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)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (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)

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 global pesticide complex has transformed over the past two decades, but social science research has not kept pace. The rise of an enormous generics sector, shifts in geographies of pesticide production, and dynamics of agrarian change have led to more pesticide use, expanding to farm systems that hitherto used few such inputs. Declining effectiveness due to pesticide resistance and anemic institutional support for non-chemical alternatives also have driven intensification in conventional systems. As an inter-disciplinary network of pesticide scholars, we (...) seek to renew the social science research agenda on pesticides to better understand this suite of contemporary changes. To identify research priorities, challenges, and opportunities, we develop the pesticide complex as a heuristic device to highlight the reciprocal and iterative interactions among agricultural practice, the agrochemical industry, civil society-shaped regulatory actions, and contested knowledge of toxicity. Ultimately, collaborations among social scientists and across the social and biophysical sciences can illuminate recent transformations and their uneven socioecological effects. A reinvigorated critical scholarship that embraces the multifaceted nature of pesticides can identify the social and ecological constraints that drive pesticide use and support alternatives to chemically driven industrial agriculture. (shrink)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (shrink)

Barry Allen, in his 2005 Knowledge and Civilization and his 2008 Artifice and Design, argues in favor of an epistemic system that is both praxical and performative; knowledge, rather than being expressed propositionally, is a kind of performance that is expressed in artifacts of all kinds, of which propositions are but an example. However, although he makes a compelling case, it is rather less clear the extent to which we are able to make judgments about the world beneath the (...) artifacts. That is to say: it seems clear that we need to provide some account of how the world is, if only so that we have some kind of coherent characterization of what it is exactly that an artifact captures. Accordingly, if we are to buy into Allen’s model, what can we subsequently say about Allen’s metaphysics? This paper is an attempt to tease out some of these concerns. (shrink)

This dissertation examines the relationship that exists between two distinct and seemingly incompatible bodies of scholarship within the field of contemporary philosophy of technology. The first, as argued by postmodern pragmatist Barry Allen, posits that our tools and what we make with them are epistemically important; disputing the idea that knowledge is strictly sentential or propositional, he claims instead that knowledge is the product of a performance that is both superlative and artefactual, rendering technology importantly world-constituting. The second, as (...) argued by Heidegger and his inheritors, is that technology is ontologically problematic; rather than technology being evidence of performative knowledge, it is instead existentially threatening by virtue of the fact that it changes the tenor of our relationship with the world-as-given. Despite the fact that these claims seem prima facie incompatible, I argue that they may be successfully reconciled by introducing a third body of scholarship: the philosophy of photography. For it is the case, I argue, that although we, qua human beings, occupy lifeworlds that are necessarily constituted by technology, technology also induces a kind of phenomenological scepticism: a concern that mediated action precludes us from the possibility of authentic experience. Arguing in favour of the sentiment that photographs serve as a kind of phenomenal anchor—a kind of machine for living—I claim that photographic images provide a panacea to this existential concern: despite being epistemically problematic, it is this selfsame epistemic “specialness” of photographs that forces us to phenomenologically recommit, if only temporarily, to the world in a serious way. Consequently, it is my belief that an analysis of our artefacts and the way they function is fundamentally incomplete without an analysis of the epistemic and ontological problems introduced of the photographic image; as I will demonstrate, the photographic image casts an extremely long shadow over the philosophy of technology. (shrink)

The merit system is based on a person’s ability to achieve. The concept of merit hence rejects a process that awards any particular entitlement explicitly based on disability. Brian Barry says that under the merit principle, people can compete for positions or advantage. This paper argues that the idea of merit, as explained by Barry, is unjust. Iris Marion Young points out that a person with cognitive disability faces a different situation compared to other people. Under normal circumstances, (...) persons can have skills that enable them to do things with ease, something that is not readily available to individuals with autism or Asperger’s syndrome. The problem is also exacerbated by policies that do not recognize the diverse needs of individuals with impairment. In this regard, practical ethics demands that a law or national policy must ensure a level playing field for everyone. (shrink)

In this paper we apply the popular Best System Account of laws to typical eternal worlds – both classical eternal worlds and eternal worlds of the kind posited by popular contemporary cosmological theories. We show that, according to the Best System Account, such worlds will have no laws that meaningfully constrain boundary conditions. It’s generally thought that lawful constraints on boundary conditions are required to avoid skeptical arguments. Thus the lack of such laws given the Best System Account may seem (...) like a severe problem for the view. We show, however, that at eternal worlds, lawful constraints on boundary conditions do little to help fend off skeptical worries. So with respect to handling these skeptical worries, the proponent of the Best System Account is no worse off than their competitors. (shrink)

For several decades, renewed interest in the connection between perception and knowledge has sustained a robust debate over external world skepticism. Recently, however, a growing consensus claims the skeptical challenge has been substantially met, and that realism in some robust form has emerged a clear victor. I invite us to rethink this consensus in a two-part response. The first forges a temporary alliance with skepticism against prominent forms of contemporary realism. That these fail to rebuff ews bolsters Barry Stroud’s (...) call for a new paradigm of objectivity. In the second part I sketch such a paradigm based upon a transactional interpretation of John Dewey’s pragmatism, and indicate its resilience to skeptical attacks. (shrink)

Modern Christians often polarize the otherwise inseparable realities of academic reading and personal reading of Scripture. While generally not declared outright, many Christians consider the two methods discontinuous. This article deems this bifurcation unnecessary and dangerous to the spiritual formation of individuals and the spiritual health of the church. It examines Bonaventure's insightful use of the quadriga in order to contribute to today's discussion of spiritual reading of Scripture. The article shall argue that Bonaventure's quadrigal method ought to be retrieved (...) today for the spiritual health of scholarship and the church. This thesis will be attained organically. It will first survey his proposed method of interpretation in his Breviloquium and Commentary on the Gospel of Luke; then, it will appeal to scriptural and pastoral support to show that his method is a helpful route for retrieval. (shrink)

The inclusion of engineering standards in US science education standards is potentially important because of how limited engineering education for K-12 learners is, despite the ubiquity of engineering in students’ lives. However, the majority of learners experience science education throughout their compulsory schooling. If improved engineering literacy is to be achieved, then its inclusion in science curricula is perhaps the most efficient means. One significant challenge that arises, however, is in the framing of engineering relative to science by both teachers (...) and curriculum. Science and engineering are both distinct and interdependent. The nature of the contributions of science and engineering to one another has been an area of some examination in philosophy of technology and engineering, but little framing of this relationship has been conducted with K-12 science and engineering education contexts in mind. Nature of science is a critical layer of scientific understanding that has been used to explicitly support literacy in K-16 science classrooms for decades. However, engineering cannot be authentically and appropriately supported by NOS framing. There is an immediate need for discourse on the nature of engineering knowledge but not in isolation of NOS. Given the increasing inclusion of engineering in science classrooms, relationships between NOS and NOEK are in need of explication and argument. Our purpose is to promote a discussion about NOS, engineering, and the relationship between them without misrepresenting engineering as a subdomain of science or as an oversimplification of itself. (shrink)

In this paper I argue that the propositional model of Divine revelation deserves renewed attention due to both criticisms stemming from misunderstanding and recent arguments in favor of the propositional model. I begin by clarifying what I mean by the propositional model of Divine revelation and by pointing out misunderstandings of the implications of this model. Subsequently, I offer a few arguments in favor of the propositional model of Divine revelation based on three assumptions that I take to be basic (...) elements of Christianity. Finally, I explain why I think the propositional model is doctrinally significant for the Christian Faith. (shrink)

This article looks at Colossians 2-3:17 and John 17:13-26 as the base texts to see the commonalities between Johannine and Pauline conceptions of Theosis. First, the article looks at indwelling and participation as the methods of Theosis in the two traditions. Second, the role of mimesis is seen to be integral in these texts' concepts of Theosis. Third, the article looks at hope and glory that believers have and look forward to as indicative of their deification. The study begins by (...) defining the term Theosis and its cognate terms - deification and divinisation - properly, within an Orthodox Christian context. CONTRIBUTION: The goal is to see and detail the concept of Theosis in Pauline and Johannine literature, looking at Colossians 2-3:17 and John 17:13-26 specifically. As such, the present study will broaden the discussion the doctrine of Theosis as it appears in the Christian scriptures. (shrink)

In recent years, there has been a distinct shift in the relationship between science and society. We have moved away from the classic unidirectional “deficit” model (Simis et al. 2016) focused on t...

The beatific vision is a subject of considerable importance both in the Christian Scriptures and in the history of Christian dogmatics. In it, humans experience and see the perfect immaterial God, which represents the final end for the saints. However, this doctrine has received less attention in the contemporary theological literature, arguably, due in part to the growing trend toward materialism and the sole emphasis on bodily resurrection in Reformed eschatology. As a piece of retrieval by drawing from the Scriptures, (...) Medieval Christianity, and Reformed Christianity, we motivate a case for the Reformed emphasis on the immaterial and intellectual aspects of human personal eschatology and offer some constructive thoughts on how to link it to the contemporary emphasis of the body. We draw a link between the soul and the body in the vision with the help of Christology as reflected in the theology of John Calvin, and, to a greater extent, the theology of both John Owen and Jonathan Edwards. (shrink)

What may seem astonishing is the near dismissal of the beatific vision doctrine in the last 50+ years of biblical and theological scholarship in contrast to the emphasis given to it throughout church history. The state of theological scholarship is changing. In what follows, we set forth a short survey of a theology of the beatific vision, while also introducing the rest of the volume on the beatific vision and theosis, of which we take to have an intimate and overlapping (...) relationship. The editorial article has four parts: it begins by (1) introducing some of the relevant biblical material on the vision, proceeding to (2) develop a theological interpretation of those passages, and then (3) offer a short historical survey of the doctrine, focusing on the relevant medieval and Reformed developments. It finally (4) introduces the articles of the issue. (shrink)

The Metaphysical Club, a gathering of intellectuals in the 1870s associated with Harvard, is widely recognized as the crucible where pragmatism, America's distinctively original philosophy, was refined and proclaimed. Louis Menand's bestseller about the group was a dramatic publishing success. However, only three actual members - Oliver Wendell Holmes Jr., Charles S. Peirce, and William James - appear in this book, alongside other thinkers such as John Dewey who were never in the Club. The Real Metaphysical Club tells the full (...) story of how this influential group shifted the course of philosophy in America. In addition to pioneering pragmatism, the group explored radical empiricism and idealism, and formulated personalism and process philosophy, equally important developments. This volume contains thirty-seven important writings dating from 1870 to 1885 by the real members of the Metaphysical Club. The first section centers on pragmatism and science; the second part collects writings of the lawyers; and the third part covers idealist and personalist philosophers. Many of these writings have never been reprinted before, and nothing like this impressive collection has ever been attempted. A general introduction provides a narrative history, and the editors' three introductions to the volume's sections vividly bring to life the intense meetings, sustained debates, and pioneering thought from the Metaphysical Club. (shrink)

There is a critical need to establish a space to engage in careful deliberation amid exciting, important, necessary, and groundbreaking technological and clinical advances in pediatric medicine. Extracorporeal membrane oxygenation (ECMO) is one such technology that began in pediatric settings nearly 50 years ago. And while not void of medical and ethical examination, both the symbolic progression of medicine that ECMO embodies and its multidimensional challenges to patient care require more than an intellectual exercise. What we illustrate, then, is a (...) person-centered framework that incorporates the philosophy and practice of palliative care and care-based ethical approaches. This person-centered framework is valuable for identifying and understanding challenges central to ECMO, guides collaborative decision-making, and recognizes the value of relationships within and between patients, families, healthcare teams, and others who impact and are impacted by ECMO. Specifically, this person-centered approach enables caregivers to provide compassionate and effective support in critical, and often urgent, situations where conflicts may emerge among healthcare team members, families, and other decision makers. By reflecting on three cases based on actual situations, we apply our person-centered framework and identify those aspects that were utilized in and informed this project. We aim to fill a current gap in the pediatric ECMO literature by presenting a person-centered framework that promotes caregiving relationships among hospitalized critically ill children, families, and the healthcare team and is supported through the philosophy and practice of palliative care and clinical ethics. (shrink)

Coronavirus disease 2019 can lead to respiratory failure. Some patients require extracorporeal membrane oxygenation support. During the current pandemic, health care resources in some cities have been overwhelmed, and doctors have faced complex decisions about resource allocation. We present a case in which a pediatric hospital caring for both children and adults seeks to establish guidelines for the use of extracorporeal membrane oxygenation if there are not enough resources to treat every patient. Experts in critical care, end-of-life care, bioethics, and (...) health policy discuss if age should guide rationing decisions. (shrink)

The negative emotions generated following stressful life events can increase one’s risk of depressive symptoms and promote higher levels of perceived stress. The process model of emotion regulation can help distinguish between adaptive and maladaptive emotion regulation strategies to determine who may be at the greatest risk of worse psychological health across the lifespan. Heart rate variability may affect these relationships as it indexes aspects of self-regulation, including emotion and behavioral regulation, that enable an individual to dynamically adapt to the (...) changing demands of both internal and external environments. In this study, we expected individual differences in resting vagally mediated HRV to moderate the influence of emotion regulatory strategies among our sample of 267 adults. We found support for the hypothesis that higher vagally mediated HRV buffers against the typical adverse effects of expressive suppression when evaluating depressive symptoms and found weak support when considering perceived stress. There was no evidence for an interaction between cognitive reappraisal and vagally mediated HRV but there was a significant, negative association between cognitive reappraisal and depressive symptoms and perceived stress. Future work may determine if intervening on either emotion regulation strategies or HRV may change these within-persons over time. (shrink)

This collection of essays, offered in honor of the distinguished career of prominent political philosophy professor Clifford Orwin, brings together internationally renowned scholars to provide a wide context and discuss various aspects of the virtue of “humanity” through the history of political philosophy.

This collection of essays, offered in honor of the distinguished career of prominent political philosophy professor Clifford Orwin, brings together internationally renowned scholars to provide a wide context and discuss various aspects of the virtue of “humanity” through the history of political philosophy.