Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and (...) information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain. (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 Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in the (...) regulation of gene expression and genome organisation. BioEssays 22:124–137, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

What is inequality? In the late 1990s there was an explosion of interest in the subject that yielded a substantial body of formal tools and results for income-distribution analysis. Nearly all of this is founded on a small set of core assumptions - such as the Principle of Transfers, scale independence, the population principle∑ - that are used to give meaning to specific concepts of inequality measurement, inequality ranking and, indeed, to inequality itself. But does the standard axiomatic structure coincide (...) with public perceptions of inequality? Or is the economist's concept of inequality a thing apart, perpetuated through serial brainwashing in the way the subject is studied and taught? In this 1999 book, Amiel and Cowell examine the evidence from a large international questionnaire experiment using student respondents. Along with basic 'cake-sharing' issues, related questions involving social-welfare rankings, the relationship between inequality and overall income growth and the meaning of poverty comparisons are considered. (shrink)

John Wilson, Barbara Cowell; The Democratic Myth, Journal of Philosophy of Education, Volume 17, Issue 1, 30 May 2006, Pages 111–117, https://doi.org/10.1111/j.

John Wilson, Barbara Cowell; The Democratic Myth, Journal of Philosophy of Education, Volume 17, Issue 1, 30 May 2006, Pages 111–117, https://doi.org/10.1111/j.

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (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)

Restoration ecology has recently emerged as a branch of scientific ecology that challenges many of the traditional tenets of environmentalism. Because the restoration of ecosystems, “applied ecology,” has the potential to advance theoretical understanding to such an extent that scientists can extensively manipulate the environment, it encourages increasingly active human participation within ecosystemsand could inhibit the preservation of areas from human influences. Despite the environmentally dangerous possibilities that this form of science and technology present, restoration offers an attractive alternative for (...) human interaction with the environment. I outline the primary claims that have been made for ecological restoration, examine inconsistencies with restorationists’ philosophical position,and propose a reassessment of the definition of restoration that may aid in the clarification and development of a system of environmental ethics that recognizes human relationships with the environment as potentially symbiotic and positive. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. 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 virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

Economic inequality has become a focus of prime interest for economic analysts and policy makers. This book provides an integrated approach to the topics of inequality and personal income distribution. It covers the practical and theoretical bases for inequality analysis, applications to real world problems and the foundations of theoretical approaches to income distribution. It also analyses models of the distribution of labour earnings and of income from wealth. The long-run development of income - and wealth - distribution over many (...) generations is also examined. Special attention is given to an assessment of the merits and weaknesses of standard economic models, to illustrating the implications of distributional mechanisms using real data and illustrative examples, and to providing graphical interpretation of formal arguments. Examples are drawn from US, UK and international sources. (shrink)

E4BP4, a mammalian basic leucine zipper (bZIP) transcription factor, was first identified through its ability to bind and repress viral promoter sequences. Subsequently, E4BP4 and homologues in other species have been implicated in a diverse range of processes including commitment to cell survival versus apoptosis, the anti‐inflammatory response and, most recently, in the mammalian circadian oscillatory mechanism. In some of these cases at least, E4BP4 appears to act antagonistically with members of the related PAR family of transcription factors with which (...) it shares DNA‐binding specificity. This diversity of function is mirrored by the regulatory pathways impinging on E4BP4, which include regulation by ras via the lymphokine IL‐3 in murine B‐cells, by thyroid hormone during Xenopus tail resorption, by glucocorticoids in murine fibroblasts and by calcium in rat smooth muscle cells. This article will cover the unfolding role/s of and regulation of E4BP4, E4BP4‐like proteins and PAR factors in species as diverse as mouse and C. elegans. BioEssays 24:1023–1029, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

Moral reasoning develops rapidly in early childhood. Recent evidence from cognitive neuroscience literature suggests that the development of moral reasoning is supported by an integration of cognitive and affective components. However, the role of culture in the development of moral reasoning in young children is under-investigated. Previous cross-cultural research suggests that culture shapes how people interpret other’s behaviors. In particular, people raised in independent cultures, such as the United States, tend to form impressions of others and attribute others’ behaviors to (...) their personal dispositions more quickly than people raised in interdependent cultures, such as Japan. In the present cross-cultural study, we examined parents’ discourse with children in Japan and the United States. Parents and their 3- to 4-year-old children were asked to view and discuss cartoon characters depicting prosocial and antisocial acts. Results indicated that in both cultures, parents discussed about moral actions of characters. Furthermore, United States parents were more likely to evaluate dispositional characteristics of characters based on their pro-social and anti-social acts, whereas Japanese parents were more likely to refer to emotion of the characters who got hurt. We discuss implications of cross-cultural differences and similarities in parental moral socialization and the development of moral reasoning in young children. (shrink)

Dialogues on moral education is directed at persons who wish to encounter many of the major issues confronting moral education in an interesting and highly readable fashion.

Abstract This paper considers the notion of ?social skills? from the viewpoint of analytic philosophy. The authors note first prejudices for and against an approach to human problems in terms of identificable ?skills?. They then stipulate a definition of ?social skills? in terms of techniques ('knowing how'), and point to other essential aspects of change and treatment which fall outside this definition (in particular, the aspects of attitude or desire and judgement). Some generalisations are attempted relevant to the question of (...) what problems are likely to yield to a ?social skills? approach, and what problems are likely to go deeper than such an approach can cure. Attention is drawn to the necessity of defining what is to count as success in such training, and the logical limits of ?social skills? training are clarified. (shrink)

We examine individuals’ distributional orderings in a number of contexts. This is done by using a questionnaire-experiment that is presented to respondents in any one of seven “flavors” or interpretations of the basic distributional problem. The flavors include inequality, risk, social welfare and justice.