Basic Formal Ontology
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Basic Formal Ontology
Basic Formal Ontology (BFO) is a top-level ontology developed by Barry Smith and his associates for the purposes of promoting interoperability among domain ontologies built in its terms through a process of downward population. A guide to building BFO-conformant domain ontologies was published by MIT Press in 2015. The ontology arose against the background of research in ontologies in the domain of geospatial information science by David Mark, Pierre Grenon, Achille Varzi and others, with a special role for the study of vagueness and of the ways sharp boundaries in the geospatial and other domains are created by fiat. BFO has passed through 4 major releases, documentehere The current revision was released in 2020, and this forms the basis of the standard, which was released by the Joint Committee of the International Standards Organization and International Electrotechnical Commission in 2021. The structure of BFO is based on a division of entities into two disjoint categor ...
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Upper Ontology
In information science, an upper ontology (also known as a top-level ontology, upper model, or foundation ontology) is an ontology (in the sense used in information science) which consists of very general terms (such as "object", "property", "relation") that are common across all domains. An important function of an upper ontology is to support broad semantic interoperability among a large number of domain-specific ontologies by providing a common starting point for the formulation of definitions. Terms in the domain ontology are ranked under the terms in the upper ontology, e.g., the upper ontology classes are superclasses or supersets of all the classes in the domain ontologies. A number of upper ontologies have been proposed, each with its own proponents. Library classification systems predate upper ontology systems. Though library classifications organize and categorize knowledge using general concepts that are the same across all knowledge domains, neither system is a repla ...
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Barry Smith (academic)
Barry Smith (born 4 June 1952) is an academic working in the fields of ontology and biomedical informatics. Smith is the author of more than 700 scientific publications, including 15 authored or edited books, and he is one of the most widely cited contemporary philosophers. Education and career From 1970 to 1973 Smith studieMathematics and Philosophyat the University of Oxford. He obtained his PhD from the University of Manchester in 1976 for a dissertation on ontology and reference in Husserl and Frege. The dissertation was supervised by Wolfe Mays. Among the cohort of graduate students supervised by Mays in Manchester were Kevin Mulligan (Geneva/Lugano), and Peter Simons (Trinity College, Dublin). Both shared with Smith an interest in analytic metaphysics and in the contributions of certain turn-of-the-century Continental philosophers and logicians to central issues of analytic philosophy. In 1979 Mulligan, Simons and Smith together founded the Seminar for Austro-German P ...
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Open Biomedical Ontologies Foundry
The Open Biological and Biomedical Ontologies (OBO) Foundry is a group of people dedicated to build and maintain ontologies related to the life sciences. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable reference ontologies in the biomedical domain. Currently, there are more than a hundred ontologies that follow the OBO Foundry principles. The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in bioinformatics. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a phenotype in a mouse model and its related phenotype in zebrafish). Introduction The Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using controlled vocabularies. Ideally, such controlled vocabularies take the form of ontologies, which ...
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Ontology For Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository. __TOC__ Scope The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration and joint ("cross-omics") analysis of experimental data, a need originally identified in the transcriptom ...
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Formal Ontology
In philosophy, the term formal ontology is used to refer to an ontology defined by axioms in a formal language with the goal to provide an unbiased (domain- and application-independent) view on reality, which can help the modeler of domain- or application-specific ontologies (information science) to avoid possibly erroneous ontological assumptions encountered in modeling large-scale ontologies. By maintaining an independent view on reality a formal ( upper level) ontology gains the following properties: *indefinite expandability: *:the ontology remains consistent with increasing content. *content and context independence: *:any kind of 'concept' can find its place. *accommodate different levels of granularity. Historical background Theories on how to conceptualize reality date back as far as Plato and Aristotle. The term 'formal ontology' itself was coined by Edmund Husserl in the second edition of his '' Logical Investigations'' (1900–01), where it refers to an ontological ...
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Ontology Engineering
In computer science, information science and systems engineering, ontology engineering is a field which studies the methods and methodologies for building ontologies, which encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities. In a broader sense, this field also includes a knowledge construction of the domain using formal ontology representations such as OWL/RDF. A large-scale representation of abstract concepts such as actions, time, physical objects and beliefs would be an example of ontological engineering. Ontology engineering is one of the areas of applied ontology, and can be seen as an application of philosophical ontology. Core ideas and objectives of ontology engineering are also central in conceptual modeling. Automated processing of information not interpretable by software agents can be improved by adding rich semantics to the corresponding resources, such as video files. One o ...
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Knowledge Representation
Knowledge representation and reasoning (KRR, KR&R, KR²) is the field of artificial intelligence (AI) dedicated to representing information about the world in a form that a computer system can use to solve complex tasks such as diagnosing a medical condition or having a dialog in a natural language. Knowledge representation incorporates findings from psychology about how humans solve problems and represent knowledge in order to design formalisms that will make complex systems easier to design and build. Knowledge representation and reasoning also incorporates findings from logic to automate various kinds of ''reasoning'', such as the application of rules or the relations of sets and subsets. Examples of knowledge representation formalisms include semantic nets, systems architecture, frames, rules, and ontologies. Examples of automated reasoning engines include inference engines, theorem provers, and classifiers. History The earliest work in computerized knowledge rep ...
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Information Science
Information science (also known as information studies) is an academic field which is primarily concerned with analysis, collection, classification, manipulation, storage, retrieval, movement, dissemination, and protection of information. Practitioners within and outside the field study the application and the usage of knowledge in organizations in addition to the interaction between people, organizations, and any existing information systems with the aim of creating, replacing, improving, or understanding the information systems. Historically, information science (informatics) is associated with computer science, data science, psychology, technology, library science, healthcare, and intelligence agencies. However, information science also incorporates aspects of diverse fields such as archival science, cognitive science, commerce, law, linguistics, museology, management, mathematics, philosophy, public policy, and social sciences. Foundations Scope and ...
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Ontology
In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped into categories and which of these entities exist on the most fundamental level. Ontologists often try to determine what the categories or highest kinds are and how they form a system of categories that encompasses classification of all entities. Commonly proposed categories include substances, properties, relations, states of affairs and events. These categories are characterized by fundamental ontological concepts, including particularity and universality, abstractness and concreteness, or possibility and necessity. Of special interest is the concept of ontological dependence, which determines whether the entities of a category exist on the most fundamental level. Disagreements within ontology are often about whether entities belonging to a certain category exist and, if so, how th ...
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Ontology (information Science)
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains of discourse. More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject. Every academic discipline or field creates ontologies to limit complexity and organize data into information and knowledge. Each uses ontological assumptions to frame explicit theories, research and applications. New ontologies may improve problem solving within that domain. Translating research papers within every field is a problem made easier when experts from different countries maintain a controlled vocabulary of jargon between each of their languages. For instance, the definition and ontology of economics is a primary concern in Marxist econ ...
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