Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network

BMC Immunology

Volumn 12, Issue , 2011, Pages

  Hur, Junguk ^a,b   Xiang, Zuoshuang ^a   Feldman, Eva L ^a,b   He, Yongqun ^a,b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRUCELLA VACCINE; CHAPERONE; PROTEIN;

ACCURACY; ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BIOGENESIS; CELL DIVISION; CELL MIGRATION; CELL REGENERATION; DOCUMENTATION; GENE IDENTIFICATION; GENE INTERACTION; INFORMATION SERVICE; MEDICAL LITERATURE; MEDLINE; NOMENCLATURE; PRODUCT RECALL; PROTEIN LOCALIZATION; PROTEIN PROCESSING; ANIMAL; BRUCELLA; BRUCELLOSIS; DATA MINING; GENE REGULATORY NETWORK; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; IMMUNOLOGY; MEDICAL INFORMATICS; MESH HEADING; METABOLISM; METHODOLOGY; MICROBIOLOGY; NATURAL LANGUAGE PROCESSING;

ABSTRACTING AND INDEXING AS TOPIC; ANIMALS; BRUCELLA; BRUCELLOSIS; DATA MINING; GENE REGULATORY NETWORKS; HOST-PATHOGEN INTERACTIONS; HUMANS; MEDICAL INFORMATICS; MEDICAL SUBJECT HEADINGS; NATURAL LANGUAGE PROCESSING; PROTEINS; PUBMED; TERMINOLOGY AS TOPIC;

EID: 80052033833     PISSN: None     EISSN: 14712172     Source Type: Journal    
DOI: 10.1186/1471-2172-12-49     Document Type: Article

References (38)

1. Almond JW. Vaccine renaissance. Nat Rev Microbiol 2007, 5(7):478-481. 10.1038/nrmicro1702, 17571456.
2. American-Diabetes-Association Economic costs of diabetes in the U.S. In 2007. Diabetes Care 2008, 31(3):596-615. American-Diabetes-Association.
3. Bradac J, Dieffenbach CW. HIV vaccine development: Lessons from the past, informing the future. IDrugs 2009, 12(7):435-439.
4. Perkins SD, Smither SJ, Atkins HS. Towards a Brucella vaccine for humans. FEMS Microbiol Rev 2010,
5. Disease NIoAaI The Jordan Report, Accelerated Development of Vaccines 2007. 2007, Disease NIoAaI.
6. Medical Subject Headings - Fact Sheet. , http://www.nlm.nih.gov/pubs/factsheets/mesh.html
7. He Y, Cowell L, Diehl AD, Mobley H, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C, et al. VO: Vaccine Ontology. International Conference on Biomedical Ontology: 2009; Buffalo, NY , http://dx.doi.org/10.1038/npre.2009.3552.1
8. Hur J, Schuyler AD, States DJ, Feldman EL. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 2009, 25(6):838-840. 10.1093/bioinformatics/btp049, 2654801, 19188191.
9. Hur J, Sullivan KA, Schuyler AD, Hong Y, Pande M, States DJ, Jagadish HV, Feldman EL. Literature-based discovery of diabetes- and ROS-related targets. BMC Medical Genomics 2010, 3:49. 10.1186/1755-8794-3-49, 2988702, 20979611.
10. Xiang Z, Zheng W, He Y. BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics 2006, 7:347. 10.1186/1471-2105-7-347, 1539029, 16842628.
11. Xiang Z, Todd T, Ku KP, Kovacic BL, Larson CB, Chen F, Hodges AP, Tian Y, Olenzek EA, Zhao B, et al. VIOLIN: vaccine investigation and online information network. Nucleic acids research 2008, (36 Database):D923-928.
12. He Y, Xiang Z. Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN. Immunome Res 2010, 6(Suppl 1):S5. 10.1186/1745-7580-6-S1-S5, 2981881, 21067547.
13. Morgan A, Lu Z, Wang X, Cohen A, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, et al. Overview of BioCreative II gene normalization. Genome Biology 2008, 9(Suppl 2):S3. 10.1186/gb-2008-9-s2-s3, 2559987, 18834494.
14. Crasta OR, Folkerts O, Fei Z, Mane SP, Evans C, Martino-Catt S, Bricker B, Yu G, Du L, Sobral BW. Genome sequence of Brucella abortus vaccine strain S19 compared to virulent strains yields candidate virulence genes. PLoS One 2008, 3(5):e2193. 10.1371/journal.pone.0002193, 2364660, 18478107.
15. Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, (34 Database):D363-368.
16. 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. 2910479, 20671958.
17. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, et al. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 2010, 26(13):1608-1615. 10.1093/bioinformatics/btq249, 2887053, 20472543.
18. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28(1):33-36. 10.1093/nar/28.1.33, 102395, 10592175.
19. Fisher RA. On the interpretation of χ2 from contingency tables, and the calculation of P. Journal of the Royal Statistical Society 1922, 85(1):87-94.
20. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
21. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255. 10.1038/nbt1346, 2814061, 17989687.
22. Xiang Z, Tian Y, He Y. PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol 2007, 8(7):R150. 10.1186/gb-2007-8-7-r150, 2323235, 17663773.
23. Chalker AF, Lupas A, Ingraham K, So CY, Lunsford RD, Li T, Bryant A, Holmes DJ, Marra A, Pearson SC, et al. Genetic characterization of gram-positive homologs of the XerCD site-specific recombinases. J Mol Microbiol Biotechnol 2000, 2(2):225-233.
24. Eskra L, Canavessi A, Carey M, Splitter G. Brucella abortus genes identified following constitutive growth and macrophage infection. Infect Immun 2001, 69(12):7736-7742. 10.1128/IAI.69.12.7736-7742.2001, 98869, 11705955.
25. Tran QT, Nawaz MS, Deck J, Foley S, Nguyen K, Cerniglia CE. Detection of type III secretion system virulence and mutations in gyrA and parC genes among quinolone-resistant strains of Pseudomonas aeruginosa isolated from imported shrimp. Foodborne Pathog Dis 2011, 8(3):451-453. 10.1089/fpd.2010.0687, 21117986.
26. Olsen SC, Boyle SM, Schurig GG, Sriranganathan NN. Immune responses and protection against experimental challenge after vaccination of bison with Brucella abortus strain RB51 or RB51 overexpressing superoxide dismutase and glycosyltransferase genes. Clin Vaccine Immunol 2009, 16(4):535-540. 10.1128/CVI.00419-08, 2668271, 19176693.
27. Winter AJ, Schurig GG, Boyle SM, Sriranganathan N, Bevins JS, Enright FM, Elzer PH, Kopec JD. Protection of BALB/c mice against homologous and heterologous species of Brucella by rough strain vaccines derived from Brucella melitensis and Brucella suis biovar 4. Am J Vet Res 1996, 57(5):677-683.
28. Doms A, Schroeder M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 2005, (33 Web Server):W783-786.
29. Vanteru BC, Shaik JS, Yeasin M. Semantically linking and browsing PubMed abstracts with gene ontology. BMC Genomics 2008, 9(Suppl 1):S10. 10.1186/1471-2164-9-S1-S10, 2559874, 18831775.
30. Dietze H, Schroeder M. GoWeb: a semantic search engine for the life science web. BMC Bioinformatics 2009, 10(Suppl 10):S7. 10.1186/1471-2105-10-S10-S7, 2788358, 19958517.
31. Muller HM, Kenny EE, Sternberg PW. Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2004, 2(11):e309. 10.1371/journal.pbio.0020309, 517822, 15383839.
32. Morgan XC, Ni S, Miranker DP, Iyer VR. Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining. BMC Bioinformatics 2007, 8:445. 10.1186/1471-2105-8-445, 2211755, 18005433.
33. Ananiadou S, Pyysalo S, Tsujii J, Kell DB. Event extraction for systems biology by text mining the literature. Trends Biotechnol 2010, 28(7):381-390. 10.1016/j.tibtech.2010.04.005, 20570001.
34. Faro A, Giordano D, Spampinato C. Combining literature text mining with microarray data: advances for system biology modeling. Briefings in bioinformatics 2011,
35. Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y. Bayesian network expansion identifies new ROS and biofilm regulators. PLoS One 2010, 5(3):e9513. 10.1371/journal.pone.0009513, 2831072, 20209085.
36. Krallinger M, Erhardt RA, Valencia A. Text-mining approaches in molecular biology and biomedicine. Drug discovery today 2005, 10(6):439-445. 10.1016/S1359-6446(05)03376-3, 15808823.
37. Ozgur A, Xiang Z, Radev DR, He Y. Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. J Biomed Biotechnol 2010, 2010:426479. 2896678, 20625487.
38. Ozgur A, Xiang Z, Radev DR, He Y. Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics 2011, 2(Suppl 2):S8. 10.1186/2041-1480-2-S2-S8, 3102897, 21624163.