the need to advance saliva research is strongly recognized by the strategic plan of the national institute of dental and craniofacial research .
the ability to monitor health status , disease onset , progression , recurrence and treatment outcome through non - invasive means is highly important to advancing health care management .
saliva ( oral fluid ) is a perfect medium to be explored , offering the potential for a non - invasive , easy to obtain means for detecting and monitoring disease .
the adoption of saliva testing would allow a patient to collect their own specimens at home , yielding savings in health costs , convenience for the patient and facilitating multiple sampling .
specimen collection is less objectionable to patients than in the case of other bodily fluids and easier in children and older individuals .
the analysis of saliva can thus provide a cost - effective approach for the screening of large populations . due to these significant advantages ,
developing biomarkers in saliva for the detection of serious illnesses such as oral and systemic cancers has been on the national healthcare agenda for several years ( government performance & results act 2008 ) .
one mandate formulated in the government performance & results act report is that by the year 2013 proof of principle will be obtained for the ability of saliva to monitor health and diagnose for one systemic disease .
a vast amount of saliva omics data has been generated by recent studies using high throughput technologies .
however , there are still barriers which researchers must overcome before such data can be exploited , such as lack of computationally accessible salivary data and information , and inability to cross - reference the salivaomics data that could potentially be made available through different proteomics , transcriptomics , genomics and metabolomics studies . for these reasons
, there is an urgent need to create the salivaomics knowledge base ( skb ) , a data management system and web resource constructed to support saliva diagnostics research , and we present below the informatics advances brought about through the skb and through the associated tools and resources .
ontologies are controlled structured vocabularies designed to provide consensus - based means to ensure consistent description of data by scientists working in disparate domains . as applied in the biomedical domain
, ontology plays a key role in providing consensus - based controlled vocabularies serving the consistent annotation of biological and medical data and information , most conspicuously within the framework of the gene ontology and now of its sister ontologies within the open biomedical ontologies foundry ( http://obofoundry.org ) .
the basic formal ontology ( bfo ) is a formal ontological framework developed by barry smith , pierre grenon and others , which serves as the starting point for some 100 ontology projects primarily in the biomedical domain ( http://www.ifomis.uni-saarland.de/bfo/ ) .
the bfo framework can be readily extended to the treatment of families of ontologies of other types , above all to the treatment of relations between ontologies of different levels of granularity , from genes to species and from a single patient to epidemics at a geographical scale ( combining applications of bfo to the medical and to the geographical domain ) .
the framework may also be used as a tool for dealing with the relations between distinct perspectives on the biomedical domain , including culturally generated perspectives of the sort which are studied by linguists and anthropologists .
two bfo - based ontologies of special significance for our work here are the ontology for biomedical investigations ( obi ) and the ontology for general medical sciences .
the obi is an ontology designed to serve the coordinated representation of designs , protocols , instrumentation , materials , processes , data and types of analysis in all areas of biological and biomedical investigation .
ontology for general medical science is an ontology of the entities involved in the clinical encounter .
thus , it includes very general terms that are used across medical disciplines , including :  disease ' ,  disorder ' ,  disease course ' ,  diagnosis ' ,  patient ' and  healthcare provider ' .
to advance the consistency of data in the dental research community , smith et al .
propose an approach to building a consensus - based ontology to support dental research ( odr ) .
in analogy to efforts in other fields , 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 .
integral to his work is a plan to allow a seamless connection between the use of ontology to support dental research in the dental domain and the use of existing ontology resources developed in other areas of biology and medicine , by reusing elements and strategies from them .
the work on dental diseases is carried out in conjunction with the development of ontology for general medical science .
the saliva ontology ( salo ) ( figure 1 ) is a 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 salo is created through cross - disciplinary interaction with saliva experts , protein experts , diagnosticians and ontologists . to aid development and testing of salo
, we develop 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 .
skb will also incorporate the results of experiments in data and text mining using the ontology .
salo will incorporate links to existing ontologies and terminology resources involving treatment of saliva - relevant phenomena .
we will also identify and represent within salo relationships to saliva - relevant types represented in ontologies such as the gene ontology , the protein ontology and the chemical entities of biological interest ontology , and also provide links to corresponding snomed ct terms where available .
each term in the ontology has its own url which points to a webpage providing definitions , pubmed sources , references to annotations to skb and to external databases .
it is cross - platform and supports many popular relational database managements systems , including mysql , oracle , postgresql , sql server and db2 .
the software is data - agnostic , and can therefore be easily adapted to existing data sets .
it is expandable and customizable through a plug - in system , and is open - source so the community can participate in deeper development .
furthermore , biomart can seamlessly connect geographically disparate databases , facilitating collaboration between different groups .
these features have catalyzed the creation of biomart central portal , a first of its kind community - supported effort to create a single access point integrating many different , independently administered biological databases .
anybody can contribute an independently maintained resource to the central portal , allowing it to be exposed to and shared with the research community , and linking it with the other resources in the portal .
users can take advantage of the common interface to quickly utilize different sources without learning a new system for each .
the system also simplifies cross - database searches that might otherwise require several complicated steps .
several integrated tools streamline common tasks , such as converting between i d formats and retrieving sequences .
the combination of a wide variety of databases , an easy - to - use interface , robust programmatic access and the array of tools make central portal a one - stop shop for biological data querying .
sdxmart is a biomart data portal that hosts salivary proteomic , transcriptomic , metabolomic and microrna data and offers access to the data by using the biomart interface and querying environment .
the sdxmart is designed to provide a variety of queries to facilitate saliva biomarker discovery including complex queries that integrate genomic , clinical and functional information .
the sdxmart holds data from projects of oral diseases and systemic diseases including oral cancer , sjgren 's syndrome , pancreatic cancer and breast cancer .
the types of datasets are : ( i ) proteomics ; ( ii ) transcriptomics ; ( iii ) microrna ; and ( iv ) metabolomics .
in addition , the sdxmart is imported with several public databases including ensembl genome database ( ensembl release 37 ) , and the number of resources is continuously growing .
it is being built in tandem with the salo and sdxmart which will allow the skb to interoperate with other omics databases as part of a general strategy to facilitate integration of heterogeneous and disparate data sources that enable system biology approaches .
either salo or sdxmart is a first and only resource of its kind in the field of dentistry .
 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 . 
Saliva research
Challenges and opportunities
Biomedical ontology
A dental research ontology consortium
Saliva ontology
BioMart
SDxMarta BioMart portal for salivaomics data
Summary