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)

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 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)

Research ethics guidelines grew out of several infamous episodes where research subjects were exploited. There is significant international synchronization of guidelines. However, indigenous groups in New Zealand, Canada and Australia have criticized these guidelines as being inadequate for research involving indigenous people and have developed guidelines from their own cultural perspectives. Whilst traditional research ethics guidelines place a lot of emphasis on informed consent, these indigenous guidelines put much greater emphasis on interdependence and trust. This article argues that traditional guidelines (...) are premised on relationships of equal power, and that often the researcher has more power that is not fully equalized by providing information. Where there is a relationship of unequal power, then focusing on interdependence and trust is more likely to achieve ethical safety. We illustrate this thesis by describing the detail of a research project looking at the use of interpreters, where we video-recorded live consultations and then interviewed the patient, interpreter and doctor. We conclude by suggesting that mainstream research ethics guidelines should pay more attention to the development of a trustworthy relationship between subject and researcher, and that, following the lead from clinical medicine, we should develop a culturally competent ethical framework for research on human subjects. (shrink)

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)

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.

Despite ample evidence of the efficacy and effectiveness of evidence-based parenting programmes (EBPPs) within research-led environments, there is very little evidence of maintenance of effectiveness when programmes are delivered as part of regular service provision. The present study examined the effectiveness of EBPPs provided during a period of sustained service-led implementation in comparison to research-led effectiveness evaluation. Data from 3706 parents who received EBPPs during sustained implementation by services were compared to data from 1390 parents who had participated in an (...) earlier researcher-led effectiveness trial of a national roll-out of EBPPs in England. In both phases, parents completed measures of child behaviour problems, parenting style and parental mental well-being prior to starting parenting programmes (pre-test), at the end of the programmes (post) and at 12-months follow up. Results from Generalised Estimating Equations controlling for potential covariates indicated significant improvements in child behaviour problems during sustained implementation, similar to the effectiveness phase; significant improvements in parenting style which were larger than the effectiveness phase at 12-month follow up; and significant improvements in parental mental well- being. Our findings demonstrate effective maintenance of gains when EBPPs are provided as part of regular provision across a large sample of English parents. Successful long-term implementation should consider effectiveness of EBPPs across the population, given the large contextual changes that take place between researcher-led evaluations and service take-up. Our findings support the integration of EBPPs in public health approaches to addressing child behaviour problems and parent well-being. (shrink)

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.

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 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)

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)

First published in 1997. Routledge is an imprint of Taylor & Francis, an informa company.

Talk about time travel is puzzling even if it isn't obviously contradictory. Philosophers however are divided about whether time travel involves empirical paradox or some deeper metaphysical incoherence. It is suggested that time travel requires a Parmenidean four-dimensionalist metaphysical conception of the world in time. The possibility of time travel is addressed (mainly) from within a Parmenidean metaphysical framework, which is accepted by David Lewis in his defence of the coherence of time travel. It is argued that time travel raises (...) formidable difficulties which are not satisfactorily resolved by Lewis's ingenious defence of time travel. Objections to time travel considered include: (1) travel to other times is impossible because there is nowhere (or “nowhen”) to go to; (2) the problem that upon setting out on a journey to the past a time machine will collide with itself; (3) time travel generates a mysterious temporal dualism between experiential time and physical time; (4) travel to the past permits reverse causation, raising the possibility of causal loops and attendant problems arising, for example, from the prospect of empirical contradiction and the possibility of someone being one of their ancestors. (shrink)

The account of natural kinds as stable property clusters is premised on the possibility of separating the epistemic value of natural kinds from their underlying metaphysics. On that account, the co-instantiation of any sub-cluster of the properties associated with a given natural kind raises the probability of the co-instantiation of the rest, and this clustering of property instantiation is invariant under all relevant counterfactual perturbations. We argue that it is not possible to evaluate the stability of a cluster of properties (...) without taking stock of the metaphysical picture used to account for that stability. Thus, even on the stable property cluster account, the epistemic value of natural kinds remains partly grounded in their metaphysical status. (shrink)

Believing in God requires not only a leap of faith but also an extension of people’s normal capacity to perceive the minds of others. Usually, people perceive minds of all kinds by trying to understand their conscious experience (what it is like to be them) and their agency (what they can do). Although humans are perceived to have both agency and experience, humans appear to see God as possessing agency, but not experience. God’s unique mind is due, the authors suggest, (...) to the uniquely moral role He occupies. In this article, the authors propose that God is seen as the ultimate moral agent, the entity people blame and praise when they receive anomalous harm and help. Support for this proposition comes from research on mind perception, morality, and moral typecasting. Interestingly, although people perceive God as the author of salvation, suffering seems to evoke even more attributions to the divine. (shrink)

First published in 1997. Routledge is an imprint of Taylor & Francis, an informa company.

Traditional accounts of perception endorse an input–output model: perception is the input from world to mind and action is the output from mind to world. In contrast, enactive accounts propose action to be constitutive of perception. We focus on Noë's sensorimotor version of enactivism, with the aim of clarifying the proper limits of enactivism more generally. Having explained Noë's particular version of enactivism, which accounts for the contents of perceptual experience in terms of sensorimotor knowledge, we use taste as a (...) test for his central thesis. We conclude that taste and other similar senses do not display the central features which Noë claims apply to all perceptual experience. (shrink)

The moral status of future persons is problematic. It is often claimed that we should take the interests of the indefinite unborn very seriously, because they have a right to a decent life. It is also claimed (often by the same people) that we should allow unrestricted access to abortion, because the indefinite unborn have no rights. In this paper I argue that these intuitions are not in fact inconsistent. The aim is to provide an account of trans-temporal concern which (...) resolves the prima facie inconsistency between commonly held intuitions about our obligations to future persons. I argue that our intuitions can be reconciled provided that we explicate obligations to the future in terms of impersonal principles subject to retroactive person-affecting constraints. (shrink)

Web 2.0 innovations may enhance informed patient decision-making, but also raise ethical concerns about inaccurate or misleading information, damage to the doctor-patient relationship, privacy and confidentiality, and health disparities. To increase the benefits and decrease the risks of these innovations, we recommend steps to help patients assess the quality of health information on the Internet; promote constructive doctor-patient communication about new information technologies; and set standards for privacy and data security in patient-controlled health records and for point-of-service advertising.

Successful social functioning requires quick and accurate processing of emotion and generation of appropriate reactions. In typical individuals, these skills are supported by embodied processing, recruiting central and peripheral mechanisms. However, emotional processing is atypical in individuals with autism spectrum disorder (ASD). Individuals with ASD show deficits in recognition of briefly presented emotional expressions. They tend to recognize expressions using rule-based, rather than template, strategies. Individuals with ASD also do not spontaneously and quickly mimic emotional expressions, unless the task encourages (...) engagement. When processing emotional scenes, ASD individuals show atypical basic motivational responses, despite intact ability to verbally determine stimulus valence. We discuss how these findings highlight the contribution of both embodied and disembodied mechanisms to typical and atypical emotional functioning. (shrink)

Collected here in a single volume for the first time, On Liberty, Utilitarianism, Considerations on Representative Government, and The Subjection of Women show Mill applying his liberal utilitarian philosophy to a range of issues that remain vital today - issues of the nature of ethics, the scope and limits of individual liberty, the merits of and costs of democratic government, and the place of women in society. In his Introduction John Gray describes these essays as applications of Mill's doctrine of (...) the Art of Life, as set out in A System of Logic. Using the resources of recent revisionist scholarship, he shows Mill's work to be far richer and subtler than traditional interpretations allow. (shrink)

A novel Protocol Ethics Tool Kit (‘Ethics Tool Kit’) has been developed by a multi-stakeholder group of the Multi-Regional Clinical Trials Center of Brigham and Women9s Hospital and Harvard. The purpose of the Ethics Tool Kit is to facilitate effective recognition, consideration and deliberation of critical ethical issues in clinical trial protocols. The Ethics Tool Kit may be used by investigators and sponsors to develop a dedicated Ethics Section within a protocol to improve the consistency and transparency between clinical trial (...) protocols and research ethics committee reviews. It may also streamline ethics review and may facilitate and expedite the review process by anticipating the concerns of ethics committee reviewers. Specific attention was given to issues arising in multinational settings. With the use of this Tool Kit, researchers have the opportunity to address critical research ethics issues proactively, potentially speeding the time and easing the process to final protocol approval. (shrink)

Although torture can establish guilt through confession, how are judgments of guilt made when tortured suspects do not confess? We suggest that perceived guilt is based inappropriately upon how much pain suspects appear to suffer during torture. Two psychological theories provide competing predictions about the link between pain and perceived blame: cognitive dissonance, which links pain to blame, and moral typecasting, which links pain to innocence. We hypothesized that dissonance might characterize the relationship between torture and blame for those close (...) to the torture, while moral typecasting might characterize this relationship for those more distant from it. Accordingly, this experiment placed participants into one of two different roles in which people may be exposed to torture. Participants in the proximal role of prison staffer saw suffering torture victims as relatively more guilty, while participants in the relatively distant role of a radio listener saw suffering victims as more innocent. (shrink)

Empowering Affected Interests brings together a group of leading contemporary democratic theorists and philosophers to debate a taken-for-granted principle at the heart of the democratic project but increasingly under strain in a global era: the idea all those affected by a decision should be included in the making of that decision.

This study focused on the influence of American and Chinese cultures on consequentialism orientation in decision-making within the broader context of psychologists’ academic roles and responsibilities. In addition, this study hypothesized that educational level would affect culturally influenced ethical decision making in both cultures. Based on the American Psychological Association Ethics Code, 20 ethical scenarios in 5 domains in psychology were created and used to examine the influence of culturally ethical beliefs on psychologists’ decision making among 181 participants. The results (...) indicated that significant cultural differences in consequentialism orientation differentiated Chinese and American participants and influenced their resolution of ethical issues. (shrink)