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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...
Autores principales: | , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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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. |
format | Online Article Text |
id | pubmed-3733925 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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