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)

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)

Offers a physical explanation of the Coriolis force. This book is useful for studying the hydrodynamics of the ocean and atmosphere. It also presents many aspects of classical mechanics/dynamics physics. It explains the complexities of this force, about which many scientists have had lingering uncertainties since it was first described in 1831.

Progressive supranuclear palsy is a movement disorder with prominent tau neuropathology. Brain diseases with abnormal tau deposits are called tauopathies, the most common of which is Alzheimer's disease. Environmental causes of tauopathies include repetitive head trauma associated with some sports. To identify common genetic variation contributing to risk for tauopathies, we carried out a genome-wide association study of 1,114 individuals with PSP and 3,247 controls followed by a second stage in which we genotyped 1,051 cases and 3,560 controls for the (...) stage 1 SNPs that yielded P ≤ 10-3. We found significant previously unidentified signals associated with PSP risk at STX6, EIF2AK3 and MOBP. We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT brain expression. The genes implicated encode proteins for vesicle-membrane fusion at the Golgi-endosomal interface, for the endoplasmic reticulum unfolded protein response and for a myelin structural component. © 2011 Nature America, Inc. All rights reserved. (shrink)

Students in 80 kindergarten to grade six classrooms photographed and captioned experiences in class which they identified as examples of democratic citizenship education. With the assistance of a teacher candidate placed in their classroom for a semester, students chose and captioned five of the photographs they considered to best represent demonstrate citizenship education. Four main categories of citizenship events emerged describing key elements associated with democratic citizenship education; shared decision making, participating in a learner-oriented classroom context in which students have (...) some individual choice of daily activities, equality of opportunity, and activities extending into the community and integrating community and classroom. Early grades students (K-3) identified activities they associated with democratic citizenship education while upper grades (4-6) students additionally presented rationales and gave evidence to support their representations. Empowerment, problem solving, and contributing to the common good were additional elements associated with democratic citizenship education in the classes sampled, although these were not strongly represented as were the four key elements. This study provides an initial portrait indicating a need for deeper investigation of K-6 students' own representations of the democratic citizenship education they experience. (shrink)

Students in 80 kindergarten to grade six classrooms photographed and captioned experiences in class which they identified as examples of democratic citizenship education. With the assistance of a teacher candidate placed in their classroom for a semester, students chose and captioned five of the photographs they considered to best represent demonstrate citizenship education. Four main categories of citizenship events emerged describing key elements associated with democratic citizenship education; shared decision making, participating in a learner-oriented classroom context in which students have (...) some individual choice of daily activities, equality of opportunity, and activities extending into the community and integrating community and classroom. Early grades students (K-3) identified activities they associated with democratic citizenship education while upper grades (4-6) students additionally presented rationales and gave evidence to support their representations. Empowerment, problem solving, and contributing to the common good were additional elements associated with democratic citizenship education in the classes sampled, although these were not strongly represented as were the four key elements. This study provides an initial portrait indicating a need for deeper investigation of K-6 students' own representations of the democratic citizenship education they experience. (shrink)