Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
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- 作者：David P Hill (1) (2)
Nico Adams (10) (3) (8)
Mike Bada (4)
Colin Batchelor (5)
Tanya Z Berardini (2) (6)
Heiko Dietze (2) (9)
Harold J Drabkin (1) (2)
Marcus Ennis (8)
Rebecca E Foulger (2) (8)
Midori A Harris (1) (2) (7)
Janna Hastings (8)
Namrata S Kale (8)
Paula de Matos (8)
Christopher J Mungall (2) (9)
Gareth Owen (8)
Paola Roncaglia (2) (8)
Christoph Steinbeck (8)
Steve Turner (8)
Jane Lomax (2) (8) - 刊名：BMC Genomics
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：14
- 期：1
- 全文大小：410KB
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Nico Adams (10) (3) (8)
Mike Bada (4)
Colin Batchelor (5)
Tanya Z Berardini (2) (6)
Heiko Dietze (2) (9)
Harold J Drabkin (1) (2)
Marcus Ennis (8)
Rebecca E Foulger (2) (8)
Midori A Harris (1) (2) (7)
Janna Hastings (8)
Namrata S Kale (8)
Paula de Matos (8)
Christopher J Mungall (2) (9)
Gareth Owen (8)
Paola Roncaglia (2) (8)
Christoph Steinbeck (8)
Steve Turner (8)
Jane Lomax (2) (8)
1. Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA
2. The Gene Ontology Consortium, Bar Harbor, ME, USA
10. CSIRO Materials Science and Engineering, Bayview Avenue, Victoria, 3168, Clayton, Australia
3. Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
8. European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
4. University of Colorado Anschutz Medical Campus, Aurora, CO, USA
5. Royal Society of Chemistry, Thomas Graham House, CB4 0WF, Cambridge, UK
6. The Arabidopsis Information Resource, Carnegie Institution for Science, Stanford, CA, 94305, USA
9. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
7. Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, CB2 1GA, Cambridge, UK
文摘
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.