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Ontologies for the Description of Mouse Phenotypes

Ontologies are becoming increasingly important for the efficient storage, retrieval and mining of biological data. The description of phenotypes using ontologies is a particularly complex problem. We outline a schema that can be used to describe phenotypes by combining orthologous axiomatic ontologi...

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Detalles Bibliográficos
Autores principales: Gkoutos, G. V., Green, E. C. J., Mallon, A.-M., Blake, A., Greenaway, S., Hancock, J. M., Davidson, D.
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2004
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447424/
https://www.ncbi.nlm.nih.gov/pubmed/18629136
http://dx.doi.org/10.1002/cfg.430
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author Gkoutos, G. V.
Green, E. C. J.
Mallon, A.-M.
Blake, A.
Greenaway, S.
Hancock, J. M.
Davidson, D.
author_facet Gkoutos, G. V.
Green, E. C. J.
Mallon, A.-M.
Blake, A.
Greenaway, S.
Hancock, J. M.
Davidson, D.
author_sort Gkoutos, G. V.
collection PubMed
description Ontologies are becoming increasingly important for the efficient storage, retrieval and mining of biological data. The description of phenotypes using ontologies is a particularly complex problem. We outline a schema that can be used to describe phenotypes by combining orthologous axiomatic ontologies. We also describe tools for storing, browsing and searching such complex ontologies. Central to this approach is that assays (protocols for measuring phenotypic characters) describe what has been measured as well as how this was done, allowing assays to link individual organisms to ontologies describing phenotypes. We have evaluated this approach by automatically annotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. We believe this approach will enable the flexible, extensible and detailed description of phenotypes from any organism.
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spelling pubmed-24474242008-07-14 Ontologies for the Description of Mouse Phenotypes Gkoutos, G. V. Green, E. C. J. Mallon, A.-M. Blake, A. Greenaway, S. Hancock, J. M. Davidson, D. Comp Funct Genomics Research Article Ontologies are becoming increasingly important for the efficient storage, retrieval and mining of biological data. The description of phenotypes using ontologies is a particularly complex problem. We outline a schema that can be used to describe phenotypes by combining orthologous axiomatic ontologies. We also describe tools for storing, browsing and searching such complex ontologies. Central to this approach is that assays (protocols for measuring phenotypic characters) describe what has been measured as well as how this was done, allowing assays to link individual organisms to ontologies describing phenotypes. We have evaluated this approach by automatically annotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. We believe this approach will enable the flexible, extensible and detailed description of phenotypes from any organism. Hindawi Publishing Corporation 2004 /pmc/articles/PMC2447424/ /pubmed/18629136 http://dx.doi.org/10.1002/cfg.430 Text en Copyright © 2004 Hindawi Publishing Corporation. http://creativecommons.org/licenses/by/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Gkoutos, G. V.
Green, E. C. J.
Mallon, A.-M.
Blake, A.
Greenaway, S.
Hancock, J. M.
Davidson, D.
Ontologies for the Description of Mouse Phenotypes
title Ontologies for the Description of Mouse Phenotypes
title_full Ontologies for the Description of Mouse Phenotypes
title_fullStr Ontologies for the Description of Mouse Phenotypes
title_full_unstemmed Ontologies for the Description of Mouse Phenotypes
title_short Ontologies for the Description of Mouse Phenotypes
title_sort ontologies for the description of mouse phenotypes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447424/
https://www.ncbi.nlm.nih.gov/pubmed/18629136
http://dx.doi.org/10.1002/cfg.430
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