PMID- 31074377 OWN - NLM STAT- MEDLINE DCOM- 20190705 LR - 20200225 IS - 1471-2105 (Electronic) IS - 1471-2105 (Linking) VI - 20 IP - Suppl 7 DP - 2019 May 1 TI - ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions. PG - 199 LID - 10.1186/s12859-019-2729-1 [doi] LID - 199 AB - BACKGROUND: Drug adverse events (AEs), or called adverse drug events (ADEs), are ranked one of the leading causes of mortality. The Ontology of Adverse Events (OAE) has been widely used for adverse event AE representation, standardization, and analysis. OAE-based ADE-specific ontologies, including ODNAE for drug-associated neuropathy-inducing AEs and OCVDAE for cardiovascular drug AEs, have also been developed and used. However, these ADE-specific ontologies do not consider the effects of other factors (e.g., age and drug-treated disease) on the outcomes of ADEs. With more ontological studies of ADEs, it is also critical to develop a general purpose ontology for representing ADEs for various types of drugs. RESULTS: Our survey of FDA drug package insert documents and other resources for 224 neuropathy-inducing drugs discovered that many drugs (e.g., sirolimus and linezolid) cause different AEs given patients' age or the diseases treated by the drugs. To logically represent the complex relations among drug, drug ingredient and mechanism of action, AE, age, disease, and other related factors, an ontology design pattern was developed and applied to generate a community-driven open-source Ontology of Drug Adverse Events (ODAE). The ODAE development follows the OBO Foundry ontology development principles (e.g., openness and collaboration). Built on a generalizable ODAE design pattern and extending the OAE and NDF-RT ontology, ODAE has represented various AEs associated with the over 200 neuropathy-inducing drugs given different age and disease conditions. ODAE is now deposited in the Ontobee for browsing and queries. As a demonstration of usage, a SPARQL query of the ODAE knowledge base was developed to identify all the drugs having the mechanisms of ion channel interactions, the diseases treated with the drugs, and AEs after the treatment in adult patients. AE-specific drug class effects were also explored using ODAE and SPARQL. CONCLUSION: ODAE provides a general representation of ADEs given different conditions and can be used for querying scientific questions. ODAE is also a robust knowledge base and platform for semantic and logic representation and study of ADEs of more drugs in the future. FAU - Yu, Hong AU - Yu H AD - Department of Pulmonary and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China. yuhong20040416@sina.com. AD - Guizhou University Medical College, Guiyang, 550025, Guizhou, China. yuhong20040416@sina.com. FAU - Nysak, Solomiya AU - Nysak S AD - College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA. FAU - Garg, Noemi AU - Garg N AD - College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA. FAU - Ong, Edison AU - Ong E AD - Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. FAU - Ye, Xianwei AU - Ye X AD - Department of Pulmonary and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China. AD - Guizhou University Medical College, Guiyang, 550025, Guizhou, China. FAU - Zhang, Xiangyan AU - Zhang X AD - Department of Pulmonary and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China. AD - Guizhou University Medical College, Guiyang, 550025, Guizhou, China. FAU - He, Yongqun AU - He Y AD - Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. yongqunh@med.umich.edu. LA - eng GR - R01 AI081062/AI/NIAID NIH HHS/United States PT - Journal Article DEP - 20190501 PL - England TA - BMC Bioinformatics JT - BMC bioinformatics JID - 100965194 RN - 0 (Anti-Bacterial Agents) RN - 0 (Antibiotics, Antineoplastic) RN - 0 (Pharmaceutical Preparations) RN - ISQ9I6J12J (Linezolid) RN - W36ZG6FT64 (Sirolimus) SB - IM MH - Adult MH - Adverse Drug Reaction Reporting Systems/*statistics & numerical data MH - Age Factors MH - Anti-Bacterial Agents/adverse effects MH - Antibiotics, Antineoplastic/adverse effects MH - Drug-Related Side Effects and Adverse Reactions/*etiology/pathology MH - Humans MH - Linezolid/*adverse effects MH - Nervous System Diseases/*chemically induced MH - Pharmaceutical Preparations/*administration & dosage/analysis MH - Sirolimus/*adverse effects MH - *Software PMC - PMC6509876 OTO - NOTNLM OT - Bioinformatics OT - Drug OT - Drug adverse event OT - ODAE OT - Ontology OT - Ontology of drug adverse events COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declare that they have no competing interests. PUBLISHER'S NOTE: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. EDAT- 2019/05/11 06:00 MHDA- 2019/07/06 06:00 PMCR- 2019/05/01 CRDT- 2019/05/11 06:00 PHST- 2019/05/11 06:00 [entrez] PHST- 2019/05/11 06:00 [pubmed] PHST- 2019/07/06 06:00 [medline] PHST- 2019/05/01 00:00 [pmc-release] AID - 10.1186/s12859-019-2729-1 [pii] AID - 2729 [pii] AID - 10.1186/s12859-019-2729-1 [doi] PST - epublish SO - BMC Bioinformatics. 2019 May 1;20(Suppl 7):199. doi: 10.1186/s12859-019-2729-1.