The Foundational Model of Anatomy Ontology

Anatomy is the structure of biological organisms. The term also denotes the scientific discipline devoted to the study of anatomical entities and the structural and developmental relations that obtain among these entities during the lifespan of an organism. Anatomical entities are the independent continuants of biomedical reality on which physiological and disease processes depend, and which, in response to etiological agents, can transform themselves into pathological entities. For these reasons, hard copy and in silico information resources in virtually all fields of biology and medicine, as a rule, make extensive reference to anatomical entities. Because of the lack of a generalizable, computable representation of anatomy, developers of computable terminologies and ontologies in clinical medicine and biomedical research represented anatomy from their own more or less divergent viewpoints. The resulting heterogeneity presents a formidable impediment to correlating human anatomy not only across computational resources but also with the anatomy of model organisms used in biomedical experimentation. The Foundational Model of Anatomy (FMA) is being developed to fill the need for a generalizable anatomy ontology, which can be used and adapted by any computer-based application that requires anatomical information. Moreover it is evolving into a standard reference for divergent views of anatomy and a template for representing the anatomy of animals. A distinction is made between the FMA ontology as a theory of anatomy and the implementation of this theory as the FMA artifact. In either sense of the term, the FMA is a spatial-structural ontology of the entities and relations which together form the phenotypic structure of the human organism at all biologically salient levels of granularity. Making use of explicit ontological principles and sound methods, it is designed to be understandable by human beings and navigable by computers. The FMA’s ontological structure provides for machine-based inference, enabling powerful computational tools of the future to reason with biomedical data

Reconsidering critical realism: an environmentalist’s perspective

In this paper, I discuss the compatibility of heterodox and ecological economics. Taking critical realism as a unifying ontology for heterodox economics, I argue that there is a radical dissonance between ontological presuppositions of ecological economics and heterodox traditions that adopt critical realist’s perspective. The dissonance lies in the need of ecologically oriented economic schools to state strict causal regularities in socio-economic realm, given the environmental intuitions about the nature of economy and the role of materiality and non-human agency in persistence of economic systems. The paper uses conceptual apparatus derived from Andrew Brown’s critique of critical realism and Bruno Latour’s Actor-network-theory.In this paper, I discuss the compatibility of heterodox and ecological economics. Taking critical realism as a unifying ontology for heterodox economics, I argue that there is a radical dissonance between ontological presuppositions of ecological economics and heterodox traditions that adopt critical realist’s perspective. The dissonance lies in the need of ecologically oriented economic schools to state strict causal regularities in socio-economic realm, given the environmental intuitions about the nature of economy and the role of materiality and non-human agency in persistence of economic systems. The paper uses conceptual apparatus derived from Andrew Brown’s critique of critical realism and Bruno Latour’s Actor-network-theory

The Method of Division and Aristotle's Criticism of Platonic Philosophy

This thesis investigates Aristotle's criticism and consequent reformulation of the Platonic method for formulating definitions called the Method of Division. For both Plato and Aristotle, the object of division is a natural kind, which consists in a class whose members stand in a homologous relationship to a single form. I argue that Aristotle's criticisms of the Method of Division fall under two categories: logical objections and ontological objections. The logical objections focus on division as a method for demonstrating definitions, a method that Aristotle wants to distinguish from his syllogistic logic, the centerpiece of his theory of scientific demonstration. The ontological objections focus on the question of whether the sort of account generated by division is sufficient to constitute a definition of its object. Aristotle's revised Method of Division is supposed to avoid the problems he raises by constructing definitions that satisfy the principles motivating his ontological objections through a logical process devised to make the resulting account a "necessary" consequence of the initial assumptions of the division. I argue that Aristotle?s ontological objections to the Method of Division reflect a deeper disparity between the Platonic and the Aristotelian notion of a form and natural kind. Underpinning Aristotle's notion of a natural kind is an ontology of discrete substances. Because the unity of substance is paramount in this ontology, Aristotle argues that a definition, which is supposed to give an account of the essence of a substance, must account for the unity of its object by itself possessing a non-accidental unity. Yet, on a Platonic ontology, a definition by division invokes a plurality of independent Forms whose conjunction does not constitute a unity. On the basis of this consideration, Aristotle argues that an ontology of abstract Forms cannot account for the unity of an individual substance. To this extent, I conclude, Aristotle's methodological objections to the Platonic Method of Division are a component of his broader criticisms of Platonic metaphysics

The evolutionary approach to entropy: Reconciling Georgescu-Roegen's natural philosophy with the maximum entropy framework

In Georgescu-Roegen's classical, though controversial discussion of entropy in relation to economics, the dualism of mechanical and subjective time plays a pivotal role. I argue that this fundamental distinction also inheres modern approaches to maximum entropy. Following Searle, I introduce the ontological dualism of observer independent and observer relative facts, and show that the notion of entropy also manifests this dualism, in the sense of the contextuality of measurements in experimental settings. Extending on the notion of observer relativity, I argue that the MaxEnt principle can be generalized into a framework of analyzing the evolution of (biological, technological etc.) functions under natural selection, if functions are equated with inference devices. Then, observer relativity is function relativity. In hierarchical evolutionary systems, this corresponds to the Maximum Entropy Production Principle, in the sense that functional evolution approximates gradients of maximum dissipation of energy. Against this background, the Georgescu-Roegen dualism of time translates into the dualism of observer independent entropy, which is the object of MEPP, and observer relative entropy, which is the object of MaxEnt. Both are two aspects under which evolution in general and economic evolution in particular can be analyzed. --Georgescu-Roegen,maximum entropy,observer relativity,time,hierarchical evolutionary systems,natural selection,physical concepts of information

Knowledge Organization and Terminology: application to Cork

This PhD thesis aims to prove the relevance of texts within the conceptual strand of terminological work. Our methodology serves to demonstrate how linguists can infer knowledge information from texts and subsequently systematise it, either through semiformal or formal representations. We mainly focus on the terminological analysis of specialised corpora resorting to semi-automatic tools for text analysis to systematise lexical-semantic relationships observed in specialised discourse context and subsequent modelling of the underlying conceptual system. The ultimate goal of this methodology is to propose a typology that can help lexicographers to write definitions. Based on the double dimension of Terminology, we hypothesise that text and logic modelling do not go hand in hand since the latter does not directly relate to the former. We highlight that knowledge and language are crucial for knowledge systematisation, albeit keeping in mind that they pertain to different levels of analysis, for they are not isomorphic. To meet our goals, we resorted to specialised texts produced within the industry of cork. These texts provide us with a test bed made of knowledge-rich data which enable us to demonstrate our deductive mechanisms employing the Aristotelian formula: X=Y+DC through the linguistic and conceptual analysis of the semi-automatically extracted textual data. To explore the corpus, we resorted to text mining strategies where regular expressions play a central role. The final goal of this study is to create a terminological resource for the cork industry, where two types of resources interlink, namely the CorkCorpus and the OntoCork. TermCork is a project that stems from the organisation of knowledge in the specialised field of cork. For that purpose, a terminological knowledge database is being developed to feed an e-dictionary. This e-dictionary is designed as a multilingual and multimodal product, where several resources, namely linguistic and conceptual ones are paired. OntoCork is a micro domain-ontology where the concepts are enriched with natural language definitions and complemented with images, either annotated with metainformation or enriched with hyperlinks to additional information, such as a lexicographic resource. This type of e-dictionary embodies what we consider a useful terminological tool in the current digital information society: accounting for its main features, along with an electronic format that can be integrated into the Semantic Web due to its interoperability data format. This aspect emphasises its contribution to reduce ambiguity as much as possible and to increase effective communication between experts of the domain, future experts, and language professionals.Cette thèse vise à prouver la pertinence des textes dans le volet conceptuel du travail terminologique. Notre méthodologie sert à démontrer comment les linguistes peuvent déduire des informations de connaissance à partir de textes et les systématiser par la suite, soit à travers des représentations semi-formelles ou formelles. Nous nous concentrons principalement sur l'analyse terminologique de corpus spécialisé faisant appel à des outils semi-automatiques d'analyse de texte pour systématiser les relations lexico-sémantiques observées dans un contexte de discours spécialisé et la modélisation ultérieure du système conceptuel sous-jacent. L’objectif de cette méthodologie est de proposer une typologie qui peut aider les lexicographes à rédiger des définitions. Sur la base de la double dimension de la terminologie, nous émettons l'hypothèse que la modélisation textuelle et logique ne va pas de pair puisque cette dernière n'est pas directement liée à la première. Nous soulignons que la connaissance et le langage sont essentiels pour la systématisation des connaissances, tout en gardant à l'esprit qu'ils appartiennent à différents niveaux d'analyse, car ils ne sont pas isomorphes. Pour atteindre nos objectifs, nous avons eu recours à des textes spécialisés produits dans l'industrie du liège. Ces textes nous fournissent un banc d'essai constitué de données riches en connaissances qui nous permettent de démontrer nos mécanismes déductifs utilisant la formule aristotélicienne : X = Y + DC à travers l'analyse linguistique et conceptuelle des données textuelles extraites semi-automatiquement. Pour l'exploitation du corpus, nous avons recours à des stratégies de text mining où les expressions régulières jouent un rôle central. Le but de cette étude est de créer une ressource terminologique pour l'industrie du liège, où deux types de ressources sont liés, à savoir le CorkCorpus et l'OntoCork. TermCork est un projet qui découle de l'organisation des connaissances dans le domaine spécialisé du liège. À cette fin, une base de données de connaissances terminologiques est en cours de développement pour alimenter un dictionnaire électronique. Cet edictionnaire est conçu comme un produit multilingue et multimodal, où plusieurs ressources, à savoir linguistiques et conceptuelles, sont jumelées. OntoCork est une micro-ontologie de domaine où les concepts sont enrichis de définitions de langage naturel et complétés par des images, annotées avec des méta-informations ou enrichies d'hyperliens vers des informations supplémentaires. Ce type de dictionnaire électronique désigne ce que nous considérons comme un outil terminologique utile dans la société de l'information numérique actuelle : la prise en compte de ses principales caractéristiques, ainsi qu'un format électronique qui peut être intégré dans le Web sémantique en raison de son format de données d'interopérabilité. Cet aspect met l'accent sur sa contribution à réduire autant que possible l'ambiguïté et à accroître l'efficacité de la communication entre les experts du domaine, les futurs experts et les professionnels de la langue

Aesthetics, Psyche and Media: A Manifold of Mimesis in the Age of Simulation

Within a dialogue with various authors, it seems that there can’t be just one universal reflection that allows us to comprehend the rising dynamism of new media. For example, Baudrillard declared the end of the traditional way of thinking about contemporary media and showed their role in the process of the endless simulation of truth. It has been shown that the contemporary world of media can be considered in dialogue with the philosophical tradition, and be evaluated in the phenomenological psychopathology (Fuchs) evaluation horizon. In this consideration, the notion of variation (Manovich), plays a key role in replacing the traditionally understood notion of mimesis. Artistic practice is precisely the main exemplar that shows the influence of new media on identity construction (simulated versions of personal identity), as well as the relationship between the artistic original and the copy. Although new digital media allows maintenance of desired (identity) simulations, its great potential is evident in enabling subjects to express their individuality, as well as in searching for new ways to improve their quality of life. This context opens a new problem, namely the one of avatar – a selected photo or image that defines the identity of entities present in the fields of the virtual agora (Baudrillard) and private chat rooms of the social media. Avatar`s function is being problematized by asking whether they represent the reduction and closure of the width of a person's beingness within the set image, or whether they facilitate and stimulate its realization by depriving them of the stress and discomfort that is caused by physical confrontation and intercourse with other persons in the living space. The given issue inevitably points to the problem of the general narcissism of our culture (Lasch), calling upon philosophical orientation to enter the discussion