Results for 'reference ontology vs. application ontology'

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  1. Ontology for the Intelligence Analyst.Barry Smith - 2012 - CrossTalk 14 (Nov/Dec):18-25.
    As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how these (...)
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  2. CARO: The Common Anatomy Reference Ontology.Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith - 2008 - In Haendel Melissa, A. Neuhaus, Fabian Osumi-Sutherland, David Mabee, Paula M., Mejino Jr José L. V., Mungall Chris, J. Smith & Barry (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer. pp. 327-349.
    The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for (...)
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  3. Easy ontology, application conditions and infinite regress.Andrew Brenner - 2018 - Analysis 78 (4):605-614.
    In a number of recent publications Thomasson has defended a deflationary approach to ontological disputes, according to which ontological disputes are relatively easy to settle, by either conceptual analysis, or conceptual analysis in conjunction with empirical investigation. Thomasson’s “easy” approach to ontology is intended to derail many prominent ontological disputes. In this paper I present an objection to Thomasson’s approach to ontology. Thomasson’s approach to existence assertions means that she is committed to the view that application conditions (...)
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  4. 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 adding semantic (...)
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  5. What particulars are referred to in EHR data? A case study in integrating referent tracking into an electronic health record application.Ron Rudnicki, Werner Ceusters, Shaid Manzoo & Barry Smith - 2007 - In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA. pp. 630-634.
    Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition (...)
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  6. Ontology-based security modeling in ArchiMate.Ítalo Oliveira, Tiago Prince Sales, João Paulo A. Almeida, Riccardo Baratella, Mattia Fumagalli & Giancarlo Guizzardi - forthcoming - Software and Systems Modeling.
    Enterprise Risk Management involves the process of identification, evaluation, treatment, and communication regarding risks throughout the enterprise. To support the tasks associated with this process, several frameworks and modeling languages have been proposed, such as the Risk and Security Overlay (RSO) of ArchiMate. An ontological investigation of this artifact would reveal its adequacy, capabilities, and limitations w.r.t. the domain of risk and security. Based on that, a language redesign can be proposed as a refinement. Such analysis and redesign have been (...)
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  7. The Ontology of Reference: Studies in Logic and Phenomenology.Barry Smith - 1976 - Dissertation, Manchester
    Abstract: We propose a dichotomy between object-entities and meaning-entities. The former are entities such as molecules, cells, organisms, organizations, numbers, shapes, and so forth. The latter are entities such as concepts, propositions, and theories belonging to the realm of logic. Frege distinguished analogously between a ‘realm of reference’ and a ‘realm of sense’, which he presented in some passages as mutually exclusive. This however contradicts his assumption elsewhere that every entity is a referent (even Fregean senses can be referred (...)
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  8. The evaluation of ontologies: Editorial review vs. democratic ranking.Barry Smith - 2008 - In Proceedings of InterOntology (Tokyo, Japan, 26-27 February 2008),. Keio University Press. pp. 127-138.
    Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to a (...)
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    (1 other version)Ontology, natural language, and information systems: Implications of cross-linguistic studies of geographic terms.M. Mark David, Kuhn Werner, Barry Smith & A. G. Turk - 2003 - In Mark David M., Werner Kuhn, Smith Barry & Turk A. G. (eds.), 6th Annual Conference of the Association of Geographic Information Laboratories for Europe (AGILE),. pp. 45-50.
    Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two (...)
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  10. What Particulars are Referred to in EHR Data? A Case Study in Integrating Referent Tracking into an Electronic Health Record Application.Ron Rudnicki - 2007 - In Proceedings of the Annual Symposium of the American Medical Informatics Association. AMIA.
    The Referent Tracking paradigm, which advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records, promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed to make it accord with the tenets of Referent Tracking. We describe the ontological principles on which such decomposition (...)
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  11. Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases.Jonathan Simon, James M. Fielding, Mariana C. Dos Santos & Barry Smith - 2005 - International Journal of Medical Informatics 75 (3-4):224-231.
    The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to (...)
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  12. Representing Mental Functioning: Ontologies for Mental Health and Disease.Janna Hastings, Werner Ceusters, Mark Jensen, 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.
    Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...)
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  13. CTO: A Community-Based Clinical Trial Ontology and Its Applications in PubChemRDF and SCAIViewH.Asiyah Yu Lin, Stephan Gebel, Qingliang Leon Li, Sumit Madan, Johannes Darms, Evan Bolton, Barry Smith, Martin Hofmann-Apitius, Yongqun Oliver He & Alpha Tom Kodamullil - 2021 - Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO) and 10th Workshop on Ontologies and Data in Life Sciences (ODLS).
    Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is (...)
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  14. Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository.Albert Goldfain, Lindsay G. Cowell & Barry Smith - 2012 - In Goldfain Albert, Cowell Lindsay G. & Smith Barry (eds.), Proceeedings of the Third International Conference on Biomedical Ontology (CEUR 897).
    A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a (...)
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  15. Ontology: minimalism and truth-conditions.Juan José Lara Peñaranda - 2013 - Philosophical Studies 162 (3):683-696.
    In this paper, I develop a criticism to a method for metaontology, namely, the idea that a discourse’s or theory’s ontological commitments can be read off its sentences’ truth- conditions. Firstly, I will put forward this idea’s basis and, secondly, I will present the way Quine subscribed to it. However, I distinguish between two readings of Quine’s famous ontological criterion, and I center the focus on the one currently dubbed “ontological minimalism”, a kind of modern Ockhamism applied to the mentioned (...)
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  16. Egalitarian vs. Elitist Plenitude.Uriah Kriegel - 2022 - Philosophical Studies 179 (10):3055-3070.
    A number of prominent metaphysicians have recently defended the idea of material plenitude: wherever there is one material object, there is in fact a great multitude of them, all coincident and sharing many properties, but differing in which of these properties they have essentially and which accidentally. The main goal of this paper is to put on the agenda an important theoretical decision that plenitudinists face, regarding whether their plenitude is egalitarian or elitist, depending on whether or not they take (...)
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  17. Communication vs. Information, an Axiomatic Neutrosophic Solution.Florentin Smarandache & Stefan Vladutescu - 2013 - Neutrosophic Sets and Systems 1:38-45.
    Study represents an application of the neutrosophic method, for solving the contradiction between communication and information. In addition, it recourse to an appropriate method of approaching the contradictions: Extensics, as the method and the science of solving the contradictions. The research core is the reality that the scientific research of communication-information relationship has reached a dead end. The bivalent relationship communicationinformation, information-communication has come to be contradictory, and the two concepts to block each other. After the critical examination of (...)
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  18. Biomedical ontology alignment: An approach based on representation learning.Prodromos Kolyvakis, Alexandros Kalousis, Barry Smith & Dimitris Kiritsis - 2018 - Journal of Biomedical Semantics 9 (21).
    While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy (...)
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  19. Foundations for a Realist Ontology of Mental Disease.Werner Ceusters & Barry Smith - 2010 - Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...)
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  20. Foundation for a Realist Ontology of Cognitive Processes.David Kasmier, David Limbaugh & Barry Smith - 2019 - In David Kasmier, David Limbaugh & Barry Smith (eds.), Proceedings of the International Conference on Biomedical Ontology (ICBO), University at Buffalo, NY.
    What follows is a first step towards an ontology of conscious mental processes. We provide a theoretical foundation and characterization of conscious mental processes based on a realist theory of intentionality and using BFO as our top-level ontology. We distinguish three components of intentional mental process: character, directedness, and objective referent, and describe several features of the process character and directedness significant to defining and classifying mental processes. We arrive at the definition of representational mental process as a (...)
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  21. Handbook of metaphysics and ontology.Hans Burkhardt & Barry Smith (eds.) - 1991 - Munich: Philosophia Verlag.
    The Handbook of Metaphysics and Ontology reflects the conviction that the history of metaphysics and current work in metaphysics and ontology can each throw valuable light on the other. Thus it is designed to serve both äs a means of making more widely accessible the results of recent scholarship in the history of philosophy, and also äs a unique work of reference in reladon to the metaphysical themes at the centre of much current debate in analyüc philosophy. (...)
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  22. Symmetry, Invariance and Ontology in Physics and Statistics.Julio Michael Stern - 2011 - Symmetry 3 (3):611-635.
    This paper has three main objectives: (a) Discuss the formal analogy between some important symmetry-invariance arguments used in physics, probability and statistics. Specifically, we will focus on Noether’s theorem in physics, the maximum entropy principle in probability theory, and de Finetti-type theorems in Bayesian statistics; (b) Discuss the epistemological and ontological implications of these theorems, as they are interpreted in physics and statistics. Specifically, we will focus on the positivist (in physics) or subjective (in statistics) interpretations vs. objective interpretations that (...)
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  23. On the False Ontological Consensus.Mudyń Krzysztof - 2015 - Polish Psychological Bulletin 46 (2):160-173.
    The objective of the research was to check whether False Consensus Effect (FCE), shown in much research,is also valid for ontological decisions. Test participants, faced with an ontological dilemma, made a choice three times,which of the 3 item set (Cracow City, Me myself, the Universe) refers to something most real. The research conducted first among psychology students (N=116), then replicated on mathematics students (N=126) and middle-aged people (N=106). Results: 1) All groups chose the Universe most seldom (4%-11% subjects), the remaining (...)
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  24. Referent tracking for treatment optimisation in schizophrenic patients.Werner Ceusters & Barry Smith - 2006 - Journal of Web Semantics 4 (3):229-236.
    The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and (...)
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  25. Beyond concepts: Ontology as reality representation.Barry Smith - 2001 - In Barry Smith & Christopher Welty (eds.), Formal Ontology in Information Systems (FOIS). ACM Press. pp. 1-12.
    The present essay is devoted to the application of ontology in support of research in the natural sciences. It defends the thesis that ontologies developed for such purposes should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws. We outline the benefits of a view along these lines by showing how it yields rigorous formal definitions of the foundational relations used in (...)
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  26. Grundgesetze and the Sense/Reference Distinction.Kevin C. Klement - 2019 - In Philip A. Ebert & Marcus Rossberg (eds.), Essays on Frege's Basic Laws of Arithmetic. Oxford: Oxford University Press. pp. 142-166.
    Frege developed the theory of sense and reference while composing his Grundgesetze and considering its philosophical implications. The Grundgesetze is thus the most important test case for the application of this theory of meaning. I argue that evidence internal and external to the Grundgesetze suggests that he thought of senses as having a structure isomorphic to the Grundgesetze expressions that would be used to express them, which entails a theory about the identity conditions of senses that is relatively (...)
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  27. Susan Stebbing, Incomplete Symbols and Foundherentist Meta-Ontology.Frederique Janssen-Lauret - 2017 - Journal for the History of Analytical Philosophy 5 (2):6-17.
    Susan Stebbing’s work on incomplete symbols and analysis was instrumental in clarifying, sharpening, and improving the project of logical constructions which was pivotal to early analytic philosophy. She dispelled use-mention confusions by restricting the term ‘incomplete symbol’ to expressions eliminable through analysis, rather than those expressions’ purported referents, and distinguished linguistic analysis from analysis of facts. In this paper I explore Stebbing’s role in analytic philosophy’s development from anti-holism, presupposing that analysis terminates in simples, to the more holist or foundherentist (...)
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  28. πολλαχῶς ἔστι; Plato’s Neglected Ontology.Mohammad Bagher Ghomi - manuscript
    This paper aims to suggest a new approach to Plato’s theory of being in Republic V and Sophist based on the notion of difference and the being of a copy. To understand Plato’s ontology in these two dialogues we are going to suggest a theory we call Pollachos Esti; a name we took from Aristotle’s pollachos legetai both to remind the similarities of the two structures and to reach a consistent view of Plato’s ontology. Based on this theory, (...)
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  29. Population thinking vs. essentialism in biology and evolutionary economics.George Liagouras - 2017 - In Evolutionary Political Economy in Action. A Cyprus Symposium, Routledge. London & New York: pp. 36-53.
    The standard perception of the dichotomy between population thinking and essentialism (typological thinking) in evolutionary economics descends from the golden age of the neo-Darwinian Synthesis. Over the last few decades the received view on population thinking has been seriously challenged in biology and its philosophy. First, the strong version of population thinking that banishes essentialism witnessed important tensions stemming from the ontological status of species. These tensions have been amplified by the demise of positivism and the rise of a new (...)
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  30. Actor Network, Ontic Structural Realism and the Ontological Status of Actants.Corrado Matta - 2014 - Proceedings of the 9th International Conference on Networked Learning 2014.
    In this paper I discuss the ontological status of actants. Actants are argued as being the basic constituting entities of networks in the framework of Actor Network Theory (Latour, 2007). I introduce two problems concerning actants that have been pointed out by Collin (2010). The first problem concerns the explanatory role of actants. According to Collin, actants cannot play the role of explanans of networks and products of the same newtork at the same time, at pain of circularity. The second (...)
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  31. Speech acts and medical records: The ontological nexus.Lowell Vizenor & Barry Smith - 2004 - In Jana Zvárová (ed.), Proceedings of the International Joint Meeting EuroMISE 2004.
    Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task of ensuring that the right sorts of information gets to the right sorts of people remains. We argue that the many efforts underway to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations. This in turn requires that the management of information and knowledge within healthcare (...)
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  32. Schemes of Historical Method in the Late 19th Century: Cross-References between Langlois and Seignobos, Bernheim, and Droysen.Arthur Alfaix Assis - 2015 - In Luiz Estevam de Oliveira Fernandes, Luísa Rauter Pereira & Sérgio da Mata (eds.), Contributions to Theory and Comparative History of Historiography German and Brazilian Perspectives. Peter Lang. pp. 105-125.
    At the end of the 19th century, most professional historians – wherever they existed – deemed history to be a form of knowledge ruled by a method that bears no resemblance with those most commonly traceable in the natural sciences. The bulk of the historian’s task was then frequently regarded as being the application of procedures frequently referred to as ‘historical method’. In the context of such an emerging interest on historical methods and methodology, at least three textbooks stand (...)
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  33. (1 other version)Word vector embeddings hold social ontological relations capable of reflecting meaningful fairness assessments.Ahmed Izzidien - 2021 - AI and Society (March 2021):1-20.
    Programming artificial intelligence to make fairness assessments of texts through top-down rules, bottom-up training, or hybrid approaches, has presented the challenge of defining cross-cultural fairness. In this paper a simple method is presented which uses vectors to discover if a verb is unfair or fair. It uses already existing relational social ontologies inherent in Word Embeddings and thus requires no training. The plausibility of the approach rests on two premises. That individuals consider fair acts those that they would be willing (...)
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  34. Blockchain et l'arbre causal de la référence.Sfetcu Nicolae - manuscript
    Dans un article précédent, The Philosophy of blockchain technology - Ontologies, j'ai parlé de l'application de la théorie narrative de Paul Ricœur dans le développement d'une ontologie de la technologie blockchain. Dans cette section, j'ai l'intention de mettre en évidence l'idée d'une analogie entre la technologie blockchain et les théories causales de la référence. Dans la mesure où la poursuite de l'élaboration de cette idée se révélera viable, je vais essayer de développer une théorie basée sur cette analogie. DOI: (...)
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  35. W poszukiwaniu ontologicznych podstaw prawa. Arthura Kaufmanna teoria sprawiedliwości [In Search for Ontological Foundations of Law: Arthur Kaufmann’s Theory of Justice].Marek Piechowiak - 1992 - Instytut Nauk Prawnych PAN.
    Arthur Kaufmann is one of the most prominent figures among the contemporary philosophers of law in German speaking countries. For many years he was a director of the Institute of Philosophy of Law and Computer Sciences for Law at the University in Munich. Presently, he is a retired professor of this university. Rare in the contemporary legal thought, Arthur Kaufmann's philosophy of law is one with the highest ambitions — it aspires to pinpoint the ultimate foundations of law by explicitly (...)
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  36. Calculus of Qualia 4: Why Something Rather than Nothing; Rather than Weakest Assumptions; Contingent Possibility vs Necessary Actuality; Possibilities of Possibilities.P. Merriam & M. A. Z. Habeeb - manuscript
    General Introduction: In [1] a Calculus of Qualia (CQ) was proposed. The key idea is that, for example, blackness is radically different than █. The former term, “blackness” refers to or is about a quale, whereas the latter term, “█” instantiates a quale in the reader’s mind and is non-referential; it does not even refer to itself. The meaning and behavior of these terms is radically different. All of philosophy, from Plato through Descartes through Chalmers, including hieroglyphics and emojis, used (...)
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  37. Needing the other: the anatomy of the Mass Noun Thesis.Lajos L. Brons - 2014 - Argument: Biannual Philosophical Journal 4 (1):103-122.
    Othering is the construction and identification of the self or in-group and the other or out-group in mutual, unequal opposition by attributing relative inferiority and/or radical alienness to the other/out-group. Othering can be “crude” or “sophisticated”, the defining difference being that in the latter case othering depends on the interpretation of the other/out-group in terms that are applicable only to the self/in-group but that are unconsciously assumed to be universal. The Mass Noun Thesis, the idea that all nouns in certain (...)
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  38. Filosofia Analitica e Filosofia Continentale.Sergio Cremaschi (ed.) - 1997 - 50018 Scandicci, Metropolitan City of Florence, Italy: La Nuova Italia.
    ● Sergio Cremaschi, The non-existing Island. I discuss the way in which the cleavage between the Continental and the Anglo-American philosophies originated, the (self-)images of both philosophical worlds, the converging rediscoveries from the Seventies, as well as recent ecumenic or anti-ecumenic strategies. I argue that pragmatism provides an important counter-instance to both the familiar self-images and to the fashionable ecumenic or anti-ecumenic strategies. My conclusions are: (i) the only place where Continental philosophy exists (as Euro-Communism one decade ago) is America; (...)
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  39. Marriages of Mathematics and Physics: A Challenge for Biology.Arezoo Islami & Giuseppe Longo - 2017 - Progress in Biophysics and Molecular Biology 131:179-192.
    The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical (...)
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  40. The Many Facets of Trust.Riccardo Baratella, Glenda Amaral, Tiago Prince Sales, Renata Guizzardi & Giancarlo Guizzardi - 1998 - In Nicola Guarino (ed.), Formal Ontology in Information Systems. IOS Press.
    Trust is an attitude that an agent (the trustor) has toward an entity (the trustee), such that the trustor counts upon the trustee to act in a way that is benefi- cial w.r.t. to the trustor’s goals. The notion of trust is relevantly discussed both in in- formation science and philosophy. Unfortunately, we still lack a satisfying account for this concept. The goal of this article is to contribute to filling this gap. First, we take issue with some central tenets (...)
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  41. Towards a Body Fluids Ontology: A unified application ontology for basic and translational science.Jiye Ai, Mauricio Barcellos Almeida, André Queiroz De Andrade, Alan Ruttenberg, David Tai Wai Wong & Barry Smith - 2011 - Second International Conference on Biomedical Ontology , Buffalo, Ny 833:227-229.
    We describe the rationale for an application ontology covering the domain of human body fluids that is designed to facilitate representation, reuse, sharing and integration of diagnostic, physiological, and biochemical data, We briefly review the Blood Ontology (BLO), Saliva Ontology (SALO) and Kidney and Urinary Pathway Ontology (KUPO) initiatives. We discuss the methods employed in each, and address the project of using them as starting point for a unified body fluids ontology resource. We conclude (...)
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  42. (1 other version)Objects are (not) ...Friedrich Wilhelm Grafe - 2024 - Archive.Org.
    My goal in this paper is, to tentatively sketch and try defend some observations regarding the ontological dignity of object references, as they may be used from within in a formalized language. -/- Hence I try to explore, what properties objects are presupposed to have, in order to enter the universe of discourse of an interpreted formalized language. -/- First I review Frege′s analysis of the logical structure of truth value definite sentences of scientific colloquial language, to draw suggestions from (...)
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  43. The Logical vs. the Ontological Understanding of Conditions.Rögnvaldur Ingthorsson - 2008 - Metaphysica 9 (2):129-137.
    According to the truth-functional analysis of conditions, to be ‘necessary for’ and ‘sufficient for’ are converse relations. From this, it follows that to be ‘necessary and sufficient for’ is a symmetric relation, that is, that if P is a necessary and sufficient condition for Q, then Q is a necessary and sufficient condition for P. This view is contrary to common sense. In this paper, I point out that it is also contrary to a widely accepted ontological view of conditions, (...)
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  44. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
    The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute (...), and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)
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  45. The Plant Ontology: A common reference ontology for plants.L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Barry Smith, Mungall Chris, A. Gandolfo Maria & Jaiswal Pankaj - 2010 - In Walls Ramona L., Cooper Laurel D., Justin Elser, Stevenson Dennis W., Smith Barry, Chris Mungall, Gandolfo Maria A. & Pankaj Jaiswal (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.
    The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and (...)
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  46. Hermeneutic fictionalism.Jason Stanley - 2001 - Midwest Studies in Philosophy 25 (1):36–71.
    Fictionalist approaches to ontology have been an accepted part of philosophical methodology for some time now. On a fictionalist view, engaging in discourse that involves apparent reference to a realm of problematic entities is best viewed as engaging in a pretense. Although in reality, the problematic entities do not exist, according to the pretense we engage in when using the discourse, they do exist. In the vocabulary of Burgess and Rosen (1997, p. 6), a nominalist construal of a (...)
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  47. CRITIQUE OF IMPURE REASON: Horizons of Possibility and Meaning.Steven James Bartlett - 2021 - Salem, USA: Studies in Theory and Behavior.
    PLEASE NOTE: This is the corrected 2nd eBook edition, 2021. ●●●●● _Critique of Impure Reason_ has now also been published in a printed edition. To reduce the otherwise high price of this scholarly, technical book of nearly 900 pages and make it more widely available beyond university libraries to individual readers, the non-profit publisher and the author have agreed to issue the printed edition at cost. ●●●●● The printed edition was released on September 1, 2021 and is now available through (...)
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  48. Warranted Diagnosis.David Limbaugh, David Kasmier, Werner Ceusters & Barry Smith - 2019 - In David Limbaugh, David Kasmier, Werner Ceusters & Barry Smith (eds.), Proceedings of the International Conference on Biomedical Ontology (ICBO), Buffalo, NY. Buffalo: pp. 1-10.
    A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...)
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  49. Using philosophy to improve the coherence and interoperability of applications ontologies: A field report on the collaboration of IFOMIS and L&C.Jonathan Simon, James Matthew Fielding & Barry Smith - 2004 - In Gregor Büchel, Bertin Klein & Thomas Roth-Berghofer (eds.), Proceedings of the First Workshop on Philosophy and Informatics. Deutsches Forschungs­zentrum für künstliche Intelligenz, Cologne: 2004 (CEUR Workshop Proceedings 112). pp. 65-72.
    The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. (...)
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  50. Ontological theory for ontological engineering: Biomedical systems information integration.James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith - 2004 - In Fielding James M., Simon Jonathan, Ceusters Werner & Smith Barry (eds.), Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning (KR2004), Whistler, BC, 2-5 June 2004. pp. 114–120.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such (...)
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