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 .