Identifying plausible adverse drug reactions using knowledge extracted from the literature

Edwards, 2000, Adverse drug reactions: definitions, diagnosis, and management, Lancet, 356, 1255, 10.1016/S0140-6736(00)02799-9 Lazarou, 1998, Incidence of adverse drug reactions in hospitalized patients, JAMA: J Amer Med Assoc, 279, 1200, 10.1001/jama.279.15.1200 Hamilton, 1998, Frequency of hospitalization after exposure to known drug–drug interactions in a medicaid population, Pharmacother: J Human Pharmacol Drug Ther, 18, 1112 Baker, 2004, The Canadian adverse events study: the incidence of adverse events among hospital patients in Canada, Can Med Assoc J, 170, 1678, 10.1503/cmaj.1040498 Bourgeois, 2009, Pediatric adverse drug events in the outpatient setting: an 11-year national analysis, Pediatrics, 124, e744, 10.1542/peds.2008-3505 DiMasi, 2003, The price of innovation: new estimates of drug development costs, J Health Econ, 22, 151, 10.1016/S0167-6296(02)00126-1 Rawlins, 1988, Spontaneous reporting of adverse drug reactions. I: The data, Brit J Clin Pharmacol, 26, 1, 10.1111/j.1365-2125.1988.tb03356.x Rawlins, 1988, Spontaneous reporting of adverse drug reactions. II:, Uses, Brit J Clin Pharmacol, 26, 7, 10.1111/j.1365-2125.1988.tb03357.x Van Puijenbroek, 2003, Application of quantitative signal detection in the Dutch spontaneous reporting system for adverse drug reactions, Drug Saf, 26, 293, 10.2165/00002018-200326050-00001 Hasford, 2002, Physicians’ knowledge and attitudes regarding the spontaneous reporting system for adverse drug reactions, J Clin Epidemiol, 55, 945, 10.1016/S0895-4356(02)00450-X Alvarez-Requejo, 1998, Under-reporting of adverse drug reactions estimate based on a spontaneous reporting scheme and a sentinel system, Europ J Clin Pharmacol, 54, 483, 10.1007/s002280050498 Wang, 2009, Active computerized pharmacovigilance using natural language processing, statistics, and electronic health records: a feasibility study, J Amer Med Info Assoc, 16, 328, 10.1197/jamia.M3028 Trifirò, 2009, Data mining on electronic health record databases for signal detection in pharmacovigilance: which events to monitor?, Pharmacoepidemiol Drug Saf, 18, 1176, 10.1002/pds.1836 Haerian, 2012, Detection of pharmacovigilance-related adverse events using electronic health records and automated methods, Clin Pharmacol Ther, 92, 228, 10.1038/clpt.2012.54 Harpaz, 2013, Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions, J Amer Med Info Assoc, 20, 413, 10.1136/amiajnl-2012-000930 Friedman, 2009, Discovering novel adverse drug events using natural language processing and mining of the electronic health record, vol. 5651, 1 Oliveira, 2013, The EU-ADR web platform: delivering advanced pharmacovigilance tools, Pharmacoepidemiol Drug Saf, 22, 459, 10.1002/pds.3375 Deftereos, 2011, Drug repurposing and adverse event prediction using high-throughput literature analysis, Wiley Interdisciplinary Rev: Systems Biol Med, 3, 323 Bauer-Mehren, 2012, Automatic filtering and substantiation of drug safety signals, PLoS Comput Biol, 8, e1002457, 10.1371/journal.pcbi.1002457 Shetty, 2011, Using information mining of the medical literature to improve drug safety, J Amer Med Info Assoc, 18, 668, 10.1136/amiajnl-2011-000096 Merck, Merck announces voluntary worldwide withdrawal of VIOXX; 2004. <http://www.merck.com/newsroom/vioxx/pdf/vioxx_press_release_final.pdf>. EMA. European medicines agency recommends suspension of Avandia, Avandamet and Avaglim, Press release; 2010. Ye, 2011, Challenges in drug discovery for thiazolidinedione substitute, Acta Pharmaceut Sinica B, 1, 137, 10.1016/j.apsb.2011.06.011 Blind, 2010, Rosiglitazone: a European regulatory perspective, Diabetologia, 54, 213, 10.1007/s00125-010-1992-5 Anderson, 2011, Correlation versus Causation? Pharmacovigilance of the analgesic flupirtine exemplifies the need for refined spontaneous ADR reporting, PLoS ONE, 6, e25221, 10.1371/journal.pone.0025221 WHO. Pharmacovigilance; 2010. <http://www.who.int/medicines/areas/quality_safety/safety_efficacy/pharmvigi/en/index.html>. Ahmad, 2003, Adverse drug event monitoring at the food and drug administration, J Gener Intern Med, 18, 57, 10.1046/j.1525-1497.2003.20130.x Kessler, 1993, Introducing MEDWatch: a new approach to reporting medication and device adverse effects and product problems, JAMA: J Amer Med Assoc, 269, 2765, 10.1001/jama.1993.03500210065033 Wysowski, 2005, Adverse drug event surveillance and drug withdrawals in the United States, 1969–2002: the importance of reporting suspected reactions, Arch Intern Med, 165, 1363, 10.1001/archinte.165.12.1363 Edwards, 1992, The WHO Database – I, Drug Info J, 26, 477, 10.1177/009286159202600403 Bate A. The use of Bayesian confidence propagation neural network in pharmacovigilance. Dissertation, Umea˚ University; 2003. Edwards, 1994, Harmonisation in pharmacovigilance, Drug Saf, 10, 93, 10.2165/00002018-199410020-00001 Collins, 2011, Reengineering translational science: the time is right, Sci Transl Med, 3, 90cm17, 10.1126/scitranslmed.3002747 Bate, 1998, A Bayesian neural network method for adverse drug reaction signal generation, Europ J Clin Pharmacol, 54, 315, 10.1007/s002280050466 Lindquist, 1999, From association to alert – a revised approach to international signal analysis, Pharmacoepidemiol Drug Saf, 8, S15, 10.1002/(SICI)1099-1557(199904)8:1+<S15::AID-PDS402>3.3.CO;2-2 Noren, 2006, Extending the methods used to screen the WHO drug safety database towards analysis of complex associations and improved accuracy for rare events, Statist Med, 25, 3740, 10.1002/sim.2473 Lindquist, 2000, A retrospective evaluation of a data mining approach to aid finding new adverse drug reaction signals in the WHO international database, Drug Saf, 23, 533, 10.2165/00002018-200023060-00004 DuMouchel, 1999, Bayesian data mining in large frequency tables, with an application to the FDA spontaneous reporting system, Amer Statist, 53, 177 DuMouchel, 2001, Empirical Bayes screening for multi-item associations, 67 Shakir, 2002, Causal association in pharmacovigilance and pharmacoepidemiology: thoughts on the application of the Austin Bradford-Hill criteria, Drug Saf, 25, 467, 10.2165/00002018-200225060-00012 Hill, 1965, The environment and disease: association or causation?, Proceed Roy Society Med, 58, 295, 10.1177/003591576505800503 Doll, 1994, Austin Bradford Hill. 8 July 1897–18 April 1991, Biogr Mem Fellows Roy Society, 40, 128, 10.1098/rsbm.1994.0032 Ward, 2009, The role of causal criteria in causal inferences: Bradford Hill's “aspects of association”, Epidemiol Perspect Innov, 6, 2, 10.1186/1742-5573-6-2 Kleinberg, 2011, A review of causal inference for biomedical informatics, J Biomed Info, 44, 1102, 10.1016/j.jbi.2011.07.001 Perrio, 2007, Application of the Bradford Hill criteria to assess the causality of cisapride-induced arrhythmia: a model for assessing causal association in pharmacovigilance, Drug Saf, 30, 333, 10.2165/00002018-200730040-00006 Swanson, 1986, Undiscovered public knowledge, Libr Quart, 103, 10.1086/601720 Swanson, 1987, Two medical literatures that are logically but not bibliographically connected, J Amer Society Info Sci, 38, 228, 10.1002/(SICI)1097-4571(198707)38:4<228::AID-ASI2>3.0.CO;2-G Weeber, 2001, Using concepts in literature-based discovery: simulating Swanson’s Raynaud-fish oil and migraine–magnesium discoveries, J Amer Society Info Sci Tech, 52, 548, 10.1002/asi.1104 Bruza, 2008 Swanson, 1986, Fish oil, Raynaud’s syndrome, and undiscovered public knowledge, Perspect Biol Med, 30, 7, 10.1353/pbm.1986.0087 Swanson, 1988, Migraine and magnesium: eleven neglected connections, Perspect Biol Med, 31, 526, 10.1353/pbm.1988.0009 Smalheiser, 1996, Linking estrogen to Alzheimer’s disease: an informatics approach, Neurology, 47, 809, 10.1212/WNL.47.3.809 Srinivasan P, Rindflesch TC. Exploring text mining from MEDLINE. In: Proceedings of the AMIA symposium; 2002. p. 722–6. Hristovski D, Friedman C, Rindflesch TC, Peterlin B. Exploiting semantic relations for literature-based discovery. In: AMIA annual symposium proceeding, vol. 2006; 2006. p. 349–53. Yetisgen-Yildiz, 2006, Using statistical and knowledge-based approaches for literature-based discovery, J Biomed Info, 39, 600, 10.1016/j.jbi.2005.11.010 Sehgal, 2008, Analyzing LBD methods using a general framework, 75 Yetisgen-Yildiz, 2009, A new evaluation methodology for literature-based discovery systems, J Biomed Info, 42, 633, 10.1016/j.jbi.2008.12.001 Rindflesch, 2003, The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text, J Biomed Info, 36, 462, 10.1016/j.jbi.2003.11.003 Chen, 2004, Extracting phenotypic information from the literature via natural language processing, Stud Health Tech Info, 107, 758 Hristovski, 2008, Literature-based knowledge discovery using natural language processing, 133, 10.1007/978-3-540-68690-3_9 Ahlers CB, Hristovski D, Kilicoglu H, Rindflesch TC. Using the literature-based discovery paradigm to investigate drug mechanisms. In: AMIA, Annual Symposium Proceedings, vol. 2007; 2007. p. 6–10. Hristovski D, Burgun-Parenthoine A, Avillach P, Rindflesch TC. Towards using literature-based discovery to explain drug adverse effects. In: Quality of life through quality of information, MIE2012; 2012a. Hristovski D, Burgun-Parenthoine A, Avillach P, Rindflesch TC. Using literature-based discovery to explain drug adverse effects. In: AMIA, annual symposium proceedings, vol. 1779; 2012b. Aronson AR. Effective mapping of biomedical text to the UMLS metathesaurus: the MetaMap program. In: Proceedings of the AMIA symposium; 2001. p. 17–21. Aronson, 2010, An overview of MetaMap: historical perspective and recent advances, J Amer Med Info Assoc, 17, 229, 10.1136/jamia.2009.002733 Rindflesch, 2005, Semantic interpretation for the biomedical research literature, 399, 10.1007/0-387-25739-X_14 Aronson AR, Rindflesch TC. Semantic knowledge representation project. A report to the Board of Scientific Counselors; 1998. Rindflesch, 2002, Semantic processing for enhanced access to biomedical knowledge, Real World Semantic Web Appl, 157 Kilicoglu H, Fiszman M, Rosemblat G, Marimpietri S, Rindflesch TC. Arguments of nominals in semantic interpretation of biomedical text. In: Proceedings of the 2010 workshop on biomedical natural language processing; 2010. p. 46–54. Lindsay, 1999, Literature-based discovery by lexical statistics, J Amer Society Info Sci, 50, 574, 10.1002/(SICI)1097-4571(1999)50:7<574::AID-ASI3>3.0.CO;2-Q Cohen, 2009, Empirical distributional semantics: methods and biomedical applications, J Biomed Info, 42, 390, 10.1016/j.jbi.2009.02.002 Cole, 2005, A bare bones approach to literature-based discovery: an analysis of the Raynaud’s/fish-oil and migraine–magnesium discoveries in semantic space, vol. 3735, 84 Gordon, 1998, Using latent semantic indexing for literature based discovery, J Amer Society Info Sci, 49, 674, 10.1002/(SICI)1097-4571(199806)49:8<674::AID-ASI2>3.0.CO;2-T Cohen, 2010, Reflective random indexing and indirect inference: a scalable method for discovery of implicit connections, J Biomed Info, 43, 240, 10.1016/j.jbi.2009.09.003 Kanerva P, Kristofersson J, Holst A. Random indexing of text samples for latent semantic analysis. In: Proceedings of the 22nd annual conference of the cognitive science society, vol. 1036; 2000. p. 1036–7. Kanerva P. What we mean when we say “What’s, the dollar of mexico?: prototypes and mapping in concept space”. In: Proc AAAI, fall symp on quantum informatics for cognitive, social, and semantic processes; 2010. Cohen, 2012, Discovering discovery patterns with predication-based semantic indexing, J Biomed Info, 45, 1049, 10.1016/j.jbi.2012.07.003 Landauer, 1997, A solution to Plato’s problem: the latent semantic analysis theory of acquisition, induction, and representation of knowledge, Psych Rev, 104, 211, 10.1037/0033-295X.104.2.211 Kuhn, 2010, A side effect resource to capture phenotypic effects of drugs, Mol Systems Biol, 6, 343, 10.1038/msb.2009.98 U.S. National Library of Medicine, National Institutes of Health, UMLS Terminology Services (UTS) API 2.0; 2012. <http://uts.nlm.nih.gov/metathesaurus.html>. Wei, 2013, Development and evaluation of an ensemble resource linking medications to their indications, J Amer Med Info Assoc, 20, 954, 10.1136/amiajnl-2012-001431 Kanerva, 2009, Hyperdimensional computing: an introduction to computing in distributed representation with high-dimensional random vectors, Cognitive Computat, 1, 139, 10.1007/s12559-009-9009-8 Widdows, 2012, Real, complex, and binary semantic vectors, 24 Kanerva, 1994, The spatter code for encoding concepts at many levels, 226 Plate, 1995, Holographic reduced representations, IEEE Trans Neural Networks, 6, 623, 10.1109/72.377968 Kanerva, 1996, Binary spatter-coding of ordered K-tuples, 869 Gayler RW. Vector symbolic architectures answer Jackendoff’s challenges for cognitive neuroscience. arXiv preprint cs/0412059. Wahle, 2012, Deterministic binary vectors for efficient automated indexing of MEDLINE/PubMed abstracts, vol. 2012 Dumais, 1991, Improving the retrieval of information from external sources, Behav Res Methods Instruments Computer, 23, 229, 10.3758/BF03203370 Cohen T, Widdows D, Schvaneveldt RW, Rindflesch TC. Discovery at a distance: farther journeys in predication space. In: Bioinformatics and biomedicine workshops (BIBMW), 2012 IEEE international conference on; 2012b. p. 218–25. Birkhoff, 1936, The logic of quantum mechanics, Ann Math, 823, 10.2307/1968621 Widdows, 2003, Word vectors and quantum logic: experiments with negation and disjunction, Math Lang, 8 Cohen, 2012, Many paths lead to discovery: analogical retrieval of cancer therapies, 90 Golub, 2012, vol. 3 National Center for Biotechnology Information, U.S. National Library of Medicine 8600 Rockville Pike, Bethesda MD, 20894 Usa, Metathesaurus – Rich Release Format (RRF); 2009. <http://www.ncbi.nlm.nih.gov/books/NBK9685/>. U.S. National Library of Medicine, National Institutes of Health, RxNorm API; 2013. <http://rxnav.nlm.nih.gov/RxNormAPI.html>. Salton, 1983, Extended Boolean information retrieval, Communications ACM, 26, 1022, 10.1145/182.358466 Manning, 2008, vol. 1 Davis J, Goadrich M. The relationship between precision–recall and ROC curves. In: Proceedings of the 23rd international conference on Machine learning; 2006. p. 233–40. Akbani, 2004, Applying support vector machines to imbalanced datasets, 39 Liu, 2012, Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs, J Amer Med Info Assoc, 19, e28, 10.1136/amiajnl-2011-000699 Hamblin, 2009, PPARs and the cardiovascular system, Antioxidants Redox Signaling, 11, 1415, 10.1089/ars.2008.2280 Cheung, 2010, Behind the rosiglitazone controversy, Exper Rev Clin Pharmacol, 3, 723, 10.1586/ecp.10.126 Lygate, 2003, The PPARγ-activator rosiglitazone does not alter remodeling but increases mortality in rats post-myocardial infarction, Cardiov Res, 58, 632, 10.1016/S0008-6363(03)00289-X Shah, 2010, Responding to an FDA, warning – geographic variation in the use of rosiglitazone, New England J Med, 363, 2081, 10.1056/NEJMp1011042 Nissen, 2007, Effect of rosiglitazone on the risk of myocardial infarction and death from cardiovascular causes, New England J Med, 356, 2457, 10.1056/NEJMoa072761 Berthet, 2011, Drug safety of rosiglitazone and pioglitazone in France: a study using the French PharmacoVigilance database, BMC Pharmacol Toxicol, 11, 5 U.S. Food and Drug Administration. Press announcements – FDA, requires removal of certain restrictions on the diabetes drug Avandia; 2013. <http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/ucm376516.htm>. Loke, 2011, Comparative cardiovascular effects of thiazolidinediones: systematic review and meta-analysis of observational studies, BMJ: Brit Med J, 342, d1309, 10.1136/bmj.d1309 Goldberg, 2005, A comparison of lipid and glycemic effects of pioglitazone and rosiglitazone in patients with type 2 diabetes and dyslipidemia, Diabetes Care, 28, 1547, 10.2337/diacare.28.7.1547 Khanderia, 2008, Thiazolidinediones in type 2 diabetes: a cardiology perspective, Ann Pharmacother, 42, 1466, 10.1345/aph.1K666 Bourg, 2012, Rosiglitazone, myocardial ischemic risk, and recent regulatory actions, Ann Pharmacother, 46, 282, 10.1345/aph.1Q400 Bodenreider, 2003, Exploring semantic groups through visual approaches, J Biomed Info, 36, 414, 10.1016/j.jbi.2003.11.002 Brackenridge, 2009, Effects of rosiglitazone and pioglitazone on lipoprotein metabolism in patients with Type 2 diabetes and normal lipids, Diabetic Med: J Brit Diabetic Assoc, 26, 532, 10.1111/j.1464-5491.2009.02729.x Sarafidis, 2005, The effect of rosiglitazone on novel atherosclerotic risk factors in patients with type 2 diabetes mellitus and hypertension. An open-label observational study, Meta: Clin Exp, 54, 1236, 10.1016/j.metabol.2005.04.010 Vessby, 1982, Diverging effects of cholestyramine on apolipoprotein B and lipoprotein Lp(a). A dose-response study of the effects of cholestyramine in hypercholesterolaemia, Atherosclerosis, 44, 61, 10.1016/0021-9150(82)90053-3 van Wijk, 2006, Rosiglitazone modulates fasting and post-prandial paraoxonase 1 activity in type 2 diabetic patients, Clin Exper Pharmacol Physiol, 33, 1134, 10.1111/j.1440-1681.2006.04505.x Gupta, 2011, Paraoxonase 1 (PON1), polymorphisms, haplotypes and activity in predicting CAD, risk in North-West Indian Punjabis, PLoS One, 6, e17805, 10.1371/journal.pone.0017805 Yoshida, 2010, Association of genetic variants with myocardial infarction in Japanese individuals with different lipid profiles, Int J Mol Med, 25, 607 Phillips, 1977, Relationship between serum sex hormones and glucose, insulin and lipid abnormalities in men with myocardial infarction, Proceed Natl Acad Sci, 74, 1729, 10.1073/pnas.74.4.1729 Kuller, 2002, Nuclear magnetic resonance spectroscopy of lipoproteins and risk of coronary heart disease in the cardiovascular health study, Arterioscler Throm Vas Biol, 22, 1175, 10.1161/01.ATV.0000022015.97341.3A Friis-Moller, 2003, Combination antiretroviral therapy and the risk of myocardial infarction, New England J Med, 349, 1993, 10.1056/NEJMoa030218 Lekhal, 2010, Tissue factor-induced thrombin generation in the fasting and postprandial state among elderly survivors of myocardial infarction, Thromb Res, 126, 353, 10.1016/j.thromres.2009.10.003 De Caterina, 2011, Strong association of the APOA5-1131T>C gene variant and early-onset acute myocardial infarction, Atherosclerosis, 214, 397, 10.1016/j.atherosclerosis.2010.11.011 Chao, 2000, Adipose tissue is required for the antidiabetic, but not for the hypolipidemic, effect of thiazolidinediones, J Clin Invest, 106, 1221, 10.1172/JCI11245 Nadeau, 2007, Discordance between intramuscular triglyceride and insulin sensitivity in skeletal muscle of Zucker diabetic rats after treatment with fenofibrate and rosiglitazone, Diabetes Obe Metab, 9, 714, 10.1111/j.1463-1326.2006.00696.x Suzuki, 2013, Characterization of actions of octanoate on porcine preadipocytes and adipocytes differentiated in vitro, Biochem Biophys Res Communications, 432, 92, 10.1016/j.bbrc.2013.01.080 Im MJ, Hoopes JE. Increases in dihydronicotinamide adenine dinucleotide (NADH) content and alpha-glycerophosphate dehydrogenase activity in epidermal wound healing. In: Proceedings of the society for experimental biology and medicine. Society for Experimental Biology and Medicine (New York, NY), vol. 173, issue no. 1; 1983. p. 17–20. Johnson, 2000, Ligand-induced stabilization of PPARÎş monitored by NMR spectroscopy: implications for nuclear receptor activation, J Mol Biol, 298, 187, 10.1006/jmbi.2000.3636 Risérus, 2005, Rosiglitazone increases indexes of stearoyl-CoA desaturase activity in humans link to insulin sensitization and the role of dominant-negative mutation in peroxisome proliferator-activated receptor-γ, Diabetes, 54, 1379, 10.2337/diabetes.54.5.1379 Otake, 2010, 4-tetrahydroisoquinoline-3-carboxylic acids: peroxisome proliferator-activated receptor α/γ dual agonists with protein-tyrosine phosphatase 1B inhibitory activity, Chem Pharmaceut Bull, 59, 1233, 10.1248/cpb.59.1233 Egerod, 2009, PPARα and PPARγ coactivation rapidly induces Egr-1 in the nuclei of the dorsal and ventral urinary bladder and kidney pelvis urothelium of rats, Toxicol Pathol, 37, 947, 10.1177/0192623309351723 Fliegner, 2008, Up-regulation of PPARγ in myocardial infarction, Europ J Heart Fail, 10, 30, 10.1016/j.ejheart.2007.11.005 Lee, 2003, Minireview: lipid metabolism, metabolic diseases, and peroxisome proliferator-activated receptors, Endocrinology, 144, 2201, 10.1210/en.2003-0288 Gao, 2007, Rosiglitazone inhibits angiotensin II-induced CTGF expression in vascular smooth muscle cells – role of PPAR-γ in vascular fibrosis, Biochem Pharmacol, 73, 185, 10.1016/j.bcp.2006.09.019 Tzameli, 2004, Regulated production of a peroxisome proliferator-activated receptor-γ ligand during an early phase of adipocyte differentiation in 3T3-L1 adipocytes, J Biol Chem, 279, 36093, 10.1074/jbc.M405346200 Tsukahara, 2005, Different residues mediate recognition of 1-O-oleyllysophosphatidic acid and rosiglitazone in the ligand binding domain of peroxisome proliferator-activated receptor, J Biol Chem, 281, 3398, 10.1074/jbc.M510843200 Kim, 2006, Antiangiogenic effect of rosiglitazone is mediated via peroxisome proliferator-activated receptor-activated Maxi-K channel opening in human umbilical vein endothelial cells, J Biol Chem, 281, 13503, 10.1074/jbc.M510357200 Muhlhausler, 2007, Increased maternal nutrition increases leptin expression in perirenal and subcutaneous adipose tissue in the postnatal lamb, Endocrinology, 148, 6157, 10.1210/en.2007-0770 Ding, 2003, Insulin-dependent adipogenesis in stromal ST2 cells derived from murine bone marrow, Biosci Biotech Biochem, 67, 314, 10.1271/bbb.67.314 Jung, 2005, The effects of rosiglitazone and metformin on the plasma concentrations of resistin in patients with type 2 diabetes mellitus, Metab: Clin Exper, 54, 314, 10.1016/j.metabol.2004.05.019 Patel, 2003, Resistin is expressed in human macrophages and directly regulated by PPAR gamma activators, Biochem Biophys Res Communications, 300, 472, 10.1016/S0006-291X(02)02841-3 Boyle, 2002, Effects of pioglitazone and rosiglitazone on blood lipid levels and glycemic control in patients with type 2 diabetes mellitus: a retrospective review of randomly selected medical records, Clin Ther, 24, 378, 10.1016/S0149-2918(02)85040-8 Chen, 2009, PubChem as a source of polypharmacology, J Chem Info Model, 49, 2044, 10.1021/ci9001876 Pauwels, 2011, Predicting drug side-effect profiles: a chemical fragment-based approach, BMC Bioinfo, 12, 169, 10.1186/1471-2105-12-169 Knox, 2011, DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs, Nucl Acids Res, 39, D1035, 10.1093/nar/gkq1126 Kanehisa, 2000, KEGG: kyoto encyclopedia of genes and genomes, Nucl Acids Res, 28, 27, 10.1093/nar/28.1.27 Huang, 2011, Predicting adverse side effects of drugs, BMC Genom, 12, S11, 10.1186/1471-2164-12-S5-S11 Tatonetti, 2012, Data-driven prediction of drug effects and interactions, Sci Transl Med, 4, 125ra31, 10.1126/scitranslmed.3003377 Kuhn, 2013, Systematic identification of proteins that elicit drug side effects, Mol Syst Biol, 9, 10.1038/msb.2013.10 Kilicoglu H, Fiszman M, Rodriguez A, Shin D, Ripple A, Rindflesch TC. Semantic MEDLINE: a web application for managing the results of PubMed Searches. In: Proceedings of the third international symposium for semantic mining in biomedicine, vol. 2008; 2008. p. 69–76. Ahlers CB, Fiszman M, Demner-Fushman D, Lang F-M, Rindflesch TC. Extracting semantic predications from Medline citations for pharmacogenomics. In: Pac symp biocomput, vol. 12; 2006. p. 209–20. U.S. Food and Drug Administration, 2007 – FDA Adds Boxed Warning for Heart-related Risks to Anti-Diabetes Drug Avandia; 2007-11-14. <http://www.fda.gov/NewsEvents/Newsroom/PressAnnouncements/2007/ucm109026.htm>. Mahaffey, 2013, Results of a reevaluation of cardiovascular outcomes in the RECORD trial, Amer Heart J, 166, 240, 10.1016/j.ahj.2013.05.004 Lopes, 2013, Methodology of a reevaluation of cardiovascular outcomes in the RECORD, trial: study design and conduct, Amer Heart J, 166, 10.1016/j.ahj.2013.05.005 Thompson D. FDA to lift restrictions on diabetes drug Avandia; 2013. <http://health.usnews.com/health-news/news/articles/2013/11/25/fda-to-lift-restrictions-on-diabetes-drug-avandia>. Herskovic JR, Bernstam EV. Using incomplete citation data for MEDLINE, results ranking. In: AMIA, annual symposium proceedings, vol. 2005; 2005. p. 316–20.