The Saliva Ontology

Ontologies are controlled structured vocabularies designed to provide consensus-based means to ensure consistent description of data by scientists working in disparate domains.The Saliva Ontology (SALO), is a more detailed ontology of this bodily fluid that is optimized to meet the needs of both the clinical diagnostic community and the cross-disciplinary community of omics researchers.

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 included in the SKB.

The SKB and the SALO initiatives are devoted to the translation of saliva data into saliva knowledge, and to the task of enabling saliva data and knowledge sharing in the broadest possible communities of researchers.

Background

Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly recognized by the National Institute of Dental and Craniofacial Research (NIDCR) and the National Cancer Institute.

As applied in the biomedical domain, ontology has been playing a key role in providing consensus-based controlled vocabularies serving the consistent annotation of biological and medical data and information.

No dedicated ontology has been defined thus far in direct relation to oral biological fluid , and the treatment of saliva in ontology and terminology resources has thus been insufficient for purposes of saliva research. 

Development

The SALO is being created through cross-disciplinary interaction between saliva experts, protein experts, diagnosticians, and ontologists. To aid development and testing of SALO, we are developing a corpus of saliva-relevant literature in SKB to assist in characterizing core terms and synonyms within the ontology, and to provide links between SALO content and relevant items in Pubmed. 

In order to build on the solid foundations of prior work on biomedical ontologies, tools, and techniques, we will work with the Open Biomedical Ontologies (OBO) Foundry, and with the developers of OBO ontologies such as GO, PRO, CHEBI, and OBI, to ensure conformity with current best practices and to guarantee non-redundant development. We follow the principles of the OBO Foundry in constructing SALO in order to ensure that SALO is semantically interoperable with the other OBO ontologies.

Updates

[05/12/2010] A pre-beta version of SALO term list including our identified 1166 human salivary proteins was released.

[04/27/2010] The SALO made her debut at the Protein Ontology 3nd Annual Meeting.

[02/10/2010] A pre-beta 2 version of SALO was created.

[01/13/2010] A pre-beta 1 version of SALO was created.

[01/05/2010] Saliva literature corpus was created. 

[12/01/2009] The SALO project started.

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