To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

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 Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (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)

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)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (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)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The past 50 years have seen an accumulation of evidence suggesting that associative learning depends on high-level cognitive processes that give rise to propositional knowledge. Yet, many learning theorists maintain a belief in a learning mechanism in which links between mental representations are formed automatically. We characterize and highlight the differences between the propositional and link approaches, and review the relevant empirical evidence. We conclude that learning is the consequence of propositional reasoning processes that cooperate with the unconscious processes involved (...) in memory retrieval and perception. We argue that this new conceptual framework allows many of the important recent advances in associative learning research to be retained, but recast in a model that provides a firmer foundation for both immediate application and future research. (shrink)

This entry considers the philosophical subject called 'metaphysics'. There have been many conceptions of metaphysics, and metaphysics has faced severe criticism throughout the history of philosophy and continues to do so. Besides discussing some major trends in analytic metaphysics - understood as 'metaphysics done by analytic philosophers' - we consider some of the criticisms and possible responses.

Struggles over precious resources such as oil, water, and land are increasingly evident in the contemporary world. States, indigenous groups, and corporations vie to control access to those resources, and the benefits they provide. These conflicts are rapidly spilling over into new arenas, such as the deep oceans and the Polar regions. How should these precious resources be governed, and how should the benefits and burdens they generate be shared? Justice and Natural Resources provides a systematic theory of natural resource (...) justice. It argues that we should use the benefits and burdens flowing from these resources to promote greater equality across the world, and share governance over many important resources. At the same time, the book takes seriously the ways in which particular resources can matter in peoples lives. It provides invaluable guidance on a series of pressing issues, including the scope of state resource rights, the claims of indigenous communities, rights over ocean resources, the burdens of conservation, and the challenges of climate change and transnational resource governance. It will be required reading for anyone interested in natural resource governance, climate politics, and global justice. (shrink)

Many contemporary philosophers rate error theories poorly. We identify the arguments these philosophers invoke, and expose their deficiencies. We thereby show that the prospects for error theory have been systematically underestimated. By undermining general arguments against all error theories, we leave it open whether any more particular arguments against particular error theories are more successful. The merits of error theories need to be settled on a case-by-case basis: there is no good general argument against error theories.

_The Good Life of Teaching_ extends the recent revival of virtue ethics to professional ethics and the philosophy of teaching. It connects long-standing philosophical questions about work and human growth to questions about teacher motivation, identity, and development. Makes a significant contribution to the philosophy of teaching and also offers new insights into virtue theory and professional ethics Offers fresh and detailed readings of major figures in ethics, including Alasdair MacIntyre, Charles Taylor, and Bernard Williams and the practical philosophies of (...) Hannah Arendt, John Dewey and Hans-Georg Gadamer Provides illustrations to assist the reader in visualizing major points, and integrates sources such as film, literature, and teaching memoirs to exemplify arguments in an engaging and accessible way Presents a compelling vision of teaching as a reflective practice showing how this requires us to prepare teachers differently. (shrink)

Philosophers often treat racist and sexist slurs as a special sort of puzzle. What is the difference between a slur and its correlates? In attempting to answer this question, a second distinction has been overlooked: that between slurs and insults. What makes a term count as a slur? This is not an unnecessary taxonomical question as long as ableist terms such as ‘moron’ are dismissed as mere insults. Attempts to resolve the insult/slur distinction by considering the communicative content of slurs (...) are not promising. A better solution is offered by speech act theory, and this paper develops a novel way to describe ordinary slurring utterances as oppressive speech acts. This can both explain the difference between slurs and insults, and challenge the dismissal of ableist terms. (shrink)

We defend Joseph Melia's thesis that the role of mathematics in scientific theory is to 'index' quantities, and that even if mathematics is indispensable to scientific explanations of concrete phenomena, it does not explain any of those phenomena. This thesis is defended against objections by Mark Colyvan and Alan Baker.

Choice architecture is heralded as a policy approach that does not coercively reduce freedom of choice. Still we might worry that this approach fails to respect individual choice because it subversively manipulates individuals, thus contravening their personal autonomy. In this article I address two arguments to this effect. First, I deny that choice architecture is necessarily heteronomous. I explain the reasons we have for avoiding heteronomous policy-making and offer a set of four conditions for non-heteronomy. I then provide examples of (...) nudges that meet these conditions. I argue that these policies are capable of respecting and promoting personal autonomy, and show this claim to be true across contrasting conceptions of autonomy. Second, I deny that choice architecture is disrespectful because it is epistemically paternalistic. This critique appears to loom large even against non-heteronomous nudges. However, I argue that while some of these policies may exhibit epistemically paternalistic tendencies, these tendencies do not necessarily undermine personal autonomy. Thus, if we are to find such policies objectionable, we cannot do so on the grounds of respect for autonomy. (shrink)

An Introduction to Philosophical Methods is the first book to survey the various methods that philosophers use to support their views. Rigorous yet accessible, the book introduces and illustrates the methodological considerations that are involved in current philosophical debates. Where there is controversy, the book presents the case for each side, but highlights where the key difficulties with them lie. While eminently student-friendly, the book makes an important contribution to the debate regarding the acceptability of the various philosophical methods, and (...) so it will also be of interest to more experienced philosophers. (shrink)

There is a recent and growing trend in philosophy that involves deferring to the claims of certain disciplines outside of philosophy, such as mathematics, the natural sciences, and linguistics. According to this trend— deferentialism , as we will call it—certain disciplines outside of philosophy make claims that have a decisive bearing on philosophical disputes, where those claims are more epistemically justified than any philosophical considerations just because those claims are made by those disciplines. Deferentialists believe that certain longstanding philosophical problems (...) can be swiftly and decisively dispatched by appeal to disciplines other than philosophy. In this paper we will argue that such an attitude of uncritical deference to any non-philosophical discipline is badly misguided. With reference to the work of John Burgess and David Lewis, we consider deference to mathematics. We show that deference to mathematics is implausible and that main arguments for it fail. With reference to the work of Michael Blome-Tillmann, we consider deference to linguistics. We show that his arguments appealing to deference to linguistics are unsuccessful. We then show that naturalism does not entail deferentialism and that naturalistic considerations even motivate some anti-deferentialist views. Finally, we set out deferentialism’s failings and present our own anti-deferentialist approach to philosophical inquiry. (shrink)

In our increasingly instrumentalist culture, debates over the privatization of schooling may be beside the point. Whether we hatch some new plan for chartering or funding schools, or retain the traditional model of government-run schools, the ongoing instrumentalization of education threatens the very possibility of public education. Indeed, in the culture of performativity, not only the public school but public life itself is hollowed out and debased. Qualities are recast as quantities, judgments replaced by rubrics, teaching and learning turned into (...) exchange values. Schools should be central to public life: key locations for the regeneration of values, the cultivation of judgment, and the creation of the conditions for positive freedom. In this article Chris Higgins, drawing on Hannah Arendt and Alasdair MacIntyre, goes beyond typical treatments of the schools as equalizer of individual opportunity to explore three aspects of educational publicity: the school as an object of communal concern, schooling as preparation for public life, and the classroom as public space. (shrink)

We consider the influence that John Forrester’s work has had on thinking in, with, and from cases in multiple disciplines. Forrester’s essay ‘If p, Then What? Thinking in Cases’ was published in History of the Human Sciences in 1996 and transformed understandings of what a case was, and how case-based thinking worked in numerous human sciences. Forrester’s collection of essays Thinking in Cases was published posthumously, after his untimely death in 2015, and is the inspiration for the special issue we (...) introduce. This comprises new research from authors working in and across the history of science and medicine, gender and sexuality studies, philosophy of science, semiotics, film studies, literary studies and comparative literature, psychoanalytic studies, medical humanities, and sociology. This research addresses what it means to reason in cases in particular temporal, spatial, or genre-focused contexts; introduces new figures into lineages of case-based reasoning; emphasizes the unfinished and unfinishable character of some case reading and autobiographical accounts; and shows the frequency with which certain kinds of reasoning attempted with cases fail. The special issue opens up new directions for thinking and working with cases and case-based reasoning in the humanities and human sciences. (shrink)

In this essay, the authors analyze and interpret facsimiles of important original documents—published here for the first time—that are deeply relevant to the education of the young Ayn Rand at the University of Petrograd. This definitive reading of source material provides significant documentation of Rand’s courses, teachers, and textbooks—and what she might have learned from them. Other original source materials are revealed to advance further investigations of this key period in Rand’s life. Recent commentary on Rand’s education in Gary H. (...) Merrill’s book, False Wisdom, is also considered. (shrink)

We address three questions raised by Cummings and Foreman regarding a model of Gitik and Sharon. We first analyze the PCF-theoretic structure of the Gitik–Sharon model, determining the extent of good and bad scales. We then classify the bad points of the bad scales existing in both the Gitik–Sharon model and other models containing bad scales. Finally, we investigate the ideal of subsets of singular cardinals of countable cofinality carrying good scales.

Do numbers exist? Do properties? Do possible worlds? Do fictional characters? Many metaphysicians spend time and effort trying to answer these and other questions about the existence of various entities. These inquiries have recently encountered opposition: a group of philosophers, drawing inspiration from Aristotle, have argued that many or all of the existence questions debated by metaphysicians can be answered trivially, and so are not worth debating. Our task is to defend existence questions from the neo-Aristotelians' attacks.

This paper distinguishes revolutionary fictionalism from other forms of fictionalism and also from other philosophical views. The paper takes fictionalism about mathematical objects and fictionalism about scientific unobservables as illustrations. The paper evaluates arguments that purport to show that this form of fictionalism is incoherent on the grounds that there is no tenable distinction between believing a sentence and taking the fictionalist's distinctive attitude to that sentence. The argument that fictionalism about mathematics is ‘comically immodest’ is also evaluated. In place (...) of those arguments, an argument against fictionalism about abstract objects of any kind is presented in the last section. This argument takes the form of a trilemma against the fictionalist. (shrink)

Analyzes the intellectual roots and philosophy of Ayn Rand. Second edition adds a new preface and an analysis of transcripts documenting Rand's education at Petrograd State University"--Provided by publisher.

Global distributive justice is now part of mainstream political debate. It incorporates issues that are now a familiar feature of the political landscape, such as global poverty, trade justice, aid to the developing world and debt cancellation. This is the first textbook to focus exclusively on issues of distributive justice on the global scale. It gives clear and up-to-date accounts of the major theories of global justice and spells out their significance for a series of important political issues, including climate (...) change, international trade, human rights and migration. These issues are brought to life through the use of case studies, which emphasise the connection of theories of justice to contemporary politics, and 'Further Issues' sections, which discuss emerging debates or controversies that are likely to command increasing attention in the coming years. (shrink)

Catcalls have been said to insult, intimidate, and silence their targets. The harms that catcalls inflict on individuals are reason enough to condemn them. This paper argues that they also inflict a type of structural harm by subordinating their targets. Catcalling initiates an unwanted conversation where none should exist. This brings the rules and norms governing conversations to bear in such a way that the catcall assigns their target a ‘subordinate discourse role’. This not only constrains the behaviour of the (...) target here and now, but also influences the norms governing future conversations. Catcalls are then not only bad because of the effects on their target, but also because of their pernicious contribution to the wider normative landscape. (shrink)

Support vector machines are being used increasingly in affective science as a data-driven classification method and feature reduction technique. Whereas traditional statistical methods typically compare group averages on selected variables, SVMs use a predictive algorithm to learn multivariate patterns that optimally discriminate between groups. In this review, we provide a framework for understanding the methods of SVM-based analyses and summarize the findings of seminal studies that use SVMs for classification or data reduction in the behavioral and neural study of emotion (...) and affective disorders. We conclude by discussing promising directions and potential applications of SVMs in future research in affective science. (shrink)

Some philosophers deny the existence of composite material objects. Other philosophers hold that whenever there are some things, they compose something. The purpose of this paper is to scrutinize an objection to these revisionary views: the objection that nihilism and universalism are both unacceptably uncharitable because each of them implies that a great deal of what we ordinarily believe is false. Our main business is to show how nihilism and universalism can be defended against the objection. A secondary point is (...) that universalism is harder to defend than nihilism. (shrink)

The Palgrave Handbook of Philosophical Methods contains twenty-six original and substantive papers examining a wide selection of philosophical methods. Drawing upon an international range of leading contributors, this Handbook will help shape future debates about how philosophy should be done. Topics explored include philosophical disagreement, thought experiments, intuitions, rational reflection, conceptual analysis, explanation, parsimony, and experimental philosophy. Written in a clear and accessible form, and drawing upon the most recent thinking in the field, the papers will be of particular interest (...) to researchers and high-level undergraduates. (shrink)

The Trompenaars database (1993) updated with Hampden-Turner (1998) has been assembled to help managers structure their cross cultural experiences in order to develop their competence for doing business and managing across the world. The database comprises more than 50,000 cases from over 100 countries and is one of the world's richest sources of social constructs. Woolliams and Trompenaars (1998) review the analysis undertaken by the authors in the last five years to develop the methodological approach underpinning the work. Recently Trompenaars (...) with Hampden-Turner (Trompenaars and Woolliams, 1999) have extended the concepts into a new model on dilemma reconciliation of cultural differences. This paper reviews these latest updates in relation to dilemmas of cross-cultural business ethics. The paper asserts that knowledge in relation to business ethics is culturally specific; and that ethnocentrism is not easy to avoid. Too great an emphasis on rational-analytic conceptions of reality may mean that syntheses, emotion, and intuition, are not adequately developed. This presents implications for doing business and managing across cultures and for resolving ethical dilemmas. (shrink)

A typical theorem of conaexive logics is Aristotle''s Thesis(A), (AA).A cannot be added to classical logic without producing a trivial (Post-inconsistent) logic, so connexive logics typically give up one or more of the classical properties of conjunction, e.g.(A & B)A, and are thereby able to achieve not only nontriviality, but also (negation) consistency. To date, semantical modellings forA have been unintuitive. One task of this paper is to give a more intuitive modelling forA in consistent logics. In addition, while inconsistent (...) but nontrivial theories, and inconsistent nontrivial logics employing prepositional constants (for which the rule of uniform substitution US fails), have both been studied extensively within the paraconsistent programme, inconsistent nontrivial logics (closed under US) do not seem to have been. This paper gives sufficient conditions for a logic containingA to be inconsistent, and then shows that there is a class of inconsistent nontrivial logics all containingA. A second semantical modelling forA in such logics is given. Finally, some informal remarks about the kind of modellingA seems to require are made. (shrink)

Popper's definition looked initially promising provided that the restriction of classical logic was removed. As we have seen, this promise is not fulfilled. The search for a satisfactory verisimilitude ordering must therefore be pursued along more mainstream lines. The present exercise ought, however, to make us aware of the possibility that breakdowns of proposed definitions might only occur because of strictly classical assumptions.

As Early Years care and education comes under closer outside scrutiny the number of practitioners moving into managerial roles is constantly increasing, this book focuses on how to make policy work in practice: clarifying the manager’s responsibilities and his or her duty to lead exploring the use of policy and procedures, why we have procedure, how to create procedures and how to put it into practice offering advice on effective planning, how to monitor progress and activity, and tips on feedback (...) and reflection providing links to Ofsted. This is a must-have for students, assessors, nursery nurses with an interest in career development into management and anyone working within a early-years environment in a managerial role. (shrink)

This book brings together the leading researchers on these issues and for the first time in literature, illustrates how a unified approach based on the idea of ...