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)

This paper will aim to accomplish two things to show Luhmann’s and Hegel’s support of language and communication as dependent on culture, but also their differences with respect to how culture is formed in conjunction with the environment. This paper will firstly show how Hegel distinguishes between the imagination and reason in a different manner from Luhmann, as Hegel considers them logically connected while Luhmann considers them as coextensive. Secondly, this paper will show how reason and imagination create culture through (...) the environment via dialectical idealism in Hegel and a poly-contextural constructivist approach in Luhmann. (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 categorical imperative inherent in Kant’s ethics has had indubitable historical influence on societies worldwide whether in the form of laws, democracy or public deliberation. The Toronto Van Attack of 2018 and its subsequent legal trial is a case example that shows how the categorical imperative can be applied to assist in understanding the reasoning for the case’s guilty verdict. This paper will convey the applicability of the categorical imperative for examining criminal case studies by closing the gap between ethical (...) theory and practice. Such closure will be shown to assist in understanding why a perpetrator of a crime can be found guilty of following a hypothetical imperative to base their actions. The rationale for the verdict in this case will be shown to be based on the perpetrator’s responsibility in the form of maintaining autonomy despite having an autism diagnosis. The perpetrator will be shown to have acted on an irrational will and yet was treated in the legal sense as a rational individual. Such rationality was maintained despite complications with their autonomy in the form of relativism and ethical solipsism. (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)

Spanish translation, introductory study and notes on Charles Leslie Stevenson’s “Persuasive Definitions”. Published in Stevenson, Charles L. “Definiciones persuasivas”. Quaderns de Filosofia, vol. VIII, n. 1 (2021), pp. 105–125. -/- [Introductory study published in Oya, Alberto. “Presentación. Las definiciones persuasivas según Charles L. Stevenson”. Quaderns de Filosofia, vol. VIII, n. 1 (2021), pp. 101–104].

Natural scientific views on the human being have the tendency to reduce selfhood toa static object. This tendency arguably derives from the need to objectify the present in which the human being is found. Phenomenology avoids such a reduction by engaging with the present instead of distancing from it for the sake of analysis. This beneficence that derives froma phenomenological view of reality is argued to be a warranted view a counseling therapist should adopt. Not only can a therapist who (...) involves phenomenological perspectives in their practice succeed in viewing their clients non-instrumentally, but such a therapist can also “Be” genuine. The paper conceives of the therapist capable of performing these phenomenological tasks in therapy as adopting a mode of Being which we highlight as akin to the ancient concept: hypostasis. This conception in turn is shown to have epistemological ramifications for the meaning of “understanding”, which is shown quite suitably in the example of therapeutic presence. Heidegger’s Dasein serves as conceptual example of self in the paper to elucidate the connection between hypostasis and understanding throughout. (shrink)

Human beings can be said to naturally seek familiarity in their environment for survival purposes, and this can explain why the mere-exposure effect, where being merely exposed to external factors in our environment, can increase preference for these factors. Familiarity in this sense can thus be framed as important for affect and preference formation and considered built upon both the subjective process of fluency and the objects of experience being processed. The feeling of uncanniness is often considered the opposite of (...) familiarity, yet within its semantic vicinity. By considering the term ‘uncanny’ as having a double meaning linked to both familiarity and unfamiliarity, however, this paper will show how this ambiguity allows for a semantic relatedness of this concept to process fluency rather than familiarity. This connection will in turn be shown to have ramifications for affect through the proposal of a fourth model of process fluency: The Embodied Fluency Model. Through consideration of Mori’s shinkawan, Freud’s notion of the uncanny, and Heidegger’s connection between uncanniness and Angst, an exploration into conceiving how fluency and uncanniness share attributes that allow for a different view on affect is propounded. (shrink)

This paper aims to uncover some of the important contributions the phenomenological method can offer to philosophical issues in literary studies. It leads us to the idea that the archetypes found in fiction are intuited phenomenologically. This idea is then linked to a social constructive attainment of meaning for reality. From the intersubjectivity provided by phenomenology, empathy with characters in fiction is then displayed as more than an intellectual activity, as it becomes known to have practical implications. It is framed (...) as involving the same processes as the empathy we have with people in the real world. This equivalency allows for the plausibility of the notion that fiction-making is a necessary process for our interpretations of reality. It designates our involvement in fiction as beneficial to our experience of the real world and supports the notion it can train us to empathize. Such training is displayed to be posssible from phenomenology’s role in the process of empathy. Phenomenology's method de-centers the Cartesian ego to prevent any impasse between internal consciousness and the external world. Since they are bridged together by intentionality, we learn that phenomenology is a method that can contribute to how we conceive of empathy. (shrink)

The conflict between aesthetic experience and the modern vision of the world frames aesthetic experience as a defender of the plurality derived from the perspectives of individuals. This signifies that aesthetic experience confronts the unilateralism of modernity’s vision. This article propounds that this role of aesthetic experience is based on its defense of subjectivity and individuality. This defense, when investigated, reveals the compatibility between phenomenology and pragmatism. This compatibility also demonstrates that aesthetic experience should be understood as a phenomenological experience. (...) Therefore, phenomenology and pragmatism reveal a comradery that permits them to work in tandem, defending subjectivity and pluralism in the face of modernity. (shrink)

The status of philosophy is contingent upon the civilizations that embrace or undermine its importance. Such status is never fully understood, nor clear, due in part to its inutility. In a goal-oriented world, philosophizing is pointless if it does not produce material results. One point of philosophy though is not only to recognize, but promote activities which are uniquely human and which therefore artificial intelligence could not possibly simulate. Improvisation, as one such activity, can reveal the importance of philosophy as (...) a discipline by maintaining the relevance of subjectivity. In order to justify the presence of philosophy in the university, one important way is to have philosophy maintain the notion that the mental cannot be reduced to the material or physical. Consequently, phenomenology in philosophy’s defense becomes more relevant the more we realize that philosophy is threatened by the interdependency of materialism, A.I. research, and the corporatization of the university. (shrink)

Narratologists commonly draw a distinction between the story and those things that tell the story- the tellings, as I will call them here. Here is an example intended to highlight that distinction. The Parable of the Sower is a parable found in the New Testament books of Matthew, Mark and Luke, and in the non-canonical Gospel of Thomas. Though the relevant pieces of text in the Gospels are remarkably similar, no two of the four are identical. The verses in Matthew, (...) Mark and Luke, have been translated and paraphrased, along with the rest of the Bible, into literally thousands of different languages and versions, all of which include the The Parable of the Sower. (shrink)

This discussion interprets William Blake's poetry and painting across the hermeneutic philosophy of Martin Heidegger and his analysis of Dasein. It shows Blake's eighteenth-century discourse to be, like Heidegger's philosophy of Dasein, a radical critique of philosophical, scientific, and artistic thinking. To better understand the connections between Blake and Heidegger, the development of aesthetic philosophy from classical aesthetics through Nietzsche is charted. The parameters of eighteenth-century aesthetics, and the rise of hermeneutics in the nineteenth and early twentieth century, are discussed (...) as a response to the limitations of the neoclassical. On this basis, ideas and practices central to Blake's poetry such as "eternity" and "Albion" are compared to Heidegger's concepts of Dasein in order to shed additional light on the pioneering nature of Blake's work, and to see that he may be understood in terms of later aesthetic philosophies. (shrink)