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)

Current challenges in medical practice, research, and administration demand physicians who are familiar with bioethics, health law, and health economics. Curriculum directors at American Association of Medical Colleges-affiliated medical schools were sent confidential surveys requesting the number of required hours of the above subjects and the years in which they were taught, as well as instructor names. The number of relevant publications since 1990 for each named instructor was assessed by a PubMed search.In sum, teaching in all three subjects combined (...) comprises less than two percent of the total hours in the American medical curriculum, and most instructors have not recently published articles in the fields they teach. This suggests that medical schools should reevaluate their curricula and instructors in bioethics, health law, and health economics. (shrink)

The issue of musical identity—of what defines works of music, gives each its unique character and distinguishes them from one another—is one of the central issues in the philosophy of music. Too often in the philosophical literature it is approached as a purely theoretical question, one that can be answered adequately through careful intellectual consideration of scores and performances. The typical philosophical approach to the performance of Western art music, particularly that composed between the Baroque and Romantic eras, is to (...) offer descriptions of how musical works come into being, what their origins may be, which of their structural and aesthetic elements must be observed and conserved in their representations, and so on. It takes the written notation of a musical work, the score, to be a kind of blueprint created by a composer, defining and describing an autonomous musical entity, the musical work, such that another person might perform it. The work is recognized paradoxically as something existing independently of, yet deriving its identity from, its origins with the composer. (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)

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)

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)

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)

Linden Lab studies massive online game "Second Life" unexpectedly gained worldwide fame after a few years after release. To the surprise of many game has met with great interest, despite the lack of promotional campaigns. It can be assumed that the reason why "second life" reached a wider audience was a special type of offered entertainment. Network game proved to be no longer a game that was known so far, but an example of a mass media, whose central element (...) is a dynamic virtual world which is an extension of our "first" reality. "Second Life" has the potential, which is challenging the widely shared rules could shake the foundations of the social world. This program is currently the most advanced example of a virtual economy. Unlike many other massive online games and their predecessors, this game is entirely based on the principles of virtual property ownership, as well as rules of conduct virtual business and service, and finally also the consumption of goods. Users of the game, just like the person providing the data in the framework of social networking sites maintained in the mainstream of Web 2.0, user-generated content constituting the virtual world, which can trade content with others linden virtual dolars that can be exchanged to real U.S. dollars. The increase in popularity of "Second Life" brings to mind the vision of the possibility of creating a better place to live for many people. Closer analysis of this phenomenon does not allow for such statements. In the following instances will be presented: information about the growth of the global market for online games and its consequences, the distinguishing features of "Second Life" from traditional online games, virtual elements of the impact of economics on social life, the concept of entertainment as a job stream properties Games 2.0 and contentious issues, which produces "second life". ** Masowa gra on-line "Second Life" studia Linden Lab nieoczekiwanie zdobyła sławȩ na całym świecie po kilku latach od premiery. Ku zaskoczeniu wielu tytuł spotkał siȩ z ogromnym zainteresowaniem mimo braku akcji promocyjnych. Można przypuszczać, że powodem dla którego "drugie życie" dotarło do szerszego grona odbiorców był szczególny typ zaoferowanej formy rozrywki. Sieciowa gra okazała siȩ nie być już gr¸a} jak¸a} znano do tej pory, lecz przykładem środka masowego przekazu, którego centralnym elementem jest dynamiczny wirtualny świat stanowi¸a}cy przedłużenie naszej, "pierwszej", rzeczywistości. "Second Life" kryje w sobie potencjał, który podważaj¸a}c podzielane powszechnie reguły może wstrz¸a}sn¸a}ć posadami świata społecznego. Program ten jest obecnie najbardziej zaawansowanym przykładem wirtualnej gospodarki. W odróżnieniu od wielu innych masowych gier on-line i ich poprzedniczek pozycja ta w całości opiera siȩ na zasadach posiadania wirtualnej własności, jak też regułach prowadzenia wirtualnej działalności gospodarczej i usługowej, i wreszcie takiej też konsumpcji dóbr. Użytkownicy gry, podobnie jak osoby udostȩpniaj¸a}ce dane w ramach internetowych serwisów społecznościowych utrzymanych w nurcie Web 2.0, generuj¸a} treści tworz¸a}ce wirtualny świat, treści którymi mog¸a} handlować z innymi pobieraj¸a}c za nie opłaty w wirtualnych dolarach lindeńskich wymiennych na realne dolary amerykańskie. Wzrost popularności "Second Life" przywodzi na myśl wizjȩ możliwości stworzenia lepszego miejsca do życia dla wielu ludzi. Bliższa analiza tego zjawiska nie pozwala już na takie stwierdzenia. W dalszej czȩści wyst¸apienia przedstawione zostan¸a: informacje o wzroście globalnego rynku gier on-line i jego konsekwencjach, cechy odróżniaj¸ace "Second Life" od tradycyjnych gier sieciowych, elementy wpływu wirtualnej gospodarki na życie społeczne, pojȩcie rozrywki jako pracy, właściwości nurtu Games 2.0 oraz sporne kwestie, jakie wywołuje "drugie życie". (shrink)

In this article, I present a two-pronged argument for the immorality of contemporary, asymmetric drone warfare, based on my new interpretations of the just war principles of “proportionality” and “moral equivalence of combatants” (MEC). The justification for these new interpretations is that drone warfare continues to this day, having survived despite arguments against it that are based on traditional interpretations of just war theory (including one from Michael Walzer). On the basis of my argument, I echo Harry Van der (...) class='Hi'>Linden’s call for “an international treaty banning all weaponized UAV [uninhabited aerial vehicles].”. (shrink)

Following Freud’s analysis of the fragile line between the uncanny double and its comic redoubling, I identify the doubling of the double found in critical moments of Hegelian dialectic as producing a kind of comic effect. It almost goes without saying that two provides greater pleasure than one, the loneliest number. Many also find two to be preferable to three, the tired trope of dialectic as a teleological waltz. Two seems to offer lightness, relieving one from her loneliness and lacking (...) the complications of a third who comes in between. And yet, we learn through Marx and Freud that the double (even the double of tragedy and farce) borders on something closer to horror than comedy. -/- In the following, I would like to explore why four is funnier than two in my staging of dialectic as the doubling of the double or, to borrow a movie title from Laurel and Hardy, “Twice Two” (Roach et al. 1933a). I will begin by exploring the formulations of the double in the form of a pair of opposites and in the form of a pair of twins. The literary tropes of the double as the odd couple, on one side, and the twins, on the other, appear to serve very different narrative functions, which incite different kinds of affective responses from the audience. However, the form of the opposed double sometimes conceals the realization that the empty or fragmented content of the first is only reduplicated in the second. The “straight man” of the odd couple cannot see himself in his counterpart “the comic.” The redoubling of the double, however, forces not only the audience, but the original double on stage to confront what was already present, but unrealized, from the beginning. To illustrate this redoubling of the double within the opening of Hegel’s Science of Logic, I consider two short films by Laurel and Hardy in which the comic duo redoubles itself. The formula (2 x 2) produces a comic excess through the dialectical redoubling of there uncanny double. (shrink)

Scholarly critiques of the just war tradition have grown in number and sophistication in recent years to the point that available publications now provide the basis for a more philosophically challenging Peace Studies course. Focusing on just a few works published in the past several years, this review explores how professional philosophers are reclaiming the terrain long dominated by the approach of political scientist Michael Walzer. On center stage are British philosopher David Rodin’s critique of the self-defensejustification for war and (...) American philosopher Andrew Fiala’s skeptical assessment of the just war tradition in its entirety. Also considered is a collection of more narrowly focused critiques by philosophers and some highly relevant extra-philosophical studies regarding the social interconnections between authority and violence. (shrink)