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)

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)

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)

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)

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (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)

Enligt ett realistiskt synsätt kan ett påstående vara sant trots att det inte ens i princip är möjligt att veta att det är sant. En sanningsteoretisk antirealist kan inte godta denna möjlighet utan accepterar en eller annan version av Dummetts vetbarhetsprincip: (K) Om ett påstående är sant, så måste det i princip vara möjligt att veta att det är sant. Det kan dock förefalla rimligt, även för en antirealist, att gå̊ med på̊ att det kan finnas sanningar som ingen faktiskt (...) vet (har vetat, eller kommer att veta) är sanna. Man kan därför tänka sig att en antirealist skulle acceptera principen (K) utan att därför gå med på den till synes starkare principen: (SK) Om ett påstående är sant, så måste det faktiskt finnas någon som vet att det är sant. Ett mycket omdiskuterat argument – som ytterst går tillbaka till Alonzo Church, men som först publicerades i en uppsats av Frederic Fitch i Journal of Symbolic Logic 1963 – tycks emellertid visa att principen (K) implicerar principen (SK). Anta nämligen att (K) är sann, medan (SK) inte är det. Men om (SK) är falsk, så finns det ett påstående som är sant men som ingen faktiskt vet är sant. Anta nu att p är ett sådant påstående. Låt Kp betyda att någon vet att p är sant. Det galler alltså̊ att p är sant samtidigt som Kp inte är det. Betrakta nu påståendet (p ∧ −Kp). Enligt antagandet är detta påstående sant. Enligt (K) måste det då vara möjligt att någon vet att (p ∧ −Kp). D.v.s., det måste vara möjligt att påståendet K(p ∧ −Kp) är sant. Men i så fall är det också̊ möjligt att påståendet Kp ∧ K−Kp är sant, vilket i sin tur implicerar att det är möjligt att Kp ∧ −Kp är sant, vilket ju är absurt. Således kan inte (K) vara sann samtidigt som (SK) är falsk. Vi tycks således kunna sluta oss till att (K) implicerar (SK). I uppsatsen diskuterar jag några olika sätt att undgå̊ Church-Fitch paradoxala slutsats. Ett tillvägagångssätt är att ersätta kunskapsoperatorn med en hierarki av kunskapspredikat. Ett annat är baserat på distinktionen mellan faktisk och potentiell kunskap och ett förkastande av den vanliga modallogiska formaliseringen av principen (K). Den senare typen av lösning betraktas både från ett realistiskt och ett icke-realistiskt perspektiv. Utifrån denna analys kommer jag fram till slutsatsen att vi, vare sig vi är realister eller antirealister rörande sanning, kan sluta oroa oss för vetbarhetsparadoxen och ändå uppskatta Church-Fitchs argument. (shrink)

Every person is equipped with both the Dionysian or life force soul (in Greek Eros), and the Apollonian or death force soul (in GreekThanatos). Dionysus was a Greek fertility god from c. 580 BCE associated with wine, music, and choral dance (Csapso 2016). In Attic art, Dionysus was often depicted as a slumping god on a ship, which had a vineover laden with grapes as a mast, surrounded by a sea with a pod of dolphins; the dolphins being the (...) rescuers of sailors (life force) (Carpenter 1990). Dionysus, who was resurrected from death, repre- sented hedonism, happiness, and the good life that he celebrated with a glass of wine. His half-brother Apollo was in many respects his polar opposite. Apollo was a cerebral god associated with the sun, light, and intellectual pursuit. Dio- nysus symbolized the ability of (wo) man to submerge him- or herself in a greater whole, the ecstatic, and the chaotic emotions. Apollo, on the contrary, symbolised his or her formally rational and reasoning mind. The Dionysian and Apollonian natural forces are complementary and one needs both to be a balanced person; one needed to be capable of creating form and struc- ture as well as being passionate and vital. Brown believed that a utopian society would primarily consist of such balanced persons who are at home in both the world of rationality and logic and of symbols and emotions. (shrink)