Scientific article
Open access

Classification and prioritization of biomedical literature for the comparative toxicogenomics database

Published inStudies in health technology and informatics, vol. 180, p. 210-214
Publication date2012

We present a new approach to perform biomedical documents classification and prioritization for the Comparative Toxicogenomics Database (CTD). This approach is motivated by needs such as literature curation, in particular applied to the human health environment domain. The unique integration of chemical, genes/proteins and disease data in the biomedical literature may advance the identification of exposure and disease biomarkers, mechanisms of chemical actions, and the complex aetiologies of chronic diseases. Our approach aims to assist biomedical researchers when searching for relevant articles for CTD. The task is functionally defined as a binary classification task, where selected articles must also be ranked by order of relevance. We design a SVM classifier, which combines three main feature sets: an information retrieval system (EAGLi), a biomedical named-entity recognizer (MeSH term extraction), a gene normalization (GN) service (NormaGene) and an ad-hoc keyword recognizer for diseases and chemicals. The evaluation of the gene identification module was done on BioCreativeIII test data. Disease normalization is achieved with 95% precision and 93% of recall. The evaluation of the classification was done on the corpus provided by BioCreative organizers in 2012. The approach showed promising performance on the test data.

  • Abstracting and Indexing as Topic/methods
  • Data Mining/methods
  • Database Management Systems
  • Databases, Chemical
  • Databases, Genetic
  • Drug Toxicity/classification
  • Humans
  • Periodicals as Topic/classification
  • Toxicogenetics/methods
  • User-Computer Interface
Citation (ISO format)
VISHNYAKOVA, Dina et al. Classification and prioritization of biomedical literature for the comparative toxicogenomics database. In: Studies in health technology and informatics, 2012, vol. 180, p. 210–214. doi: 10.3233/978-1-61499-101-4-210
Main files (1)
Article (Accepted version)
ISSN of the journal0926-9630

Technical informations

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