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

University of California at Los Angeles School of Dentistry, University of California, Los Angeles, CA 90095-1668, USA.
BMC Bioinformatics (Impact Factor: 2.58). 06/2010; 11(1):302. DOI: 10.1186/1471-2105-11-302
Source: PubMed


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).
We define the Saliva Ontology (SALO; 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.
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.

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Available from: Barry Smith, Jan 29, 2014
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    • "In analogy to efforts in other fields,11 a consortium of research groups specializing in different areas of study would undertake such an effort, each building different components of ontology to support dental research. Initial efforts in this direction, by scientists in dental research and biomedical ontology at University at Buffalo and University of California, include work on the ontology of oral pathology, oral maxillofacial anatomy, dental disease and dental procedures, and as we discuss below, the Saliva Ontology.13 "
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    ABSTRACT: There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva diagnostics made possible by the Saliva Ontology and SDxMart.International Journal of Oral Science (2012) 4, doi:10.1038/ijos.2012.26; published online 15 June 2012.
    International Journal of Oral Science 06/2012; 4(2). DOI:10.1038/ijos.2012.26 · 2.53 Impact Factor
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    • "Just recently, the Salivaomics Knowledge Base (SKB) has been created by aligning the salivary biomarker discovery and validation resources at UCLA (Figure 1) with the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry (, including the new Saliva Ontology (SALO) (Ai et al., 2010). The SKB is a data repository, management system and web resource constructed to support human salivary proteomics, transcriptomics, miRNA, metabolomics and microbiome research. "
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    ABSTRACT: For the past two decades, salivary diagnostic approaches have been developed to monitor oral diseases such as periodontal diseases and to assess caries risk. Recently, the combination of emerging biotechnologies and salivary diagnostics has extended the range of saliva-based diagnostics from the oral cavity to the whole physiologic system as most compounds found in blood are also present in saliva. Accordingly, saliva can reflect the physiologic state of the body, including emotional, endocrinal, nutritional and metabolic variations and acts as a source for the monitoring of oral and also systemic health. This review presents an update on the status of saliva diagnostics and delves into their applications to the discovery of biomarkers for cancer detection and therapeutic applications. Translating scientific findings of nucleic acids, proteins and metabolites in body fluids to clinical applications is a cumbersome and challenging journey. Our research group is pursuing the biology of salivary analytes and the development of technologies for detection of distinct biomarkers with high sensitivity and specificity. The avenue of saliva diagnostics incorporating transcriptomic, proteomic and metabolomic findings will enable us to connect salivary molecular analytes to monitor therapies, therapeutic outcomes, and finally disease progression in cancer.
    Oral Diseases 12/2010; 17(4):345-54. DOI:10.1111/j.1601-0825.2010.01773.x · 2.43 Impact Factor
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    • "and via LinkOut from the National Center for Biotechnology Information ( PRO serves as a reference ontology, for example, for the Dendritic Cell Ontology (22), The Saliva Ontology (23) and the GO (24). "
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    ABSTRACT: The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein research. PRO ( is part of the Open Biomedical Ontology Foundry.
    Nucleic Acids Research 10/2010; 39(Database issue):D539-45. DOI:10.1093/nar/gkq907 · 9.11 Impact Factor
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