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)

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)

This selection of reviews and papers is intended to stimulate renewed reflection on the fundamental and practical aspects of probability in physics.

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)

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)

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)

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)

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)

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)

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)