BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btt639 Data and text mining Advance Access publication November 13, 2013 CheNER: chemical named entity recognizer

Motivation: Chemical named entity recognition is used to automat-ically identify mentions to chemical compounds in text and is the basis for more elaborate information extraction. However, only a small number of applications are freely available to identify such mentions. Particularly challenging and useful is the identification of International Union of Pure and Applied Chemistry (IUPAC) chemical compounds, which due to the complex morphology of IUPAC names requires more advanced techniques than that of brand names. Results: We present CheNER, a tool for automated identification of systematic IUPAC chemical mentions. We evaluated different systems using an established literature corpus to show that CheNER has a superior performance in identifying IUPAC names specifically, and that it makes better use of computational resources