Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.
Highlights
The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context
One informatics resource that has transformed the analysis of large biological datasets is the Gene Ontology (GO) [3], which provides a computable description of the functional aspects of an increasing number of genes and gene products spanning a diverse range of species
Inherent GO chemical ontology Before comparing the GO to an external chemical ontology, the inherent chemical representations in the GO were checked for internal consistency
Summary
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. David P Hill1,2*, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale, Paula de Matos, Christopher J Mungall, Gareth Owen, Paola Roncaglia, Christoph Steinbeck, Steve Turner and Jane Lomax
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