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)

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 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)

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)

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)

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)

Over 200 health journals call on the United Nations (UN), political leaders and health professionals to recognise that climate change and biodiversity loss are one indivisible crisis and must be tackled together to preserve health and avoid catastrophe. This overall environmental crisis is now so severe as to be a global health emergency. The world is currently responding to the climate crisis and the nature crisis as if they were separate challenges. This is a dangerous mistake. The 28th Conference of (...) the Parties (COP) on climate change is about to be held in Dubai while the 16th COP on biodiversity is due to be held in Turkey in 2024. The research communities that provide the evidence for the two COPs are unfortunately largely separate, but they were brought together for a workshop in 2020 when they concluded that: ‘Only by considering climate and biodiversity as parts of the same... (shrink)

This essay examines the Mission paléontologique française of the 1920s, a series of scientific expeditions into the Ordos Desert in Inner Mongolia in which a team of Jesuit scholar-scientists worked with local collaborators to provide material for the Muséum d’Histoire Naturelle in Paris. The case study shows that the global and colonial expansion of Western science in the early twentieth century provided space for traditional scientific institutions, such as universalizing metropolitan collections and clerical scholarly networks, to extend their research projects. (...) The linking of approaches, agendas, and geographic regions was facilitated by the concepts and practices of the deep-time sciences of geology, paleontology, and human prehistory. These were based on the interchange of expertise, common projects of unveiling the development of life, and the alignment of different regions and specimens. Moreover, the expeditions did not just conduct research based around global movement and transmission. They also conceptualized the ancient development of life in terms of movement, migration, and exchange. The act of forming research networks that linked Asia and Europe also led scientists to conceive of these regions as bound by deep natural processes. Circulation and transfer became important actors’ categories used to understand the origins and history of life. (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 article focuses on the interweaving of constructive praxis with communication inontogenesis, inphylogenesisand in biocultural niche evolution (ecogenesis), within anEvoDevoSocioframework. I begin by discussing the nature of symbolization, its evolution from communicative signaling and its elaboration into semantic systems. I distinguish between thesymbol-readyand thelanguage-readybrain, leading to a discussion of linguistic conceptualization and itsdual groundingin organism and language system. There follows an outline account of the interpenetration in the human biocultural niche-complex ofsemiosphereandtechnosphere,mediated by the evolution of the niche of infancy. Symbolization (...) (the foundation of the semiosphere) is by definition normative; the normative character of the technosphere is demonstrated by the interrelations in human development between affordance, action schema and canonical functional object schema. A model of the neuro-computational implementation of dual grounding is proposed. (shrink)

The impact of neoliberal reforms of education systems on the work of teachers and school leaders, particularly in relation to high-stakes accountability frameworks, has been extensively studied in recent decades. One significant aspect of neoliberal schooling is the emergence of quasi-autonomous public schools (such as Academies in England, Charter Schools in the USA and Independent Public Schools in Australia), characterised by heterarchical governance models, the promotion of entrepreneurial leadership cultures, and the promotion of a discourse of pursuing educational equity by (...) means of ‘achievement for all’. This paper explores the emergence of a mode of teacher professionalism characteristic of these quasi-autonomous schools, and conceptualises this as being ‘neo-performative’. The neo-performative profession is shaped by the shift in the focus of the regulation and management of schools from ‘governing to governance’, and the consequential rise of the ‘responsibilised profession’, and marked by the emergence of an entrepreneurial model of school leadership. The paper argues that this new conceptualisation of teacher professionalism requires further, more focused, empirical study in order to explore how neoperformative teachers and school leaders articulate their vision of educational equity and social justice, and how they enact this vision in an increasingly intensified high-stakes accountability culture. (shrink)

Using a vague predicate can make commitments about the appropriate use of that predicate in the remaining part of the discourse. For instance, if I assert that some particular pig is fat, I am committed to judging any fatter pig to be fat as well. We can model this update effect by recognizing that truth depends both on the state of the world and on the state of the discourse: the truth conditions of ‘This pig is fat’ rule out evaluation (...) points for which the pig in question in world w is thinner than the cutoff for fatness in the discourse d. Then disagreements about taste are disagreements about the discourse. Unlike disagreements about the world, disagreements about the discourse can be faultless, given that none of the discourse participants has privileged authority to make pronouncements about conventions for appropriate use of a predicate. Thus on the dynamic view developed here, whether or not a dispute about taste turns out to be faultless depends in part on predictable features of the previous discourse. On this account, faultless disagreement involving predicates of personal taste does not force relativizing truth to a judge or assessor. (shrink)

By making plausible the Diversity Thesis (different people have systematically different and incompatible packages of epistemic intuitions), experimental epistemology raises the specter of the shifting-sands problem: the evidence base for epistemology contains systematic inconsistencies. In response to this problem, some philosophers deny the Diversity Thesis, while others flirt with denying the Evidence Thesis (in normal circumstances, the epistemic intuition that p is prima facie evidence that p is true). We propose to accept both theses. The trick to living with the (...) shifting-sands problem is to expand epistemology’s evidential base so as to include scientific evidence. This evidence can provide principled grounds on which to decide between incompatible intuitions. The idea of resolving inconsistencies in an evidential base by adding more independent lines of evidence is commonplace in science. And in philosophy, it is simplyWide Reflective Equilibrium.We contend that the idea that epistemology would depend crucially on scientific evidence seems radical because many traditional epistemologists practice reflective equilibrium that is WINO, Wide In Name Only. We suggest five different lines of scientific evidence that can be, and have been, used in support of non-WINO epistemological theories. (shrink)

Drawing from my previous experiences as an Approved Social Worker and my current experiences as a social work educator, this paper will explore the issues that mental health professionals, and specifically social workers, will face when confronted with the requirement to make decisions that are contrary to the emancipatory values that may have been inculcated in them during their period of training. The controlling nature of statutory social work in particular will be investigated and an assessment of its impact will (...) be offered. The legislative system in the United Kingdom dictates that one piece of legislation can override another in certain instances. In applying this phenomenon, the argument will be made that social workers are increasingly required to override certain values to accomplish the desired outcomes of their position. Ethical issues and the concept of care versus control will be assessed in an attempt to rationalize the problems faced by many of today's mental health social workers. (shrink)

I propose the first strictly compositional semantic account of same. New data, including especially NP-internal uses such as two men with the same name, suggests that same in its basic use is a quantificational element taking scope over nominals. Given type-lifting as a generally available mechanism, I show that this follows naturally from the fact that same is an adjective. Independently-motivated assumptions extend the analysis to standard examples such as Anna and Bill read the same book via a mechanism I (...) call PARASITIC SCOPE, in which the scope of same depends on the scope of some other scopetaking element in the sentence. Although I will initially discuss the analysis in terms of a familiar Quantifier Raising framework, I go on to implement the analysis within an innovative continuation-based Type-Logical Grammar. The empirical payoff for dealing in continuations is that a simple generalization of the basic analysis gives the first ever formal account of cases in which same distributes over objects other than NP denotations, as in the relevant interpretation of John hit and killed the same man. (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)

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.

The Cambridge Handbook of the Psychology of Prejudice: Concise Student Edition aims to answer the questions: why is prejudice so persistent? How does it affect people exposed to it? And what can we do about it? With cutting-edge research from top scholars in the field, the chapters present an overview of psychological models of prejudice and investigate key domains such as racism, sexism, and the criminal justice system. This student edition of the award-winning Handbook includes new pedagogical features such as (...) learning objectives, core terms and definitions, summary points, discussion questions, recommended readings, and instructor's test bank. It also features a new conclusion chapter that analyzes eight hard problems currently faced by researchers and activists, thus engaging students in deep, forward-thinking discussion. Developed specifically for use in Psychology of Prejudice courses at the undergraduate and graduate levels, the Concise Student Edition is an essential teaching and learning resource. (shrink)

Preface to Philosophy of Science 82 (5). This volume contains a selection of contributed papers presented at the Philosophy of Science Association Meeting held in Chicago on November 6–9, 2014.

From gender and identity to welfare and consumerism, sociology is the study of how societies are organized and what helps them function or go wrong. Questions posed include: What is my "tribe"? Why do people commit crimes? Who decides if someone has a mental illness? What's work for? Does aid do any good? Heads Up Sociology explores these fascinating questions and more.

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)

Semantic composition in language must be closely related to semantic composition in thought. But the way the two processes are explained differs considerably. Focusing primarily on propositional content, language theorists generally take semantic composition to be a truth‐conditional process. Focusing more on extensional content, cognitive theorists take it to be a form of concept combination. But though deep, this disconnect is not irreconcilable. Both areas of theory assume that extensional (i.e., denotational) meanings must play a role. As this article demonstrates, (...) they also have the potential to fulfill a mediative function. What is shown is that extensional meanings are themselves inherently compositional. On this basis, it becomes possible to model semantic composition without assuming the existence of any specifically linguistic/conceptual apparatus. Examples are presented to demonstrate this direct style of modeling. Abstract connections between composition in thought and language can then be made, raising the prospect of a more unified, theoretical account of semantic composition. (shrink)

Historically Wales has been regarded as a country with relatively low levels of school exclusion, particularly in comparison with England. This has been used as an indicator of Wales’ commitment to the UN Convention on the Rights of the Child, which foregrounds a rights-based agenda that would argue school exclusion is a consequence of broader socio-economic structures than individual actions. However, simple analyses may mask a different picture of school exclusions in Wales. In this article, we study more detailed information (...) on formal school exclusions by looking at ‘instances’ of school exclusion, which considers the frequency and length of formal school exclusions in Wales, and alongside recorded school absence. The article also demonstrates that the pupils ‘at risk’ of formal school exclusion varies by when they experience school exclusion during their educational lifecourse. The article concludes by highlighting that patterns of school exclusion are complex, and that interpretation of these patterns depends on what kind of measure of school exclusion is used. By publishing these results, the article hopes to persuade policymakers and practitioners to re-examine their processes of exclusion to ensure they are commensurate with the law and to prevent unnecessary school exclusions. (shrink)