Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (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)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (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)

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)

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)

Written by five scholars whose expertise extends across the disciplines of biblical, historical, systematic, and philosophical theology, this is a careful and ...

It is a daunting task to tell the story of the lives emotions lead, how they are rooted in the deeper folds of the person’s psyche and wax and wane over a lifetime. Wollheim’s book is at times a daring attempt to cast an analytic philosopher in the role of narrator of this fascinating but hard to follow story. Two related story lines run through his book. One repeatedly criticizes contemporary philosophers for turning a blind eye to the psychological reality (...) and developmental nature of desire and emotion. The other, containing the book’s main project, develops an account of the characteristic history of an emotion from its origins in a satisfied or frustrated desire, to the formation of an attitude that lies at the core of an emotion, and finally to the fantasized critic in moral emotions such as shame and guilt. How we rate the success of the project depends in no small part on how we assess the relation between these two themes. (shrink)

The reliable covariation between numerosity and spatial extent is considered as a strong constraint for inferring the successor principle in numerical cognition. We suggest that children can derive a general number concept from the (experientially) infinite succession of spatial positions during object manipulation.

An accessible selection of Professor Gombrich's best and most characteristic writing.

Contents/Inhalt: Preface. Vorwort. Abbreviations/Siglen. I. JASPERS ON WORLD PHILOSOPHY AND WORLD HISTORY OF PHILOSOPHY/JASPERS ÜBER WELT-PHILOSOPHIE UND WELTGESCHICHTE DER PHILOSOPHIE. Nekrolog von Karl Jaspers selbst verfaßt. Obituary by Karl Jaspers himself. Karl JASPERS: Weltgeschichte der Philosophie - Zweites Buch: Geschichte der Gehalte: Einleitung. Karl JASPERS: World History of Philosophy - Second Volume: History of the Substantive Contents of Philosophic Thought. Introduction. II. INTRODUCTION/EINLEITUNG. Leonard H. EHRLICH: Opening Remarks. Introduction of Jeanne Hersch, Honorary President of the Conference. Jeanne HERSCH: Von der (...) Wirkung einer "philosophia negativa". III. LEGACY AND TASK. VERMÄCHTNIS UND AUFGABE. Leonard H. EHRLICH: Ausblick: Vernunft, Geist, Geschichte. Sawako HANYU: the Concept of the "Encompassing" in World Philosophy. Andreas RINOFNER: Periechontologie und Weltgeschichte der Philosophie. Systematische Bemerkungen zu einem aufschlußreichen Verhältnis. Richard WISSER: Projekt und Vision einer "Weltgeschichte der Philosophie" und "Weltphilosophie" als Folgen der "Grundverfassung" von Karl Jaspers. IV. DIMENSIONS OF COMMUNICATION/RÄUME DER KOMMUNIKATION. Andreas CESANA: Grenzen der Rationalität und Kommunikation. Brenio ONETTO-BÄCHLER: Existentielle Kommunikation bei Jaspers. Czes_awa PIECUCH: Es ist gleichgültig, wer die Wahrheit ausspricht. Über die Uneigennützigkeit der existentiellen Kommunikation. Oswald O. SCHRAG: Existence, Existenz, and Social Organization. Vladimir KATASONOV: The Gadfly, Stinging the Sluggish Horse: The Socratic Mission of Jaspers's Philosophy. V. COMMUNICATIVE WORLD HISTORY OF PHILOSOPHY/KOMMUNIKATIVE WELTGESCHICHTE DER PHILOSOPHIE. Albrecht KIEL: Die Weisen des Umgreifenden, die der Mensch ist: Wege zu Jaspers' Periechontologie. Maria Luisa BASSO: K. Jaspers - N. Berdiaeff: une confrontation entre deux philosophies de l'histoire. Convergence et divergence d'affirmations. Inigo BOCKEN: Kommunikation und Mutmaßung. Versuch eines Vergleichs zwischen Jaspers' Idee einer Philosophie der Kommunikation und Nikolaus von Kues' Kunst der Mutmaßungen. Boles_aw ANDRZEJEWSKI: Jaspers' Stellung zur Romantik im Lichte seiner Sprachphilosophie. Endre KISS: Karl Jaspers' Auslegung Nietzsches als eines Metaphysikers der Immanenz. Danièle MOYAL-SHARROCK: Genie et Folie selon Jaspers. Milan UZELAC: The World and Existence. Pablo LÓPEZ-LÓPEZ: Das Studium der Philosophie als Studium der Weltgeschichte der Philosophie. VI. COMMUNICATIVE WORLD PHILOSOPHY: EAST AND WEST/KOMMUNIKATIVE WELTPHILOSOPHIE: OST UND WEST. Wonjae LEE: Karl Jaspers und das Weltproblem des interreligiösen Dialogs. Silvia MARZANO: Comunicazione mondiale, kantismo e frattura dell'essere in Karl Jaspers. Una "terza via" fra Occidente e Oriente? Indu SARIN: Jaspers's Quest for Existential Communication. Mohammed MARUF: Jaspers and Iqbal on Self, Freedom and Communication. Subhadr PANYADEEP: Ich und Nicht-Ich bei Jaspers und im Buddhismus. Kazuteru FUKUI: Das Wesen des Buddhismus und Jaspers' Philosophie. Yukio MASUBUCHI: Jaspers und Nishida. Eine Theorie des "Topos" in der Lehre von der Kommunikation. Hans SANER: Weltphilosophie und Globalkultur im interkulturellen Vergleich mit den Konzepten "Weltmusik" und "Weltkunst". Gerhard RAUCHE: The Paradox of " Das Scheitern " as a World Formula. VII. COMMUNICATIVE WORLD PHILOSOPHY: FREEDOM AND TOLERANCE/KOMMUNIKATIVE WELTPHILOSOPHIE: FREIHEIT UND TOLERANZ. Anna MASÓ-MONCLÚS: Libertad y autoridad en Hannah Arendt y Karl Jaspers. Otmar KLEIN: "Weltverabsolutierung" und Verantwortungsverlust. Kurt SALAMUN: Grenzen der Toleranz. Zum Offenheits- und Toleranzparadigma in der Philosophie von Karl Jaspers. Giorgio PENZO: Politik als Ethos und das Problem der Freiheit bei Jaspers. Gerhard KNAUSS: Von der Weimarer Republik zur Weltpolitik. Wandlungen in Jaspers' Auffassung und Wertung der Politik von der Heidelberger Frühschrift "Die geistige Situation der Zeit" bis zu den Basler Spätschriften. Hermann-Josef SEIDENECK: Freiheit und Wiedervereinigung auf dem Prüfstand. Prognose und Ergebnis unter dem Blickwinkel von existentieller Kommunikation im Welthorizont. Appendix/Anhang. (shrink)

The aim of this article is to describe the phenomenon of male rape from the victims’ perspectives. The methodology employed relied on transcendental phenomenology in order to create the rich descriptions of the lived experiences of three male survivors of rape. From the descriptions elicited from the formulation of an open-ended question, it was discovered that the phenomenon of male rape has a dominant structure that is related to the destruction and reconstruction of the masculine self. The research also revealed (...) several textural themes that include the characteristics of the assault, treatment and support that victims receive, the effects of the assault on the self, disclosure, the learning and life changes brought about by the assault, the victims’ feelings towards their assailants and the effect of the assault on the victims’ relationships. This study hopes to facilitate further descriptive research on the phenomenon of male rape in order that greater knowledge be gleaned and applied regarding its prevention and healing processes. (shrink)

The contributions to this volume, selected papers from several conferences held in conjunction with the centenary of Karl Jaspers's birth, constitute the first reassessment of his significance as philosopher and scholar since his death in 1969.

The contributions to this volume, selected papers from several conferences held in conjunction with the centenary of Karl Jaspers's birth, constitute the first reassessment of his significance as philosopher and scholar since his death in 1969.