Results for 'Protein Ontology'

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  1. 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 (...)
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  2. 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 (...)
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  3. Protein Ontology: Enhancing and scaling up the representation of protein entities.Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross & Alan Ruttenberg - 2017 - Nucleic Acids Research 45 (D1):D339-D346.
    The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and (...)
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  4. Framework for a protein ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed (...)
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  5. Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology (...)
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  6. TGF-beta signaling proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. (...)
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  7. Protein-centric connection of biomedical knowledge: Protein Ontology research and annotation tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Landgrebe Jobst & Smith Barry (eds.), Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and (...)
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  8. The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants (...)
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  9. A framework for protein classification.Anand Kumar & Barry Smith - 2003 - In Anand Kumar & Barry Smith (eds.), Proceedings of the 2003 German Conference on Bioinformatics, Vol. II. pp. 55-57.
    It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed (...)
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  10. 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 Alexander P. Cox, Mark Jensen, William Duncan, Bianca Weinstock-Guttman, Kinga Szigeti, Alan Ruttenberg, Barry Smith & Alexander D. Diehl (eds.), 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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  11. Where Do You Get Your Protein? Or: Biochemical Realization.Tuomas E. Tahko - 2020 - British Journal for the Philosophy of Science 71 (3):799-825.
    Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...)
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  12. (1 other version)Wanting what we don't want to want: Representing Addiction in Interoperable Bio-Ontologies.Janna Hastings, Nicolas Le Novère, Werner Ceusters, Kevin Mulligan & Barry Smith - 2012 - In Janna Hastings, Werner Ceusters, Mark Jensen, Kevin Mulligan & Barry Smith (eds.), Towards an Ontology of Mental Functioning (ICBO Workshop). CEUR. pp. 56-60.
    Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience and pharmacology (...)
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  13. An improved ontological representation of dendritic cells as a paradigm for all cell types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop (...)
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  14. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian Athey & Barry Smith - 2022 - Journal of Biomedical Semantics 13 (1):25.
    The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...)
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  15. Ontology as the core discipline of biomedical informatics: Legacies of the past and recommendations for the future direction of research.Barry Smith & Werner Ceusters - 2007 - In Gordana Dodig Crnkovic & Susan Stuart (eds.), Computation, Information, Cognition: The Nexus and the Liminal.f. Cambridge Scholars Press. pp. 104-122.
    The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...)
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  16. 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.
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  17. 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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  18. VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In Barry Smith (ed.), ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo: NCOR.
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced (...)
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  19. Towards a proteomics meta-classification.Anand Kumar & Barry Smith - 2004 - In Kumar Anand & Smith Barry (eds.), IEEE Fourth Symposium on Bioinformatics and Bioengineering, Taichung, Taiwan. IEEE Press. pp. 419–427.
    that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...)
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  20. Biometaphysics.Barry Smith - 2009 - In Robin Le Poidevin, Simons Peter, McGonigal Andrew & Ross P. Cameron (eds.), The Routledge Companion to Metaphysics. New York: Routledge. pp. 537-544.
    While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other (...)
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  21. Molecular Interactions. On the Ambiguity of Ordinary Statements in Biomedical Literature.Stefan Schulz & Ludger Jansen - 2009 - Applied ontology (4):21-34.
    Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions (...)
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  22. Is the Cell Really a Machine?Daniel J. Nicholson - 2019 - Journal of Theoretical Biology 477:108–126.
    It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...)
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  23. Messy Chemical Kinds.Joyce C. Havstad - 2018 - British Journal for the Philosophy of Science 69 (3):719-743.
    Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be made more complicated (...)
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  24. A new framework for host-pathogen interaction research.Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrell, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhiping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K. Handelman, Jonathan Sexton, Kathryn Eaton, Gerry Higgins, Gilbert S. Omenn, Brian Athey, Barry Smith, Luonan Chen & Yongqun He - 2022 - Frontiers in Immunology 13.
    COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...)
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  25.  40
    How a sense of place may return the Social License to Operate concept back to an ethics of responsiblity within a neoliberal framework — a Tasmanian salmon story.Larelle Bossi - 2023 - Research in Ethical Issues in Organizations.
    This chapter is a journey into the ontological significance of place in consideration of the Atlantic Tasmanian salmon industry and its challenges to the ethical discourse around the social license to operate (SLO) beyond the oxymoron of a name. It centres the discourse around the salmon itself. A once totem animal, responsible for the balance of Canada’s abundant ecosystem, now reduced to a mere source of protein, manipulated, and commodified by Tasmania’s ‘big business’ and against the SLO of Flanagan’s (...)
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  26. Lmn-2 interacts with Elf-2. On the meaning of common statements in biomedical literature.Stefan Schulz & Ludger Jansen - 2006 - In Stefan Schulz & Ludger Jansen (eds.), Lmn-2 interacts with Elf-2. On the meaning of common statements in biomedical literature. MD. pp. 37-45.
    Statements about the behavior of biological entities, e.g. about the interaction between two proteins, abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that is necessary to take into account in the practice of biomedical ontology engineering. Several concurring formalizations are proposed. Emphasis is laid on the discussion of biological dispositions.
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  27. Introduction: What is Ontology for?Katherine Munn - 2008 - In Katherine Munn & Barry Smith (eds.), Applied Ontology: An Introduction. Frankfurt: ontos. pp. 7-19.
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  28. Debunking Rationalist Defenses of Common-Sense Ontology: An Empirical Approach.Robert Carry Osborne - 2016 - Review of Philosophy and Psychology 7 (1):197-221.
    Debunking arguments typically attempt to show that a set of beliefs or other intensional mental states bear no appropriate explanatory connection to the facts they purport to be about. That is, a debunking argument will attempt to show that beliefs about p are not held because of the facts about p. Such beliefs, if true, would then only be accidentally so. Thus, their causal origins constitute an undermining defeater. Debunking arguments arise in various philosophical domains, targeting beliefs about morality, the (...)
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  29. The question of ontology.Kit Fine - 2009 - In Ryan Wasserman, David Manley & David Chalmers (eds.), Metametaphysics: New Essays on the Foundations of Ontology. Oxford, England: Oxford University Press. pp. 157--177.
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  30. The Essences of Objects: Explicating a Theory of Essence in Object-Oriented Ontology.Stanford Howdyshell - 2020 - Open Philosophy 3 (1):01-10.
    In this paper, I will discuss the need for a theory of essences within Object-Oriented Ontology (OOO) and then formulate one. I will do so by drawing on Graham Harman’s work on OOO and Martin Heidegger’s thought on the essence of being, presented in his Introduction to Metaphysics. Harman touches on essences, describing them as the tension between a withdrawn object and its withdrawn qualities, but fails to distinguish between essential and inessential qualities within this framework. To fill in (...)
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  31. The GRW Flash Theory: A Relativistic Quantum Ontology of Matter in Space-Time?Michael Esfeld & Nicolas Gisin - 2014 - Philosophy of Science 81 (2):248-264.
    John Bell proposed an ontology for the GRW modification of quantum mechanics in terms of flashes occurring at space- time points. This article spells out the motivation for this ontology, inquires into the status of the wave function in it, critically examines the claim of its being Lorentz invariant, and considers whether it is a parsimonious but nevertheless physically adequate ontology.
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  32. Unveiling Ezumezu logic as a framework for process ontology and Yorùbá ontology.Emmanuel Ofuasia - 2019 - Filosofia Theoretica: Journal of African Philosophy, Culture and Religions 8 (2):63-84.
    Ezumezu, a prototype African logic, developed by Jonathan Chimakonam as a framework which mediates thought, theory and method in the African place, is according to him, extendable and applicable in places non-African too. This seems to underscore the universal character of the logic. I interrogate, in this piece, the logic to see if it truly mediates thought, theory and method in Yorùbá ontology on the one hand, and process ontology on the other hand. Through critical analysis, I discern (...)
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  33. Fundamental Quantification and the Language of the Ontology Room.Daniel Z. Korman - 2013 - Noûs 49 (2):298-321.
    Nihilism is the thesis that no composite objects exist. Some ontologists have advocated abandoning nihilism in favor of deep nihilism, the thesis that composites do not existO, where to existO is to be in the domain of the most fundamental quantifier. By shifting from an existential to an existentialO thesis, the deep nihilist seems to secure all the benefits of a composite-free ontology without running afoul of ordinary belief in the existence of composites. I argue that, while there are (...)
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  34. What is Individualism in Social Ontology? Ontological Individualism vs. Anchor Individualism.Brian Epstein - 2014 - In Julie Zahle & Finn Collin (eds.), Rethinking the Individualism-Holism Debate. Cham: Springer.
    Individualists about social ontology hold that social facts are “built out of” facts about individuals. In this paper, I argue that there are two distinct kinds of individualism about social ontology, two different ways individual people might be the metaphysical “builders” of the social world. The familiar kind is ontological individualism. This is the thesis that social facts supervene on, or are exhaustively grounded by, facts about individual people. What I call anchor individualism is the alternative thesis that (...)
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  35. Ficta and Virtuality: An Ingardenian Ontology of Virtualized Ficta.Hicham Jakha - 2024 - Rivista di Estetica 85 (1):199-212.
    In my paper, I establish an Ingardenian phenomenological ontology of "virtualized ficta", i.e., fictional entities introduced to virtual gaming. The first Section of my paper provides an ontology of virtualized ficta, focusing primarily on their ‘‘existential moments’’. But in order to have a firm grasp of the ontological aspects grounding the virtual work, it’s important to engage its strata. This is what I attempt to do in Section 1.2. Virtualized ficta’s intentional dependencies are strongly manifest in what I (...)
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    On the Semantics and the Ontology of the Mass-Count Distinction.Friederike Moltmann - forthcoming - Philosophy Compass.
    The mass-count distinction is a morpho-syntactic distinction among nouns in English and many other languages and is generally taken to have semantic content or reflect a semantic mass-count distinction. At the center of the semantic mass-count distinction is, in some way or another, a notion of unity or being a single entity, the basis of countability. There is little unanimity, however, of how that notion is to be understood and thus what the semantic mass-count distinction consists in. The paper gives (...)
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  37. Using a two-dimensional model from social ontology to explain the puzzling metaphysical features of words.Jared S. Oliphint - 2022 - Synthese 200 (3):1-10.
    I argue that a two-dimensional model of social objects is uniquely positioned to deliver explanations for some of the puzzling metaphysical features of words. I consider how a type-token model offers explanations for the metaphysical features of words, but I give reasons to find the model wanting. In its place, I employ an alternative model from social ontology to explain the puzzling data and questions that are generated from the metaphysical features of words. In the end I chart a (...)
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  38. Carnap on Analyticity and Existence: A Clarification, Defense, and Development of Quine’s Reading of Carnap’s Views on Ontology.Gary Ebbs - 2019 - Journal for the History of Analytical Philosophy 7 (5):1-31.
    Does Carnap’s treatment of philosophical questions about existence, such as “Are there numbers?” and “Are there physical objects?”, depend on his analytic–synthetic distinction? If so, in what way? I answer these questions by clarifying, defending, and developing the reading of Carnap’s paper “Empiricism, Semantics, and Ontology” that W. V. Quine proposes, with little justification or explanation, in his paper “On Carnap’s Views on Ontology”. The primary methodological value of studying Quine’s reading of “Empiricism, Semantics, and Ontology” is (...)
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  39. Variance Theses in Ontology and Metaethics.Matti Eklund - 2019 - In Alexis Burgess, Herman Cappelen & David Plunkett (eds.), Conceptual Engineering and Conceptual Ethics. New York, USA: Oxford University Press.
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  40. The ImmPort Antibody Ontology.William Duncan, Travis Allen, Jonathan Bona, Olivia Helfer, Barry Smith, Alan Ruttenberg & Alexander D. Diehl - 2016 - Proceedings of the International Conference on Biological Ontology 1747.
    Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...)
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  41. Emerging into the rainforest: Emergence and special science ontology.Alexander Franklin & Katie Robertson - 2024 - European Journal for Philosophy of Science 14 (4):1-26.
    Scientific realists don’t standardly discriminate between, say, biology and fundamental physics when deciding whether the evidence and explanatory power warrant the inclusion of new entities in our ontology. As such, scientific realists are committed to a lush rainforest of special science kinds (Ross, 2000). Viruses certainly inhabit this rainforest – their explanatory power is overwhelming – but viruses’ properties can be explained from the bottom up: reductive explanations involving amino acids are generally available. However, reduction has often been taken (...)
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  42. The Reality of Brands: Towards an Ontology of Marketing.Wolfgang Grassl - 1999 - American Journal of Economics and Sociology 58:313-360.
    The ontology of marketing, particularly the question of what products and brands are, is still largely unexplored. The ontological status of brands hinges on their relationship with products. Idealists about brands see perceptual or cognitive acts of consumers grouped under the heading ‘brand awareness’ or ‘brand image’ as constitutive for the existence of brands so that, in their view, tools of the marketing mix can influence relevant mental dispositions and attitudes. Brand realists, on the other hand, reject the view (...)
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  43. (1 other version)Vital anti-mathematicism and the ontology of the emerging life sciences: from Mandeville to Diderot.Charles T. Wolfe - 2017 - Synthese:1-22.
    Intellectual history still quite commonly distinguishes between the episode we know as the Scientific Revolution, and its successor era, the Enlightenment, in terms of the calculatory and quantifying zeal of the former—the age of mechanics—and the rather scientifically lackadaisical mood of the latter, more concerned with freedom, public space and aesthetics. It is possible to challenge this distinction in a variety of ways, but the approach I examine here, in which the focus on an emerging scientific field or cluster of (...)
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  44. The Eucharist according to Gunk-relational Ontology.Damiano Migliorini - 2023 - Münchener Theologische Zeitschrift 74 (3):315-330.
    The rational explanation of the Eucharist is at the centre of a revived debate in philosophical theology. After describing gunk-relational ontology, I show how it allows us to understand transubstantiation differently than other traditional and contemporary accounts, from which it draws a few points but combining them in a new way. In gunk-relational ontology every substance is its own relations, which constitute a gunky fundamental reality. The liturgical celebration of the Last Supper therefore creates a new relational situation (...)
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  45. Kind Instantiation and Kind Change - A Problem for Four-Category Ontology.Markku Keinänen & Jani Hakkarainen - 2017 - Studia Neoaristotelica 14 (2):139-165.
    In Lowe’s Four-Category Ontology, instantiation is a basic formal ontological relation between particulars (objects, modes) and their kinds (kinds, attributes). Therefore, instantiation must be considered as a metaphysically necessary relation, which also rules out the metaphysical possibility of kind change. Nevertheless, according to Lowe, objects obtain their identity conditions in a more general level than specific natural kinds, which allows for kind change. There also seems to be actual examples of kind change. The advocate of Four-Category Ontology is (...)
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  46. Non-Existent Objects and Epistemological Ontology.William J. Rapaport - 1985 - Grazer Philosophische Studien 25-26 (1):61-95.
    This essay examines the role of non-existent objects in "epistemological ontology"--the study of the entities that make thinking possible. An earlier revision of Meinong's Theory of Objects is reviewed, Meinong's notions of Quasisein and Aussersein are discussed, and a theory of Meinongian objects as "combinatorially possible" entities is presented.
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  47. Eleaticism and Socratic Dialectic: On Ontology, Philosophical Inquiry, and Estimations of Worth in Plato’s Parmenides, Sophist and Statesman.Jens Kristian Larsen - 2019 - Études Platoniciennes 19 (19).
    The Parmenides poses the question for what entities there are Forms, and the criticism of Forms it contains is commonly supposed to document an ontological reorientation in Plato. According to this reading, Forms no longer express the excellence of a given entity and a Socratic, ethical perspective on life, but come to resemble concepts, or what concepts designate, and are meant to explain nature as a whole. Plato’s conception of dialectic, it is further suggested, consequently changes into a value-neutral method (...)
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  48. Searle and De Soto: The New Ontology of the Social World.Barry Smith - 2008 - In Barry Smith, David M. Mark & Isaac Ehrlich (eds.), The Mystery of Capital and the Construction of Social Reality. Open Court. pp. 35-51.
    Consider a game of blind chess between two chess masters that is recorded in some standard chess notation. The recording is a representation of the game. But what is the game itself? This question is, we believe, central to the entire domain of social ontology. We argue that the recorded game is a special sort of quasi-abstract pattern, something that is: (i) like abstract entities such as numbers or forms, in that it is both nonphysical and nonpsychological; but at (...)
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  49. "I that is we, we that is I," perspectives on contemporary Hegel : social ontology, recognition, naturalism, and the critique of Kantian constructivism.Italo Testa & Luigi Ruggiu (eds.) - 2016 - Boston: Brill.
    In _"I that is We, We that is I"_ leading scholars analyze the many facets of Hegel’s formula for the intersubjective structure of human life and explores its relevance for debates on social ontology, recognition, action theory, constructivism, and naturalism.
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  50. Bohmian mechanics without wave function ontology.Albert Solé - 2013 - Studies in History and Philosophy of Science Part B: Studies in History and Philosophy of Modern Physics 44 (4):365-378.
    In this paper, I critically assess different interpretations of Bohmian mechanics that are not committed to an ontology based on the wave function being an actual physical object that inhabits configuration space. More specifically, my aim is to explore the connection between the denial of configuration space realism and another interpretive debate that is specific to Bohmian mechanics: the quantum potential versus guidance approaches. Whereas defenders of the quantum potential approach to the theory claim that Bohmian mechanics is better (...)
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