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Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes

Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomyce...

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Autores principales: Gkoutos, Georgios V, Hoehndorf, Robert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448529/
https://www.ncbi.nlm.nih.gov/pubmed/23046642
http://dx.doi.org/10.1186/2041-1480-3-S2-S6
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author Gkoutos, Georgios V
Hoehndorf, Robert
author_facet Gkoutos, Georgios V
Hoehndorf, Robert
author_sort Gkoutos, Georgios V
collection PubMed
description Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following our proposed patterns. We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser. Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast.
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spelling pubmed-34485292012-09-24 Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes Gkoutos, Georgios V Hoehndorf, Robert J Biomed Semantics Proceedings Ontologies are widely used in the biomedical community for annotation and integration of databases. Formal definitions can relate classes from different ontologies and thereby integrate data across different levels of granularity, domains and species. We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following our proposed patterns. We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes across species available in the PhenomeBrowser. Furthermore, we utilize our definitions and the yeast phenotype annotations to suggest novel functional annotations of gene products in yeast. BioMed Central 2012-09-21 /pmc/articles/PMC3448529/ /pubmed/23046642 http://dx.doi.org/10.1186/2041-1480-3-S2-S6 Text en Copyright ©2012 Gkoutos and Hoehndorf; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Gkoutos, Georgios V
Hoehndorf, Robert
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
title Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
title_full Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
title_fullStr Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
title_full_unstemmed Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
title_short Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes
title_sort ontology-based cross-species integration and analysis of saccharomyces cerevisiae phenotypes
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448529/
https://www.ncbi.nlm.nih.gov/pubmed/23046642
http://dx.doi.org/10.1186/2041-1480-3-S2-S6
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