Print Email Facebook Twitter A dictionary to identify small molecules and drugs in free text Title A dictionary to identify small molecules and drugs in free text Author Hettne, K.M. Stierum, R.H. Schuemie, M.J. Hendriksen, P.J.M. Schijvenaars, B.J.A. van Mulligen, E.M. Kleinjans, J. Kors, J.A. TNO Kwaliteit van Leven Publication year 2009 Abstract Motivation: From the scientific community, a lot of effort has been spent on the correct identification of gene and protein names in text, while less effort has been spent on the correct identification of chemical names. Dictionary-based term identification has the power to recognize the diverse representation of chemical information in the literature and map the chemicals to their database identifiers. Results: We developed a dictionary for the identification of small molecules and drugs in text, combining information from UMLS, MeSH, ChEBI, DrugBank, KEGG, HMDB and ChemIDplus. Rule-based term filtering, manual check of highly frequent terms and disambiguation rules were applied. We tested the combined dictionary and the dictionaries derived from the individual resources on an annotated corpus, and conclude the following: (i) each of the different processing steps increase precision with a minor loss of recall; (ii) the overall performance of the combined dictionary is acceptable (precision 0.67, recall 0.40 (0.80 for trivial names); (iii) the combined dictionary performed better than the dictionary in the chemical recognizer OSCAR3; (iv) the performance of a dictionary based on ChemIDplus alone is comparable to the performance of the combined dictionary. © The Author 2009. Published by Oxford University Press. All rights reserved. Subject HealthBiomedical Research To reference this document use: http://resolver.tudelft.nl/uuid:7eaced5d-a12a-4574-a17f-ac63390c1f6b DOI https://doi.org/10.1093/bioinformatics/btp535 TNO identifier 248245 ISSN 1367-4803 Source Bioinformatics, 25 (22), 2983-2991 Document type article Files To receive the publication files, please send an e-mail request to TNO Library.