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Variation Ontology for annotation of variation effects and mechanisms

Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological an...

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Autor principal: Vihinen, Mauno
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912426/
https://www.ncbi.nlm.nih.gov/pubmed/24162187
http://dx.doi.org/10.1101/gr.157495.113
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author Vihinen, Mauno
author_facet Vihinen, Mauno
author_sort Vihinen, Mauno
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description Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism.
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spelling pubmed-39124262014-02-18 Variation Ontology for annotation of variation effects and mechanisms Vihinen, Mauno Genome Res Resource Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism. Cold Spring Harbor Laboratory Press 2014-02 /pmc/articles/PMC3912426/ /pubmed/24162187 http://dx.doi.org/10.1101/gr.157495.113 Text en © 2014 Vihinen; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/3.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Resource
Vihinen, Mauno
Variation Ontology for annotation of variation effects and mechanisms
title Variation Ontology for annotation of variation effects and mechanisms
title_full Variation Ontology for annotation of variation effects and mechanisms
title_fullStr Variation Ontology for annotation of variation effects and mechanisms
title_full_unstemmed Variation Ontology for annotation of variation effects and mechanisms
title_short Variation Ontology for annotation of variation effects and mechanisms
title_sort variation ontology for annotation of variation effects and mechanisms
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912426/
https://www.ncbi.nlm.nih.gov/pubmed/24162187
http://dx.doi.org/10.1101/gr.157495.113
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