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 2,000 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.
• VO Download: Download the most updated Vaccine Ontology OWL format (Protégé 4.0 beta 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).

     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.

• 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.
• Nov 10-12, 2009: Dr. Oliver He and Allen Xiang attended the “UTMB Sealy Center for Vaccine Development Symposium” in Galveston, Texas. Dr. He presented a talk in how to use VIOLIN and VO to analyze Brucella vaccines (http://www.utmb.edu/scvd/2009Symposium.pdf).
• September 21, 2009: An Notice of Award (NoA) was issued by NIH-NIAID to officially award Oliver He (PI) and his team and collaborators an R01 grant with the title: "Ontology-based Information Network to Support Vaccine Research" (Grant Number: R01AI081062). This is a four-year grant with an aim to develop VO and apply it for ontology-based literature mining and analysis of vaccine-induced protective immune networks.
• September 19, 2009: VO has been accepted to be listed in the OBO Foundry website: http://www.obofoundry.org/. The summary page of VO in OBO Foundry is here: http://www.obofoundry.org/cgi-bin/detail.cgi?id=vaccine.
• July 24-26, 2009: Oliver and two lab members attended the 1st International Conference on Biomedical Ontology (ICBO) conference in Buffalo, NY. Two posters and one software demo were presented, all related to Vaccine Ontology (VO) development and application. One poster is introduction of VO, the other is on using VO for literature mining. The software demo is about OntoFox, which a side project derived from the VO development. OntoFox is used for VO development. More details can be seen in the I CBO proceedings.
• June 23, 2009: A new web server OntoFox has been developed by Allen Xiang and Oliver He in He Group with constructive suggestions and comments from Alan Ruttenberg and Melanie Courtot. OntoFox facilitates ontology development by automatically fetching ontology terms and their annotations from existing ontologies and saving the results in an importable RDF/OWL format. OntoFox is developed based on the MIREOT principle. OntoFox is used in VO development.
• May 1, 2009: The VO Browser is re-designed and available in this VO website.
• Feb 17 - Mar 31, 2009: Dr. Oliver He submitted seven more updated version to NCBO BioPortal. The VO website in NCBO BioPortal is HERE.
• March Feb 17, 2009: Dr. Oliver He and Allen Xiang submitted the Vaccine Ontology (VO, version 0.6) to the NCBO BioPortal for the first time. The information about this VO submission is HERE. Allen has also updated the VOBrowse based on this updated version. This VO version contains many licensed veterinary vaccines.
• Feb 9, 2009: Dr. Oliver He updated the Vaccine Ontology. The VO is downloadable in the VO Download page and viewable in the VO Browser. This update incorporated many suggestions and comments received from the OBI 2009 Vancouver Workshop, especially from Drs. Bjoern Peters, Richard H. Scheuermann, and Alan Ruttenberg. Many new terms have been added. Some terms (e.g., software) were deleted from previous version since those terms would not fit in with the currernt VO scope. More term and relationship definitions have also been made.
• Feb 2-6, 2009: Oliver attended the OBI 2009 Vancouver Workshop. Oliver communicated with OBI and discussed with the OBI development team how to improve VO using OBI and possibly improve OBI by using vaccine investigation as a user case in OBI development. Oliver presented a talk with a title "VO and OBI" during the workshop. Oliver has also joined the OBI Consortium and represeents the vaccine community in the OBI development.

More VO News