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Bioinformatics Advance Access originally published online on April 28, 2005
Bioinformatics 2005 21(14):3191-3192; doi:10.1093/bioinformatics/bti475
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text

Burr Settles

Department of Computer Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison Madison, WI 52706, USA

Summary: ABNER (A Biomedical Named Entity Recognizer) is an open source software tool for molecular biology text mining. At its core is a machine learning system using conditional random fields with a variety of orthographic and contextual features. The latest version is 1.5, which has an intuitive graphical interface and includes two modules for tagging entities (e.g. protein and cell line) trained on standard corpora, for which performance is roughly state of the art. It also includes a Java application programming interface allowing users to incorporate ABNER into their own systems and train models on new corpora.

Availability: ABNER is available as an executable Java archive and source code from http://www.cs.wisc.edu/~bsettles/abner/

Contact: bsettles{at}cs.wisc.edu

Received on April 1, 2005; revised on April 21, 2005; accepted on April 26, 2005

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