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. 2010 Jun 3:11:302.
doi: 10.1186/1471-2105-11-302.

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

Jiye Ai  1 , Barry Smith, David T Wong
Affiliations

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

Jiye Ai et al. BMC Bioinformatics. .

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/) 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.

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Figures

Figure 1
Figure 1
The SKB architecture. The SKB is based on a three-layer architecture. Data sources are stored in the data layer. In the ontology layer data elements from these data sources are mapped to nodes in controlled vocabularies. The interface layer allows query, browsing and submission. For instance, the interface layer receives user requests, submits queries to the data layer through the ontology layer and obtains corresponding results. The three layers connect data from consumers (users submitting query) with data providers (data sources) via ontologies.
Figure 2
Figure 2
A fragment of SALO in its current form.
Figure 3
Figure 3
A result of entity chunking recognition for the text of one sample article.
Figure 4
Figure 4
Links between SALO and other ontologies.
Figure 5
Figure 5
Relations involved in a saliva-specific genetic marker for Sjögren's syndrome.
See this image and copyright information in PMC

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