TY - JOUR AU - Vlachos, A. AU - Craven, M. PY - 2012 DA - 2012// TI - Biomedical event extraction from abstracts and full papers using search-based structured prediction JO - BMC Bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-S11-S5 DO - 10.1186/1471-2105-13-S11-S5 ID - Vlachos2012 ER - TY - CHAP AU - Riedel, S. AU - McClosky, D. AU - Surdeanu, M. AU - McCallum, A. AU - Manning, C. D. PY - 2011 DA - 2011// TI - Model combination for event extraction in BioNLP 2011 BT - Proceedings of the BioNLP Shared Task 2011 Workshop PB - Association for Computational Linguistics CY - Portland, Oregon ID - Riedel2011 ER - TY - CHAP AU - Björne, J. AU - Salakoski, T. PY - 2011 DA - 2011// TI - Generalizing biomedical event extraction BT - Proceedings of the BioNLP Shared Task 2011 Workshop PB - Association for Computational Linguistics CY - Portland, Oregon ID - Björne2011 ER - TY - JOUR AU - Bui, Q. C. AU - Katrenko, S. AU - Sloot, P. M. PY - 2011 DA - 2011// TI - A hybrid approach to extract protein–protein interactions JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btq620 DO - 10.1093/bioinformatics/btq620 ID - Bui2011 ER - TY - JOUR AU - Kim, S. AU - Yoon, J. AU - Yang, J. AU - Park, S. PY - 2010 DA - 2010// TI - Walk-weighted subsequence kernels for protein–protein interaction extraction JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-107 DO - 10.1186/1471-2105-11-107 ID - Kim2010 ER - TY - JOUR AU - Miwa, M. AU - Sætre, R. AU - Miyao, Y. AU - Tsujii, J. PY - 2009 DA - 2009// TI - Protein–protein interaction extraction by leveraging multiple kernels and parsers JO - Int J Med Inform VL - 78 UR - https://doi.org/10.1016/j.ijmedinf.2009.04.010 DO - 10.1016/j.ijmedinf.2009.04.010 ID - Miwa2009 ER - TY - JOUR AU - Airola, A. AU - Pyysalo, S. AU - Björne, J. AU - Pahikkala, T. AU - Ginter, F. AU - Salakoski, T. PY - 2008 DA - 2008// TI - All-paths graph kernel for protein–protein interaction extraction with evaluation of cross-corpus learning JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-S11-S2 DO - 10.1186/1471-2105-9-S11-S2 ID - Airola2008 ER - TY - JOUR AU - Pyysalo, S. AU - Airola, A. AU - Heimonen, J. AU - Björne, J. AU - Ginter, F. AU - Salakoski, T. PY - 2008 DA - 2008// TI - Comparative analysis of five protein–protein interaction corpora JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-S3-S6 DO - 10.1186/1471-2105-9-S3-S6 ID - Pyysalo2008 ER - TY - CHAP AU - Tudor, C. O. AU - Vijay-Shanker, K. PY - 2012 DA - 2012// TI - RankPref: Ranking sentences describing relations between biomedical entities with an application BT - Proceedings of the 2012 Workshop on Biomedical Natural Language Processing PB - Association for Computational Linguistic CY - Montreal, Canada ID - Tudor2012 ER - TY - JOUR AU - Cohen, K. B. AU - Verspoor, K. AU - Johnson, H. L. AU - Roeder, C. AU - Ogren, P. V. AU - Baumgartner, W. A. AU - White, E. AU - Tipney, H. AU - Hunter, L. PY - 2011 DA - 2011// TI - High-precision biological event extraction: effects of system and of data JO - Comput Intell VL - 27 UR - https://doi.org/10.1111/j.1467-8640.2011.00405.x DO - 10.1111/j.1467-8640.2011.00405.x ID - Cohen2011 ER - TY - JOUR AU - Hakenberg, J. AU - Leaman, R. AU - Ha Vo, N. AU - Jonnalagadda, S. AU - Sullivan, R. AU - Miller, C. AU - Tari, L. AU - Baral, C. AU - Gonzalez, G. PY - 2010 DA - 2010// TI - Efficient extraction of protein–protein interactions from full-text articles JO - IEEE/ACM Trans Comput Biol Bioinform (TCBB) VL - 7 UR - https://doi.org/10.1109/TCBB.2010.51 DO - 10.1109/TCBB.2010.51 ID - Hakenberg2010 ER - TY - JOUR AU - Hu, Z. Z. AU - Narayanaswamy, M. AU - Ravikumar, K. E. AU - Vijay-Shanker, K. AU - Wu, C. H. PY - 2005 DA - 2005// TI - Literature mining and database annotation of protein phosphorylation using a rule-based system JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti390 DO - 10.1093/bioinformatics/bti390 ID - Hu2005 ER - TY - CHAP AU - Kilicoglu, H. AU - Bergler, S. PY - 2011 DA - 2011// TI - Adapting a general semantic interpretation approach to biological event extraction BT - Proceedings of the BioNLP Shared Task 2011 Workshop PB - Association for Computational Linguistics CY - Portland, Oregon ID - Kilicoglu2011 ER - TY - CHAP AU - Quirk, C. AU - Choudhury, P. AU - Gamon, M. AU - Vanderwende, L. PY - 2011 DA - 2011// TI - MSR-NLP entry in BioNLP shared task 2011 BT - Proceedings of the BioNLP Shared Task 2011 Workshop PB - Association for Computational Linguistics CY - Portland, Oregon ID - Quirk2011 ER - TY - JOUR AU - Kim, J. AU - Rebholz-Schuhmann, D. PY - 2011 DA - 2011// TI - Improving the extraction of complex regulatory events from scientific text by using ontology-based inference JO - J Biomed Semantics VL - 2 UR - https://doi.org/10.1186/2041-1480-2-S5-S3 DO - 10.1186/2041-1480-2-S5-S3 ID - Kim2011 ER - TY - JOUR AU - Fundel, K. AU - Küffner, R. AU - Zimmer, R. PY - 2007 DA - 2007// TI - RelEx – relation extraction using dependency parse trees JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl616 DO - 10.1093/bioinformatics/btl616 ID - Fundel2007 ER - TY - JOUR AU - Rinaldi, F. AU - Schneider, G. AU - Kaljurand, K. AU - Hess, M. AU - Andronis, C. AU - Konstandi, O. AU - Persidis, A. PY - 2007 DA - 2007// TI - Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach JO - Artif Intell Med VL - 39 UR - https://doi.org/10.1016/j.artmed.2006.08.005 DO - 10.1016/j.artmed.2006.08.005 ID - Rinaldi2007 ER - TY - JOUR AU - Hunter, L. AU - Lu, Z. AU - Firby, J. AU - Baumgartner, W. A. AU - Johnson, H. L. AU - Ogren, P. V. AU - Cohen, K. B. PY - 2008 DA - 2008// TI - OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-78 DO - 10.1186/1471-2105-9-78 ID - Hunter2008 ER - TY - CHAP AU - Schabes, Y. PY - 1992 DA - 1992// TI - Stochastic lexicalized tree-adjoining grammars BT - Proceedings of the 14th conference on Computational linguistics-Volume 2 PB - Association for Computational Linguistics CY - Nantes, France UR - https://doi.org/10.3115/992133.992136 DO - 10.3115/992133.992136 ID - Schabes1992 ER - TY - BOOK AU - Pollard, C. AU - Sag, I. A. PY - 1994 DA - 1994// TI - Head-driven phrase structure grammar PB - University of Chicago Press CY - Chicago ID - Pollard1994 ER - TY - BOOK AU - Bresnan, J. PY - 2001 DA - 2001// TI - Lexical-functional syntax PB - Wiley-Blackwell CY - Hoboken ID - Bresnan2001 ER - TY - CHAP AU - Kipper, K. AU - Korhonen, A. AU - Ryant, N. AU - Palmer, M. PY - 2006 DA - 2006// TI - Extending VerbNet with novel verb classes BT - Proceedings of LREC; Genova, Italy, Volume 2006 ID - Kipper2006 ER - TY - CHAP AU - Chen, J. AU - Vijay-Shanker, K. PY - 2005 DA - 2005// TI - Automated extraction of TAGs from the Penn Treebank BT - New Developments in Parsing Technology, Volume 23 PB - Springer CY - New York ID - Chen2005 ER - TY - STD TI - The XTAG Research Group: A lexicalized tree adjoining grammar for English. Tech. rep., Technical Report IRCS-01-03, IRCS, University of Pennsylvania 2001 ID - ref24 ER - TY - BOOK AU - Levin, B. PY - 1993 DA - 1993// TI - English verb classes and alternations: a preliminary investigation PB - University of Chicago Press CY - Chicago ID - Levin1993 ER - TY - STD TI - Dolbey AE: BioFrameNet: a FrameNet extension to the domain of molecular miology. PhD thesis. University of California: Berkeley; 2009 ID - ref26 ER - TY - JOUR AU - Rebholz-Schuhmann, D. AU - Jimeno-Yepes, A. AU - Arregui, M. AU - Kirsch, H. PY - 2010 DA - 2010// TI - Measuring prediction capacity of individual verbs for the identification of protein interactions JO - J Biomed Inform VL - 43 UR - https://doi.org/10.1016/j.jbi.2009.09.007 DO - 10.1016/j.jbi.2009.09.007 ID - Rebholz-Schuhmann2010 ER - TY - JOUR AU - Lippincott, T. AU - Rimell, L. AU - Verspoor, K. AU - Korhonen, A. PY - 2013 DA - 2013// TI - Approaches to verb subcategorization for biomedicine JO - J Biomed Inform VL - 46 UR - https://doi.org/10.1016/j.jbi.2012.12.001 DO - 10.1016/j.jbi.2012.12.001 ID - Lippincott2013 ER - TY - JOUR AU - Rimell, L. AU - Lippincott, T. AU - Verspoor, K. AU - Johnson, H. L. AU - Korhonen, A. PY - 2013 DA - 2013// TI - Acquisition and evaluation of verb subcategorization resources for biomedicine JO - J Biomed Inform VL - 46 UR - https://doi.org/10.1016/j.jbi.2013.01.001 DO - 10.1016/j.jbi.2013.01.001 ID - Rimell2013 ER - TY - STD TI - EvidenceFinder. http://labs.europepmc.org/evf, UR - http://labs.europepmc.org/evf ID - ref30 ER - TY - CHAP AU - Jonnalagadda, S. AU - Gonzalez, G. PY - 2010 DA - 2010// TI - BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction BT - AMIA Annual Symposium Proceedings; Washington, DC, Volume 2010 ID - Jonnalagadda2010 ER - TY - CHAP AU - Miwa, M. AU - Saetre, R. AU - Miyao, Y. AU - Tsujii, J. PY - 2010 DA - 2010// TI - Entity-focused sentence simplification for relation extraction BT - Proceedings of the 23rd International Conference on Computational Linguistics PB - Beijing CY - China ID - Miwa2010 ER - TY - CHAP AU - Peng, Y. AU - Tudor, C. O. AU - Torii, M. AU - Wu, C. H. AU - Vijay-Shanker, K. PY - 2012 DA - 2012// TI - iSimp: A sentence simplification system for biomedical text BT - IEEE International Conference on Bioinformatics and Biomedicine (BIBM2012) PB - Philadelphia CY - PA ID - Peng2012 ER - TY - STD TI - Ogren PV: Coordination resolution in biomedical texts. PhD thesis. University of Colorado at Boulder; 2011 ID - ref34 ER - TY - JOUR AU - Jimeno-Yepes, A. AU - Jiménez-Ruiz, E. AU - Berlanga-Llavori, R. AU - Rebholz-Schuhmann, D. PY - 2009 DA - 2009// TI - Reuse of terminological resources for efficient ontological engineering in life sciences JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-S10-S4 DO - 10.1186/1471-2105-10-S10-S4 ID - Jimeno-Yepes2009 ER - TY - JOUR AU - Van Landeghem, S. AU - Björne, J. AU - Abeel, T. AU - De Baets, B. AU - Salakoski, T. AU - Van de Peer, Y. Z. PY - 2012 DA - 2012// TI - Semantically linking molecular entities in literature through entity relationships JO - BMC Bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-S11-S6 DO - 10.1186/1471-2105-13-S11-S6 ID - Van Landeghem2012 ER - TY - JOUR AU - Miwa, M. AU - Thompson, P. AU - Ananiadou, S. PY - 2012 DA - 2012// TI - Boosting automatic event extraction from the literature using domain adaptation and coreference resolution JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts237 DO - 10.1093/bioinformatics/bts237 ID - Miwa2012 ER - TY - CHAP AU - Van Landeghem, S. AU - Pyysalo, S. AU - Ohta, T. AU - Van de Peer, Y. PY - 2010 DA - 2010// TI - Integration of static relations to enhance event extraction from text BT - Proceedings of the 2010 Workshop on Biomedical Natural Language Processing PB - Association for Computational Linguistics CY - Uppsala, Sweden ID - Van Landeghem2010 ER - TY - CHAP AU - Narayanaswamy, M. AU - Ravikumar, K. AU - Vijay-Shanker, K. PY - 2003 DA - 2003// TI - A biological named entity recognizer BT - Proceedings of the Pacific Symposium on Biocomputing PB - Kauai CY - Hawaii ID - Narayanaswamy2003 ER - TY - CHAP AU - Miller, J. E. AU - Torii, M. AU - Vijay-Shanker, K. PY - 2007 DA - 2007// TI - Building domain-specific taggers without annotated (domain) data BT - Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning PB - Prague CY - Czech Republic ID - Miller2007 ER - TY - BOOK AU - Levin, B. PY - 2005 DA - 2005// TI - Hovav MR: Argument realization PB - Cambridge University Press CY - Cambridge, UK UR - https://doi.org/10.1017/CBO9780511610479 DO - 10.1017/CBO9780511610479 ID - Levin2005 ER - TY - JOUR AU - Smith, N. A. PY - 2001 DA - 2001// TI - Ellipsis happens, and deletion is how JO - Univ Md Working Papers Linguist VL - 11 ID - Smith2001 ER - TY - JOUR AU - Gerber, M. AU - Chai, J. Y. PY - 2012 DA - 2012// TI - Semantic role labeling of implicit arguments for nominal predicates JO - Comput Linguist VL - 38 UR - https://doi.org/10.1162/COLI_a_00110 DO - 10.1162/COLI_a_00110 ID - Gerber2012 ER - TY - CHAP AU - Tsuruoka, Y. AU - Tsujii, J. PY - 2005 DA - 2005// TI - Bidirectional inference with the easiest-first strategy for tagging sequence data BT - Proceedings of the Conference on Human Language Technology and Empirical Methods in Natural Language Processing 2005 PB - Vancouver CY - Canada UR - https://doi.org/10.3115/1220575.1220634 DO - 10.3115/1220575.1220634 ID - Tsuruoka2005 ER - TY - CHAP AU - De Marneffe, M. C. AU - Manning, C. D. PY - 2008 DA - 2008// BT - Stanford typed dependencies manual ID - De Marneffe2008 ER - TY - BOOK AU - Huddleston, R. AU - Pullum, G. K. PY - 2002 DA - 2002// TI - The Cambridge grammar of the English language PB - Cambridge University Press CY - Cambridge, UK ID - Huddleston2002 ER - TY - STD TI - Siddharthan A: Syntactic simplification and text cohesion. University of Cambridge 2003 ID - ref47 ER - TY - BOOK AU - Hartmann, R. R. K. AU - Stork, F. C. PY - 1972 DA - 1972// TI - Dictionary of language and linguistics PB - Wiley CY - New York ID - Hartmann1972 ER - TY - BOOK AU - Hearst, M. A. PY - 1992 DA - 1992// TI - Automatic acquisition of hyponyms from large text corpora PB - Association for Computational Linguistics CY - Nantes, France UR - https://doi.org/10.3115/992133.992154 DO - 10.3115/992133.992154 ID - Hearst1992 ER - TY - JOUR AU - Snow, R. AU - Jurafsky, D. AU - Ng, A. Y. PY - 2004 DA - 2004// TI - Learning syntactic patterns for automatic hypernym discovery JO - Adv Neural Inform Process Syst VL - 17 ID - Snow2004 ER - TY - JOUR AU - Kim, J. D. AU - Nguyen, N. AU - Wang, Y. AU - Tsujii, J. AU - Takagi, T. AU - Yonezawa, A. PY - 2012 DA - 2012// TI - The genia event and protein coreference tasks of the BioNLP shared task 2011 JO - BMC Bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-S11-S1 DO - 10.1186/1471-2105-13-S11-S1 ID - Kim2012 ER - TY - CHAP AU - Kim, J. D. AU - Yue, W. AU - Yamamoto, Y. PY - 2013 DA - 2013// TI - The Genia event extraction shared task, 2013 edition - Overview BT - Proceedings of the Workshop on BioNLP Shared Task 2013 PB - Sofia CY - Bulgaria ID - Kim2013 ER - TY - CHAP AU - Stenetorp, P. AU - Topić, G. AU - Pyysalo, S. AU - Ohta, T. AU - Kim, J. D. AU - Tsujii, J. PY - 2011 DA - 2011// TI - BioNLP shared task 2011: Supporting resources BT - Proceedings of the Workshop on BioNLP Shared Task 2011 PB - Portland CY - Oregon ID - Stenetorp2011 ER - TY - STD TI - McClosky D: Any domain parsing: automatic domain adaptation for natural language parsing. PhD thesis. Department of Computer Science, Brown University 2009 ID - ref54 ER - TY - CHAP AU - Tateisi, Y. AU - Yakushiji, A. AU - Ohta, T. AU - Tsujii, J. PY - 2005 DA - 2005// TI - Syntax annotation for the GENIA corpus BT - Proceedings of the Workshop on the 1st International Joint Conference on Natural Language Processing (IJCNLP). Volume 5 PB - Jeju Island CY - Korea ID - Tateisi2005 ER - TY - CHAP AU - Levy, R. AU - Andrew, G. PY - 2006 DA - 2006// TI - Tregex and Tsurgeon: tools for querying and manipulating tree data structures BT - Proceedings of the Fifth International Conference on Language Resources and Evaluation PB - Genoa CY - Italy ID - Levy2006 ER - TY - JOUR AU - Lappin, S. AU - Leass, H. J. PY - 1994 DA - 1994// TI - An algorithm for pronominal anaphora resolution JO - Comput Linguist VL - 20 ID - Lappin1994 ER - TY - CHAP AU - Qiu, L. AU - yen Kan, M. AU - seng Chua, T. PY - 2004 DA - 2004// TI - A public reference implementation of the rap anaphora resolution algorithm BT - Proceedings of the Fourth International Conference on Language Resources and Evaluation (LREC 2004) PB - Lisbon CY - Portugal ID - Qiu2004 ER - TY - STD TI - BioNLP-ST 2013 GE task results. http://bionlp-st.dbcls.jp/GE/2013/results, UR - http://bionlp-st.dbcls.jp/GE/2013/results ID - ref59 ER - TY - JOUR AU - Narayanaswamy, M. AU - Ravikumar, K. AU - Vijay-Shanker, K. PY - 2005 DA - 2005// TI - Beyond the clause: extraction of phosphorylation information from medline abstracts JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1011 DO - 10.1093/bioinformatics/bti1011 ID - Narayanaswamy2005 ER -