DOI 10.1093bioinformaticsbth904 Protein.pdf

BIOINFORMATICS Vol. 20 Suppl. 1 2004, pages i241–i247 DOI: 10.1093/bioinformatics/bth904 Protein names precisely peeled off free text Sven Mika1,2,3,? and Burkhard Rost1,2 1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA, 2Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St. Nicholas Avenue, New York, NY 10032, USA and 3Institute of Physical Biochemistry, University Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany Received on January 15, 2004; accepted on March 1, 2004 ABSTRACT Motivation: Automatically identifying protein names from the scientific literature is a pre-requisite for the increasing demand in data-mining this wealth of information. Existing approaches are based on dictionaries, rules and machine-learning. Here, we introduced a novel system that combines a pre-processing dictionary- and rule-based filtering step with several separately trained support vector machines (SVMs) to identify protein names in the MEDLINE abstracts. Results: Our new tagging-system NLProt is capable of extract- ing protein names with a precision (accuracy) of 75% at a recall (coverage) of 76% after training on a corpus, which was used before by other groups and contains 200 annotated abstracts. For our estimate of sustained performance, we considered partially identified names as false positives. One important issue frequently ignored in the literature is the redundancy in evaluation sets. We suggested some guidelines for removing overly inadequate overlaps between training and testing sets. Applying these new guidelines, our program appeared to sig- nificantly out-perform other methods tagging protein names. NLProt was so successful due to the SVM-building blocks that succeeded in utilizing the local context of protein names in the scientific literature. We challenge that our system may consti- tute the most general and prec