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Introduction to Vaccine Ontology

     In this page, we start with introducing the basic concepts of biomedical ontologies and their applications. The basic information of the Vaccine Ontology and its applications is then summarized.

Biomedical Ontologies and their Applications:

     Ontologies 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 is closely related to the Infectious Disease Ontology (IDO), initiated by Drs. Cowell and Smith. 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.

VO screen shot
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.

     A prototype of the VO has been created through our collaborative efforts. Current focuses in the 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 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 VO now contains more than 1000 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).

Applications of the Vaccine Ontology (VO):

     Like other biomedical ontologies, Vaccine Ontology can be used in various applications. We have formed many Vaccine Ontology user groups with many user case studies. For example, 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. We have formed the University of Michigan Vaccine Informatics and Resource Advisory Committee (VIRAC) with many interests of applying the Vaccine Ontology for variuos research goals. The Vaccine Ontology has also been considered for vaccine industry applications.

References:

  1. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25 (11): 1251-5. (PMID 17989687).
  2. Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. (2005). Relations in biomedical ontologies. Genome Biol 6 (5): R46. (PMID 15892874).