Systematic Drug Repurposing Through Text Mining

Methods in Molecular Biology

Volumn 1159, Issue , 2014, Pages 253-267

  Tari, Luis B ^a   Patel, Jagruti H ^a  

^a NONE

Author keywords

Alternative drug indications; Drug repositioning; Drug repurposing

Indexed keywords

DIPYRIDAMOLE; TAZAROTENE;

AMINO ACID SEQUENCE; ANGIOGENESIS; APOPTOSIS; ARTICLE; CELL PROLIFERATION; DATA MINING; DRUG INDICATION; DRUG REPOSITIONING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; LEARNING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; ANIMAL; BIBLIOGRAPHIC DATABASE; HUMAN; PROCEDURES;

ANIMALS; DATA MINING; DATABASES, BIBLIOGRAPHIC; DRUG REPOSITIONING; HUMANS;

EID: 84927558406     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0709-0_14     Document Type: Article

References (27)

1. DiMasi JA, Hansen RW, Grabowski HG (2003) The price of innovation: new estimates of drug development costs. J Health Econ 22:151-185. doi:10.1016/S0167-6296(02)00126-1
2. Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3:673-683. doi:10.1038/nrd1468
3. Ghofrani HA, Osterloh IH, Grimminger F (2006) Sildenafil: from angina to erectile dysfunction to pulmonary hypertension and beyond. Nat Rev Drug Discov 5:689-702. doi:10.1038/nrd2030
4. Dubus E, Ijjaali I, Barberan O, Petitet F (2009) Drug repositioning using in silico compound profiling. Future Med Chem 1:1723-1736. doi:10.4155/fmc.09.123
5. Yang L, Agarwal P (2011) Systematic drug repositioning based on clinical side-effects. PLoS One 6(12)
6. Duran-Frigola M, Aloy P (2012) Recycling side-effects into clinical markers for drug repositioning. Genome Med 4(1):3
7. Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ (2011) Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. Sci Transl Med 3:96ra76
8. Hurle MR, Yang L, Xie Q, Rajpal DK, Sanseau P, Agarwal P (2013) Computational drug repositioning: from data to therapeutics. Clin Pharmacol Ther 93(4):335-341
9. Deftereos SN, Andronis C, Friedla EJ, Persidis A, Persidis A (2011) Drug repurposing and adverse event prediction using high-throughput literature analysis. Wiley Interdiscip Rev Syst Biol Med 3:323-334. doi:10.1002?wsbm.147
10. Swanson DR (1990) Medical literature as a potential source of new knowledge. Bull Med Libr Assoc 78:29-37
11. Swanson DR (1986) Fish oil, Raynaud’s syndrome, and undiscovered public knowledge. Perspect Biol Med 30:7-18
12. Weeber M, Vos R, Klein H, DeJong-VanDen Berg LTW, Aronson AR et al (2003) Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide. J Am Med Inform Assoc 10:252-259. doi:10.1197/jamia.M1158
13. Yetisgen-Yildiz M, Pratt W (2006) Using statistical and knowledge-based approaches for literature-based discovery. J Biomed Inform 39:600-611. doi:10.1016/j.jbi.2005.11.010
14. Fu C, Jin G, Gao J, Zhu R, Ballesteros-Villagrana E, Wong ST (2013) DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies. Bioinformatics 29(14):1834-1836. doi:10.1093?bioinformatics/btt279
15. The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25-29
16. Knox C, Law V, Jewison T et al (2011) DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs. Nucleic Acids Res 39(Database issue):D1035-D1041
17. Klein TE, Chang JT, Cho MK, Easton KL, Fergerson R et al (2001) Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J 1:167-170
18. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A et al (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res 38:D525-D531. doi:10.1093/nar/gkp878
19. Tari L, Tu PH, Hakenberg J, Chen Y, Son TC et al (2010) Incremental information extraction using relational databases. IEEE Trans Knowledge Data Eng 24:86-99. doi:10.1109?TKDE.2010.214
20. Klein D, Manning CD (2003) Accurate unlexicalized parsing. Proceedings of the 41st Annual meeting on association for computational linguistics (ACL’03), Vol 1, pp 423-430. doi:10.3115/1075096.1075150
21. Leaman R, Gonzalez G (2008) BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput. pp 652-663
22. Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G (2008) Inter-species normalization of gene mentions with GNAT. Bioinformatics 24:i126-i132. doi:10.1093?bioinformatics/btn299
23. Gelfond M, Lifschitz V (1988) The stable model semantics for logic programming. In International symposium on logic programming, pp 1070-1080
24. Gelfond M, Lifschitz V (1991) Classical negation in logic programs and disjunctive databases. New Generation Computing 9:365-387
25. Baral C (2003) Knowledge representation, reasoning and declarative problem solving. Cambridge University Press, New York
26. Gebser M, Ostrowski M, Schaub T (2009) Constraint answer set solving. In Proceedings of the 25th International conference on logic programming (ICLP’09), Vol 5649, pp 235-249. doi:10.1007/978-3-642-02846-5
27. Tari L, Vo N, Liang S, Patel J, Baral C, Cai J (2012) Identifying novel drug indications through automated reasoning. PLoS One 7(7):e40946