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Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to i...

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Autores principales: Hill, David P, Adams, Nico, Bada, Mike, Batchelor, Colin, Berardini, Tanya Z, Dietze, Heiko, Drabkin, Harold J, Ennis, Marcus, Foulger, Rebecca E, Harris, Midori A, Hastings, Janna, Kale, Namrata S, de Matos, Paula, Mungall, Christopher J, Owen, Gareth, Roncaglia, Paola, Steinbeck, Christoph, Turner, Steve, Lomax, Jane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733925/
https://www.ncbi.nlm.nih.gov/pubmed/23895341
http://dx.doi.org/10.1186/1471-2164-14-513
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author Hill, David P
Adams, Nico
Bada, Mike
Batchelor, Colin
Berardini, Tanya Z
Dietze, Heiko
Drabkin, Harold J
Ennis, Marcus
Foulger, Rebecca E
Harris, Midori A
Hastings, Janna
Kale, Namrata S
de Matos, Paula
Mungall, Christopher J
Owen, Gareth
Roncaglia, Paola
Steinbeck, Christoph
Turner, Steve
Lomax, Jane
author_facet Hill, David P
Adams, Nico
Bada, Mike
Batchelor, Colin
Berardini, Tanya Z
Dietze, Heiko
Drabkin, Harold J
Ennis, Marcus
Foulger, Rebecca E
Harris, Midori A
Hastings, Janna
Kale, Namrata S
de Matos, Paula
Mungall, Christopher J
Owen, Gareth
Roncaglia, Paola
Steinbeck, Christoph
Turner, Steve
Lomax, Jane
author_sort Hill, David P
collection PubMed
description BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. RESULTS: We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. CONCLUSIONS: The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl.
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spelling pubmed-37339252013-08-06 Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology Hill, David P Adams, Nico Bada, Mike Batchelor, Colin Berardini, Tanya Z Dietze, Heiko Drabkin, Harold J Ennis, Marcus Foulger, Rebecca E Harris, Midori A Hastings, Janna Kale, Namrata S de Matos, Paula Mungall, Christopher J Owen, Gareth Roncaglia, Paola Steinbeck, Christoph Turner, Steve Lomax, Jane BMC Genomics Methodology Article BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. RESULTS: We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. CONCLUSIONS: The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. BioMed Central 2013-07-29 /pmc/articles/PMC3733925/ /pubmed/23895341 http://dx.doi.org/10.1186/1471-2164-14-513 Text en Copyright © 2013 Hill 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
Hill, David P
Adams, Nico
Bada, Mike
Batchelor, Colin
Berardini, Tanya Z
Dietze, Heiko
Drabkin, Harold J
Ennis, Marcus
Foulger, Rebecca E
Harris, Midori A
Hastings, Janna
Kale, Namrata S
de Matos, Paula
Mungall, Christopher J
Owen, Gareth
Roncaglia, Paola
Steinbeck, Christoph
Turner, Steve
Lomax, Jane
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
title Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
title_full Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
title_fullStr Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
title_full_unstemmed Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
title_short Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
title_sort dovetailing biology and chemistry: integrating the gene ontology with the chebi chemical ontology
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733925/
https://www.ncbi.nlm.nih.gov/pubmed/23895341
http://dx.doi.org/10.1186/1471-2164-14-513
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