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Open Access Highly Accessed Research article

Saliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base

Jiye Ai1, Barry Smith2 and David T Wong1*

  • * Corresponding author: David T Wong dtww@ucla.edu

  • † Equal contributors

Author affiliations

1 University of California at Los Angeles School of Dentistry and Dental Research Institute, 73-017 Center for Health Sciences, 10833 Le Conte Avenue, University of California, Los Angeles, CA 90095-1668 USA

2 Department of Philosophy, 135 Park Hall, University at Buffalo, Buffalo, NY 14260 USA

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Citation and License

BMC Bioinformatics 2010, 11:302  doi:10.1186/1471-2105-11-302

Published: 3 June 2010

Abstract

Background

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO).

Results

We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/ webcite) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry.

Conclusions

The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB.