{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T15:31:38Z","timestamp":1773156698710,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2854,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: While text mining technologies for biomedical research have gained popularity as a way to take advantage of the explosive growth of information in text form in biomedical papers, selecting appropriate natural language processing (NLP) tools is still difficult for researchers who are not familiar with recent advances in NLP. This article provides a comparative evaluation of several state-of-the-art natural language parsers, focusing on the task of extracting protein\u2013protein interaction (PPI) from biomedical papers. We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system.<\/jats:p>\n               <jats:p>Results: All the parsers attained improvements in accuracy of PPI extraction. The levels of accuracy obtained with these different parsers vary slightly, while differences in parsing speed are larger. The best accuracy in this work was obtained when we combined Miyao and Tsujii's Enju parser and Charniak and Johnson's reranking parser, and the accuracy is better than the state-of-the-art results on the same data.<\/jats:p>\n               <jats:p>Availability: The PPI extraction system used in this work (AkanePPI) is available online at http:\/\/www-tsujii.is.s.u-tokyo.ac.jp\/downloads\/downloads.cgi. The evaluated parsers are also available online from each developer's site.<\/jats:p>\n               <jats:p>Contact: \u00a0yusuke@is.s.u-tokyo.ac.jp<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn631","type":"journal-article","created":{"date-parts":[[2008,12,11]],"date-time":"2008-12-11T01:13:35Z","timestamp":1228958015000},"page":"394-400","source":"Crossref","is-referenced-by-count":107,"title":["Evaluating contributions of natural language parsers to protein\u2013protein interaction extraction"],"prefix":"10.1093","volume":"25","author":[{"given":"Yusuke","family":"Miyao","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenji","family":"Sagae","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rune","family":"S\u00e6tre","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takuya","family":"Matsuzaki","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun'ichi","family":"Tsujii","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"},{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"},{"name":"1 Department of Computer Science, University of Tokyo, Tokyo, Japan, 2Institute for Creative Technologies, University of Southern California, CA, USA, 3School of Computer Science, University of Manchester and 4National Center for Text Mining, Manchester, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,12,9]]},"reference":[{"key":"2023013110031861300_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3115\/1572306.1572308","article-title":"A graph kernel for protein-protein interaction extraction.","volume-title":"Proceedings of BioNLP.","author":"Airola","year":"2008"},{"key":"2023013110031861300_B2","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1162\/0891201042544929","article-title":"Intricacies of Collins' parsing model","volume":"30","author":"Bikel","year":"2004","journal-title":"Comput. 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