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Ontology: Gene Ontology
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Ontology (the "science of being") is a word, like metaphysics, that is used in many different senses. It is sometimes considered to be identical to metaphysics, but we prefer to use it in a more specific sense, as that part of metaphysics that specifies the most fundamental categories of existence, the elementary substances or structures out of which the world is made. Ontology will ... analyse the most general and abstract concepts or distinctions that underlie every more specific description of any phenomenon in the world, e.g. time, space, matter, process, cause and effect, system.
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"The Gene Ontology (GO) project was established to provide a common language to describe aspects of a gene product's biology. The use of a consistent vocabulary allows genes from different species to be compared based on their GO annotations. The objective of GO is to provide controlled vocabularies for the description of the biological process, molecular function, and cellular component of gene products. These terms are to be used as attributes of gene products by organism databases, facilitating uniform queries across them. The controlled vocabularies of terms are structured to allow annotation of gene products to GO terms at varying levels of detail and to query for gene products that are involved in similar processes, function and components."
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In more modern and contemporary philosophy, Ontology was taken up by physicists who were already asking very similar questions using the scientific method. Ontology is being done today, though not under its ancient name, in many branches of Physics and the other sciences. Quantum mechanics, String theory, and quantum philosophy in general, are direct descendants of the ontological traditions, which naturally grew beyond the historical distinctions between universals and particulars, into questions of particle states, dimensions and probabilities. The basic ontological questions of the nature of existence are even more relevant to quantum mechanics, as notions of solid matter and distinct, separate existence of objects are challenged by new discoveries.
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The Sequence Ontology is developed and archived using OBO format. OBO stands for Open Biomedical Ontologies. It is a collection of structured controlled vocabularies for shared use across the biomedical domain, such as Gene Ontology. A file format for sharing ontologies has been developed by the OBO group.
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Gene Ontology