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)

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)

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)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

The purpose of this book is to provide you with tools to become a better reader of nonfiction, argumentative texts.

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)

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 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)

Wie finden Medien Eingang in die Theorie der Rhetorik? Und wie findet Rhetorik Eingang in die Praxis der Medien? Der vorliegende Band erschließt die Beziehung zwischen der Rhetorik und den Medien sowohl historisch und systematisch als auch in aktuellen Fallstudien. Im ersten Teil wird dargelegt, wie die mediale Grundstruktur der Rhetorik reflektiert wurde – in die Bedeutung von Medien für das überzeugende Handeln von der Antike und Spätantike über Mittelalter, Renaissance, Barock sowie Aufklärung und Moderne bis zu gegenwärtigen Theorien. Im (...) systematischen Teil wird erörtert, wie das Verhältnis von Rhetorik und Medien in Bezug auf unterschiedliche Medienträger wie Bild, Rede, Musik, Architektur, Werbung, Websites etc. spezifiziert werden kann. Die Fallstudien stellen an konkreten Beispielen vor, wie sich die Mediengestaltung von heute der Rhetorik bedienen kann. Der Band liefert so einen umfassenden Einblick und ist somit für jeden Medienschaffenden eine wichtige Grundlage. (shrink)

Introduction: Conversion and the practice of transformation -- The philosophical structure of Jonathan Edwards's religious affections -- Habit, habit change, and conversion in C.S. Peirce -- Reconstructing faith : religious overcoming in Dewey's pragmatism -- Transforming obligation in William James -- Dwelling in absence: the reflective origin of conversion -- Creative transformation : the work of conversion -- The evasion of conversion in recent American philosophy.

Comment devient-on philosophe? Par quel sursaut un Aristoclès se fait-il Platon, jusqu'à s'imposer dans la liste des " auteurs philo " Il faut enquêter, non pas sur la vie privée, mais sur la vie intime : rumination intellectuelle, ton sur lequel on parle, motivations amoureuses... Ce qui fait un philosophe, c'est un immense travail sur soi, et la rencontre d'autres philosophes, vivants, de leurs problématiques. Mémoire sémantique + obsession métaphysique, voilà le code génétique du philosophe. Il débute par un attentat (...) religieux, puisqu'il commence sa carrière en niant tel ou tel sacré. Bien sûr, il vaut mieux être mâle, communiquer par les livres adopter la langue dominante, écrire quand on est célibataire. Comment gagner sa vie? Pas forcément en étant enseignant, comme c'est le cas aujourd'hui. Le profil du philosophe nous le révèle orphelin, vivant à l'étranger, souvent laid, jamais fou, et serial thinker, prêt à changer de philosophie pourvu qu'il reste, lui, à menacer le monde donnera ou donnera pas du sens à notre vie? Le philosophe est l'être inquiet qui pense inquiéter l'Être par deux trois mots bien aiguisés. (shrink)

The philosophy of Epictetus, a freed slave in the Roman Empire, has been profoundly influential on Western thought: it offers not only stimulating ideas but practical guidance in living one's life. A. A. Long, a leading scholar of later ancient philosophy, gives the definitive presentation of the thought of Epictetus for a broad readership. Long's fresh and vivid translations of a selection of the best of Epictetus' discourses show that his ideas are as valuable and striking today as they were (...) amost two thousand years ago. This is a book for anyone interested in what we can learn from ancient philosophy about how to live our lives. (shrink)

We present the opinion of some authors who believe there is no force between a stationary charge and a stationary resistive wire carrying a constant current. We show that this force is different from zero and present its main components: the force due to the charges induced in the wire by the test charge and a force proportional to the current in the resistive wire. We also discuss briefly a component of the force proportional to the square of the current (...) which should exist according to some models and another component due to the acceleration of the conduction electrons in a curved wire carrying a dc current (centripetal acceleration). Finally, we analyze experiments showing the existence of the electric field proportional to the current in resistive wires. (shrink)

Decisions by industry sponsors to end clinical trials early for commercial reasons have been the subject of controversy. I argue that the principal consideration in assessing these decisions ought to be the way in which the termination would affect the trial’s risk–benefit relationship. If there is not yet sufficient benefit to be gained from the study to offset the risks to which participants were exposed and it is expected that important scientific information would be obtained if the trial were continued, (...) early termination constitutes an unethical alteration of the risk−benefit relationship. This violates the grounds on which permission is given to conduct human research, patients consent to participate, and investigators agree to conduct studies. These knowable and avoidable changes in risk–benefit relationship should generally be seen as impermissible. (shrink)

A general theory of acts leads to a theory of cognition distinguishing between formation of apriorical knowledge about values, norms, and cognitive beliefs, based on conditioning by means of rewards and punishments, and formation of aposteriorical knowledge based on conscious, theoretical analysis of observations. The latter, rational layer of consciousness can be built on the former, irrational layer only, if certain conditions are fulfilled. It is shown that rational cognition of values presupposes a notion of aposteriorical value, which challenges some (...) conventions of the 'value-free' social science, in particular, the so called guillotine of Hume. (shrink)