title: Recognition of chemical entities: combining dictionary-based and grammar-based approaches.
abstract: BACKGROUND
  The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstructured texts. The BioCreative CHEMDNER challenge invites the development of systems for the automatic recognition of chemicals in text (CEM task) and for ranking the recognized compounds at the document level (CDI task). We investigated an ensemble approach where dictionary-based named entity recognition is used along with grammar-based recognizers to extract compounds from text. We assessed the performance of ten different commercial and publicly available lexical resources using an open source indexing system (Peregrine), in combination with three different chemical compound recognizers and a set of regular expressions to recognize chemical database identifiers. The effect of different stop-word lists, case-sensitivity matching, and use of chunking information was also investigated. We focused on lexical resources that provide chemical structure information. To rank the different compounds found in a text, we used a term confidence score based on the normalized ratio of the term frequencies in chemical and non-chemical journals.
  
  
  RESULTS
  The use of stop-word lists greatly improved the performance of the dictionary-based recognition, but there was no additional benefit from using chunking information. A combination of ChEBI and HMDB as lexical resources, the LeadMine tool for grammar-based recognition, and the regular expressions, outperformed any of the individual systems. On the test set, the F-scores were 77.8% (recall 71.2%, precision 85.8%) for the CEM task and 77.6% (recall 71.7%, precision 84.6%) for the CDI task. Missed terms were mainly due to tokenization issues, poor recognition of formulas, and term conjunctions.
  
  
  CONCLUSIONS
  We developed an ensemble system that combines dictionary-based and grammar-based approaches for chemical named entity recognition, outperforming any of the individual systems that we considered. The system is able to provide structure information for most of the compounds that are found. Improved tokenization and better recognition of specific entity types is likely to further improve system performance.
authors: Department of Medical Informatics, Erasmus University Medical Center, P.O. Box 2040, Rotterdam, CA 3000, The Netherlands.
authors: Saber A
authors: SA
authors: Akhondi
authors: Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, Leiden, RC 2300, The Netherlands.
authors: Kristina M
authors: KM
authors: Hettne
authors: Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, Leiden, RC 2300, The Netherlands.
authors: Eelke
authors: E
authors: van der Horst
authors: Department of Medical Informatics, Erasmus University Medical Center, P.O. Box 2040, Rotterdam, CA 3000, The Netherlands.
authors: Erik M
authors: EM
authors: van Mulligen
authors: Department of Medical Informatics, Erasmus University Medical Center, P.O. Box 2040, Rotterdam, CA 3000, The Netherlands.
authors: Jan A
authors: JA
authors: Kors
keywords: BioCreative; CHEMDNER; Chemical compounds; Chemical databases; Chemical dictionaries; Chemical identifiers; Chemical structure; Drugs; MOL files; Named entity recognition