PMID- 29880031
OWN - NLM
STAT- MEDLINE
DCOM- 20190731
LR  - 20190731
IS  - 2041-1480 (Electronic)
VI  - 9
IP  - 1
DP  - 2018 Jun 7
TI  - Ontology-based literature mining and class effect analysis of adverse drug 
      reactions associated with neuropathy-inducing drugs.
PG  - 17
LID - 10.1186/s13326-018-0185-x [doi]
LID - 17
AB  - BACKGROUND: Adverse drug reactions (ADRs), also called as drug adverse events 
      (AEs), are reported in the FDA drug labels; however, it is a big challenge to 
      properly retrieve and analyze the ADRs and their potential relationships from 
      textual data. Previously, we identified and ontologically modeled over 240 drugs 
      that can induce peripheral neuropathy through mining public drug-related 
      databases and drug labels. However, the ADR mechanisms of these drugs are still 
      unclear. In this study, we aimed to develop an ontology-based literature mining 
      system to identify ADRs from drug labels and to elucidate potential mechanisms of 
      the neuropathy-inducing drugs (NIDs). RESULTS: We developed and applied an 
      ontology-based SciMiner literature mining strategy to mine ADRs from the drug 
      labels provided in the Text Analysis Conference (TAC) 2017, which included drug 
      labels for 53 neuropathy-inducing drugs (NIDs). We identified an average of 243 
      ADRs per NID and constructed an ADR-ADR network, which consists of 29 ADR nodes 
      and 149 edges, including only those ADR-ADR pairs found in at least 50% of NIDs. 
      Comparison to the ADR-ADR network of non-NIDs revealed that the ADRs such as 
      pruritus, pyrexia, thrombocytopenia, nervousness, asthenia, acute lymphocytic 
      leukaemia were highly enriched in the NID network. Our ChEBI-based ontology 
      analysis identified three benzimidazole NIDs (i.e., lansoprazole, omeprazole, and 
      pantoprazole), which were associated with 43 ADRs. Based on ontology-based drug 
      class effect definition, the benzimidazole drug group has a drug class effect on 
      all of these 43 ADRs. Many of these 43 ADRs also exist in the enriched NID ADR 
      network. Our Ontology of Adverse Events (OAE) classification further found that 
      these 43 benzimidazole-related ADRs were distributed in many systems, primarily 
      in behavioral and neurological, digestive, skin, and immune systems. CONCLUSIONS: 
      Our study demonstrates that ontology-based literature mining and network analysis 
      can efficiently identify and study specific group of drugs and their associated 
      ADRs. Furthermore, our analysis of drug class effects identified 3 benzimidazole 
      drugs sharing 43 ADRs, leading to new hypothesis generation and possible 
      mechanism understanding of drug-induced peripheral neuropathy.
FAU - Hur, Junguk
AU  - Hur J
AUID- ORCID: 0000-0002-0736-2149
AD  - Department of Department of Biomedical Sciences, University of North Dakota 
      School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA. 
      junguk.hur@med.und.edu.
FAU - Ozgur, Arzucan
AU  - Ozgur A
AD  - Department of Computer Engineering, Bogazici University, 34342, Istanbul, Turkey.
FAU - He, Yongqun
AU  - He Y
AD  - Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, 
      University of Michigan Medical School, Ann Arbor, MI, 48109, USA. 
      yongqunh@med.umich.edu.
AD  - Department of Microbiology and Immunology, University of Michigan Medical School, 
      Ann Arbor, MI, 48109, USA. yongqunh@med.umich.edu.
AD  - Center for Computational Medicine and Bioinformatics, University of Michigan 
      Medical School, Ann Arbor, MI, 48109, USA. yongqunh@med.umich.edu.
AD  - Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, 
      MI, 48109, USA. yongqunh@med.umich.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20180607
PL  - England
TA  - J Biomed Semantics
JT  - Journal of biomedical semantics
JID - 101531992
MH  - *Biological Ontologies
MH  - Data Mining/*methods
MH  - *Drug-Related Side Effects and Adverse Reactions
MH  - Peripheral Nervous System Diseases/*chemically induced
PMC - PMC5991464
COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: 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- 2018/06/09 06:00
MHDA- 2019/08/01 06:00
PMCR- 2018/06/07
CRDT- 2018/06/09 06:00
PHST- 2018/02/06 00:00 [received]
PHST- 2018/05/18 00:00 [accepted]
PHST- 2018/06/09 06:00 [entrez]
PHST- 2018/06/09 06:00 [pubmed]
PHST- 2019/08/01 06:00 [medline]
PHST- 2018/06/07 00:00 [pmc-release]
AID - 10.1186/s13326-018-0185-x [pii]
AID - 185 [pii]
AID - 10.1186/s13326-018-0185-x [doi]
PST - epublish
SO  - J Biomed Semantics. 2018 Jun 7;9(1):17. doi: 10.1186/s13326-018-0185-x.