Development of a classification scheme for disease-related enzyme information

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Söhngen, Carola ^a   Chang, Antje ^a   Schomburg, Dietmar ^a  

^a TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; ARTIFICIAL INTELLIGENCE; DATA MINING; DIAGNOSIS; ENZYMES; LEARNING SYSTEMS;

AUTOMATIC SEARCHES; CLASSIFICATION SCHEME; DISEASE RELATED ENZYMES; ENTITY RECOGNITION; INFORMATION DATABASE; RELATION CLASSIFICATIONS; THERAPEUTIC APPLICATION; TWO-STEP PROCEDURE;

CLASSIFICATION (OF INFORMATION);

ARTICLE; ARTIFICIAL INTELLIGENCE; DATA MINING; DISEASES; ENZYMOLOGY; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MEDLINE; NEOPLASM; PROTEIN DATABASE;

ARTIFICIAL INTELLIGENCE; DATA MINING; DATABASES, PROTEIN; DISEASE; HIV INFECTIONS; HUMANS; NEOPLASMS; PUBMED;

EID: 79961145412     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-329     Document Type: Article

References (27)

1. Krallinger M, Leitner F, Valencia A. Analysis of biological processes and diseases using text mining approaches. Methods Mol Biol 2010, 593:341-382. 10.1007/978-1-60327-194-3_16, 19957157.
2. Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet 2006, 7:119-129. 10.1038/nrg1768, 16418747.
3. Krallinger M, Izarzugaza JMG, Rodriguez-Penagos C, Valencia A. Extraction of human kinase mutations from literature, databases and genotyping studies. BMC Bioinformatics 2009, 10(Suppl 8):S1. 10.1186/1471-2105-10-S8-S1, 20151484.
4. Yeniterzi S, Sezerman U. EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts. BMC Bioinformatics 2009, 10(Suppl 8):S2.. 2788353, 19958512.
5. Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004, 36:664. 10.1038/ng0704-664, 15226743.
6. Kim J-J, Pezik P, Rebholz-Schuhmann D. MedEvi: retrieving textual evidence of relations between biomedical concepts from Medline. Bioinformatics 2008, 24:1410-1412. 10.1093/bioinformatics/btn117, 2387223, 18400773.
7. Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2010,
8. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2010, 38:D5-16. 10.1093/nar/gkp967, 2808881, 19910364.
9. Germain DP. Fabry disease. Orphanet J Rare Dis 2010, 5:30. 10.1186/1750-1172-5-30, 3009617, 21092187.
10. Debouck C. The HIV-1 protease as a therapeutic target for AIDS. AIDS Res Hum Retroviruses 1992, 8:153-164. 10.1089/aid.1992.8.153, 1540403.
11. Saif MW, Alexander D, Wicox CM. Serum Alkaline Phosphatase Level as a Prognostic Tool in Colorectal Cancer: A Study of 105 patients. J Appl Res 2005, 5:88-95. 2741323, 19750205.
12. Dosaka-Akita H, Kinoshita I, Yamazaki K, Izumi H, Itoh T, Katoh H, Nishimura M, Matsuo K, Yamada Y, Kohno K. N-acetylgalactosaminyl transferase-3 is a potential new marker for non-small cell lung cancers. Br J Cancer 2002, 87:751-755. 10.1038/sj.bjc.6600536, 2364253, 12232759.
13. Hofmann O, Schomburg D. Concept-based annotation of enzyme classes. Bioinformatics 2005, 21:2059-2066. 10.1093/bioinformatics/bti284, 15661799.
14. Sewell W. MEDICAL SUBJECT HEADINGS IN MEDLARS. Bull Med Libr Assoc 1964, 52:164-170. 198088, 14119288.
15. Dumais S, Platt J, Heckerman D, Sahami M. Inductive learning algorithms and representations for text categorization. Proceedings of the seventh international conference on Information and knowledge management 1998, 148-155. Bethesda, Maryland, United States: ACM.
16. Joachims T. Making large-Scale SVM Learning Practical. Advances in Kernel Methods - Support Vector Learning 1999, 169-184. Cambridge, MA: MIT Press, Schölkopf B, Burges C, Smola A.
17. Jirapongsananuruk O, Niemela JE, Malech HL, Fleisher TA. CYBB mutation analysis in X-linked chronic granulomatous disease. Clin Immunol 2002, 104:73-76. 10.1006/clim.2002.5230, 12139950.
18. Scagliotti GV, Selvaggi G, Novello S, Hirsch FR. The biology of epidermal growth factor receptor in lung cancer. Clin Cancer Res 2004, 10:4227s-4232s. 10.1158/1078-0432.CCR-040007, 15217963.
19. Whitfield JB. Gamma glutamyl transferase. Crit Rev Clin Lab Sci 2001, 38:263-355. 10.1080/20014091084227, 11563810.
20. Saw S, Aw TC. Age-related reference intervals for free and total prostate-specific antigen in a Singaporean population. Pathology 2000, 32:245-249.
21. Yeh KC, Deutsch PJ, Haddix H, Hesney M, Hoagland V, Ju WD, Justice SJ, Osborne B, Sterrett AT, Stone JA, Woolf E, Waldman S. Single-dose pharmacokinetics of indinavir and the effect of food. Antimicrob Agents Chemother 1998, 42:332-338. 105409, 9527781.
22. Salton G, Wong A, Yang CS. A vector space model for automatic indexing. Commun ACM 1975, 18:613-620.
23. Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics 2005, 21:3940-3941. 10.1093/bioinformatics/bti623, 16096348.
24. Pastores GM. Recombinant glucocerebrosidase (imiglucerase) as a therapy for Gaucher disease. BioDrugs 2010, 24:41-47. 10.2165/11318540-000000000-00000, 20055531.
25. Perrone MG, Scilimati A, Simone L, Vitale P. Selective COX-1 inhibition: A therapeutic target to be reconsidered. Curr Med Chem 2010, 17:3769-3805. 10.2174/092986710793205408, 20858219.
26. Kwon KH, Barve A, Yu S, Huang M-T, Kong A-NT. Cancer chemoprevention by phytochemicals: potential molecular targets, biomarkers and animal models. Acta Pharmacol Sin 2007, 28:1409-1421. 10.1111/j.1745-7254.2007.00694.x, 17723174.
27. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, Tzur D, Gautam B, Hassanali M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 2008, 36:D901-906. 2238889, 18048412.