Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions

Journal of Biomedical Semantics

Volumn 6, Issue 1, 2015, Pages

  Hur, Junguk ^a   Özgür, Arzucan ^b   Xiang, Zuoshuang ^c   He, Yongqun ^a,c  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b BOGAZICI UNIVERSITY   (Turkey)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Biomedical ontology; Gene gene interaction; Interaction enrichment; Interaction network ontology; Literature mining

Indexed keywords

EID: 84938805888     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-6-2     Document Type: Article

References (30)

1. Ozgur A, Xiang Z, Radev D, He Y: Literature-based discovery of IFN-γ and vaccine-mediated gene interaction networks. J Biomed Biotechnol 2010, 2010:426413. Article ID 426479
2. Jenssen TK, Laegreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28:21-8.
3. Joachims T: Making large-scale support vector machine learning practical. In Advances in Kernel Methods: Support Vector Learning. Edited by: Schölkopf CJB B, Smola AJ. Cambridge, MA: MIT Press; 1999:169-84.
4. Erkan G, Ozgur A, Radev DR: Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing. In Proceedings of the Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL). Prague: Czech Republic; 2007:228-37. Association for Computational Linguistics
5. He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, et al.: VO: Vaccine Ontology. In The 1st International Conference on Biomedical Ontology (ICBO-2009); july 24-26. Buffalo, NY, USA: Nature Precedings; 2009. http://precedings.nature.com/documents/3552/version/1
6. 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.
7. Kim JD, Ohta T, Tateisi Y, Tsujii J: GENIA corpus-semantically annotated corpus for bio-textmining. Bioinformatics 2003,19(Suppl 1):i180-2. 10.1093/bioinformatics/btg1023
8. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25:1251-5. 10.1038/nbt1346
9. Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y: OntoFox: web-based support for ontology reuse. BMC Res Notes 2010, 3:175. 10.1186/1756-0500-3-175
10. 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). Buffalo, NY, USA: CEUR Workshop Proceedings; 2011:279-81. [ http://ceur-ws.org/Vol-833/paper48.pdf ]
11. Hur J, Schuyler AD, States DJ, Feldman EL: SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 2009, 25:838-40. 10.1093/bioinformatics/btp049
12. 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. 10.1186/1471-2172-12-49
13. de Marneffe MC, Maccartney B, Manning CD: Generating Typed Dependency Parses from Phrase Structure Parses. In Proceedings of LREC-06. Genoa, Italy; 2006:449-54.
14. Hosack DA, Dennis G Jr, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70. 10.1186/gb-2003-4-10-r70
15. Sartor MA, Mahavisno V, Keshamouni VG, Cavalcoli J, Wright Z, Karnovsky A, et al.: ConceptGen: a gene set enrichment and gene set relation mapping tool. Bioinformatics 2010, 26:456-63. 10.1093/bioinformatics/btp683
16. Banerjee S, Pedersen T: The design, implementation, and Use of the ngram statistic package. In Proceedings of the Fourth International Conference on Intelligent Text Processing and Computational Linguistics. Mexico City, Mexico; 2003:370-81. [ http://www.d.umn.edu/~tpederse/Pubs/cicling2003-2.pdf ]
17. Grenon P, Smith B: SNAP and SPAN: towards dynamic spatial ontology. Spat Cogn Comput 2004, 4:69-103.
18. He Y, Xiang Z: HINO: a BFO-aligned ontology representing human molecular interactions and pathways. arXiv 2013, arXiv:1311. 3355
19. Xiang Z, He Y: HINO: BFO-Aligned Ontology Representation of Human Molecular Interactions and Pathways. In International Conference on Biomedical Ontology 2013 (ICBO 2013); july 7-12, 2013. Montreal, Canada: CEUR ICBO Workshop Proceedings; 2013:122. [ http://ceur-ws.org/Vol-1060/icbo2013_submission_70.pdf ]
20. Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, et al.: The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 2013, 41:D456-63. 10.1093/nar/gks1146
21. He Y, Liu Y, Zhao B: OGG: A Biological Ontology for Representing Genes and Genomes in Specific Organisms. In Proceedings of the 2014 International Conference on Biomedical Ontologies (ICBO 2014); October 6-9. Houston, TX, USA; 2014:1-6. In press
22. Chen X, O'Donnell MA, Luo Y: Dose-dependent synergy of Th1-stimulating cytokines on bacille calmette-guerin-induced interferon-gamma production by human mononuclear cells. Clin Exp Immunol 2007, 149:178-85. 10.1111/j.1365-2249.2007.03413.x
23. Wynn TA, Oswald IP, Eltoum IA, Caspar P, Lowenstein CJ, Lewis FA, et al.: Elevated expression of Th1 cytokines and nitric oxide synthase in the lungs of vaccinated mice after challenge infection with schistosoma mansoni. J Immunol 1994, 153:5200-9.
24. Green SJ, Scheller LF, Marletta MA, Seguin MC, Klotz FW, Slayter M, et al.: Nitric oxide: cytokine-regulation of nitric oxide in host resistance to intracellular pathogens. Immunol Lett 1994, 43:87-94. 10.1016/0165-2478(94)00158-8
25. Kim J-D, Ohta T, Pyysalo S, Kano Y, Tsujii J: Overview of BioNLP'09 Shared Task on Event Extraction. In Book Overview of BioNLP'09 Shared Task on Event Extraction (Editor ed.eds.). City: Association for Computational Linguistics; 2009:1-9.
26. Mastroeni P, Harrison JA, Chabalgoity JA, Hormaeche CE: Effect of interleukin 12 neutralization on host resistance and gamma interferon production in mouse typhoid. Infect Immun 1996, 64:189-96.
27. Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC: Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. AMIA Annual Symp Proc 2013, 2013:164-73.
28. Chen RT, Rastogi SC, Mullen JR, Hayes SW, Cochi SL, Donlon JA, et al.: The vaccine adverse event reporting system (VAERS). Vaccine 1994, 12:542-50. 10.1016/0264-410X(94)90315-8
29. Zhang Y, Tao C, He Y, Kanjamala P, Liu H: Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J Biomed Semantics 2013, 4:33. 10.1186/2041-1480-4-33
30. Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, et al.: Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS One 2012, 7:e49941. 10.1371/journal.pone.0049941