This paper looks at the specific proposed amendments to European directive 2007/36/EC and 2013/34/EU, and evaluates as to how such amendments alter shareholders’ moral responsibilities. To be responsible is here simply to be understood as being under an obligation, where an obligation is a requirement on an agent to either act or refrain from acting in a given way. In order to determine whether changes to the proposed directives alter shareholders’ moral responsibilities the following analysis argues that we need to (...) look at three factors: whether such changes do in fact alter the subject matter of shareholders’ obligations, a closer look at the agent i.e. shareholders to whom the obligation is to apply and thirdly whether they do actually apply. (shrink)

In this paper I argue that Christopher Kutz misapplies his theory of joint action when he attributes shareowners responsibilities on the basis of their intentional participation in the corporations in which they invest. Instead I propose that his theory of joint action should be used to attribute shareowners responsibilities on the basis of their intentional participation in the stock market. If shareholders’ accountability is grounded in their intentional participation in the stock market, then shareholders cannot take responsibility for corporation’s individual (...) actions. Instead they are solely responsible for the benefits they gain from holding shares if these are a result of moral wrongdoing and for this they should be held accountable. (shrink)

In this paper we have two main aims. First, we present an account of mood-congruent delusions in depression (hereafter, depressive delusions). We propose that depressive delusions constitute acknowledgements of self-related beliefs acquired as a result of a negatively biased learning process. Second, we argue that depressive delusions have the potential for psychological and epistemic benefits despite their obvious epistemic and psychological costs. We suggest that depressive delusions play an important role in preserving a person’s overall coherence and narrative identity at (...) a critical time, and thus can be regarded as epistemically innocent. (shrink)

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The article analyses the history of the Einfühlung concept. Theories of ‘feeling into’ Nature, works of art or feelings and behaviours of other persons by German philosophers of the second half of the nineteenth century Robert and Friedrich Vischer and Theodor Lipps are evoked, as well as similar theory of understanding (Verstehen) by Wilhelm Dilthey and Friedrich Schleiermacher, to which Dilthey refers. The meaning of the term Einfühlung within Edith Stein’s thought is also analysed. Both Einfühlung and Verstehen were criticized (...) as non-objective and naive methods consisting only in the identification of the subject with the object or the projection of feelings onto the object. The article refers to criticism by Georg Gadamer and Bertolt Brecht and proposes ways to restitute the concept of Einfühlung after this criticism, recalling the theory of empathy by Dominick Lacapra, in terms of its advantages for the historical enquiry, or the myth of Narcissus analyzed in the spirit of psychoanalysis by Julia Kristeva. The article proposes a reformulation of the concept of mimesis, connected to the Einfühlung, understood as the identification, analogy, imitation of feelings (as it was described by Lipss and Vischer). Mimesis does not necessarily mean a passive repetition and reconstruction of the feelings of the object, but serves only as a starting point for the interest of the subject for the outside world or for experiences of historical protagonists. Then there is no identification or projection of feelings, but the creative, active and critical reformulation of knowledge. It is stated that empathy is not a passive, uncritical process, but that it deals with the critical choice of the object of empathy and with an active approach to the perceived feelings and appearances. In addition to this cognitive aspect, empathy may also contribute to the analytical and valuable introspection. Furthermore empathy allows us to connect the analysis of the facts with a personal narrative and understanding of individual identity in historical knowledge. (shrink)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, and (...) modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

The article considers the problem of images and the role they play in our reflection turning to evidence provided by two seemingly very distant theories of mind together with two sorts of corresponding visions: dreams as analyzed by Freud who claimed that they are pictures of our thoughts, and their mechanical counterparts produced by neural networks designed for object recognition and classification. Freud’s theory of dreams has largely been ignored by philosophers interested in cognition, most of whom focused solely on (...) the linguistic incarnation of thoughts, but even though commonly neglected by respectable theories of thinking, dream images may prove to be the key to the black box of thought. As argued in this article, when seen from the right perspective and approached with the right set of questions, oneiric visions yield groundbreaking insights into the mechanism of how concepts and judgments are formed. Support for this conclusion comes from a tradition seemingly remote, if not opposed to psychoanalysis: the mechanical model of the mind conceived by information sciences and embodied in the form of artificial neural nets which mirror the activity of human visual cortex producing visions strikingly similar to those created by the sleeping mind. These purely mechanical, artificial ‘dreams’ constitute byproducts of algorithms designed for object recognition and classification, which, as I shall argue, reveals the true purpose of our own oneiric visual formations. Just like their mechanical counterparts produced by neural networks, condensations and displacements encountered in dreams are in fact visual universals. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

W niniejszym artykule opisany i zbadany został jeden z wyznaczników dowcipu słownego, jakim jest szeroko pojęta wieloznaczność. Technika wykorzystywana w przypadku dowcipu polisemicznego polega na neutralizacji czynników, które sygnalizują w tekście różne znaczenia każdego wieloznacznego wyrazu. Elementem wyodrębniającym jedno konkretne znaczenie jest kontekst, czyli najbliższe leksykalne lub syntaktyczne otoczenie wyrazu kluczowego. W przypadku dowcipu polisemantycznego kompozycja kontekstu charakteryzuje się dużą różnorodnością – kontekst jest maksymalnie neutralny i sygnalizuje znaczenie, które nie może być zrealizowane.

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

In this article we introduce the notion of non-home as an attempt of meaningful insight into the migrants' dwelling constructed from elements of different provenance, depending on tenants housing experiences, definitions and the very materiality of a living space. In developing the idea of a non-home we refer to the theoretical concepts of non-places and heterotopias.

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

In this paper I investigate whether there are any cases in which it is rational for a person to hold inconsistent beliefs and, if there are, just what implications this might have for the theory of epistemic justification. A number of issues will crop up along the way – including the relation between justification and rationality, the nature of defeat, the possibility of epistemic dilemmas, the importance of positive epistemic duties, and the distinction between transitional and terminal attitudes.

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...) needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

Research on research ethics—regarding both the governance and practice of the ethical review of human subjects research—has a tumultuous history in North America and Europe. Much of the academic literature focuses on issues to do with regulating the conduct and quality of ethics review of research protocols by ethics committees (research ethics boards (REBs) in Canada and institutional review boards (IRBs) in the United States). In addition, some of the literature attends to issues particular to the review of qualitative research, (...) and still other literature addresses the challenges posed by and the need for research on REBs/IRBs. It is this third group of literature within which our article is situated. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

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 greatly benefits application ontologies. To this end r®, 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 project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (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)

En la obra de Hegel la filosofía de lo bello es eminentemente filosofía del espíritu. Uno de los temas insoslayables acerca de la belleza es su presencia en la naturaleza y en el arte. En las Lecciones de Estética la belleza del arte se pondera como la más excelente. En este punto la postura hegeliana diverge llamativamente de la de Schelling; quien trató explícitamente de la relación de las artes plásticas con la naturaleza, como consta en el texto que lleva (...) este tema por título (generalmente llamado “discurso de la academia”). Su propuesta es clara: la superioridad de la naturaleza frente a las artes plásticas. Lo más interesante de esta disputa no es el desacuerdo en sí mismo, sino las argumentaciones que uno y otro autor alegan a favor de sus tesis respectivas. (cuánto se parece y cuánto divergen) A través de ellas se pueden ver los diversos matices en torno a los conceptos de belleza y de espíritu. A esta cuestión es a lo que se dedicará esta comunicación: a analizar brevemente algunos argumentos de ambos autores acerca de la belleza en la naturaleza y en el arte. A lo largo de este artículo se lleva a cabo una comparación de textos, de algunas discrepancias concretas: en todas ellas lo llamativo es cómo son a la vez tan cercanos y tan contrarios. Tanto para Schelling como para Hegel, la belleza es del espíritu: lo más bello es lo que está penetrado de espíritu y es vivificado por él. Pero más allá de estos principios comunes hay mil matices que acaban desembocando en dos posturas contrapuestas. (shrink)

In this paper I aim to undermine Stoic and Neo-Stoic readings of Benedict de Spinoza by examining the latter’s strong agreements with Epicurus (a notable opponent of the Stoics) on the nature and ethical role of pleasure in living a happy life. Ultimately, I show that Spinoza and Epicurus are committed to three central claims which the Stoics reject: (1) pleasure holds a necessary connection to healthy natural being, (2) pleasure manifests healthy being through positive changes in state and states (...) of healthy being per se, and (3) pleasure is by nature good. The Stoics reject these three claims due to their views on pleasant sensations as preferred moral indifferents and passionate pleasures as diseases of the soul, views which Spinoza (due to the abovementioned commitments) is strongly opposed to, thereby placing him (at least on the subject of pleasure) outside the realm of merely following or improving on Stoic doctrines. From this comparative analysis we also gain deeper insight into both Spinoza’s engagement with ancient Greek philosophy and the value of Epicureanism and Spinozism in helping us achieve and maintain happiness in the present day, particularly with respect to the benefits and harms of bodily and mental pleasures. (shrink)

Purpose of review: What is the relationship between rationality and mental health? By considering the psychological literature on depressive realism and unrealistic optimism it was hypothesized that, in the context of judgments about the self, accurate cognitions are psychologically maladaptive and inaccurate cognitions are psychologically adaptive. Recent studies recommend being cautious in drawing any general conclusion about style of thinking and mental health. Recent findings: Recent investigations suggest that people with depressive symptoms are more accurate than controls in tasks involving (...) time perception and estimates of personal circumstances, but not in other tasks. Unrealistic optimism remains a robust phenomenon across a variety of tasks and domains, and researchers are starting to explore its neural bases. However, the challenge is to determine to what extent and in what way unrealistic optimism is beneficial. Summary: We should revisit the hypothesis that optimistic cognitions are psychologically adaptive, whereas realistic thinking is not. Realistic beliefs and expectations can be conducive to wellbeing and good functioning, and wildly optimistic cognitions have considerable psychological costs. (shrink)

A belief one has is safe if either (i) it could not easily be false or (ii) in any nearby world in which it is false, it is not formed using the method one uses to form one’s actual belief. It seems our mathematical beliefs are safe if mathematical pluralism is true: if, loosely put, almost any consistent mathematical theory is true. It seems, after all, that in any nearby world where one’s mathematical beliefs differ from one’s actual beliefs, one (...) would believe some other true, consistent theory. Focusing on Justin Clarke-Doane’s recent discussion, I argue the thesis that mathematical beliefs are safe given pluralism faces some obstacles. I argue (i) is true of mathematical belief given pluralism only if we deny plausible claims about the interpretation of non-pluralists who many of us could easily be. Unless strong metasemantic theses are true, it is plausible many of us could easily deny or refuse to believe a consistent and true mathematical theory we actually believe. Since philosophical arguments and controversies permeate the methodology of foundational mathematics, I argue we cannot confidently distinguish the methods we use in mathematics between worlds, thus raising doubts about (ii). (shrink)

As health systems around the world turn towards highly distributed, specialized and cooperative structures to increase quality and safety of care as well as efficiency and efficacy of delivery processes, there is a growing need for supporting communication and collaboration of all parties involved with advanced ICT solutions. The Electronic Health Record (EHR) provides the information platform which is maturing towards the eHealth core application. To meet the requirements for sustainable, semantically interoperable, and trustworthy EHR solutions, different standards and different (...) national strategies have been established. The workshop summarizes the requirements for such advanced EHR systems and their underlying architecture, presents different strategies and solutions advocated by corresponding protagonists, discusses pros and cons as well as harmonization and migration strategies for those approaches. It particularly highlights a turn towards ontology-driven architectures. (shrink)

This essay concerns the question of how we make genuine epistemic progress through conceptual analysis. Our way into this issue will be through consideration of the paradox of analysis. The paradox challenges us to explain how a given statement can make a substantive contribution to our knowledge, even while it purports merely to make explicit what one’s grasp of the concept under scrutiny consists in. The paradox is often treated primarily as a semantic puzzle. However, in “Sect. 1” I argue (...) that the paradox raises a more fundamental epistemic problem, and in “Sects.1 and 2” I argue that semantic proposals—even ones designed to capture the Fregean link between meaning and epistemic significance—fail to resolve that problem. Seeing our way towards a real solution to the paradox requires more than semantics; we also need to understand how the process of analysis can yield justification for accepting a candidate conceptual analysis. I present an account of this process, and explain how it resolves the paradox, in “Sect. 3”. I conclude in “Sect. 4” by considering the implications for the present account concerning the goal of conceptual analysis, and by arguing that the apparent scarcity of short and finite illuminating analyses in philosophically interesting cases provides no grounds for pessimism concerning the possibility of philosophical progress through conceptual analysis. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...) performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (shrink)

Lockheed Martin Corp. has funded research to generate a framework and methodology for developing semantic reasoning applications to support the discipline oflntelligence Analysis. This chapter outlines that framework, discusses how it may be used to advance the information sharing and integrated analytic needs of the Intelligence Community, and suggests a system I software architecture for such applications.

Grasping the identity of hybrids, that is beings which cross the binarism of nature and technology (e.g. genetically-modified organisms (GMOs), syn-bio inventions, biomimetic projects), is problematic since it is still guided by self-evident dualistic categories, either as artefacts or as natural entities. To move beyond the limitations of such a one-sided understanding of hybrids, we suggest turning towards the categories of affordances and the juxtaposition of needs and patterns of proper use, as inspired by the Heideggerian version of phenomenology. Drawing (...) upon selected concepts by Heidegger, we argue that hybrids can be conceptualised as a regenerative design and use to serve the planet. We argue that the ideal type of non-exploitative account of hybrids consists of the adaptive approach to the environment, which does not, however, exclude the possibility of designing and constructing new beings. We also point out that hybrids undermine the divide of being destructive/regenerative which marks the boundaries of nature and technology. (shrink)

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)