224
Views
10
CrossRef citations to date
0
Altmetric
Reviews

Ontology-supported research on vaccine efficacy, safety and integrative biological networks

References

  • He Y, Rappuoli R, De Groot AS, Chen RT. Emerging vaccine informatics. J Biomed Biotechnol 2010;2010:218590
  • Pizza M, Scarlato V, Masignani V, et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 2000;287(5459):1816-20
  • Althoff E, Gassenbach N. Novartis submits Bexsero®, a multi-component meningococcal B vaccine, for regulatory review in Europe. Novartis Media releases, USA; 2010. Available from: www.novartis.com/newsroom/media-releases/en/2010/1475256.shtml
  • He Y, Xiang Z, Mobley HL. Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development. J Biomed Biotechnol 2010;2010:297505
  • He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res 2010;6(Suppl 1):S5
  • Xiang Z, He Y. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia Vaccinol 2009;1(1):23-9
  • Gomez G, Pei J, Mwangi W, et al. Immunogenic and invasive properties of Brucella melitensis 16M outer membrane protein vaccine candidates identified via a reverse vaccinology approach. PLoS One 2013;8(3):e59751
  • He Y. Genome-based computational vaccine discovery by reverse vaccinology. In: Flower DR, editors. Immunomic discovery of adjuvants and candidate subunit vaccines. Springer; New York: 2013
  • Pereira UP, Soares SC, Blom J, et al. In silico prediction of conserved vaccine targets in Streptococcus agalactiae strains isolated from fish, cattle, and human samples. Genet Mol Res 2013;12(3):2902-12
  • Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics 2013;14(Suppl 4):S2
  • Van Regenmortel MH. Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol 2012;3:194
  • Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunol 2011;12:49
  • Bagnoli F, Baudner B, Mishra RP, et al. Designing the next generation of vaccines for global public health. OMICS 2011;15(9):545-66
  • He Y. Analyses of Brucella pathogenesis, host immunity, and vaccine targets using systems biology and bioinformatics. Front Cell Infect Microbiol 2012;2:2
  • Sayers S, Ulysse G, Xiang Z, He Y. Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development. J Biomed Biotechnol 2012;2012:831486
  • Racz R, Li X, Patel M, et al. DNAVaxDB: the first web-based DNA vaccine database and its data analysis. BMC Bioinformatics 2014;15(Suppl 4):S2
  • Poland GA, Ovsyannikova IG, Jacobson RM. Application of pharmacogenomics to vaccines. Pharmacogenomics 2009;10(5):837-52
  • Sarntivijai S, Xiang Z, Shedden KA, et al. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS One 2012;7(11):e49941
  • Bonhoeffer J, Black S, Izurieta H, et al. Current status and future directions of post-marketing vaccine safety monitoring with focus on USA and Europe. Biologicals 2012;40(5):393-7
  • Vaccine adverse event reporting system. Available from: www.vaers.hhs.gov
  • Chen RT, Rastogi SC, Mullen JR, et al. The vaccine adverse event reporting system (VAERS). Vaccine 1994;12(6):542-50
  • Varricchio F, Iskander J, Destefano F, et al. Understanding vaccine safety information from the vaccine adverse event reporting system. Pediatr Infect Dis J 2004;23(4):287-94
  • Frequently asked questions. Available from: www.vaers.hhs.gov/about/faqs
  • Brown EG. Methods and pitfalls in searching drug safety databases utilising the medical dictionary for regulatory activities (MedDRA). Drug Saf 2003;26(3):145-58
  • Brown SH, Elkin PL, Bauer BA, et al. SNOMED CT: utility for a general medical evaluation template. AMIA Annu Symp Proc 2006:101-5
  • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10(1):57-63
  • Nakaya HI, Li S, Pulendran B. Systems vaccinology: learning to compute the behavior of vaccine induced immunity. Wiley Interdiscip Rev Syst Biol Med 2012;4(2):193-205
  • Pulendran B, Li S, Nakaya HI. Systems vaccinology. Immunity 2010;33(4):516-29
  • Nakaya HI, Wrammert J, Lee EK, et al. Systems biology of vaccination for seasonal influenza in humans. Nat Immunol 2011;12(8):786-95
  • Poland GA, Ovsyannikova IG, Jacobson RM. Personalized vaccines: the emerging field of vaccinomics. Expert Opin Biol Ther 2008;8(11):1659-67
  • Poland GA, Ovsyannikova IG, Kennedy RB, et al. Vaccinomics and a new paradigm for the development of preventive vaccines against viral infections. OMICS 2011;15(9):625-36
  • He Y, Xiang Z. Databases and in silico tools for vaccine design. Methods Mol Biol 2013;993:115-27
  • US FDA vaccines. Available from: www.fda.gov/BiologicsBloodVaccines/Vaccines/default.htm
  • USDA veterinary biological products, licensees and permittees, prepared April 9, 2014. Available from: www.aphis.usda.gov/animal_health/vet_biologics/publications/CurrentProdCodeBook.pdf
  • Edlich RF, Martin ML, Foley ML, et al. Vaccine information statements. Revolutionary but neglected educational advances in healthcare in the United States. J Long Term Eff Med Implants 2005;15(1):91-114
  • Vaccine resource library. Available from: www.path.org/vaccineresources/
  • Saleh JA, Yusuph H, Zailani SB, Aji B. Malaria vaccine: the pros and cons. Niger J Med 2010;19(1):8-13
  • Vita R, Zarebski L, Greenbaum JA, et al. The immune epitope database 2.0. Nucleic Acids Res 2010,38(Database issue):D854-62
  • Immune epitope database and analysis resource. Available from: www.iedb.org
  • Rammensee H, Bachmann J, Emmerich NP, et al. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999;50(3-4):213-19
  • Lefranc MP. Immunoglobulin and T Cell receptor genes: IMGT((R)) and the birth and rise of immunoinformatics. Front Immunol 2014;5:22
  • The international immunogenetics information system. Available from: www.imgt.org
  • The nonhuman primate HIV/SIV vaccine trials database. Available from: www.hiv.lanl.gov/content/vaccine/home.html
  • Xiang Z, Todd T, Ku KP, et al. VIOLIN: vaccine investigation and online information network. Nucleic Acids Res 2008;36(Database issue):D923-8
  • VIOLIN. Available from: www.violinet.org
  • He Y, Racz R, Sayers S, et al. Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res 2014;42(1):D1124-32
  • Yang B, Sayers S, Xiang Z, He Y. Protegen: a web-based protective antigen database and analysis system. Nucleic Acids Res 2011;39(Database issue):D1073-8
  • Jaiswal V, Chanumolu SK, Gupta A, et al. Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions. BMC Bioinformatics 2013;14:211
  • W3C: OWL 2 web ontology language document overview. 2009. Available from: www.w3.org/TR/2009/REC-owl2002-overview-20091027/ Last accessed March 2009
  • Tirmizi SH, Aitken S, Moreira DA, et al. Mapping between the OBO and OWL ontology languages. J Biomed Semantics 2011;2(Suppl 1):S3
  • Xiang Z, Courtot M, Brinkman RR, et al. OntoFox: web-based support for ontology reuse. BMC Res Notes 2010;3:175
  • Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007;25(11):1251-5
  • OBO Foundry wiki. Introduction of the NCBITaxon ontology. Available from: www.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page
  • Rosse C, Mejino JL Jr. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003;36(6):478-500
  • Demir E, Cary MP, Paley S, et al. The BioPAX community standard for pathway data sharing. Nat Biotechnol 2010;28(9):935-42
  • Smith B, Ceusters W. Ontological realism: a methodology for coordinated evolution of scientific ontologies. Appl Ontol 2010;5:139-88
  • He Y, Cowell L, Diehl AD, et al. VO: vaccine ontology. In: The 1st International Conference on Biomedical Ontology (ICBO-2009): Nature Precedings; 2009. 24-26 July 2009.Buffalo, NY, USA. Available from: precedings.nature.com/documents/3552/version/3551
  • Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. J Biomed Semantics 2012;3(1):17
  • Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000;25(1):25-9
  • Bettembourg C, Diot C, Burgun A, Dameron O. GO2PUB: querying PubMed with semantic expansion of gene ontology terms. J Biomed Semantics 2012;3(1):7
  • Doms A, Schroeder M. GoPubMed: exploring PubMed with the gene ontology. Nucleic Acids Res 2005;33(Web Server issue):W783-6
  • Plake C, Royer L, Winnenburg R, et al. GoGene: gene annotation in the fast lane. Nucleic Acids Res 2009;37(Web Server issue):W300-4
  • Hur J, Ozgur A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. J Biomed Semantics 2012;3(1):18
  • Ozgur A, Xiang Z, Radev DR, He Y. Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology. J Biomed Semantics 2011;2(Suppl 2):S8
  • The VO in the OBO Foundry ontology library. Available from: www.obofoundry.org/cgi-bin/detail.cgi?id=vaccine
  • Xiang Z, Mungall C, Ruttenberg A, He Y. Ontobee: a linked data server and browser for ontology terms. In: The 2nd International Conference on Biomedical Ontologies (ICBO): 2011; CEUR Workshop Proceedings Buffalo, NY, USA;2013. Pages 279-81 Available from: ceur-ws.org/Vol-833/paper248.pdf
  • VO statistics shown in Ontobee. Available from: www.ontobee.org/ontostat.php?ontology=VO
  • Kazakov Y, Krötzsch M, Simancík F. ELK reasoner: architecture and evaluation. In: Proceedings of the OWL Reasoner Evaluation Workshop (ORE 2012): July 1,2012. Manchester,UK.12 pages
  • Sirin E, Parsia B, Grau BC, et al. Pellet: a practical OWL-DL reasoner. Web Semant 2007;5:51-3
  • Tsarkov D, Horrocks I. FaCT++ description logic reasoner: system description. Proc of the Int Joint Conf on Automated Reasoning (IJCAR 2006) 2006. 4130 of Lecture Notes in Artificial Intelligence, 292-7
  • Zhang Y, Tao C, He Y, et al. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J Biomed Semantics 2013;4(1):33
  • Lipscomb CE. Medical Subject Headings (MeSH). Bull Med Libr Assoc 2000;88(3):265-6
  • Srinivasan P. MeSHmap: a text mining tool for MEDLINE. Proc AMIA Symp 2001;642-6
  • Djebbari A, Karamycheva S, Howe E, Quackenbush J. MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. Bioinformatics Oxford, England 2005;21(15):3324-6
  • Osborne JD, Zhu LJ, Lin SM, Kibbe WA. Interpreting microarray results with gene ontology and MeSH. Methods Mol Biol 2007;377:223-42
  • Hur J, Schuyler AD, States DJ, Feldman EL. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics Oxford, England 2009;25(6):838-40
  • Genomesh. Available from: www.genomesh.hegroup.org
  • Xiang Z, Qin T, Qin Z, He Y. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks. BMC Syst Biol 2013;7(Suppl 3):S9
  • Joachims T. Making large-scale support vector machine learning practical. In: Schölkopf B CJB, Smola AJ, editors. Advances in kernel methods: support vector learning. MIT Press; Cambridge, MA: 1999. 169-84
  • Ozgur A, Xiang Z, Radev D, He Y. Literature-based discovery of IFN-γ and vaccine-mediated gene interaction networks. J Biomed Biotechnol 2010;2010: article id 426479 426413
  • He Y, Xiang Z, Sarntivijai S, et al. AEO: a realism-based biomedical ontology for the representation of adverse events. In: Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO-2011). CEUR Workshop Proceedings. 26-30 July 2011; Buffalo, NY, USA; Pages 309-15. Available from: www.ceur-ws.org/Vol-833/paper359.pdf
  • Marcos E, Zhao B, He Y. The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. J Biomed Semantics 2013;4:40
  • Lee JA, Spidlen J, Boyce K, et al. MIFlowCyt: the minimum information about a flow cytometry experiment. Cytometry A 2008;73(10):926-30
  • Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001;29(4):365-71
  • Todd TE, Tibi O, Lin Y, et al. Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. BMC Bioinformatics 2013;14(Suppl 6):S3
  • Brinkman RR, Courtot M, Derom D, et al. Modeling biomedical experimental processes with OBI. J Biomed Semantics 2010;1(Suppl 1):S7
  • He Y, Xiang Z, Todd T, et al. Ontology representation and ANOVA analysis of vaccine protection investigation. In: Bio-Ontologies 2010: Semantic Applications in Life Sciences: CEUR Workshop Proceedings, 11-13July 2010.Boston, MA, USA. Pages 1-8 Available from: www.ceur-ws.org/Vol-754/he_krmed2010.pdf]
  • Glass GV. Primary, secondary, and meta-analysis of research. Educ Res 1976;5:3-8
  • Altman DG. Statistics in medical journals: some recent trends. Stat Med 2000;19(23):3275-89
  • Lean IJ, Rabiee AR, Duffield TF, Dohoo IR. Invited review: use of meta-analysis in animal health and reproduction: methods and applications. J Dairy Sci 2009;92(8):3545-65
  • Lukk M, Kapushesky M, Nikkila J, et al. A global map of human gene expression. Nat Biotechnol 2010;28(4):322-4
  • Zheng-Bradley X, Rung J, Parkinson H, Brazma A. Large scale comparison of global gene expression patterns in human and mouse. Genome Biol 2010;11(12):R124
  • Bizer C, Heath T, Berners-Lee T. Linked Data-the story so far. Int J Semantic Web Information Systems 2009;5(3):22
  • Design issues: linked data. Available from: www.w3.org/DesignIssues/LinkedData
  • Belleau F, Nolin MA, Tourigny N, et al. Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008;41(5):706-16
  • Yamamoto Y, Yamaguchi A, Yonezawa A. Building linked open data towards integration of biomedical scientific literature with DBpedia. J Biomed Semantics 2013;4(1):8
  • Grenon P, Smith B. SNAP and SPAN: towards dynamic spatial ontology. Spat Cogn Comput 2004;4(1):69-103
  • Futuyma DJ. Evolutionary Biology, 3rd edition: Sinauer Associates, USA 1997
  • Baluska F, Volkmann D, Barlow PW. Eukaryotic cells and their cell bodies: cell Theory revised. Ann Bot (Lond) 2004;94(1):9-32
  • Mazzarello P. A unifying concept: the history of cell theory. Nat Cell Biol 1999;1(1):E13-15
  • Perelson AS. Immune network theory. Immunol Rev 1989;110:5-36
  • Moore KL. Essentials of Human Embryology. B.C. Decker, Inc; Toronto, Canada: 1988
  • Friedman N, Linial M, Nachman I, Pe’er D. Using Bayesian networks to analyze expression data. J Comput Biol 2000;7(3-4):601-20
  • He Y, Xiang Z. miniTUBA: a web-based dynamic Bayesian network analysis system and an application in host-pathogen interaction analysis. In: Rebai A, editors. Bayesian Network, Sciyo 2010. Available from: www.intechopen.com/articles/show/title/minituba-a-web-based-dynamic-bayesian-network-analysis-system
  • Hodges AP, Dai D, Xiang Z, et al. Bayesian network expansion identifies new ROS and biofilm regulators. PLoS One 2010;5(3):e9513
  • Pearl J. Causality. 2nd edition Cambridge University Press; New York, NY, USA: 2009
  • Croft D, O’Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011;39(Database issue):D691-7
  • Kanehisa M, Goto S, Kawashima S, et al. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004;32(Database issue):D277-80
  • Latendresse M, Paley S, Karp PD. Browsing metabolic and regulatory networks with BioCyc. Methods Mol Biol 2012;804:197-216
  • BioCarta apoptosis pathway. Available from: www.biocarta.com/genes/Apoptosis.asp
  • HarshaRani GV, Vayttaden SJ, Bhalla US. Electronic data sources for kinetic models of cell signaling. J Biochem 2005;137(6):653-7
  • He Y, Xiang Z. HINO: a BFO-aligned ontology representing human molecular interactions and pathways. arXiv 2013; arXiv:1311.3355
  • DARPA: Big mechanism. DARPA Broad Agency Announcement 2014;DARPA-BAA-14-14
  • Hastings J, de Matos P, Dekker A, et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 2013;41(Database issue):D456-63
  • Announcement of the ontology of genes and genomes (OGG). Available from: https://groups.google.com/forum/#!topic/ogg-discuss/wy0132CCdNA
  • Diehl AD, Augustine AD, Blake JA, et al. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform 2011;44(1):75-9
  • Sarntivijai S, Lin Y, Xiang Z, et al. CLO: the cell line ontology. J Biomed Semantics 2014; In press
  • Xiang Z, Lin Y, He Y. Ontorat web server for automatic generation and annotations of new ontology terms. In: The 3rd International Conference on Biomedical Ontologies (ICBO): CEUR Workshop Proceedings. 24-27July 2012; Graz, Austria;2012. Available from: www.ceur-ws.org/Vol-897/poster_812.pdf
  • Zheng J, Xiang Z, SJC J, et al. Ontodog: a web-based ontology community view generator. Bioinformatics 2013; In press
  • Tan PL, Jacobson RM, Poland GA, et al. Twin studies of immunogenicity--determining the genetic contribution to vaccine failure. Vaccine 2001;19(17-19):2434-9
  • The protege ontology editor. Available from: www.protege.stanford.edu/

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.