Results for 'biological ontology'

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  1. Is Evolution Fundamental When It Comes to Defining Biological Ontology?Ellen Clarke - forthcoming - In Shamik Dasgupta & Brad Westlake (eds.), Current Controversies in Philosophy of Science. Routledge.
    I argue for the usefulness of the evolutionary kind of biological individual.
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  2. The Ontology of Biological and Clinical Statistics (OBCS) for Standardized and Reproducible Statistical Analysis.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Lin Yu, Alfred Hero, Barry Smith & Yongqun He - 2016 - Journal of Biomedical Semantics 7 (53).
    Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data (...)
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  3. Biological Explanations, Realism, Ontology, and Categories.Matthew J. Barker - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):617-622.
    This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main conclusions (...)
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  4. OBCS: The Ontology of Biological and Clinical Statistics.Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith & Yongqun He - 2014 - Proceedings of the Fifth International Conference on Biomedical Ontology 1327:65.
    Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community (...)
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  5. Ontology-Based Knowledge Representation of Experiment Metadata in Biological Data Mining.Scheuermann Richard, Kong Megan, Dahlke Carl, Cai Jennifer, Lee Jamie, Qian Yu, Squires Burke, Dunn Patrick, Wiser Jeff, Hagler Herb, Herb Hagler, Barry Smith & David Karp - 2009 - In Jake Chen & Stefano Lonardi (eds.), Biological Data Mining. Boca Raton: Chapman Hall / Taylor and Francis. pp. 529-559.
    According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...)
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  6. The Environment Ontology: Contextualising Biological and Biomedical Entities.Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis - 2013 - Journal of Biomedical Semantics 4 (43):1-9.
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. (...)
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  7. The Non-Coding RNA Ontology : A Comprehensive Resource for the Unification of Non-Coding RNA Biology.Huang Jingshan, Eilbeck Karen, Barry Smith, A. Blake Judith, Dou Dejing, Huang Weili, A. Natale Darren, Ruttenberg Alan, Huan Jun & T. Zimmermann Michael - 2016 - Journal of Biomedical Semantics 7 (1).
    In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...)
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  8. Semantics in Support of Biodiversity: An Introduction to the Biological Collections Ontology and Related Ontologies.Ramona L. Walls, John Deck, Robert Guralnik, Steve Baskauf, Reed Beaman, Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Barry Smith & Others - 2014 - PLoS ONE 9 (3):1-13.
    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the (...)
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  9. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as (...)
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  10. An Improved Ontological Representation of Dendritic Cells as a Paradigm for All Cell Types.Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Liebermann, Chris Mungall, Richard H. Scheuermann, Barry Smith & Lindsay Cowell - 2009 - BMC Bioinformatics 10 (1):70.
    Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure (...)
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  11. The Ontology of Organisms: Mechanistic Modules or Patterned Processes?Christopher J. Austin - 2016 - Biology and Philosophy 31 (5):639-662.
    Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our (...)
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  12. An Essay on the Ontological Foundations and Psychological Realization of Forgetting.Stan Klein - 2019 - Psychology of Consciousness: Theory, Research, and Practice 6 (292-305).
    I argue that appreciation of the phenomenon of forgetting requires serious attention to its origins and place in nature. This, in turn, necessitates metaphysical inquiry as well as empirical backing – a combination likely to be eschewed by psychological orthodoxy. But, if we hope to avoid the conceptual vacuity that characterizes too much of contemporary psychological inquiry (e.g., Klein, 2012, 2014a, 2015a, 2016a), a “big picture” approach to phenomena of interest is essential. Adopting this investigative posture turns the “received view” (...)
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  13. Ontological Choices and the Value-Free Ideal.David Ludwig - 2015 - Erkenntnis (6):1-20.
    The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species, race, memory, intelligence, depression, or obesity are true or false relative to the choice of a biological, psychological, or medical ontology. Second, I show that ontological choices often depend on non-epistemic values. On the (...)
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  14. Ontologies and Politics of Biogenomic 'Race'.Rasmus Grønfeldt Winther & Jonathan Michael Kaplan - 2013 - Theoria. A Journal of Social and Political Theory (South Africa) 60 (3):54-80.
    All eyes are turned towards genomic data and models as the source of knowledge about whether human races exist or not. Will genomic science make the final decision about whether racial realism (e.g., racial population naturalism) or anti-realism (e.g., racial skepticism) is correct? We think not. We believe that the results of even our best and most impressive genomic technologies underdetermine whether bio-genomic races exist, or not. First, different sub-disciplines of biology interested in population structure employ distinct concepts, aims, measures, (...)
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  15. Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
    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 (...)
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  16. Applied Ontology: An Introduction.Katherine Munn & Barry Smith (eds.) - 2008 - Frankfurt: ontos.
    Ontology is the philosophical discipline which aims to understand how things in the world are divided into categories and how these categories are related together. This is exactly what information scientists aim for in creating structured, automated representations, called 'ontologies,' for managing information in fields such as science, government, industry, and healthcare. Currently, these systems are designed in a variety of different ways, so they cannot share data with one another. They are often idiosyncratically structured, accessible only to those (...)
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  17. A Biologically Informed Hylomorphism.Christopher J. Austin - 2017 - In William M. R. Simpson, Robert C. Koons & Nicholas J. Teh (eds.), Neo-Aristotelian Perspectives on Contemporary Science. Routledge. pp. 185-210.
    Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...)
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  18. Everything Flows: Towards a Processual Philosophy of Biology.Daniel J. Nicholson & John Dupré (eds.) - 2018 - Oxford University Press.
    This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, (...)
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  19. Ontological Realism: A Methodology for Coordinated Evolution of Scientific Ontologies.Barry Smith & Werner Ceusters - 2010 - Applied ontology 5 (3):139-188.
    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes (...)
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  20. Biodynamic Ontology: Applying BFO in the Biomedical Domain.Barry Smith, Pierre Grenon & Louis Goldberg - 2004 - Studies in Health and Technology Informatics 102:20–38.
    Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that (...)
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  21. The Ontology of the Gene Ontology.Barry Smith, Jennifer Williams & Steffen Schulze-Kremer - 2003 - In AMIA 2003 Symposium Proceedings. Washington, DC: AMIA. pp. 609-613.
    The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of (...)
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  22. Code Biology and the Problem of Emergence.Arran Gare - 2021 - Biosystems 208.
    It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...)
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  23. A Manifesto for a Processual Philosophy of Biology.John A. Dupre & Daniel J. Nicholson - 2018 - In Daniel J. Nicholson & John A. Dupre (eds.), Everything Flows: Towards a Processual Philosophy of Biology.
    This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been associated (...)
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  24. Ontologically Significant Aggregation: Process Structural Realism (PSR).Joseph E. Earley - 2008 - In Weber (ed.), Handbook of Whiteheadian Process Thought. De Gruyter. pp. 2--179.
    Combinations of molecules, of biological individuals, or of chemical processes can produce effects that are not simply attributable to the constituents. Such non-redundant causality warrants recognition of those coherences as ontologically significant whenever that efficacy is relevant. With respect to such interaction, the effective coherence is more real than are the components. This ontological view is a variety of structural realism and is also a kind of process philosophy. The designation ‘process structural realism’ (PSR) seems appropriate.
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  25.  22
    Metabolism Instead of Machine: Towards an Ontology of Hybrids.Julia Rijssenbeek, Vincent Blok & Zoë Robaey - 2022 - Philosophy and Technology 35 (3):1-23.
    The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of (...)
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  26. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson, Barry Smith & Others - 2013 - Plant and Cell Physiology 54 (2):1-23..
    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 (...)
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  27. Relations in Biomedical Ontologies.Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, , Fabian Neuhaus, Alan Rector & Cornelius Rosse - 2005 - Genome Biology 6 (5):R46.
    To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
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  28. Functions in Basic Formal Ontology.Andrew D. Spear, Werner Ceusters & Barry Smith - 2016 - Applied ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of (...)
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  29. Ontologies for the Life Sciences.Steffen Schulze-Kremer & Barry Smith - 2005 - In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, vol. 4. Wiley.
    Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...)
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  30. Protein Ontology: A Controlled Structured Network of Protein Entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). (...)
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  31. The Protein Ontology: A Structured Representation of Protein Forms and Complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of (...)
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  32. Ontologies of Living Beings: Introduction.Adam Ferner & Thomas Pradeu - 2017 - Philosophy, Theory, and Practice in Biology 9 (4).
    Part of a special issue, Ontologies of Living Beings, guest-edited by A. M. Ferner and Thomas Pradeu.
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  33. Do Organisms Have an Ontological Status?Charles T. Wolfe - 2010 - History and Philosophy of the Life Sciences 32 (2-3):195-232.
    The category of ‘organism’ has an ambiguous status: is it scientific or is it philosophical? Or, if one looks at it from within the relatively recent field or sub-field of philosophy of biology, is it a central, or at least legitimate category therein, or should it be dispensed with? In any case, it has long served as a kind of scientific “bolstering” for a philosophical train of argument which seeks to refute the “mechanistic” or “reductionist” trend, which has been perceived (...)
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  34. Biological Roots of Musical Epistemology: Functional Cycles, Umwelt, and Enactive Listening.Mark Reybrouck - 2001 - Semiotica 2001 (134):599-633.
    This article argues for an epistemology of music, stating that dealing with music can be considered as a process of knowledge acquisition. What really matters is not the representation of an ontological musical reality, but the generation of music knowledge as a tool for adaptation to the sonic world. Three major positions are brought together: the epistemological claims of Jean Piaget, the biological methodology of Jakob von Uexküll, and the constructivistic conceptions of Ernst von Glasersfeld, each ingstress the role (...)
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  35. Ontology and Values Anchor Indigenous and Grey Nomenclatures: A Case Study in Lichen Naming Practices Among the Samí, Sherpa, Scots, and Okanagan.Catherine Kendig - 2020 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 84:101340.
    Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may (...)
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  36.  9
    An Essay on the Ontological Foundations and Psychological Realization of Forgetting.Stanely Bernard Klein - forthcoming - Psychology of Consciousness: Theory, Research, and Practice.
    NOTE: This is the penultimate version. The finalized MS will be available a few weeks from now and when in hand I will remove this version and put the final version on line. I anticipate very few changes of substance. ---------------------------------------------------------------------------------------------------- -------------------- -/- I argue that appreciation of the phenomenon of forgetting requires serious attention to its origins and place in nature. This, in turn, necessitates metaphysical inquiry as well as empirical backing – a combination likely to be eschewed by psychological (...)
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  37. Ontologies for the Study of Neurological Disease.Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl - 2012 - In Towards an Ontology of Mental Functioning (ICBO Workshop), Third International Conference on Biomedical Ontology. Graz:
    We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry (...)
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  38. Biology and Theology in Malebranche's Theory of Organic Generation.Karen Detlefsen - 2014 - In Ohad Nachtomy & Justin E. H. Smith (eds.), The Life Sciences in Early Modern Philosophy. Oxford University Press. pp. 137-156.
    This paper has two parts: In the first part, I give a general survey of the various reasons 17th and 18th century life scientists and metaphysicians endorsed the theory of pre-existence according to which God created all living beings at the creation of the universe, and no living beings are ever naturally generated anew. These reasons generally fall into three categories. The first category is theological. For example, many had the desire to account for how all humans are stained by (...)
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  39. The Industrial Ontologies Foundry Proof-of-Concept Project.Evan Wallace, Dimitris Kiritsis, Barry Smith & Chris Will - 2018 - In Ilkyeong Moon, Gyu M. Lee, Jinwoo Park, Dimitris Kiritsis & Gregor von Cieminski (eds.), Advances in Production Management Systems. Smart Manufacturing for Industry 4.0. IFIP. pp. 402-409.
    The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an (...)
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  40. An ontology of weak entity realism for HPC kinds.Reuben Sass - 2021 - Synthese 198 (12):11861-11880.
    This paper defends an ontology of weak entity realism for homeostatic property cluster (HPC) theories of natural kinds, adapted from Bird’s (Synthese 195(4):1397–1426, 2018) taxonomy of such theories. Weak entity realism about HPC kinds accepts the existence of natural kinds. Weak entity realism denies two theses: that (1) HPC kinds have mind-independent essences, and that (2) HPC kinds reduce to entities, such as complex universals, posited only by metaphysical theories. Strong entity realism accepts (1) and (2), whereas moderate entity (...)
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  41. Toward an Ontological Treatment of Disease and Diagnosis.Richard H. Scheuermann, Werner Ceusters & Barry Smith - 2009 - In Proceedings of the 2009 AMIA Summit on Translational Bioinformatics. American Medical Informatics Association.
    Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...)
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  42. The Organism as Ontological Go-Between. Hybridity, Boundaries and Degrees of Reality in its Conceptual History.Charles T. Wolfe - 2014 - Studies in History and Philosophy of Biological and Biomedical Sciences 1:http://dx.doi.org/10.1016/j.shps.
    The organism is neither a discovery like the circulation of the blood or the glycogenic function of the liver, nor a particular biological theory like epigenesis or preformationism. It is rather a concept which plays a series of roles – sometimes overt, sometimes masked – throughout the history of biology, and frequently in very normative ways, also shifting between the biological and the social. Indeed, it has often been presented as a key-concept in life science and the ‘theorization’ (...)
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  43. Ontology and the Future of Dental Research Informatics.Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick - 2010 - Journal of the American Dental Association 141 (10):1173-75.
    How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy (...)
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  44. The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.Ramona Lynn Walls, Laurel Cooper, Justin Lee Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis William Stevenson & Pankaj Jaiswal - 2019 - Frontiers in Plant Science 10.
    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 (...)
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  45. How to Count Biological Minds: Symbiosis, the Free Energy Principle, and Reciprocal Multiscale Integration.Matthew Sims - 2020 - Synthese 8:1-1.
    The notion of a physiological individuals has been developed and applied in the phi- losophy of biology to understand symbiosis, an understanding of which is key to theorising about the major transition in evolution from multi-organismality to multi- cellularity. The paper begins by asking what such symbiotic individuals can help to reveal about a possible transition in the evolution of cognition. Such a transition marks the movement from cooperating individual biological cognizers to a function- ally integrated cognizing unit. Somewhere (...)
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  46.  60
    Transbiopolitics: Ontology and Metatheory of Managed Evolution.Valentin Cheshko & Kuz Oleh - 2021 - Epistemological studies in Philosophy, Social and Political Sciences 4 (1):1-11.
    Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the anthropic principle (...)
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  47. TOWARDS ONTOLOGY FOR A UNIFIED KNOWLEDGE: THE HYPOTHESIS OF LOGICAL QUANTA.Meskos George - 2007.08.23 - Metanexus.Net.
    The suggestion of Logical Quanta (LQ) is a bidirectional synthesis of the theory of logos of Maximus the Confessor and the philosophical interpretation of quantum mechanics. The result of such a synthesis is enrichment to the ontology of classical mechanics that enable us to have a unified view and an explanatory frame of the whole cosmos. It also enables us to overcome the Cartesian duality both on biology and the interaction of body and mind. Finally, one can reconstruct a (...)
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  48. Animated Persona: The Ontological Status of a Deceased Person Who Continues to Appear in This World.Masahiro Morioka - 2021 - European Journal of Japanese Philosophy 6:115-131.
    In this paper, I propose the concept of the “animated persona,” a soundless voice that says, “I am here” and appears on the surface of someone or something. This concept can bring clarity to the experience of perceiving a kind of personhood on a corpse, a wooden mask, or even a tree. In the first half of this paper, I will examine some Japanese literature and a work of Viktor Frankl’s that discuss these phenomena. In the second half, I will (...)
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  49.  76
    Virus Ontology: Thing, Being, Process, or Information?Sfetcu Nicolae - manuscript
    The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241.
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  50. Methodology and Ontology in Microbiome Research.John Huss - 2014 - Biological Theory 9 (4):392-400.
    Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing (...)
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