Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (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)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

The 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)

Since its publication in 1965, Brian Barry's seminal work has occupied an important role in the revival of Anglo-American political philosophy. A number of ideas and terms in it have become part of the standard vocabulary, such as the distinction between "ideal-regarding" and "want-regarding" principles and the division of principles into aggregative and distributive. The book provided the first precise analysis of the concept of political values having trade-off relations and its analysis of the notion of the public interest (...) has also been significant. (shrink)

This interpretation of Zhuangzi's Dao, particularly in the "Qi Wu Lun," as "background noise" begins from Zhuangzi's question as to whether any human statements-and human language itself-can ultimately be distinguished from the "peeps of baby birds." The essay explores a tentative model of Dao that sees it as neither fully "linguistic" nor "non-linguistic" but as "pre-linguistic," the potential ground of emergence of words, statements, and meanings. To develop this model we turn to the notion of background noise in physics, especially (...) as discussed by Michel Serres in his discussion of chaos and information theory. A crucial feature of the Serresian chaos-theory model and also, it is suggested here, of Zhuangzi's Dao is the tendency of hyper-order to return (or switch) back to the initial state of disorder. (shrink)

Bioregionalists have championed the utility of the concept of the watershed as an organizing framework for thought and action directed to understanding and implementing appropriate and respectful human interaction with particular pieces of land. In a creative analogue to the watershed, permaculturist Arthur Getz has recently introduced the term “foodshed” to facilitate critical thought about where our food is coming from and how it is getting to us. We find the “foodshed” to be a particularly rich and evocative metaphor; but (...) it is much more than metaphor. Like its analogue the watershed, the foodshed can serve us as a conceptual and methodological unit of analysis that provides a frame for action as well as thought. Food comes to most of us now through a global food system that is destructive of both natural and social communities. In this article we explore a variety of routes for the conceptual and practical elaboration of the foodshed. While corporations that are the principal beneficiaries of a global food system now dominate the production, processing, distribution, and consumption of food, alternatives are emerging that together could form the basis for foodshed development. Just as many farmers are recognizing the social and environmental advantages to sustainable agriculture, so are many consumers coming to appreciate the benefits of fresh and sustainably produced food. Such producers and consumers are being linked through such innovative arrangements as community supported agriculture and farmers markets. Alternative producers, alternative consumers, and alternative small entrepreneurs are rediscovering community and finding common ground in municipal and community food councils. Recognition of one's residence within a foodshed can confer a sense of connection and responsibility to a particular locality. The foodshed can provide a place for us to ground ourselves in the biological and social realities of living on the land and from the land in a place that we can call home, a place to which we are or can become native. (shrink)

This article investigates the propensity for academic dishonesty by university students using the partitioning method of decision tree analysis. A set of prediction rules are presented, and conclusions are drawn. To provide context for the decision tree approach, the partition process is compared with results of more traditional probit regression models. Results of the decision tree analysis complement the probit models in terms of predictive accuracy and confirm results previously found in the literature. In particular, students’ moral character—whether they believe (...) cheating is acceptable—is found to be the most important factor in determining the propensity for academic dishonesty. (shrink)

Cyclic nucleotides can regulate the sensitivity of retinal rods to light through phosducin. The phosphorylation state of phosducin determines the amount of G available for activation by Rho*. Phosducin phosphorylation is regulated by cyclic nucleotides through their activation of cAMP-dependent protein kinase. The regulation of phosphodiesterase activity by the noncatalytic cGMP binding sites as well as Ca2+/calmodulin dependent regulation of cGMP binding to the cation channel are also discussed.

: This interpretation of Zhuangzi's Dao, particularly in the "Qi Wu Lun," as "background noise" begins from Zhuangzi's question as to whether any human statements—and human language itself—can ultimately be distinguished from the "peeps of baby birds." The essay explores a tentative model of Dao that sees it as neither fully "linguistic" nor "non-linguistic" but as "pre-linguistic," the potential ground of emergence of words, statements, and meanings. To develop this model we turn to the notion of background noise in physics, (...) especially as discussed by Michel Serres in his discussion of chaos and information theory. A crucial feature of the Serresian chaos-theory model and also, it is suggested here, of Zhuangzi's Dao is the tendency of hyper-order to return (or switch) back to the initial state of disorder. (shrink)

This interpretation of Zhuangzi's Dao, particularly in the "Qi Wu Lun," as "background noise" begins from Zhuangzi's question as to whether any human statements-and human language itself-can ultimately be distinguished from the "peeps of baby birds." The essay explores a tentative model of Dao that sees it as neither fully "linguistic" nor "non-linguistic" but as "pre-linguistic," the potential ground of emergence of words, statements, and meanings. To develop this model we turn to the notion of background noise in physics, especially (...) as discussed by Michel Serres in his discussion of chaos and information theory. A crucial feature of the Serresian chaos-theory model and also, it is suggested here, of Zhuangzi's Dao is the tendency of hyper-order to return (or switch) back to the initial state of disorder. (shrink)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

Ludwig Traube has remarked that ‘ Einer der sonderbarsten Abschnitte in der von Emil Baehrens rekonstruierten Anthologia latina ist der, welcher die Gedichte Römischer Kaiser zusammenfasst, carmen 122–127 .” Of these six poems he points out that Nos. 125 and 126 are early mediaeval epitaphs, No. 127, Hermaphroditus, is later mediaeval, and that Nos. 123 and 124, which were favourites in the Middle Ages, are improperly ascribed to the Emperor Hadrian. Of the remaining poem, No 122, he says nothing. It (...) was first printed by Hermann Hagen in the Rheinisches Museum, xxxv, pp. 569 sqq. , from the Berne MS. No. 109, a tenth century MS. of French origin, partly written in Tironian notes. Hagen gives a facsimile of the entry in the MS. which bears the title Octa. aug. This is the authority for attributing the poem to Augustus. (shrink)

This volume represents the proceedings of the annual Lectures on Moral Values in a Free Society at the University of Texas at Dallas, presented in 1983 on November 14 through 16.

Counterfactuals all the way down? Content Type Journal Article DOI 10.1007/s11016-010-9437-9 Authors Jim Woodward, History and Philosophy of Science, 1017 Cathedral of Learning, University of Pittsburgh, Pittsburgh, PA 15260, USA Barry Loewer, Department of Philosophy, Rutgers University, New Brunswick, NJ 08901, USA John W. Carroll, Department of Philosophy and Religious Studies, North Carolina State University, Raleigh, NC 27695-8103, USA Marc Lange, Department of Philosophy, University of North Carolina at Chapel Hill, CB#3125—Caldwell Hall, Chapel Hill, NC 27599-3125, USA Journal Metascience (...) Online ISSN 1467-9981 Print ISSN 0815-0796 Journal Volume Volume 20 Journal Issue Volume 20, Number 1. (shrink)