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

Roncaglia, Paola; Martone, Maryann E.; Hill, David P.; Berardini, Tanya Z.; Foulger, Rebecca E.; Imam, Fahim T.; Drabkin, Harold; Mungall, Christopher J.; Lomax, Jane

doi:10.1186/2041-1480-4-20

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

Journal Article · Tue Jan 01 00:00:00 EST 2013 · Journal of Biomedical Semantics

DOI:https://doi.org/10.1186/2041-1480-4-20· OSTI ID:1626675

Roncaglia, Paola ^[1]; Martone, Maryann E. ^[2]; Hill, David P. ^[3]; Berardini, Tanya Z. ^[4]; Foulger, Rebecca E. ^[5]; Imam, Fahim T. ^[2]; Drabkin, Harold ^[6]; Mungall, Christopher J. ^[7]; Lomax, Jane ^[5]

Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI); Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI). The Gene Ontology Consortium; DOE/OSTI
Univ. of California, San Diego, CA (United States). Center for Research in Biological Systems. Dept. of Neurosciences
Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI). The Gene Ontology Consortium; The Jackson Lab., Bar Harbor, ME (United States)
Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI). The Gene Ontology Consortium; Carnegie Inst. for Science, Stanford, CA (United States). Dept.of Plant Biology. The Arabidopsis Information Resource
Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI); Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI). The Gene Ontology Consortium
Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI). The Gene Ontology Consortium; The Jackson Lab., Bar Harbor, ME (United States); Univ. of Delaware, Newark, DE (United States). Dept. of Computer and Information Science. Protein Ontology
Wellcome Trust Genome Campus, Hinxton (United Kingdom). European Molecular Biology Lab. European Bioinformatics Inst. (EMBL-EBI). The Gene Ontology Consortium; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division

Background: The Gene Ontology (GO) (http://www.geneontology.org/) 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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626675

Journal Information:: Journal of Biomedical Semantics, Journal Name: Journal of Biomedical Semantics Journal Issue: 1 Vol. 4; ISSN 2041-1480

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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

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