Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2018-06-01
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| Series: | Journal of Biomedical Semantics |
| Online Access: | http://link.springer.com/article/10.1186/s13326-018-0185-x |
| _version_ | 1819225574504136704 |
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| author | Junguk Hur Arzucan Özgür Yongqun He |
| author_facet | Junguk Hur Arzucan Özgür Yongqun He |
| author_sort | Junguk Hur |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-23T10:11:46Z |
| format | Article |
| id | doaj.art-5437919d3b22449997413f9cf09a4d32 |
| institution | Directory Open Access Journal |
| issn | 2041-1480 |
| language | English |
| last_indexed | 2024-12-23T10:11:46Z |
| publishDate | 2018-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Semantics |
| spelling | doaj.art-5437919d3b22449997413f9cf09a4d322022-12-21T17:50:56ZengBMCJournal of Biomedical Semantics2041-14802018-06-019111010.1186/s13326-018-0185-xOntology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugsJunguk Hur0Arzucan Özgür1Yongqun He2Department of Department of Biomedical Sciences, University of North Dakota School of Medicine and Health SciencesDepartment of Computer Engineering, Bogazici UniversityUnit for Laboratory Animal Medicine, Department of Microbiology and Immunology, University of Michigan Medical SchoolAbstract 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.http://link.springer.com/article/10.1186/s13326-018-0185-x |
| spellingShingle | Junguk Hur Arzucan Özgür Yongqun He Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs Journal of Biomedical Semantics |
| title | Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs |
| title_full | Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs |
| title_fullStr | Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs |
| title_full_unstemmed | Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs |
| title_short | Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs |
| title_sort | ontology based literature mining and class effect analysis of adverse drug reactions associated with neuropathy inducing drugs |
| url | http://link.springer.com/article/10.1186/s13326-018-0185-x |
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