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The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

Paola Roncaglia12*, Maryann E Martone3, David P Hill24, Tanya Z Berardini25, Rebecca E Foulger12, Fahim T Imam3, Harold Drabkin247, Christopher J Mungall26 and Jane Lomax12

Author Affiliations

1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK

2 The Gene Ontology Consortium, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK

3 Department of Neurosciences, Center for Research in Biological Systems, University of California, San Diego, CA, USA

4 The Jackson Laboratory, Bar Harbor, ME 04609, USA

5 The Arabidopsis Information Resource, Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA

6 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

7 Protein Ontology, Center for Bioinformatics & Computational Biology, Department of Computer and Information Sciences, University of Delaware, 15 Innovation Way, room 205, Newark DE19711, USA

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Journal of Biomedical Semantics 2013, 4:20  doi:10.1186/2041-1480-4-20

Published: 7 October 2013

Abstract

Background

The Gene Ontology (GO) (http://www.geneontology.org/ webcite) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience.

Description

Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases.

Conclusions

In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community.

Keywords:
Gene ontology; Cellular component ontology; Subcellular anatomy ontology; Neuroscience; Annotation; Ontology language; Ontology integration; Neuroscience information framework