title: Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature.
abstract: BACKGROUND
  Systems approaches to studying drug-side-effect (drug-SE) associations are emerging as an active research area for both drug target discovery and drug repositioning. However, a comprehensive drug-SE association knowledge base does not exist. In this study, we present a novel knowledge-driven (KD) approach to effectively extract a large number of drug-SE pairs from published biomedical literature.
  
  
  METHODS
  For the text corpus, we used 21,354,075 MEDLINE records (119,085,682 sentences). First, we used known drug-SE associations derived from FDA drug labels as prior knowledge to automatically find SE-related sentences and abstracts. We then extracted a total of 49,575 drug-SE pairs from MEDLINE sentences and 180,454 pairs from abstracts.
  
  
  RESULTS
  On average, the KD approach has achieved a precision of 0.335, a recall of 0.509, and an F1 of 0.392, which is significantly better than a SVM-based machine learning approach (precision: 0.135, recall: 0.900, F1: 0.233) with a 73.0% increase in F1 score. Through integrative analysis, we demonstrate that the higher-level phenotypic drug-SE relationships reflects lower-level genetic, genomic, and chemical drug mechanisms. In addition, we show that the extracted drug-SE pairs can be directly used in drug repositioning.
  
  
  CONCLUSIONS
  In summary, we automatically constructed a large-scale higher-level drug phenotype relationship knowledge, which can have great potential in computational drug discovery.
authors: Rong
authors: R
authors: Xu
authors: QuanQiu
authors: Q
authors: Wang
mesh_terms: D001185:Artificial Intelligence; D064229:Biological Ontologies; D057225:Data Mining / Q000379:methods*; D062313:Databases, Pharmaceutical; D055808:Drug Discovery; D058492:Drug Repositioning; D064420:Drug-Related Side Effects and Adverse Reactions / Q000145:classification*; D006801:Humans; D051188:Knowledge Bases; D016239:MEDLINE; D010506:Periodicals as Topic; D004364:Pharmaceutical Preparations; D010641:Phenotype; D057386:Search Engine
chemical_list: D004364:Pharmaceutical Preparations