Bioinformatics advances in saliva diagnostics

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. A knowledge base to retrieve, integrate and analyze multiple data types collected from saliva samples promises to transform healthcare. Saliva is ideally suited to non-invasive detection and monitoring of disease. However, the absence of a free resource that cross-references disease-based changes in the levels of biomolecules has hamstrung progress in identifying biomarkers of specific illnesses. To address this issue, a team led by Ji-Ye Ai and David Wong at the University of California in Los Angeles are spearheading the creation of the Salivaomics Knowledge Base (SKB), a data management system and web resource to facilitate the discovery of saliva biomarkers using systems biology. The researchers first defined a common and structured vocabulary to describe the diverse data types; now, they are creating a common interface to integrate protein, RNA and metabolite data from multiple independent databases.