In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Although fairness is a key moral trait, limited research focuses on participants' observed fairness behavior because moral traits are generally measured through self-report. This experiment focused on day-to-day interpersonal fairness rather than impersonal justice, and fairness was assessed as observed behavior. The experiment investigated whether a self-reported fairness trait would moderate a situational influence on observed fairness behavior, such that individuals with a stronger fairness trait would be less affected by a situational influence than those with a weaker fairness trait. (...) We used an iterated resource game in which participants could withdraw resources as they chose, and we manipulated the number of resources bogus players withdrew. The number of resources participants withdrew was the behavioral measure of fairness. Results confirmed the expected moderation of the unfairness manipulation by a fairness trait on observed behavior. Those reporting a stronger fairness trait were unaffected by the manipulation, whereas those reporting a weaker fairness trait were more strongly influenced. (shrink)

By combining normative philosophy and empirical social science, we craft a research framework for assessing differential expectations embodied in normative conceptions of the economic social contract in the United States. We argue that there are distinctviews of such a contract grounded in individualist and communitarian philosophical ideologies. We apply this framework to organizational downsizing, postulating that certain human resource practices, in combination with the respective ideological orientations, will affect perceptions of the justice of downsizing policies.Living up to one’s word is (...) a decisive measure of moral character. Within the microsocial realm of the family, promises and commitments derive their social force and cultural meaning from the idea that love or biology binds people together in an absolute way. But outside of this world, in the larger society, the only thing binding people together is a sense that there is a social contract, a set of common obligations held collectively by society as a whole. But today’s workers say no one seems to care whether these promises are kept. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Books ReceivedThe Ahmadis: Community, Gender, and Politics in a Muslim Society. By Antonio Gualtieri. Montreal and Kingston: McGill-Queen's University Press, 2004. Pp. xvi + 192. Hardcover $65.00. Paper Cdn $24.95 / U.S. $19.95.American Knees. By Shawn Wong. Seattle and London: University of Washington Press, 2005. Pp. xxi + 229. Paper $14.95.The Art of Worldly Wisdom. By Baltasar Gracian and translated by Joseph Jacobs. Mineola, NY: Dover Publications, 2005. Pp. (...) xiii + 114. Paper $5.95.Bashō's Journey: The Literary Prose of Matsuo Bashō. Translated by David Landis Barnhill. Albany: State University of New York Press, 2005. Pp. xvii + 191. Hardcover $59.50. Paper $17.95.Bringing the Gods to Mind: Mantra and Ritual in Early Indian Sacrifice. By Laurie L. Patton. Berkeley: University of California Press, 2005. Pp. xv + 289. Hardcover $49.95/£32.50.Buddhist Inclusivism: Attitudes Towards Religious Others. By Kristin Beise Kiblinger. Burlington, VT: Ashgate Publishing Company, 2005. Pp. viii + 145. Hardcover $89.95.A Chinese Ethics for the New Century: The Ch'ien Mu Lectures in History and Culture, and Other Essays on Science and Confucian Ethics. By Donald J. Munro. Hong Kong: Chinese University Press, 2005. Pp. xlv + 158. Hardcover $33.00.Chinese Theories of Reading and Writing: A Route to Hermeneutics and Open Poetics. By Ming Dong Gu. Albany: State University of New York Press, 2005. Pp. xiv + 334. Hardcover $85.00.A Dictionary of Cantonese Slang: The Language of Hong Kong Movies, Street Gangs, and City Life. By Christopher Hutton and Kingsley Bolton. Honolulu: University of Hawai'i Press, 2005. Pp. xxiv + 492. Paper $28.00.Ghazālī and the Poetics of Imagination. By Ebrahim Moosa. Chapel Hill and London: University of North Carolina Press, 2005. Pp. xiii + 349. Hardcover $59.95. Paper $22.50.Going Forth: Visions of Buddhist Vinaya. Edited by William M. Bodiford. Honolulu: University of Hawai'i Press, 2005. Pp. x + 317. Hardcover $48.00.The Harem: Inside the Grand Seraglio of the Turkish Sultans. By N. M. Penzer. Mineola, NY: Dover Publications, 2005. Pp. 277. Paper $14.95.Ideals of the East: The Spirit of Japanese Art. By Kakuzo Okakura. Mineola, NY: Dover Publications, 2005. Pp. xiv + 106. Paper $5.95. [End Page 365]An Illustrated Chinese Materia Medica. By Jing-Nuan Wu. New York: Oxford University Press, 2005. Pp. 706. Price not given.Jews and Arabs: A Concise History of Their Social and Cultural Relations. By S. D. Goitein. Mineola, NY: Dover Publications, 2005. Pp. xv + 263. Paper $12.95.The Logic of Nothingness: A Study of Nishida Kitarō. By Robert J. J. Wargo. Honolulu: University of Hawai'i Press, 2005. Pp xi + 241. Paper $25.00.The Moral and Political Thought of Mahatma Gandhi. By Raghavan N. Iyer. New Delhi: Oxford University Press, 2000. Pp. xiii + 449. Paper Rs 520.00.Nietzsche's Epic of the Soul: Thus Spoke Zarathustra. By T. K. Seung. Lanham, MD: Lexington Books, 2005. Pp. xxviii + 370. Hardcover $83.00. Paper $27.95.Of Guilds, Companies, Corporations, and Governance: A Conceptual Sketch. By Leonardo R. Silos. Makati City, Philippines: Asian Institute of Management, 2005. Pp. xvi + 238. Price not given.The Path to Rome. By Hilaire Belloc. Mineola, NY: Dover Publications, 2005. Pp. ix + 251. Paper $12.95.The Philosophy of the Bhagavadgātā : A Study based on the Evaluation of the Commentaries of Śamkara, Rāmānuja and Madhva. By S. M. Srinivasa Chari. New Delhi: Munshiram Manoharlal Publishers, 2005. Pp. xxvi + 294. Hardcover Rs 575.00.The Philosophy of Rabindranath Tagore. By Kalyan Sen Gupta. Burlington, VT: Ash-gate Publishing Company, 2005. Pp. ix + 103. Hardcover $79.95.The Pristine Dao: Metaphysics in Early Daoist Discourse. By Thomas Michael. Albany: State University of New York Press, 2005. Pp. xi + 170. Hardcover $60.00. Paper $21.95.Three Mountains and Seven Rivers: Prof. Musashi Tachikawa's Felicitation Volume. Edited by Shoun Hino and Toshihiro Wada. Delhi: Motilal Banarsidass Publishers. 2004. Pp. xx + 903. Hardcover Rs. 1800.The Unity of Mystical Traditions: The Transformation of Consciousness in Tibetan and German Mysticism. By Randall Studstill. Leiden and Boston: Brill, 2005. Pp. xii + 304. Hardcover @89/$127.00.Writing the World: On Globalization. Edited by David... (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)

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)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (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)

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)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Over the past decade, teaching and learning in virtual worlds has been at the forefront of many higher education institutions around the world. The DEHub Virtual Worlds Working Group (VWWG) consisting of Australian and New Zealand higher education academics was formed in 2009. These educators are investigating the role that virtual worlds play in the future of education and actively changing the direction of their own teaching practice and curricula. 47 academics reporting on 28 Australian higher education institutions present an (...) overview of how they have changed directions through the effective use of virtual worlds for diverse teaching and learning activities such as business scenarios and virtual excursions, role-play simulations, experimentation and language development. The case studies offer insights into the ways in which institutions are continuing to change directions in their teaching to meet changing demands for innovative teaching, learning and research in virtual worlds. This paper highlights the ways in which the authors are using virtual worlds to create opportunities for rich, immersive and authentic activities that would be difficult or not possible to achieve through more traditional approaches. (shrink)

Human experience is not confined to waking life. Do experiences in dreams matter? Humans are not the only living beings who have experiences. Does nonhuman experience matter? The Buddhist philosopher Vasubandhu, writing during the late fourth and early fifth centuries C.E., argues in his work The Twenty Verses that these alternative contexts ought to inform our understanding of mind and world. Vasubandhu invites readers to explore experiences in dreams and to inhabit the experiences of nonhuman beings—animals, hungry ghosts, and beings (...) in hell. Other Lives offers a deep engagement with Vasubandhu’s account of mind in a global philosophical perspective. Sonam Kachru takes up Vasubandhu’s challenge to think with perspective-diversifying contexts, showing how his novel theory draws together action and perception, minds and worlds. Kachru pieces together the conceptual system in which Vasubandhu thought to show the deep originality of the argument. He reconstructs Vasubandhu’s ecological concept of mind, in which mindedness is meaningful only in a nexus with life and world, to explore its ongoing philosophical significance. Engaging with a vast range of classical, modern, and contemporary Asian and Western thought, Other Lives is both a groundbreaking work in Buddhist studies and a model of truly global philosophy. The book also includes an accessible new translation of The Twenty Verses, providing a fresh introduction to one of the most influential works of Buddhist thought. (shrink)

In The Othering of Women in Silent Film: Cultural, Historical, and Literary Contexts, Barbara Tepa Lupack explores the rampant racial and gender stereotyping in early cinema and demonstrates how that imagery helped shape American attitudes and practices.

'Foot stands out among contemporary ethical theorists because of her conviction that virtues and vices are more central ethical notions than rights, duties, justice, or consequences - the primary focus of most other contemporary theorists. This volume brings together a dozen essays published between 1957 and 1977, and includes two new ones as well. In the first, Foot argues explicitly for an ethic of virtue, and in the next five discusses abortion, euthanasia, free will/determination, and the ethics of Hume and (...) Nietzsche. The final eight essays chart her growing disenchantment with emotivism and prescriptivism and their account of moral arguments. All the essays embody to some extent her commitment to an ethics of virtue... Foot's style is straightforward and readable, her arguments subtle, ingenious, and some of them important.' Choice. (shrink)

This chapter develops a perceptual solution to the epistemological problem of other minds, relying on central ideas from Maurice Merleau-Ponty's phenomenology. The Merleau-Pontian account is contrasted with another attempted perceptual solution to the other minds problem, and it is argued that only the former meets the phenomenologists' desideratum of providing an alternative to inferential solutions. The chapter also provides responses to various objections to the perceptual solution, including a pair of objections recently put forward by Alec Hyslop.

Dan Zahavi engages with classical phenomenology, philosophy of mind, and a range of empirical disciplines to explore the nature of selfhood. He argues that the most fundamental level of selfhood is not socially constructed or dependent upon others, but accepts that certain dimensions of the self and types of self-experience are other-mediated.

Introduction -- Otherness in contemporary European cinema -- Potential and limits of a new European in Nicolas Echevarría's Cabeza de vaca -- Migrants in Europe: breaking the boundaries? -- Inspiration from abroad? cultural boundaries in Chicano cinema -- Conclusion.

In his recent book Reflective Democracy, Robert Goodin argues that 'external-collaborative' models of democratic deliberation procedures need to be supplemented by 'internal-reflective' deliberation. The exercise of the moral imagination plays a central role in Goodin's account of 'democratic deliberation within'. By imaginatively putting ourselves in the place of a range of others, he argues, including those who maybe not be able to represent their own interests, we can make their points of view 'communicatively present' in deliberation. Goodin's argument emphasizes the (...) role of art and other forms of cultural representation in helping to bring about this expansion of moral imagination. Drawing on debates in philosophy of mind concerning the scope and limits of our capacities to simulate other minds, I argue that Goodin's analysis of 'democratic deliberation within' conflates different kinds of imaginative project. In doing so, it underestimates both the difficulties of imaginatively putting ourselves in the place of others and the political risks in doing so. I argue, alternatively, that moral engagement with others involves the capacity for sympathy and that art and other forms of cultural representation can enlarge the scope of our sympathies, by assisting us to overcome imaginative resistance to alien points of view. In developing this argument, I provide a qualified defense of Iris Young's claim that respect for others involves 'asymmetrical reciprocity'. (shrink)

To what extent do we and can we understand others--other peoples, species, times, and places? What is the role of others within ourselves, epitomized in the notion of unconscious forces? Can we come to terms with our internalized others in ways that foster mutual understanding and counteract the tendency to scapegoat, project, victimize, and indulge in prejudicial and narcissistic impulses? How do various fields or disciplines address or avoid such questions? And, in the light of recent developments, have these questions (...) become particularly pressing and not in the least confined to other peoples, times, and places? Making selective and critical use of the thought of such important figures as Sigmund Freud, Jacques Derrida, and Mikhail Bakhtin, the book investigates a series of crucial topics from the current state of deconstruction, trauma studies, and the humanities to newer fields such as animal studies and posthumanist scholarship. A feature of the book is the effort to bring critical historical thought into a provocative engagement with politics and our current political climate. (shrink)

Wrestling and arguing with God: between insider and outsider African perspectives -- Introduction to Richard Kearney's intellectual autobiography: where do you come from, Richard Kearney? -- Where I speak from: a short intellectual autobiography -- Phenomenology in South Africa: an indirect encounter with Richard Kearney -- Transcendence and anatheism -- Response to Richard Kearney's Anatheism: Anatheism and holy folly -- Kearney between poles: is too much lost in the middle? -- Strangers, Gods and Africa: in dialogue with Richard Kearney on (...) Otherness -- Approaching the threshold: hospitality as a pedagogical wager in the work of Richard Kearney -- God-talk, the biblical prophets and Richard Kearney -- 'Strange' theology: engaging with Richard Kearney -- Trinitarian theology and Richard Kearney's anatheism: an engagement -- After God but behind the Cross: the procession as a way to re-encounter God in a culture beyond classical liturgy -- Touch gives rise to thought: Paul Ricoeur and Pumla Gobodo-Madikizela on mutual recognition and carnal hermeneutics -- Towards hospitality between enemies -- Across oceans: a conversation on otherness, hospitality and welcoming a strange God. (shrink)

Although'Otherness' is an extremely common phenomenon in every society, related research is still at its beginnings.'Otherness' in the Middle Ages is a versatile and complex theme that covers a great number of different aspects, facets, and approaches: from non-human monsters and cultural strangers from remote places up to foreigners from another country or another town; it can refer to ethnic, cultural, political, social, sexual, or religious'Otherness', inside or outside one's own community. In any case, however,'Otherness' is (...) a subjective phenomenon depending on personal views and ascriptions, an issue of'imagination' and experience rather than'reality'. There is neither one single model of alterity nor is'Otherness' a stable phenomenon, but it changes over time and according to the cultural context. All this calls for methodological reflection and needs thorough investigation.00The methodological introduction and the 18 contributions of this volume demonstrate the great diversity of the theme and its different manifestations and perspectives. They tackle the problem from distinct angles and disciplines (history, art history, archaeology, literary history, and philology) in a wide chronological and thematic frame, using different methodological approaches, dealing with different areas (from Northern and Southern Europe to Byzantium and India), perspectives (including law, social order, the past, a sea), and diverse kinds of sources. They examine all kinds of'Otherness' mentioned above, highlight demarcation and rejection, aversion or acceptance, assimilation and integration, thus relativizing a strict dichotomy between'the Self' and'the Other' or between inside and outside. This volume is so far the most comprehensive attempt to tackle the huge problem of'Otherness' in the Middle Ages. (shrink)