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)

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)

It is argued that a number of important, and seemingly disparate, types of representation are species of a single relation, here called structural representation, that can be described in detail and studied in a way that is of considerable philosophical interest. A structural representation depends on the existence of a common structure between a representation and that which it represents, and it is important because it allows us to reason directly about the representation in order to draw conclusions about the (...) phenomenon that it depicts. The present goal is to give a general and precise account of structural representation, then to use that account to illuminate several problems of current philosophical interest — including some that do not initially seem to involve representation at all. In particular, it is argued that ontological reductions (like that of the natural numbers to sets), compositional accounts of semantics, several important sorts of mental representation, and (perhaps) possible worlds semantics for intensional logics are all species of structural representation and are fruitfully studied in the framework developed here. (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)

This article focuses on the concept of worldviews, arguing that a change in managerial worldviews is the key lever for addressing the social and global challenges facing humanity. We draw from a new synthesis of science and spirituality, with the addition of “other ways of knowing” that go beyond rational-empirical analysis, to suggest that what we call Quantum Worldviews are capable of generating the prosocial and pro-environmental behavior consistent with humanistic management. Using the yin-yang symbol as a metaphor, we suggest (...) that a transformation in consciousness, at the level of the paradigmatic assumptions held by managers about the nature of reality, can be understood through adult development theory. We also go beyond the metaphor to propose a quantum worldview based on a more literal interpretation of quantum science to fundamentally re-conceptualize what it means to be human, drawing on quantum research that suggests ontological wholeness and interdependence of all. Quantum Worldviews can help leaders, and the various systems of which they are a part, transition to a new science-based consciousness - long intuited by indigenous and nonwestern spiritual leaders - of an interconnected and dynamically coherent world. We identify a variety of practices that give managers a direct experience of Oneness, changing who they are at the deepest level of self-concept. Our research suggests that only when using such practices, and in sufficient numbers, will business leaders become agents of world benefit with the collective influence to bring about meaningful solutions to climate change and other wicked problems—in other words, needed system transformation. (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.

It is a common idea that morality, or moral truths, if there are any, must have some sort of source, or grounding. It has also been claimed that constructivist theories in metaethics have an advantage over realist theories in that the former but not the latter can provide such a grounding. This paper has two goals. First, it attempts to show that constructivism does not in fact provide a complete grounding for morality, and so is on a par with realism (...) in this respect. Second, it explains why it seems that morality in fact couldn't have a source. (shrink)

According to the argument from self-sacrifice, standard, unrestricted desire-based theories of welfare fail because they have the absurd implication that self-sacrifice is conceptually impossible. I attempt to show that, in fact, the simplest imaginable, completely unrestricted desire-based theory of well-being is perfectly compatible with the phenomenon of self-sacrifice – so long as the theory takes the right form. I go on to consider a new argument from self-sacrifice against this simple theory, which, I argue, also fails. I conclude that, contrary (...) to popular opinion, considerations of self-sacrifice do not pose a problem for preferentist theories of welfare. (shrink)

Narrativism, as represented by Hayden White and Frank Ankersmit, can fruitfully be analyzed as an inversion of two brands of positivism. First, narrativist epistemology can be regarded as an inversion of empiricism. Its thesis that narratives function as metaphors which do not possess a cognitive content is built on an empiricist, "picture view" of knowledge. Moreover, all the non-cognitive aspects attributed to narrative as such are dependent on this picture theory of knowledge and a picture theory of representation. Most of (...) the epistemological characteristics that White and Ankersmit attribute to historical narratives therefore share the problems of this picture theory.The article's second thesis is that the theories of narrative explanation can also fruitfully be analyzed as inversions of positivist covering-law theory. Ankersmit's brand of narrativism is the most radical in this respect because it posits an opposition between narrative and causal modes of comprehension while simultaneously eliminating causality from narrativist historical understanding. White's brand of narrativism is more of a hybrid than is Ankersmit's as far as its theory of explanation is concerned; nevertheless, it can also be fruitfully interpreted as an inversion of covering-law theory, replacing it by an indefinite multitude of explanatory strategies.Most of the striking characteristics of both White's and Ankersmit's narrativism presuppose positivism in these two senses, especially their claim that historical narratives have a metaphorical structure and therefore no truth-value. These claims are hard to reconcile with the factual characteristics of debates by historians; this problem can be tracked down to the absence in "metaphorical" narrativism of a conceptual connection between historical narratives and historical research. (shrink)

Many recent attacks on consequentialism and several defenses of pluralism have relied on arguments for the incommensurability of value. Such arguments have, generally, turned on empirical appeals to aspects of our everyday experience of value conflict. My intention, largely, is to bypass these arguments and turn instead to a discussion of the conceptual apparatus needed to make the claim that values are incommensurable. After delineating what it would mean for values to be incommensurable, I give an a priori argument that (...) such is impossible. It is widely accepted that value is conceptually tied to desire. I argue that, more specifically, it is proportional to merited desire strength. This connection gives one a metric of all value if there is any such thing. This metric entails that value is a complete ordering over all states of affairs, or, in other words, that value is commensurable. (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)

In this paper, I develop a view on set-theoretic ontology I call Universe-Indeterminism, according to which there is a unique but indeterminate universe of sets. I argue that Solomon Feferman’s work on semi-constructive set theories can be adapted to this project, and develop a philosophical motivation for a semi-constructive set theory closely based on Feferman’s but tailored to the Universe-Indeterminist’s viewpoint. I also compare the emergent Universe-Indeterminist view to some more familiar views on set-theoretic ontology.

Metaethical non-naturalists maintain that normative or evaluative properties cannot be reduced to, or otherwise explained in terms of, natural properties. They thus have difficulty explaining what these irreducibly normative properties are supposed to be, other than by saying what they are not. I offer a partial, positive characterization of irreducible normativity in naturalistic terms. At a first pass, it is this: that to attribute a normative property to something is necessarily to commend or condemn that thing, due to the nature (...) of the property attributed. This theory characterizes normativity in terms of the natural phenomenon of performing certain familiar speech acts. The hypothesis does other explanatory work as well: it provides for an account of the "queerness" of normative properties, one superior to other accounts; it explains why metaethical reductionism is bound to fail, in a way friendly to non-naturalism (as opposed to non-cognitivism); and it can help deflect arguments against non-naturalism from the "essential practicality" of normativity. (shrink)

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.

This encyclopedia entry provides an introduction to the literature on transmission failure.

An argument that science is indeed 'socially constructed' but in a way that exposes it to a Darwinian version of variability and selection which ensures its success.

Many of the existing ethical analyses of genetic engineering technologies (GET) focus on how they can be used to enhance individuals—to improve individual well-being, health and cognition. There is a gap in the current literature about the specific ways enhancement technologies could be used to improve our populations and species, viewed as a whole. In this paper, I explore how GET may be used to enhance the species through improvements in the gene pool. I argue one aspect of the species (...) that may be desirable to enhance is ‘persistence’ or long-term viability. I then look at some of the ways in which GET could be used to improve human persistence and argue that the use of GET to secure benefits for individuals may compromise persistence. This suggests conflicts between uses of GET to enhance individuals and uses to promote the persistence of the species may occur. As GET are further developed, the likelihood that these conflicts will actually arise, and how we should resolve them if they do, will need to be considered. (shrink)

The bounded arithmetic theories R2i, S2i, and T2i are closely connected with complexity theory. This paper is motivated by the questions: what are the Σi+1b-definable multifunctions of R2i? and when is one theory conservative over another? To answer these questions we consider theories , and where induction is restricted to prenex formulas. We also define which has induction up to the 0 or 1-ary L2-terms in the set τ. We show and and for . We show that the -multifunctions of (...) are FPΣip and that those of are FPΣip. For -definability we get FPΣi+k+1p for all these theories. Write for the set of terms 2min,t) where ℓ is a finite product of terms in τ and tL2. We prove and we show - INDτ provided τO2. This gives a proof theoretic proof that S2iΔi+1b-LIND and -LLIND solving an open problem. For τO2, we define using weak replacement axioms and show . We show if or if or if where τ′ has an unbounded term then PH=B. We separate PΣip from PΣip for behaved ℓ and deduce theory separations. We lastly introduce a notion of a model separating two theories and derive some consequences. (shrink)