OAE: The Ontology of Adverse Events

Journal of Biomedical Semantics

Volumn 5, Issue 1, 2014, Pages

  He, Yongqun ^a   Sarntivijai, Sirarat ^a,b   Lin, Yu ^a   Xiang, Zuoshuang ^a   Guo, Abra ^a   Zhang, Shelley ^a   Jagannathan, Desikan ^a   Toldo, Luca ^c   Tao, Cui ^d   Smith, Barry ^e  

^a UNIVERSITY OF MICHIGAN   (United States)

^b CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

^c MERCK KGAA   (Germany)

^d UNIVERSITY OF TEXAS   (United States)

^e UNIVERSITY AT BUFFALO   (United States)

Author keywords

Adverse event; Design pattern; Drug; Drug adverse event; OAE; Ontology; Ontology of adverse events; Vaccine; Vaccine adverse event; VAERS

Indexed keywords

EID: 84927925404     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-5-29     Document Type: Article

References (49)

1. Scheuermann RH, Ceusters W, Smith B. Toward an Ontological Treatment of Disease and Diagnosis. Proceedings of the 2009 AMIA Summit on Translational Bioinformatics 2009, 116-120.
2. Varricchio F, Iskander J, Destefano F, Ball R, Pless R, Braun MM, Chen RT. Understanding vaccine safety information from the Vaccine Adverse Event Reporting System. Pediatr Infect Dis J 2004, 23(4):287-294.
3. FDA U FDA Adverse Event Reporting System (FAERS) (formerly AERS). 2013, URL: http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/default.htm, accessed on June 21, 2013, FDA U.
4. Brown EG, Wood L, Wood S. The medical dictionary for regulatory activities (MedDRA). Drug Saf 1999, 20(2):109-117.
5. NCI Common Terminology Criteria for Adverse Events (CTCAE). http://ctep.cancer.gov/reporting/ctc.html. Accessed on May 15, 2013.
6. WHO's Adverse Reaction Terminology (WHO-ART). http://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/WHO/. Accessed on March 17, 2013.
7. Brown EG. Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA). Drug Saf 2003, 26(3):145-158.
8. Sarntivijai S, Xiang Z, Shedden KA, Markel H, Omenn GS, Athey BD, He Y. Ontology-based combinatorial comparative analysis of adverse events associated with killed and live influenza vaccines. PLoS One 2012, 7(11):e49941.
9. He Y, Cowell L, Diehl AD, Mobley HL, Peters B, Ruttenberg A, Scheuermann RH, Brinkman RR, Courtot M, Mungall C, Xiang Z, Chen F, Todd T, Colby LA, Rush H, Whetzel T, Musen MA, Athey BD, Omenn GS, Smith B. VO: Vaccine Ontology. The 1st International Conference on Biomedical Ontology (ICBO-2009): July 24-26 2009 2009, Buffalo, NY, USA: Nature Precedings, http://precedings.nature.com/documents/3552/version/1.
10. Lin Y, He Y. Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses. J Biomed Semantics 2012, 3(1):17.
11. Ceusters W, Capolupo M, de Moor G, Devlies J, Smith B. An evolutionary approach to realism-based adverse event representations. Methods Inf Med 2011, 50(1):62-73.
12. He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. AEO: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO-2011): July 26-30 2011 2011, 309-315. Buffalo, NY, USA: CEUR Workshop Proceedings, http://ceur-ws.org/Vol-833/paper359.pdf.
13. Courtot M, Brinkman RR, Ruttenberg A. The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective. PLoS One 2014, 9(3):e92632.
14. Hur J, Ozgur A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. J Biomed Semantics 2012, 3(1):18.
15. Gurulingappa H, Mateen-Rajput A, Toldo L. Extraction of potential adverse drug events from medical case reports. J Biomed Semantics 2012, 3(1):15.
16. Gurulingappa H, Rajput AM, Roberts A, Fluck J, Hofmann-Apitius M, Toldo L. Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. J Biomed Inform 2012, 45(5):885-892.
17. Gurulingappa H, Toldo L, Rajput AM, Kors JA, Taweel A, Tayrouz Y. Automatic detection of adverse events to predict drug label changes using text and data mining techniques. Pharmacoepidemiol Drug Saf 2013, 22(11):1189-1194.
18. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255.
19. Courtot M, Goldfain A, He Y, Ruttenberg A. Adverse Event Representation Workshop. International Conference on Biomedical Ontologies 2011 (ICBO 2011) 2011; University at Buffalo, NY 2011, http://icbo.buffalo.edu/2011/workshop/adverse-events.
20. He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). J Biomed Semantics 2012, 3(1):12.
21. Tao C, He Y, Arabandi S. A 2013 Workshop: Vaccine and Drug Ontology Studies (VDOS 2013). J Biomed Semantics 2014, 5(1):16.
22. Zhou W, Pool V, Iskander JK, English-Bullard R, Ball R, Wise RP, Haber P, Pless RP, Mootrey G, Ellenberg SS, Braun MM, Chen RT. Surveillance for safety after immunization: Vaccine Adverse Event Reporting System (VAERS)-United States, 1991-2001. MMWR Surveill Summ 2003, 52(1):1-24.
23. Burnstead B, Furlan G. Unifying drug safety and clinical databases. Curr Drug Saf 2013, 8(1):56-62.
24. Smith B, Ceusters W. Ontological realism: A methodology for coordinated evolution of scientific ontologies. Appl Ontol 2010, 5:139-188.
25. Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Res Notes 2010, 3:175.
26. Grenon P, Smith B. SNAP and SPAN: Towards Dynamic Spatial Ontology. Spat Cogn Comput 2004, 4(1):69-103.
27. MacKenzie SH, Clark AC. Death by caspase dimerization. Adv Exp Med Biol 2012, 747:55-73.
28. Marcos E, Zhao B, He Y. The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines. J Biomed Semantics 2013, 4:40.
29. Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Uberon, an integrative multi-species anatomy ontology. Genome Biol 2012, 13(1):R5.
30. Rosse C, Mejino JL. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform 2003, 36(6):478-500.
31. NCBI Taxonomy ontology. http://www.obofoundry.org/cgi-bin/detail.cgi?id=ncbi_taxonomy. Accessed on March 17, 2013.
32. Naranjo CA, Busto U, Sellers EM, Sandor P, Ruiz I, Roberts EA, Janecek E, Domecq C, Greenblatt DJ. A method for estimating the probability of adverse drug reactions. Clin Pharmacol Ther 1981, 30(2):239-245.
33. Evans SJ, Waller PC, Davis S. Use of proportional reporting ratios (PRRs) for signal generation from spontaneous adverse drug reaction reports. Pharmacoepidemiol Drug Saf 2001, 10(6):483-486.
34. Heaney RP, Kopecky S, Maki KC, Hathcock J, Mackay D, Wallace TC. A review of calcium supplements and cardiovascular disease risk. Advances in nutrition 2012, 3(6):763-771.
35. Pearl J. Causality (2nd edition) 2009, Cambridge University Press.
36. Tao C, He Y, Yang H, Gregory PA, Chute CG. Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis. J Biomed Semantics 2012, 3(1):13.
37. Lin Y, He Y. The Ontology of Genetic Susceptibility Factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events. J Biomed Semantics 2014, 5:19.
38. The protege ontology editor. http://protege.stanford.edu/.
39. Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Annu Symp Proc 2010, 2010:787-791.
40. U.S. Food and Drug Administration Vaccines Licensed for Immunization and Distribution in the US with Supporting Documents. URL: http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM093830.htm, accessed on April 3, 2013, U.S. Food and Drug Administration.
41. US FDA Afluria package insert information. URL: http://www.fda.gov/downloads/BiologicsBloodVaccines/Vaccines/ApprovedProducts/UCM263239.pdf. Accessed on April 18, 2014.
42. Vrethem M, Malmgren K, Lindh J. A patient with both narcolepsy and multiple sclerosis in association with Pandemrix vaccination. J Neurol Sci 2012, 321(1-2):89-91.
43. Reif DM, McKinney BA, Motsinger AA, Chanock SJ, Edwards KM, Rock MT, Moore JH, Crowe JE. Genetic basis for adverse events after smallpox vaccination. J Infect Dis 2008, 198(1):16-22.
44. He Y. Updates on the development of the Ontology of Adverse Events (OAE) and its applications. The 2012 Vaccine and Drug Oontology in the Study of Mechanism and Effect (VDOSME) workshop 2012, Graz, Austria, http://kr-med.org/icbofois2012/vdosme/docs/presentations/OAE_VDOSME2012_He.pdf.
45. Abernethy DR, Woodcock J, Lesko LJ. Pharmacological mechanism-based drug safety assessment and prediction. Clin Pharmacol Ther 2011, 89(6):793-797.
46. Bai JP, Abernethy DR. Systems pharmacology to predict drug toxicity: integration across levels of biological organization. Annu Rev Pharmacol Toxicol 2013, 53:451-473.
47. Sarntivijai S, Lin Y, Blair E, Burkhart KK, He Y, Omenn GS, Athey BD, Abernethy DR. The ontology representation of adverse events with composite symptoms: expanding Ontology of Adverse Events to describe drug-induced cardiotoxicity. American Society for Clinical Pharmacology and Therapeutics 2014 Annual Meeting (ASCPT-2014) 2014, Atlanta, Georgia, http://www.ascpt.org/Portals/8/docs/Meetings/2014%2020Annual%2020Meeting/Speaker%2020Presentations/Thursday/TKI_Sirarat%2020Sarntivijai.pdf.
48. Sarntivijai S, Hur J, Ozgur A, Burkhart KK, He Y, Omenn GS, Athey BD, Abernethy DR. Predicting gene interactions of tyrosine kinase inhibitor-induced cardiotoxicity with ontology of adverse events-assisted bioinformatics. American Society for Clinical Pharmacology and Therapeutics 2014 Annual Meeting (ASCPT-2014) 2014, Atlanta, Georgia.
49. Bousquet C, Henegar C, Louet AL, Degoulet P, Jaulent MC. Implementation of automated signal generation in pharmacovigilance using a knowledge-based approach. Int J Med Inform 2005, 74(7-8):563-571.