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Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

BACKGROUND: The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all sp...

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Autores principales: Deegan (née Clark), Jennifer I, Dimmer, Emily C, Mungall, Christopher J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098089/
https://www.ncbi.nlm.nih.gov/pubmed/20973947
http://dx.doi.org/10.1186/1471-2105-11-530
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author Deegan (née Clark), Jennifer I
Dimmer, Emily C
Mungall, Christopher J
author_facet Deegan (née Clark), Jennifer I
Dimmer, Emily C
Mungall, Christopher J
author_sort Deegan (née Clark), Jennifer I
collection PubMed
description BACKGROUND: The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation. RESULTS: We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology. CONCLUSIONS: Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855.
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spelling pubmed-30980892011-07-08 Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development Deegan (née Clark), Jennifer I Dimmer, Emily C Mungall, Christopher J BMC Bioinformatics Methodology Article BACKGROUND: The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation. RESULTS: We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology. CONCLUSIONS: Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855. BioMed Central 2010-10-25 /pmc/articles/PMC3098089/ /pubmed/20973947 http://dx.doi.org/10.1186/1471-2105-11-530 Text en Copyright ©2010 Deegan (née Clark) 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 Methodology Article
Deegan (née Clark), Jennifer I
Dimmer, Emily C
Mungall, Christopher J
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
title Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
title_full Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
title_fullStr Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
title_full_unstemmed Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
title_short Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
title_sort formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098089/
https://www.ncbi.nlm.nih.gov/pubmed/20973947
http://dx.doi.org/10.1186/1471-2105-11-530
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