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Welcome to Vaccine Ontology!A community-based effort to develop the Vaccine Ontology (VO) has been initiated. Here we introduce biomedical ontologies and their applications, the VO development effort and its progress, and relevant tool development and links. Biomedical Ontologies and their ApplicationsOntologies are consensus-based controlled vocabularies of terms and relations, with associated definitions which are logically formulated in such a way as to promote automated reasoning. Ontologies are being used in the following ways: (1) Reference for naming things. The Gene Ontology (GO) is the canonical example of an ontology created for the primary purpose of providing controlled and standardized terms for naming things. Creating such ontology-based annotations is highly valuable for both querying databases and analyzing high throughput data. (2) Representation of encyclopedic knowledge. For example, the Foundational Model of Anatomy (FMA) is a comprehensive ontology of human anatomy. FMA contains more than 70,000 entitles that describes the elements of canonical human morphology, providing declarative descriptions of detailed anatomic structures. (3) Specification of an information model (database/knowledgebase schema). Ontologies provide an explicit specification of the terms used to express information in biomedical domain. They make relationships among data types in databases explicit and support automated reasoning such as deducing subsumption among classes. Representations of information models using ontologies can be published on the Semantic Web in the format of the Web Ontology Language (OWL). (4) Specification of a data exchange format, such as BioPax for pathway data exchange. (5) Representation of semantics of data for information integration. Ontologies can streamline the process of integrating and accessing data across diverse resources. (6) Computer reasoning with data. The Vaccine Ontology (VO)A bottleneck in vaccine research and development is the lack of a Vaccine Ontology for vaccine data standardization, integration, and analysis. Dr. Yongqun "Oliver" He and the VIOLIN team are working with Dr. Barry Smith (University at Buffalo and the National Center for Biomedical Ontology) and Dr. Lindsay Cowell (Duke University) to develop the Vaccine Ontology (VO). The Vaccine Ontology will also become a sub-domain specific extension of the Infectious Disease Ontology (IDO). IDO was initiated by Drs. Cowell and Smith, and Dr. He is a member of the IDO consortium. Like IDO, VO development will follow the OBO Foundry principles [1]. Examples of these principles include: a) ontologies are developed in a collaborative effort, b) ontologies use common relations that are unambiguously defined, c) ontologies provide procedures for user feedback and for identifying successive versions, and d) ontologies have a clearly bounded subject-matter. The OBOFoundry principles are summarized in the OBOFoundry website. New OBO Foundry principles have also been proposed. 
Protege screenshots of VO (Click to enlarge)
The Vaccine Ontology (VO) utilizes the Basic Formal Ontology (BFO) and the Relation Ontology [2]. BFO is a highest-common-denominator upper ontology that is designed to support interoperability between domain ontologies for shared use of scientific research data across disciplinary boundaries. BFO has been used and tested extensively within biomedical sciences. Derived from BFO, VO will include a disease neutral core VO that contains general terms such as ‘adjuvant’, and disease-specific extensions containing terms for each disease domain such as ‘Brucella abortus vaccine RB51’ and ’Escherichia coli T cell epitope’. A prototype of the core VO has been created through our collaborative efforts. Current focuses in the core VO development are on vaccine categorization, vaccine components, vaccine quality, and vaccine-induced host responses. The screenshorts included in this web page demonstrate the overall hierarchies of the core VO (middle screenshot), the vaccine categorization (left screenshot) and the host responses to vaccines (right screenshot). Future directions will include ontology resources for vaccine design, preparation, evaluation, and administration. The core VO now contains more than 500 terms. VO not only contains many vaccine-specific terms, but it also includes many terms cross-referenced from other existing ontologies, such as the Phenotypic Quality Ontology (PATO). Like other biomedical ontologies, Vaccine Ontology can be used in various applications. Currently we are collaborating with Drs. David States, Brian Athey, and Gil Omenn (University of Michigan and the National Center for Integrative Biomedical Informatics) to apply Vaccine Ontology to natural language processing (NLP)-driven literature mining for vaccine specific research. Vaccine Ontology will also be used for standardization of vaccine data stored in the VIOLIN vaccine database. The applications of Vaccine Ontology in VIOLIN will facilitate to establish VIOLIN as a web-based vaccine resource center for vaccine data integration, annotation, standardization, storage, query, and analysis. The successful development and applications of Vaccine Ontology are not easy tasks, and we just started. Oliver will introduce and discuss the Vaccine Ontology development at the 2008 Infectious Disease Ontology (IDO) meeting in September 2008. We will seek new ideas to improve Vaccine Ontology and its integration with IDO in this meeting. We have recently formed the University of Michigan Vaccine Informatics and Resource Advisory Committee (VIRAC) with an aim to help develop and use Vaccine Ontology. Support from the broad vaccine research and development community is also needed and welcome. If you plan to join us or have any suggestions and comments, please contact Oliver He. Thank you. VO Downloads and BrowserThe current core VO is available for download in Protege and OWL formats: You can also browse the structure and documentation of the Vaccine Ontology using the Vaccine Ontology Browser. References
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