The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (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 Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Consent remains a crucial, yet challenging, cornerstone of clinical practice. The ethical, legal and professional understandings of this construct have evolved away from a doctor-centred act to a patient-centred process that encompasses the patient’s values, beliefs and goals. This alignment of consent with the philosophy of shared decision-making was affirmed in a recent high-profile Supreme Court ruling in England. The communication of information is central to this model of health care delivery but it can be difficult for doctors to gauge (...) the information needs of the individual patient. The aim of this paper is to describe ‘core information sets’ which are defined as a minimum set of consensus-derived information about a given procedure to be discussed with all patients. Importantly, they are intended to catalyse discussion of subjective importance to individuals. The model described in this paper applies health services research and Delphi consensus-building methods to an idea orginally proposed 30 years ago. The hypothesis is that, first, large amounts of potentially-important information are distilled down to discrete information domains. These are then, secondly, rated by key stakeholders in multiple iterations, so that core information of agreed importance can be defined. We argue that this scientific approach is key to identifying information important to all stakeholders, which may otherwise be communicated poorly or omitted from discussions entirely. Our methods apply systematic review, qualitative, survey and consensus-building techniques to define this ‘core information’. We propose that such information addresses the ‘reasonable patient’ standard for information disclosure but, more importantly, can serve as a spring board for high-value discussion of importance to the individual patient. The application of established research methods can define information of core importance to informed consent. Further work will establish how best to incorporate this model in routine practice. (shrink)

ABSTRACTDifficulties with inhibiting fear have been associated with the emergence of anxiety problems and poor response to cognitive–behavioural treatment. Fear inhibition problems measured using experimental paradigms involving aversive stimuli may be inappropriate for vulnerable samples and may not capture fear inhibition problems evident in everyday life. We present the Fear Inhibition Questionnaire, a self-report measure of fear inhibition abilities. We assess the FIQ’s factor structure across two cultures and how well it correlates with fear inhibition indices derived experimentally. Adolescent participants (...) from Hong Kong and England completed the FIQ, with the English participants also completing a conditioning and extinction task to assess fear inhibition problems. Across both cultures, the FIQ showed a single factor structure and low FIQ scores, or worse fear inhibition problems, were associated with self-reports of heightened anxiety. Correlation of FIQ scores with experimental indices, whi... (shrink)

When the COVID-19 surge hit New York City hospitals, the Division of Medical Ethics at Weill Cornell Medical College, and our affiliated ethics consultation services, faced waves of ethical issues sweeping forward with intensity and urgency. In this article, we describe our experience over an eight-week period (16 March through 10 May 2020), and describe three types of services: clinical ethics consultation (CEC); service practice communications/interventions (SPCI); and organizational ethics advisement (OEA). We tell this narrative through the prism of time, (...) describing the evolution of ethical issues and trends as the pandemic unfolded. We delineate three phases: anticipation and preparation, crisis management, and reflection and adjustment. The first phase focused predominantly on ways to address impending resource shortages and to plan for remote ethics consultation, and CECs focused on code status discussions with surrogates. The second phase was characterized by the dramatic convergence of a rapid increase in the number of critically ill patients, a growing scarcity of resources, and the reassignment/ redeployment of staff outside their specialty areas. The third phase was characterized by the recognition that while the worst of the crisis was waning, its medium- and long-term consequences continued to pose immense challenges. We note that there were times during the crisis that serving in the role of clinical ethics consultant created a sense of dis-ease as novel as the coronavirus itself. In retrospect we learned that our activities far exceeded the familiar terrain of clinical ethics consultation and extended into other spheres of organizational life in novel ways that were unanticipated before this pandemic. To that end, we defined and categorized a middle level of ethics consultation, which we have termed service practice communication intervention (SPCI). This is an underappreciated dimension of the work that ethics consult services are capable of in times of crisis. We believe that the pandemic has revealed the many enduring ways that ethics consultation services can more robustly contribute to the ethical life of their institutions moving forward. (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)

The chief sources of groundwater contamination on farms come from point sources and diffuse sources. Possible point sources are feedlots, poorly-sited manure piles, septic sewage-treatment systems—all of which can release nitrate, phosphates and bacteria— and sites of chemical spills. Diffuse sources are typified by excess fertilizer leaching from a number of arable fields. The basis of quality standards for drinking-water is discussed in relation to common contaminants present on farms. Samples of drinking-water were collected in 1991–1992 from wells on about (...) 1,200 farms in order to study the quality of rural groundwater in Ontario. Analysis showed that approximately one third of wells were contaminated with bacteria, 14% were contaminated with nitrate, two wells were contaminated with pesticide, but 40% were considered unsafe because of the presence of at least one contaminant. These values were similar to those reported for similar regions in the U.S. There was no significant effect of agricultural practice on the proportion of contaminated samples. One response of Ontario's farmers to information on water quality has been to initiate their own program, the Environmental Farm Plan, which has 23 modules by which the risk of environmental contamination can be assessed. Government policies for agriculture can be expected to influence farming practices. However, the literature suggests that the consequences of policies aimed at reducing environmental contamination are poorly understood, not least because the instruments used for implementation can have widely differing impacts. The need for discussions on the ethics surrounding the relationship between food producers and consumers with regard to environmental contamination is identified. (shrink)

Corporate social responsibility (CSR) is about the moral purpose of business and its proper relationship to society. We map the logical structure of CSR—its canonical core—and identify the view of CSR that is most consistent with CSR as driven by moral purpose as Moral CSR (CSRM). The numerous perspectives of CSR, which we term CSR memes, are complements to CSRM. A meme is an idea or usage diffusing within communities. Moral norms and what we term normatively injunctive warrants are implicit (...) in many CSR memes but have received a relative lack of explicit and systematic attention. A norm is an accepted standard for behavior. A warrant is an authoritative or authorizing instruction for behavior. All CSR memes contain three elements—a corporate actor, a relation, and nonmoral normative warrants, which we term constructive warrants. We argue that any CSR meme should include a fourth element—moral normative (injunctive) warrants linking explicitly to moral reasoning. Through sorting key CSR memes by their epistemological and compositional characteristics, we reveal the paucity of explicit attention to injunctive warrants. We resort memes according to social gains or losses, which are the outcomes of societal demand for and business supply of CSR. This analysis yields two proposed improvements for CSR reasoning. The first is a clearer picture of variable use of the term CSR in extant research. The second is how scholars can incorporate more explicitly moral elements of CSR in future work. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Co-authored letter to the APA to take a lead role in the recognition of teaching in the classroom, based on the participation in an interdisciplinary Conference on the Role of Advocacy in the Classroom back in 1995. At the time of this writing, the late Myles Brand was the President of Indiana University and a member of the IU Department of Philosophy.

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The authors of this article are previous or current members of the Clinical Ethics Consultation Affairs (CECA) Committee, a standing committee of the American Society for Bioethics and Humanities (ASBH). The committee is composed of seasoned healthcare ethics consultants (HCECs), and it is charged with developing and disseminating education materials for HCECs and ethics committees. The purpose of this article is to describe the educational research and development processes behind our teaching materials, which culminated in a case studies book called (...) A Case-Based Study Guide for Addressing Patient-Centered Ethical Issues in Health Care (hereafter, the Study Guide). In this article, we also enumerate how the Study Guide could be used in teaching and learning, and we identify areas that are ripe for future work. (shrink)

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

A collection of newly commissioned papers on themes from David Albert's Time and Chance (HUP, 2000), with replies by Albert. Introduction [Barry Loewer, Brad Weslake, and Eric Winsberg] I. Overview of Time and Chance 1. The Mentaculus: A Probability Map of the Universe [Barry Loewer] II. Philosophical Foundations 2. The Metaphysical Foundations of Statistical Mechanics: On the Status of PROB and PH [Eric Winsberg] 3. The Logic of the Past Hypothesis [David Wallace] 4. In What Sense Is the Early Universe (...) Fine-Tuned? [Sean M. Carroll] 5. The Meta-Reversibility Objection [Christopher J. G. Meacham] 6. Typicality versus Humean Probabilities as the Foundation of Statistical Mechanics [Dustin Lazarovici] 7. The Past Hypothesis and the Nature of Physical Laws [Eddy Keming Chen] 8. On the Albertian Demon [Tim Maudlin] III. Underwriting the Asymmetries of Knowledge and Intervention 9. Reading the Past in the Present [Nick Huggett] 10. Causes, Randomness, and the Past Hypothesis [Mathias Frisch] 11. Time, Flies, and Why We Can’t Control the Past [Alison Fernandes] 12. The Concept of Intervention in Time and Chance [Sidney Felder] Conclusion [David Albert]. (shrink)

In 2005, President George Bush read John Barry’s The Great Influenza: The Story of the Deadliest Pandemic in History. After his experiences of 9/11 and Hurricane Katrina, Bush began the first White...

Frankena, W. K. Morality and moral philosophy.--Soltis, J. F. Men, machines and morality.--Chazan, B. I. The moral situation.--Phenix, P. H. Ethics and the will of God.--Moore, G. E. The indefinability of good.--Morgenbesser, S. Approaches to ethical objectivity.--Sartre, J. P. Existentialism and ethics.--Hare, R. M. Decisions of principle.--Singer, M. G. Moral rules and principles.--Hare, R. M. Adolescents into adults.--Wilson, J. Assessing the morally educated person.--Kohlberg, L. The child as a moral philosopher.--Frankena, W. K. Toward a philosophy of moral education.--Archambault, R. D. (...) Criteria for success in moral instruction.--Raths, L., Harmin, M., and Simon, S. Teaching for value clarity.--Bibliography (p. 188-192). (shrink)

Some patients with schizophrenia are not told their diagnosis. The moral, clinical and practical issues involved in telling or not telling the patient are discussed. In some cases a relative is told the diagnosis but not the patient. The implications for the family and clinical outcome are outlined. A case history illustrating some of these issues is presented.

Outstanding translations by leading contemporary scholars--many commissioned especially for this volume--are presented here in the first single edition to include the entire surviving corpus of works attributed to Plato in antiquity. In his introductory essay, John Cooper explains the presentation of these works, discusses questions concerning the chronology of their composition, comments on the dialogue form in which Plato wrote, and offers guidance on approaching the reading and study of Plato's works. Also included are concise introductions by Cooper and Hutchinson (...) to each translation, meticulous annotation designed to serve both scholar and general reader, and a comprehensive index. This handsome volume offers fine paper and a high-quality Smyth-sewn cloth binding in a sturdy, elegant edition. (shrink)

The idea of human cruelty to animals so consumes novelist Elizabeth Costello in her later years that she can no longer look another person in the eye: humans, especially meat-eating ones, seem to her to be conspirators in a crime of stupefying magnitude taking place on farms and in slaughterhouses, factories, and laboratories across the world. Costello's son, a physics professor, admires her literary achievements, but dreads his mother’s lecturing on animal rights at the college where he teaches. His colleagues (...) resist her argument that human reason is overrated and that the inability to reason does not diminish the value of life; his wife denounces his mother’s vegetarianism as a form of moral superiority. At the dinner that follows her first lecture, the guests confront Costello with a range of sympathetic and skeptical reactions to issues of animal rights, touching on broad philosophical, anthropological, and religious perspectives. Painfully for her son, Elizabeth Costello seems offensive and flaky, but—dare he admit it?—strangely on target. In this landmark book, Nobel Prize–winning writer J. M. Coetzee uses fiction to present a powerfully moving discussion of animal rights in all their complexity. He draws us into Elizabeth Costello’s own sense of mortality, her compassion for animals, and her alienation from humans, even from her own family. In his fable, presented as a Tanner Lecture sponsored by the University Center for Human Values at Princeton University, Coetzee immerses us in a drama reflecting the real-life situation at hand: a writer delivering a lecture on an emotionally charged issue at a prestigious university. Literature, philosophy, performance, and deep human conviction—Coetzee brings all these elements into play. As in the story of Elizabeth Costello, the Tanner Lecture is followed by responses treating the reader to a variety of perspectives, delivered by leading thinkers in different fields. Coetzee’s text is accompanied by an introduction by political philosopher Amy Gutmann and responsive essays by religion scholar Wendy Doniger, primatologist Barbara Smuts, literary theorist Marjorie Garber, and moral philosopher Peter Singer, author of Animal Liberation. Together the lecture-fable and the essays explore the palpable social consequences of uncompromising moral conflict and confrontation. (shrink)