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)

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 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)

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)

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)

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)

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)

Isidore Etymologiae Vol. II. Books XI-XX.

The nature/nurture debate is not dead. Dichotomous views of development still underlie many fundamental debates in the biological and social sciences. Developmental systems theory offers a new conceptual framework with which to resolve such debates. DST views ontogeny as contingent cycles of interaction among a varied set of developmental resources, no one of which controls the process. These factors include DNA, cellular and organismic structure, and social and ecological interactions. DST has excited interest from a wide range of researchers, from (...) molecular biologists to anthropologists, because of its ability to integrate evolutionary theory and other disciplines without falling into traditional oppositions. The book provides historical background to DST, recent theoretical findings on the mechanisms of heredity, applications of the DST framework to behavioral development, implications of DST for the philosophy of biology, and critical reactions to DST. (shrink)

Stem cells derived from pluripotent cells offer the hope of new treatments for diseases for which current therapy is inadequate. Clinical trials are essential in developing effective and safe stem cell therapies and fulfilling this promise. However, such clinical trials raise ethical issues that are more complex than those raised in clinical trials using drugs, cord blood stem cells, or adult stem cells. Several clinical trials are now being carried out with stem cells derived from pluripotent cells, and many more (...) can be expected in light of the rapid scientific progress in the field.Degenerative neurological diseases are desirable targets for stem cell clinical trials. The FDA has approved Phase 1 clinical trials of neural stem cell transplantation for Batten Disease, Pelizaeus-Merzbacher Disease, and spinal cord injury. In Parkinson Disease, stem cell transplantation could correct the primary pathophysiological defect — inadequate levels of the neurotransmitter dopamine. Current treatment is unsatisfactory in late-stage PD. (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.

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

The uncanny valley—the unnerving nature of humanlike robots—is an intriguing idea, but both its existence and its underlying cause are debated. We propose that humanlike robots are not only unnerving, but are so because their appearance prompts attributions of mind. In particular, we suggest that machines become unnerving when people ascribe to them experience, rather than agency. Experiment 1 examined whether a machine’s humanlike appearance prompts both ascriptions of experience and feelings of unease. Experiment 2 tested whether a machine capable (...) of experience remains unnerving, even without a humanlike appearance. Experiment 3 investigated whether the perceived lack of experience can also help explain the creepiness of unfeeling humans and philosophical zombies. These experiments demonstrate that feelings of uncanniness are tied to perceptions of experience, and also suggest that experience—but not agency—is seen as fundamental to humans, and fundamentally lacking in machines. (shrink)

There has recently been a flurry of activity in the philosophy of language on how to best account for the unique features of epithets. One of these features is that epithets can be appropriated (that is, the offense-grounding potential of a term can be removed). We argue that attempts to appropriate an epithet fundamentally involve a violation of language-governing rules. We suggest that the other conditions that make something an attempt at appropriation are the same conditions that characterize acts of (...) civil disobedience. Accounting for attempts at appropriation is thus both a linguistic and socio-political endeavor. We demonstrate how these two facets of attempts at appropriation also help us understand the communicative features of civil disobedience. (shrink)

In an increasingly complex world with increasingly powerful organisations it seems inevitable that society – or groups in society – would become anxious about whether these organisations could be encouraged to match that power with an appropriate responsibility. This is the function of accountability – to require individuals and organisations to present an account of those actions for which society holds them – or would wish to hold them – responsible. And the history of social accounting, at its most fundamental, (...) is a history of attempts to develop this accountability. It seems to me that the widespread and systematic practice of social and environmental accounting is a deeply essential element in any well‐functioning, complex democracy. The corollary is that the absence of such mechanisms raises fundamental questions about the nature of modern democracies. This article briefly outlines what I believe to be the three strands of social accounting. It then identifies a few of the lessons that we may be able to learn from current experience and, in particular, how social accounting is related to accountability, democracy and sustainability. The central issue of the tension between accountability and control is touched upon: I then illustrate how the stakeholder model can be used to help define the social account, and conclude with a few words on attestation. (shrink)

When someone steps on your toe on purpose, it seems to hurt more than when the person does the same thing unintentionally. The physical parameters of the harm may not differ—your toe is flattened in both cases—but the psychological experience of pain is changed nonetheless. Intentional harms are premeditated by another person and have the specific purpose of causing pain. In a sense, intended harms are events initiated by one mind to communicate meaning (malice) to another, and this could shape (...) the recipient’s experience. This study examined whether self-reported pain is indeed higher when the events producing the pain are understood as intentionally (as opposed to unintentionally) caused by another person. Although pain was traditionally conceived to be solely physical in nature (Aydede, 2005), its experience varies substantially with psychological context. The placebo analgesia effect, for example, is the reduction of pain without a change in physical stimulation when context, expectations, or sugar pills challenge the interpretation of a sensation as painful (e.g., Fields, 2008). The nocebo effect, in turn, is the experience of pain without any physical stimulation—as when participants report headaches when told that a (nonexistent) electric current is passing through their heads (Schweiger & Parducci, 1981). These variations in pain experience seem to depend on the meaning of the stimulus: A sugar pill is meant to decrease pain, whereas electric current is meant to increase pain. In an interpersonal context, the meaning of an action is derived from the would complete. perceiver’s perceptions of the actor’s intention (Clark, 1996). (shrink)

Our experiences of heat and cold are usually thought to represent states of things: their hotness and coldness. I propose a novel account according to which their contents are not states of things but processes, more specifically, the opposite processes of thermal energy being transmitted to and from the body, respectively. I call this account the Heat Exchange Model of heat perception. Having set out the evidence in support of the proposal, I conclude by showing how it provides a new (...) perspective on some old problems. (shrink)

The first part of this paper surveys the current literature in the history of nineteenth-century mathematics in order to show that the question “Did the increasing abstraction of mathematics lead to a sense of anxiety?” is a new and valid question. I argue that the mathematics of the nineteenth century is marked by a growing appreciation of error leading to a note of anxiety, hesitant at first but persistent by 1900. This mounting disquiet about so many aspects of mathematics after (...) 1850 is seldom discussed. The second part explores the issue of anxiety in mathematical life through an interesting account of an address made by a mathematician in 1911, Oscar Perron. The third and final part ventures some conclusions about the value of anxiety as a question for historians of mathematics to pursue. (shrink)

Acquiring expertise in a task is often thought of as an automatic process that follows inevitably with practice according to the log‐log law (aka: power law) of learning. However, as Ericsson, Chase, and Faloon (1980) showed, this is not true for digit‐span experts and, as we show, it is certainly not true for Tetris players at any level of expertise. Although some people may simply “twitch” faster than others, the limit to Tetris expertise is not raw keypress time but the (...) techniques acquired by players that allow them to use the tools provided by the hardware and software to compensate for the game's relentlessly increasing drop speed. Unfortunately, these increases in drop speed between Tetris levels make performance plateaus very short and quickly followed by game death. Hence, a player's success at discovering, exploring, and practicing new techniques for the tasks of board preparation, board maintenance, optimal placement discovery, zoid rotation, lateral movement of zoids, and other tasks important to expertise in Tetris is limited. In this paper, we analyze data collected from 492 Tetris players to reveal the challenges they confronted while constructing expertise via the discovery of new techniques for gameplay at increasingly difficult levels of Tetris. (shrink)

This volume presents an English translation of Nietzsche's Unzeitgemasse Betrachtungen or, Unfashionable Observations. The common impulse that links up these four essays is Nietzsche's attitude towards all mainstream and popular movements that constituted contemporary European, and especially German culture. The work offers the foundations for Nietzsche's whole philosophy, prefiguring both his characteristic philosophical style and many of the major ideas he develops in his later writings.

Two proposals have recently, and independently, been made about a space of possible sensory modalities. In this paper I examine these different proposals, and offer one of my own. I suggest that there are several spaces associated with distinct kinds of sensory modality.