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Towards improving phenotype representation in OWL

BACKGROUND: Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definit...

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Detalles Bibliográficos
Autores principales: Loebe, Frank, Stumpf, Frank, Hoehndorf, Robert, Herre, Heinrich
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448528/
https://www.ncbi.nlm.nih.gov/pubmed/23046625
http://dx.doi.org/10.1186/2041-1480-3-S2-S5
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author Loebe, Frank
Stumpf, Frank
Hoehndorf, Robert
Herre, Heinrich
author_facet Loebe, Frank
Stumpf, Frank
Hoehndorf, Robert
Herre, Heinrich
author_sort Loebe, Frank
collection PubMed
description BACKGROUND: Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. METHODS: We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. RESULTS: In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. CONCLUSION: Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions.
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spelling pubmed-34485282012-09-24 Towards improving phenotype representation in OWL Loebe, Frank Stumpf, Frank Hoehndorf, Robert Herre, Heinrich J Biomed Semantics Proceedings BACKGROUND: Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. METHODS: We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. RESULTS: In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. CONCLUSION: Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions. BioMed Central 2012-09-21 /pmc/articles/PMC3448528/ /pubmed/23046625 http://dx.doi.org/10.1186/2041-1480-3-S2-S5 Text en Copyright ©2012 Loebe et al.; 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
Loebe, Frank
Stumpf, Frank
Hoehndorf, Robert
Herre, Heinrich
Towards improving phenotype representation in OWL
title Towards improving phenotype representation in OWL
title_full Towards improving phenotype representation in OWL
title_fullStr Towards improving phenotype representation in OWL
title_full_unstemmed Towards improving phenotype representation in OWL
title_short Towards improving phenotype representation in OWL
title_sort towards improving phenotype representation in owl
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448528/
https://www.ncbi.nlm.nih.gov/pubmed/23046625
http://dx.doi.org/10.1186/2041-1480-3-S2-S5
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