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Journal of Biomedical Semantics

, 4:20

Biomedical Ontologies

Abstract

BackgroundThe 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.

DescriptionRecently, 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.

ConclusionsIn 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.

KeywordsGene ontology Cellular component ontology Subcellular anatomy ontology Neuroscience Annotation Ontology language Ontology integration Neuroscience information framework AbbreviationsBPBiological process

CCCellular component

CCDBCell centered database

GO-CCOGene ontology cellular component ontology

CILCell image Library

CLCell ontology

GOGene ontology

MFMolecular function

MPMammalian phenotype

NDPONeurodegenerative disease phenotype Ontology

NIFSTDNeuroscience information framework standard

OBOOpen biological ontologies

OWLWeb ontology language

SAOSubcellular anatomy ontology.

Electronic supplementary materialThe online version of this article doi:10.1186-2041-1480-4-20 contains supplementary material, which is available to authorized users.

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Autor: Paola Roncaglia - Maryann E Martone - David P Hill - Tanya Z Berardini - Rebecca E Foulger - Fahim T Imam - Harold Dra

Fuente: https://link.springer.com/



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