Welcome to Vaccine Ontology!
Model biomedical research is data-intensive. The post-genomics era has brought up a proliferation in data, databases, and an exponential growth in published literature. Researchers must now assimilate and integrate an ever increasing amount of diverse information to do their research. Computers have been used to help researchers to manage the information explosion. Ontologies are able to structure complex biomedical domains and relate the myriad of data to shared understanding of biomedicine. The most successful ontology is the Gene Ontology (GO), which was initiated in 1998 as a collaborative effort to address the need for consistent descriptions of gene products in three model organism databases. GO has been widely used in various GO-based applications, such as gene expression data analysis and literature mining. Its importance can be demonstrated by more than 3,000 peer-revieweed publications out of a direct search of "Gene Ontology" in PubMed.
To ensure consistent representation of vaccine knowledge and to support automated reasoning, a community-based effort to develop the Vaccine Ontology (VO) has been initiated. This international collaborative VO development effort has been joined by many institutes and disciplines around the world. The Vaccine Ontology is also being used in a variety of applications by many user groups in academia and industry.
This site currently include the following components:
- Introduction: Introduction of biomedical ontologies, the Vaccine Ontology, and their applications.
- Statistics: Statistics of most updated Vaccine Ontology.
- VO News: Documentation of Vaccine Ontology-related news.
- VO at SourceForge: VO development site at SourceForge.net. Features include mailing list, bug tracker, code version control, forum etc.
- VO Development Team: Introduction of the international, multiple-institute, and multidiscipline Vaccine Ontology development team.
- VO Users: Vaccine Ontology user case studies and user groups. The Vaccine Ontology can not only be used for representation of vaccine terms and their relationships, but also be used in various applications, inclusing vaccine data analysis, literature mining, and network prediction, and so on.
- VOBrowser: Search and browse Vaccine Ontology terms and relationships.
- VO SPARQL Query: Use SPARQL to query VO RDF file.
Download the most updated Vaccine Ontology OWL format (Protégé 4.x is recommanded for opening this file).
- FAQs: Frequently asked questions related to the Vaccine Ontology.
- Links: Useful links.
- Contact Us: Information how to contact us, and a web form for direct input of your feedback.
- VO in VIOLIN: Introduction of the development and applications of the Vaccine Ontology in the VIOLIN project (Vaccine Investigation and Online Information Network).
Publications and Citation: Please check HERE for a list of VO-associated papers we have pubished. Also, VO has been cited by many other papers: Search "Vaccine Ontology" in Google Scholar.
The successful development and applications of the Vaccine Ontology are not easy tasks, and we just started. Its success requires determination and intelligent work. Support from the broad vaccine research and development community is greatly appreciated.
Listed are the news related to VO development and its applications. Please submit your news to us and we will have it posted here. Thank you.
- 5/2/2012: Oliver presented a Webinar presentation in NCBO Webinar Series. His presentation title is: "Vaccine Ontology (VO) and its application in literature mining of vaccine-gene interaction networks".
- 8/26/2011: Another paper using VO was accepted for publication: Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. 12(1):49 2011 Aug 26. PMID: 21871085.
- 6/20/2011: A comprehensive 26-page review article titled "Emerging Vaccine Informatics" in the Journal of Biomedicine and Biotechnology 2010 special issue on vaccine informatics was published. Oliver is a co-author of this article. This review also introduces VIOLIN and VO.
- 5/17/2011: A paper using VO was accepted for publication: Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163.
- 12/8-9/2010: Oliver, Allen, and Asiyah (Yu Lin) attended the IDO Workshop 2010. Asiyah presented Brucellosis Ontology, Allen presented OntoBee, and Oliver updated the development of Vaccine Ontology (VO).
- 9/28/2010: A new paper about the application of VIOLIN and VO in analysis/prediction of Brucella vaccines and vaccine targets was published. The PubMed ID is: 20875156.
- 9/26-28/2010: Oliver He attended InCoB2010 in Tokyo, Japan. He presented a talk on how to use VIOLIN to analyze and predict Brucella vaccines and vaccine targets.
- 7/9-10/2010: Arzucan Ozgur presented a talk in the conference: Ozgur A, Xiang Z, Radev D, He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper.
- 7/9-10/2010: Oliver presented a talk in the conference: He Y, Xiang Z, Todd T, Courtot M, Brinkman R, Zheng J, Stoeckert CJ, Malone J, Rocca-Serra P, Sansone S, Fostel J, Soldatova LN, Peters B, Rutternberg A. Ontology representation and ANOVA analysis of vaccine protection investigation. Proceeding of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB, July 9-10, 2010. Boston, MA, USA. Full length paper. This talk used OBI and VO for representing vaccine protection investigation and used ANOVA to evaluate meta-analyzed data.
- 7/9-10/2010: Junguk Hur presented a poster in the conference: Hur J, Xiang Z, Feldman E, He Y. Ontology-based vaccine literature mining and indexing. Bio-Ontologis 2010: Semantic Applications in Life Sciences. July 9-10, 2010, Boston, Massachusetts, USA. This poster used VO for Brucella vaccine literature mining and indexing.
- 3/22-25/2010: Allen Xiang attended the OBI Spring 2010 Workshop at Vancouver, Canada. He presented a use case on vaccine protection investigation using ontology (OBI and VO)-based ANOVA analysis of literature mined data.
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