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Ontology: So Cvs
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The Gene Ontology is a collection of terms used to describe gene products. It is divided into three aspects, cellular location, biological process and molecular function. A gene product may be described by one or more terms from each of the aspects. The characterization of gene products in this way enhances many large scale analyses. The Sequence Ontology ... is used to catalog the features and properties of biological sequence, and how these features relate to each other. It captures the subclass hierarchy of these features, the meronomies, that is what features are parts of other features, and also topological relationships like adjacent_to. Using SO and GO together to catalogue the kinds of gene products and the features of the sequence will mean that queries such as “Give me the 3’UTR sequence of all transcription factors in the X pathway” will be trivial.
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In philosophy, Ontology, the most fundamental branch of metaphysics, is the study of being or existence as well as the basic categories thereof. A being is anything that can be said to 'be' in various senses of the word 'be'. The verb to be has many different meanings and can therefore be rather ambiguous. Because "to be" has so many different meanings, there are, accordingly, many different ways of being.
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The term is originally borrowed from philosophy, where Ontology (uncountable term with a capital o) is described as a systematic account of existence. In the computer science area, specifically in the AI community, it is considered an engineering artifact, constituted by a specific vocabulary used to describe a certain reality, plus a set of explicit assumptions regarding the intended meaning of the vocabulary words. The assumptions has usually the form of a first order logical theory where vocabulary words appear as unary (concepts) or binary (relations) predicate names. In its simplest form an ontology will describe a hierarchy of concepts, as it gets mores sophisticated suitable axioms are added. [Lassila & McGuinness, 2001] present an excellent description of this spectrum.
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