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 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)

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)

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)

Achieving understanding of nature is one of the aims of science. In this paper we offer an analysis of the nature of scientific understanding that accords with actual scientific practice and accommodates the historical diversity of conceptions of understanding. Its core idea is a general criterion for the intelligibility of scientific theories that is essentially contextual: which theories conform to this criterion depends on contextual factors, and can change in the course of time. Our analysis provides a general account of (...) how understanding is provided by scientific explanations of diverse types. In this way, it reconciles conflicting views of explanatory understanding, such as the causal-mechanical and the unificationist conceptions. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

There is a need to better understand how individuals in different religious groups construct and maintain their worldviews. This study explores how religious practices, beliefs, and relationships create and sustain the worldviews of five British Muslims. Semi-structured interviews were inductively analyzed using interpretative phenomenological analysis (IPA) to idiographically explore the participants’ lived experiences. This analysis developed multiple subordinate themes that formed two superordinate themes: “Submitting to Allah” and “Being a British Muslim.” The participants’ experiences of being raised in Muslim families (...) strongly shaped their beliefs and they each strongly identify themselves as both Muslim and British. These important relationships taught them to follow the teachings of the Qur’an and to live their lives in submission to God. The analysis suggests the belief that the Qur’an is the authoritative and enduring revelation of God to mankind provided the core of their worldview and that this belief had far-reaching implications for every aspect of their lives. Their social relationships and religious practices both continually affirmed this fundamental belief in their sacred text and created a social reality in which the participants experienced God and submitted to the will of Allah. The combination of many different religious practices, social relationships, and personal experiences imbued the Qur’an with the power and authority to shape the participants’ lives and sustained their religious community. The participants’ intratextually fundamentalist approach to the Qur’an helped them create coherent worldviews that were filled with meaning and purpose. (shrink)

Providing in-utero treatments to target specific conditions in the fetus is a relatively new approach in perinatal care, with the vast majority of these treatments being used off-label. The high degree of off-label medication use in the perinatal and neonatal settings raises concern for the safety of both the fetuses and expectant mothers. This report presents two examples of intra-amniotic drug administration based on reported clinical cases. From the ethical framework of medical principlism, we examine the competing ethical duties of (...) autonomy, beneficence, and non-maleficence in this setting. We then lay out three fundamental ethical principles for obtaining informed consent and maximizing clinical benefit. (shrink)

The Aristotelian dictum that desire is the starting point of practical reasoning that ends in action can of course be denied. Its denial is a commonplace of moral theory in the tradition of Kant. But in this essay I am concerned with that issue only indirectly. I shall not contend that rational action always or necessarily does involve desire as its starting point; nor shall I deny it. My question concerns instead the possibility of its ever beginning in desire. For (...) there is a question whether it is even possible for reasoning to begin in desire, a question arising from the nature of desire and its objects, which to my knowledge has not been articulated. If we can see how desire can provide the arche of action, then we can consider later, and from that vantage point, whether it is necessary that it should do so. It will, I think, be possible eventually to argue that if practical reasoning has the character it must have, if it can begin in desire, then its starting point can be nothing but desire. (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)

This study proposes a conceptual model to explain persistent, accepted-as-normal corporate wrongdoing (hereafter banality of wrongdoing), particularly for high performance organizations. The model describes five explanatory variables: the culture of competition, ends-biased leadership, missionary zeal, legitimizing myth, and the corporate cocoon. Our thesis is that the nature of competition drives both legitimate and illegitimate goal-seeking to adopt an iconoclastic (rule-breaking) orientation. High performance organizations are favorable hosts for wrongdoing because high performance requires aggressive behavior at the ethical margins of what (...) is acceptable. The way leadership reacts to competition sets the stage for ethical or unethical cultures to develop. Ends-biased leadership will project strong vision, using ideology and legitimizing myth as tools to inspire and motivate. The resulting missionary zeal justifies using questionable means because of the perceived value of the end. One critical method for building strong culture is creating a sense of being separate and apart from the ordinary. This cocoon effect may create a self-referential value system that is significantly at odds with mainstream culture and in which wrongdoing is banal. We intend an empirical study of the variables described in this model. (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 textbook offers a unique and accessible approach to ethical decision-making for practicing pharmacists and student pharmacists. Unlike other texts, it gives clear guidance based on the fundamental principles of moral philosophy, explaining them in simple language and illustrating them with abundant clinical examples and case studies. The strength of this text is in its emphasis on normative ethics and critical thinking, and that there is truly a best answer in the vast majority of cases, no matter how complex. The (...) authors place high trust in a pharmacist’s moral judgment. This teaches the reader how to think, based on ethical principles, not necessarily what to think. This means navigating between the two extremes of overly theoretical and excessively prescriptive. The cogent framework given in this text uses the language of competing duties, identifying the moral principles at stake that create duties for the pharmacist. This is the balancing act of normative ethics, and of deciding which duties should prevail in a given clinical situation. This work presents a clear-cut pathway for resolving ethical dilemmas encountered by pharmacists, based on foundational principles and critical thinking. Presents a clear-cut pathway for resolving the ethical dilemmas encountered by pharmacists, based on foundational principles and critical thinking. Jon E. Sprague, RPh, PhD, Director of Science and Research for the Ohio Attorney General. (shrink)

Reductionism, in the sense of the doctrine that theories on different levels of reality should exhibit strict and general relations of deducibility, faces well-known difficulties. Nevertheless, the idea that deeper layers of reality are responsible for what happens at higher levels is well-entrenched in scientific practice. We argue that the intuition behind this idea is adequately captured by the notion of supervenience: the physical state of the fundamental physical layers fixes the states of the higher levels. Supervenience is weaker than (...) traditional reductionism, but it is not a metaphysical doctrine: one can empirically support the existence of a supervenience relation by exhibiting concrete relations between the levels. Much actual scientific research is directed towards finding such inter-level relations. It seems to be quite generally held that the importance of such relations between different levels is that they are explanatory and give understanding: deeper levels provide deeper understanding, and this justifies the search for ever deeper levels. We shall argue, however, that although achieving understanding is an important aim of science, its correct analysis is not in terms of relations between higher and lower levels. Connections with deeper layers of reality do not generally provide for deeper understanding. Accordingly, the motivation for seeking deeper levels of reality does not come from the desire to find deeper understanding of phenomena, but should be seen as a consequence of the goal to formulate ever better, in the sense of more accurate and more-encompassing, empirical theories. (shrink)