In the present review we focus on what we take to be some remaining issues with the Behaviour Change Intervention Ontology (BCIO). We are in full agreement with the authors’ endorsement of the principles of best practice for ontology development In particular, we agree that an ontology should be “logically consistent and having a clear structures [sic], preferably a well-organised hierarchical structure,” and that “Maximising the new ontology’s interoperability with existing ontologies by reusing entities from existing ontologies where appropriate” is (...) critically important (Wright et al., 2020, p. 17). Our remaining concerns with BCIO relate directly to these two principles. First, we identify a number of issues with some of the classifications and definitions in BCIO that seem to be in tension with the just-mentioned principle . Second, we note some reservations about the reuse of certain classes in BCIO, namely from the Gazetteer (GAZ), the Ontology of Medically Related Social Entities (OMRSE), and the Information Artifact Ontology (IAO). While the latter principle of “reuse” is important, it is also important not to let the reuse of existing classes (or their corresponding definitions) compromise the logical integrity or the realist nature of one’s ontology. (shrink)

In “Ontologies Relevant to behaviour change interventions: A Method for their Development” Wright, et al. outline a step by step process for building ontologies of behaviour modification – what the authors call the Refined Ontology Developmental Method (RODM) – and demonstrate its use in the development of the Behaviour Change Intervention Ontology (BCIO). RODM is based on the principles of good ontology building used by the Open Biomedical Ontology (OBO) Foundry in addition to those outlined in (Arp, Smith, and Spear (...) 2015). BCIO uses as its top-level ontology Basic Formal Ontology (BFO). The methods outlined in Wright, et al. are a valuable contribution to the field, especially the use of formal mechanisms for literature annotation and expert stakeholder review, and the BCIO will certainly play an important role in the extension of OBO Foundry ontologies into the behavioural domain. (shrink)

Independently of whether an object of experience becomes a candidate for being a part of the self or a part of the external world, it is always given to us as just an object of experience. The observer-observed relation can be seen as a type of relation with many instances, both between the self and different objects of experience and between any given object of experience and different selves. The self is situated in a spatial grid, where the latter can (...) be characterised as an array of relations, of which the relata include both observers and observed. The world, understood as independent existence, including the self, is empty. However, Paolo Bozzi’s method for identifying the self and delimiting its independent existence from the external world has taught us just the opposite lesson. Bozzi’s project is to teach us how to use them, and to recognise that they allow a self to be situated in a world of objects. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

This article argues that we could improve the design of research protocols by developing an awareness of and a responsiveness to the social contexts of all the actors in the research enterprise, including subjects, investigators, sponsors, and members of the community in which the research will be conducted. ?Social context? refers to the settings in which the actors are situated, including, but not limited to, their social, economic, political, cultural, and technological features. The utility of thinking about social contexts is (...) introduced and exemplified by the presentation of a hypothetical case in which one central issue is limitation of the probability of injury to subjects by selection of individuals who are not expected to live long enough for the known risks of the study to become manifest as harms. Benefits of such considerations may include enhanced subject satisfaction and cooperation, community acceptance, and improved data quality, among other desirable consequences. (shrink)

This article argues that we could improve the design of research protocols by developing an awareness of and a responsiveness to the social contexts of all the actors in the research enterprise, including subjects, investigators, sponsors, and members of the community in which the research will be conducted. “Social context” refers to the settings in which the actors are situated, including, but not limited to, their social, economic, political, cultural, and technological features. The utility of thinking about social contexts is (...) introduced and exemplified by the presentation of a hypothetical case in which one central issue is limitation of the probability of injury to subjects by selection of individuals who are not expected to live long enough for the known risks of the study to become manifest as harms. Benefits of such considerations may include enhanced subject satisfaction and cooperation, community acceptance, and improved data quality, among other desirable consequences. (shrink)

This collection of essays on themes in the work of John Locke , George Berkeley , and David Hume , provides a deepened understanding of major issues raised in the Empiricist tradition. In exploring their shared belief in the experiential nature of mental constructs, The Empiricists illuminates the different methodologies of these great Enlightenment philosophers and introduces students to important metaphysical and epistemological issues including the theory of ideas, personal identity, and skepticism. It will be especially useful in courses devoted (...) to the history of modern philosophy. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

During the latter half of the twentieth century political realism dominated national and international landscapes. The twenty-first century has seen the rise of neo‐conservatism, what Charles Krauthammer has called “democratic realism” and what others see as a re-birth of Wilsonianism—making the world safe for democracy. Robert M. Gates, U.S. Secretary of Defense, in a speech on Sept. 17, 2007 in Williamsburg, VA, at the World Forum on the Future of Democracy, acknowledged these different strains of current U.S. policy, saying (...) that “once again [people are] talking about the competing impulses in U.S. foreign policy: realism versus idealism, freedom versus security, values versus interests.” These competing concerns—but especially fear about terrorism coupled with asense of retributive justice—have divided much of the world. Nonetheless, it is clear that no matter what terms one gives to domestic and foreign policies, they are all in one way or another mired in the attitude that the end justifies the means, an attitude that will remain both morally and politically bankrupt until such time as people, policies, and programs embrace the concept of principled nonviolence, if not principled nonviolence itself. (shrink)

This book shows that the repeated announcements of the death of Hegel's philosophical system have been premature. Hegel's Philosophy of Freedom, Reality, and God brings to light accomplishments for which Hegel is seldom given credit: unique arguments for the reality of freedom, for the reality of knowledge, for the irrationality of egoism, and for the compatibility of key insights from traditional theism and naturalistic atheism. The book responds in a systematic manner to many of the major criticisms leveled at Hegel's (...) system, from Feuerbach and Kierkegaard to Heidegger and Charles Taylor. It provides detailed interpretations of Hegel's Philosophy of Spirit, large parts of his indispensable Science of Logic, and important parts of his Philosophy of Nature and Philosophy of Right. Unlike many academic books on Hegel, this one treats him very much as a 'live' thinker, whom we can learn from today. (shrink)