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Vaccine Ontology News

• VO-related PubMed publications: https://www.ncbi.nlm.nih.gov/pubmed/?term=%22Vaccine+Ontology%22.
• VO-related Google Scholar citations: https://scholar.google.com/scholar?hl=en&as_sdt=0%2C23&q=%22Vaccine+Ontology%22.
• Note: This page is not routinely updated.
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• 4/1/2018: Oliver moved the VO source code from sourceforge to GitHub: https://github.com/vaccineontology/VO.
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• ... Note: Although a lot down on VO development, the VO news was not regularly maintained ... ...
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• 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.
• 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 (Allen and Sira) 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: A new VO Browser is re-designed by Oliver He and Allen, and implemented by Allen. The previous version is based on OWLDoc. The new version uses Virtuoso.
• Feb 17 - Mar 31, 2009: Dr. Oliver He submitted seven more updated version to NCBO BioPortal. The VO website in NCBO BioPortal is HERE.
• 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.
• Jan 21, 2009: Oliver updated the Vaccine Ontology (VO). One error was corrected. More terms were added, esp. the term 'gene related to vaccine' and many terms under it. The new version of VO is downloadable in the VO Download page. Allen Xiang has also updated the VO Browser correspondingly.
• Dec 9, 2008: Dr. Oliver He presented an oral presentation in the 2nd Vaccine Congress organized by the International Society for Vaccines (ISV) and the journal Vaccine. His presentation title is: "Vaxign: a web-based vaccine target design program for reverse vaccinology". In his talk, Oliver introduced the Vaccine Ontology to the attendees and received many positive feedback, encouragements, and possible collaborations.
• Nov 25, 2008: Dr. Oliver He updated the Vaccine Ontology, which includes more terms and updated relationships. More term definitions have also been made. The VO is downloadable in the VO Download page and viewable in the VO Browser.
• Sept 25, 2008: An expended Vaccine Ontology Development Team is established.
• Sept 23, 2008: Based on the feedback and suggestions from experts, particularly Alan Ruttenberg, Bjoern Peters, Richard Scheuermann, Barry Smith, Alexander Diehl, and many others (Thanks!), during the IDO 2008 workshop, Oliver updated the Vaccine Ontology a lot. Now it contains 1241 terms. Beside the BFO and Ration Ontology (RO) terms, the VO contains 874 vaccine-specific terms. The term relationships and general structure design have improved a lot. It also contains a large number of bacterial and viral vaccines, including those licensed for human use in the USA.
• 09/16-17/2008: Oliver He attended the Infectious Disease Ontology (IDO) 2008 workshop. In the workshop Oliver presented a talk on the progress of the Vaccine Ontology.
• Aug 18, 2008: The Vaccine Ontology version now contains 617 terms and is published in the VO web page.
• Aug 14, 2008: Dr. Oliver He gave a speaker presentation in the Cambridge Healthtech Institute (CHI) conference "Novel Vaccines: Bridging Research, Development & Production", which is part of the Immunotherapeutics& Vaccine Summit--ImVacS. His presentation title is "An Ontology-based Information Network to Support Vaccine Research".
• July 10, 2008: The Vaccine Ontology web site has been moved from VIOLIN Wiki to a new site: http://www.violinet.org/vaccineontology/. The VO browsing tool VOBrowser is also launched.
• May 12, 2008: A lot of new terms have been added to Vaccine Ontology by Oliver He. It now contains 460 terms. The focuses are vaccine-induced immune responses and vaccine phenotypes.
• July 19, 2008: We presented the VIOLIN and Vaccine Ontology project in ISMB2008 and here is a PDF version.
• July 18, 2008: Oliver attended the ISMB 2008 tutorial "How to Make Useful Ontologies for Biomedicine", presented by Drs. Nigam Shah (Stanford University) and Barry Smith.
• April 12-13, 2008: Both Dr. Oliver He and Zuoshuang (Allen) Xiang in Dr. He's lab attended the training course by Dr. Barry Smith: "An Introduction to Biomedical Ontology" in Buffalo, NY, USA. Dr. Smith introduced ontology with special reference to applications in biomedical research, including Vaccine Ontology.
• Nov 2007 to Jan, 2008: Oliver started to collaborate with Drs. Harry Mobley, David States, and Brian Athey at University of Michigan on the area of applying VO in vaccine literature mining. Brucella and E. coli were chosen as two use case models.
• Nov 2007 to Jan 12, 2008: Oliver proposed specific vaccine terms for VO development to Barry and Linday. After intensive discussions among all three, a first draft of VO was developed, and it contained ~60 vaccine specific terms.
• Jan 10, 2008: VIOLIN Wiki was created. The collaborative effort of Vaccine Ontology development was described in the Wiki site.
• Nov 9-10, 2007: Oliver emailed Dr. Barry Smith to propose specific development of VO and possible NIH grant application. Drs. Smith and Cowell agreed to participate.
• Oct 31, 2007: The VIOLIN vaccine database and analysis paper was officially accepted for publication in Nucleic Acid Research (NAR).
• Sep 19-20, 2007: Dr. Oliver He attended the Workshop on Infectious Disease Ontology (IDO) at the Cold Spring Harbor, which was co-organized by Drs. Lindsay Cowell (Duke University), and Barry Smith (University at Baffulo). In the last discussion section of the IDO workshop, Oliver proposed to develop a Vaccine Ontology (VO).