurative and lyrical use of scriptural language to express a deep personal relationship with God. The development of vernacular mysticism, and its adoption (...) of this scriptural model, is then explored through a detailed consideration of four mystical poets (Dante, Jacopone, Hadewijch, and Angelus Silesius). The interaction of poetic form and spiritual content is elaborated throughout, with the aim of demonstrating how poetics allows the mystical writer to achieve a result for the reader otherwise not possible in discursive forms of communication. (shrink)

A central element of Hölderlin’s poetic project was to find a new language for transcendence in an age of immanence. To do so, he turned not to philosophy or theology, but to poetics. Its rhythmic nature, he argued, was capable of re-presenting the transcendent. This examination will begin with a brief historical consideration of the relation of transcendence and immanence, with particular attention to the influential philosophies of Spinoza and Fichte. It then proceeds to Hölderlin’s consideration of the loss of (...) the language of transcendence, and his project to develop a new one. The final section will examine how Hölderlin aimed to achieve this in his poetics. (shrink)

As the sequential stages of the 2020 COVID-19 pandemic have unfolded, so have its complexities. What initially presented as a health emergency, has revealed itself to be a phenomenon of many facets. As the situation continues to advance, the question for many is whether the crisis will be grasped as an opportunity to address deep structural, ecological and social challenges. This introductory chapter briefly addresses why and how the fields of ecology and theology can play an important and vital role (...) in addressing the challenges and its transformative possibilities presented by the COVID-19 pandemic. (shrink)

More, Henry (1614-1687), an English philosopher, theologian and poet. The most important member of the Cambridge Platonists, a group of seventeenth century thinkers associated with the University of Cambridge. Accepting of the developments of Galilean science, Cartesianism and atomism, they sought an alternative to the faltering philosophical foundation of Aristotelianism by looking to the Platonic tradition, viewed through the framework of Renaissance perennial philosophy. More’s Christian apologetics argued for the existence of God, the immortality of the soul, and the veracity (...) of Christian ethics in light of the atheistic, mechanistic, and fatalistic conclusions drawn from the thought of Spinoza and Hobbes. (shrink)

This consideration characterises the crisis and opportunity of COVID-19 in three parts: First, it sets out the problematic conceptualisation of nature in the modern social imaginary by focusing upon the buffered self in terms of its sense of identity, agency and authority. Second, it sets out how the pandemic fundamentally disrupts these three facets of the self in terms of the fragilization of economic values, the notion of unique human agency, and the limitation of the authority of discursive reason. Finally, (...) it concludes by outlining the opportunity for a renewed relationship with nature by proposing the recovery of the premodern concepts of metaphysical participation, teleology, and rational intuition. In doing so, the pandemic crisis is considered in the wider context of the ecological crisis of the modern age, and as an opportunity for rethinking our collective concept of nature, and the place of our selves within it. (shrink)

In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...) the relationships between (1) particulars and types, and (2) continuants and occurrents. (shrink)

An ontology of geographic kinds is designed to yield a better understanding of the structure of the geographic world, and to support the development of geographic information systems that are conceptually sound. This paper first demonstrates that geographical objects and kinds are not just larger versions of the everyday objects and kinds previously studied in cognitive science. Geographic objects are not merely located in space, as are the manipulable objects of table-top space. Rather, they are tied intrinsically to space, and (...) this means that their spatial boundaries are in many cases the most salient features for categorization. The ontology presented here will accordingly be based on topology (the theory of boundary, contact and separation) and on mereology (the theory of extended wholes and parts). Geographic reality comprehends mesoscopic entities, many of which are best viewed as shadows cast onto the spatial plane by human reasoning and language. Because of this, geographic categories are much more likely to show cultural differences in category definitions than are the manipulable objects of table-top space. (shrink)

The fact that there is such a thing as a degree of formedness [Gestaltung], that every Gestalt has a certain Gestalt level, is of fundamental significance. A rose is a Gestalt of higher level than a heap of sand: this we recognize just as immediately as that red is a fuller, more lively colour than grey. The higher Gestalten are distinguished further from the lower by the fact that the product of unity and multiplicity [Einheit und Mannigfaltigkeit] is in their (...) case greater. (shrink)

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

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (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)

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

The Repugnant Conclusion served an important purpose in catalyzing and inspiring the pioneering stage of population ethics research. We believe, however, that the Repugnant Conclusion now receives too much focus. Avoiding the Repugnant Conclusion should no longer be the central goal driving population ethics research, despite its importance to the fundamental accomplishments of the existing literature.

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

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

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)

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

The 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.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

This is the second part of a two-part series on the logic of hyperlogic, a formal system for regimenting metalogical claims in the object language (even within embedded environments). Part A provided a minimal logic for hyperlogic that is sound and complete over the class of all models. In this part, we extend these completeness results to stronger logics that are sound and complete over restricted classes of models. We also investigate the logic of hyperlogic when the language is enriched (...) with hyperintensional operators such as counterfactual conditionals and belief operators. (shrink)

While it is a point of agreement in contemporary republican political theory that property ownership is closely connected to freedom as non-domination, surprisingly little work has been done to elucidate the nature of this connection or the constraints on property regimes that might be required as a result. In this paper, I provide a systematic model of the boundaries within which republican property systems must sit and explore some of the wider implications that thinking of property in these terms may (...) have for republicans. The boundaries I focus on relate to the distribution of property and the application of types of property claims over particular kinds of goods. I develop this model from those elements of non-domination most directly related to the operation of a property regime: (a) economic independence, (b) limiting material inequalities, and (c) the promotion of common goods. The limits that emerge from this analysis support intuitive judgments that animate much republican discussion of property distribution. My account diverges from much orthodox republican theory, though, in challenging the primacy of private property rights in the realization of economic independence. The value of property on republican terms can be realized without private ownership of the means of production. (shrink)

Recent discussions of emergence in physics have focussed on the use of limiting relations, and often particularly on singular or asymptotic limits. We discuss a putative example of emergence that does not fit into this narrative: the case of phonons. These quasi-particles have some claim to be emergent, not least because the way in which they relate to the underlying crystal is almost precisely analogous to the way in which quantum particles relate to the underlying quantum field theory. But there (...) is no need to take a limit when moving from a crystal lattice based description to the phonon description. Not only does this demonstrate that we can have emergence without limits, but also provides a way of understanding cases that do involve limits. (shrink)

In the Critique of Pure Reason, Kant states that ideas give us the rule for organizing experience and ideals serve as archetypes or standards against which one can measure copies. Further, he states that ideas and ideals can be practical. Understanding how precisely these concepts should function presents a challenging and understudied philosophical puzzle. I offer a reconstruction of how ideas and ideals might be practical in order to uphold, to my mind, a conceptually worthy distinction. A practical idea, I (...) argue, is best understood as a reference to the categorical imperative (and its various formulations), which guides conduct directly as a rule. A practical ideal, by contrast, I think is a substrate that serves two functions: one that (a) helps us gauge moral deficiencies and another that (b) reveals the potential for moral improvement. In response to well-grounded sceptical concerns, I argue that ideals are indirectly practical in that they ground the possibility to recognise moral states of affairs and be moral in the first place. (shrink)

Die klassische bikategoriale Ontologie von Substanzen und Akzidentien ist für die Festlegung der Strukturen menschlichen und tierischen Verhaltens nicht hinreichend, da die Umwelten dieses Verhaltens sich nicht in dieses klassische System einfügen. Wir bieten dementsprechend den Grundriß einer Theorie der besonderen Gebilde, die die Alltagswelten menschlicher und tierischer Verhalten konstituieren. Die Ausgangsüberlegung ist die folgende, Wir sind alle (Schau)spieler, und diese brauchen eine Bühne. Unsere Bühne ist die jeweilige Umwelt, in der wir leben und handeln. Der Terminus ‘Umwelt’ wird hierbei (...) in Analogie zu Husserls Begriff der Lebenswelt verwendet. Er bezeichnet dementsprechend einen strukturierten Teil der Welt, in den sich ein Lebewesen, z.B. ein Mensch, einpaßt. Die Umwelt ist, wenn man so will, demnach die Bühne, auf welcher sich unser Verhalten abspielt. Der Versuch, das Wesen solcher Umwelten ontologisch festzulegen, bringt allerdings ein schwieriges Problem mit sich - ein Problem so alt wie Platons Höhlengleichnis und so neu wie gegenwärtige Reflexionen amerikanischer Philosophen zur Metaphysik der virtuellen Realität und zum Gedankenexperiment des Gehirns im Tank. Es gibt nämlich in manchen Fällen grobe Inkonsistenzen zwischen (1) der Umwelt, wie wir sie uns gerade vorstellen, und (2) der Umwelt als Bestandteil der wirklichen Welt. Das Problem, zwischen diesen beiden Umweltklassen einen Ausgleich zu finden, wird im letzten Teil des Aufsatzes behandelt. (shrink)

I argue that embodied understanding and conceptual-representational understanding interact through schematic structure. I demonstrate that common conceptions of these two kinds of understanding, such as developed by Wheeler (2005, 2008) and Dreyfus (2007a, b, 2013), entail a separation between them that gives rise to significant problems. Notably, it becomes unclear how they could interact; a problem that has been pointed out by Dreyfus (2007a, b, 2013) and McDowell (2007) in particular. I propose a Kantian strategy to close the gap between (...) them. I argue that embodied and conceptual-representational understanding are governed by schemata. Since they are governed by schemata, they can interact through a structure that they have in common. Finally, I spell out two different ways to conceive of the schematic interaction between them—a close, grounding relationship and a looser relationship that allows for a minimal interaction, but preserves the autonomy of both forms of understanding. (shrink)

Contrary to the popular assumption that linguistically mediated social practices constitute the normativity of action (Kiverstein and Rietveld, 2015; Rietveld, 2008a,b; Rietveld and Kiverstein, 2014), I argue that it is affective care for oneself and others that primarily constitutes this kind of normativity. I argue for my claim in two steps. First, using the method of cases I demonstrate that care accounts for the normativity of action, whereas social practices do not. Second, I show that a social practice account of (...) the normativity of action has unwillingly authoritarian consequences in the sense that humans act only normatively if they follow social rules. I suggest that these authoritarian consequences are the result of an uncritical phenomenology of action and the fuzzy use of “normative”. Accounting for the normativity of action with care entails a realistic picture of the struggle between what one cares for and often repressive social rules. (shrink)

Recent work in formal philosophy has concentrated over-whelmingly on the logical problems pertaining to epistemic shortfall - which is to say on the various ways in which partial and sometimes incorrect information may be stored and processed. A directly depicting language, in contrast, would reflect a condition of epistemic perfection. It would enable us to construct representations not of our knowledge but of the structures of reality itself, in much the way that chemical diagrams allow the representation (at a certain (...) level of abstractness) of the structures of molecules of different sorts. A diagram of such a language would be true if that which it sets out to depict exists in reality, i.e. if the structural relations between the names (and other bits and pieces in the diagram) map structural relations among the corresponding objects in the world. Otherwise it would be false. All of this should, of course, be perfectly familiar. (See, for example, Aristotle, Metaphysics, 1027 b 22, 1051 b 32ff.) The present paper seeks to go further than its predecessors, however, in offering a detailed account of the syntax of a working universal characteristic and of the ways in which it might be used. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

This essay narrates what I have learned from Søren Kierkegaard & John Dewey about teaching philosophy. It consists of three sections: 1) a Deweyan pragmatist’s translation of Kierkegaard’s religious insights on Christianity, as a way of life, into ethical insights on philosophy, as a way of life; 2) a brief description of the introductory course that I teach most frequently: Ethics, Happiness, & The Good Life; and 3) an exploration of three spiritual exercises from the course: a) self-cultivation by means (...) of writing in an Ethics Notebook, b) an “existential experiment” in which we practice one of Aristotle’s virtues for a week, and c) a 15-hour service-learning component. (shrink)

Do mountains exist? The answer to this question is surely: yes. In fact, ‘mountain’ is the example of a kind of geographic feature or thing most commonly cited by English speakers (Mark, et al., 1999; Smith and Mark 2001), and this result may hold across many languages and cultures. But whether they are considered as individuals (tokens) or as kinds (types), mountains do not exist in quite the same unequivocal sense as do such prototypical everyday objects as chairs or (...) people. (shrink)