TY - JOUR AU - Verspoor, K. AU - Cohen, K. B. AU - Hunter, L. PY - 2009 DA - 2009// TI - The textual characteristics of traditional and Open Access scientific journals are similar JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-183 DO - 10.1186/1471-2105-10-183 ID - Verspoor2009 ER - TY - JOUR AU - Blaschke, C. AU - Valencia, A. PY - 2001 DA - 2001// TI - Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study JO - Comparative and Functional Genomics VL - 2 UR - https://doi.org/10.1002/cfg.91 DO - 10.1002/cfg.91 ID - Blaschke2001 ER - TY - STD TI - Shah PK, Perez-Iratxeta C, Bork P, Andrade MA: Information extraction from full text scientific articles: Where are the keywords? BMC Bioinformatics 2003., 4(20): ID - ref3 ER - TY - JOUR AU - Corney, D. P. AU - Buxton, B. F. AU - Langdon, W. B. AU - Jones, D. T. PY - 2004 DA - 2004// TI - BioRAT: extracting biological information from full-length papers JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth386 DO - 10.1093/bioinformatics/bth386 ID - Corney2004 ER - TY - JOUR AU - Friedman, C. AU - Kra, P. AU - Yu, H. AU - Krauthammer, M. AU - Rzhetsky, A. PY - 2001 DA - 2001// TI - GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.suppl_1.S74 DO - 10.1093/bioinformatics/17.suppl_1.S74 ID - Friedman2001 ER - TY - CHAP AU - Lin, J. PY - 2009 DA - 2009// TI - Is searching full text more effective than searching abstracts? BT - BMC Bioinformatics ID - Lin2009 ER - TY - CHAP AU - McIntosh, T. AU - Curran, J. R. PY - 2009 DA - 2009// TI - Challenges for automatically extracting molecular interactions from full-text articles BT - BMC Bioinformatics ID - McIntosh2009 ER - TY - JOUR AU - Agarwal, S. AU - Yu, H. PY - 2009 DA - 2009// TI - Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp548 DO - 10.1093/bioinformatics/btp548 ID - Agarwal2009 ER - TY - CHAP AU - Tanabe, L. AU - Wilbur, W. J. PY - 2002 DA - 2002// TI - Tagging gene and protein names in full text articles BT - Natural language processing in the biomedical domain UR - https://doi.org/10.3115/1118149.1118151 DO - 10.3115/1118149.1118151 ID - Tanabe2002 ER - TY - JOUR AU - Hersh, W. AU - Voorhees, E. PY - 2008 DA - 2008// TI - TREC genomics special issue overview JO - Information Retrieval VL - 12 UR - https://doi.org/10.1007/s10791-008-9076-6 DO - 10.1007/s10791-008-9076-6 ID - Hersh2008 ER - TY - JOUR AU - Hirschman, L. AU - Yeh, A. AU - Blaschke, C. AU - Valencia, A. PY - 2005 DA - 2005// TI - Overview of BioCreAtIvE: critical assessment of information extraction for biology JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-S1-S1 DO - 10.1186/1471-2105-6-S1-S1 ID - Hirschman2005 ER - TY - JOUR AU - Krallinger, M. AU - Morgan, A. AU - Smith, L. AU - Leitner, F. AU - Tanabe, L. AU - Wilbur, J. AU - Hirschman, L. AU - Valencia, A. PY - 2008 DA - 2008// TI - The BioCreative II - critical assessment for information extraction in biology challenge JO - Genome Biology VL - 9 UR - https://doi.org/10.1186/gb-2008-9-s2-s1 DO - 10.1186/gb-2008-9-s2-s1 ID - Krallinger2008 ER - TY - BOOK AU - Jurafsky, D. AU - Martin, J. H. PY - 2008 DA - 2008// TI - Speech and language processing: An introduction to natural language processing, computational linguistics, and speech recognition ID - Jurafsky2008 ER - TY - CHAP AU - Nakov, P. I. AU - Schwartz, A. S. AU - Hearst, M. A. PY - 2004 DA - 2004// TI - Citances: Citation sentences for semantic analysis of bioscience text BT - SIGIR'04 Workshop on Search and Discovery in Bioinformatics ID - Nakov2004 ER - TY - JOUR AU - Baumgartner, W. A. AU - Lu, Z. AU - Johnson, H. L. AU - Caporaso, J. G. AU - Paquette, J. AU - Lindemann, A. AU - White, E. K. AU - Medvedeva, O. AU - Cohen, K. B. AU - Hunter, L. PY - 2008 DA - 2008// TI - Concept recognition for extracting protein interaction relations from biomedical text JO - Genome Biology VL - 9 UR - https://doi.org/10.1186/gb-2008-9-s2-s9 DO - 10.1186/gb-2008-9-s2-s9 ID - Baumgartner2008 ER - TY - STD TI - A design methodology for a biomedical literature indexing tool using the rhetoric of science BioLINK 2004, Linking biological literature, ontologies and databases 77–84. ID - ref16 ER - TY - CHAP AU - Elhadad, N. PY - 2006 DA - 2006// TI - User-sensitive text summarization: Application to the medical domain BT - PhD thesis ID - Elhadad2006 ER - TY - CHAP AU - Chapman, W. AU - Bridewell, W. AU - Hanbury, P. AU - Cooper, G. AU - Buchanan, B. PY - 2001 DA - 2001// TI - Evaluation of negation phrases in narrative clinical reports BT - Proceedings of the AMIA Symposium 2001 ID - Chapman2001 ER - TY - JOUR AU - Chapman, W. AU - Bridewell, W. AU - Hanbury, P. AU - Cooper, G. AU - Buchanan, B. PY - 2001 DA - 2001// TI - A simple algorithm for identifying negated findings and diseases in discharge summaries JO - Journal of Biomedical Informatics VL - 34 UR - https://doi.org/10.1006/jbin.2001.1029 DO - 10.1006/jbin.2001.1029 ID - Chapman2001 ER - TY - CHAP AU - Goldin, I. AU - Chapman, W. PY - 2003 DA - 2003// TI - Learning to detect negation with 'not' in medical texts BT - Proceedings of the ACM SIGIR ID - Goldin2003 ER - TY - JOUR AU - Mutalik, P. G. AU - Deshpande, A. AU - Nadkarni, P. M. PY - 2001 DA - 2001// TI - Use of general-purpose negation detection to augment concept indexing of medical documents JO - Journal of the American Medical Informatics Association VL - 8 UR - https://doi.org/10.1136/jamia.2001.0080598 DO - 10.1136/jamia.2001.0080598 ID - Mutalik2001 ER - TY - CHAP AU - Gasperin, C. PY - 2006 DA - 2006// TI - Semi-supervised anaphora resolution in biomedical texts BT - Linking natural language processing and biology: towards deeper biological literature analysis UR - https://doi.org/10.3115/1567619.1567640 DO - 10.3115/1567619.1567640 ID - Gasperin2006 ER - TY - CHAP AU - Gasperin, C. AU - Karamanis, N. AU - Seal, R. PY - 2007 DA - 2007// TI - Annotation of anaphoric relations in biomedical full-text articles using a domain-relevant scheme BT - Proceedings of DAARC 2007 ID - Gasperin2007 ER - TY - CHAP AU - Szmrecsányi, B. M. PY - 2004 DA - 2004// TI - On operationalizing syntactic complexity BT - JADT 2004: 7es Journées internationales d'Analyse statistique des Données Textuelles ID - Szmrecsányi2004 ER - TY - CHAP AU - Leroy, G. AU - Helmreich, S. AU - Cowie, J. R. AU - Miller, T. AU - Zheng, W. PY - 2008 DA - 2008// TI - Evaluating online health information: Beyond readability formulas BT - AMIA 2008 Symposium Proceedings ID - Leroy2008 ER - TY - JOUR AU - Settles, B. PY - 2005 DA - 2005// TI - ABNER: an open source tool for automatically tagging genes, proteins, and other entity names in text JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti475 DO - 10.1093/bioinformatics/bti475 ID - Settles2005 ER - TY - CHAP AU - Leaman, R. AU - Gonzalez, G. PY - 2008 DA - 2008// TI - BANNER: An executable survey of advances in biomedical named entity recognition BT - Pac Symp Biocomput ID - Leaman2008 ER - TY - CHAP AU - Alias-i PY - 2008 DA - 2008// BT - LingPipe 3.1.2 ID - Alias-i2008 ER - TY - JOUR AU - Caporaso, J. G. AU - W, A. B. AU - Randolph, D. A. AU - Cohen, K. B. AU - Hunter, L. PY - 2007 DA - 2007// TI - MutationFinder: A high-performance system for extracting point mutation mentions from text JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm235 DO - 10.1093/bioinformatics/btm235 ID - Caporaso2007 ER - TY - CHAP AU - Klein, D. AU - Manning, C. PY - 2003 DA - 2003// TI - Accurate unlexicalized parsing BT - Proceedings of the 41st Annual Meeting of the Association for Computational Linguistics ID - Klein2003 ER - TY - CHAP AU - Abney, S. AU - Flickenger, S. AU - Gdaniec, C. AU - Grishman, C. AU - Harrison, P. AU - Hindle, D. AU - Ingria, R. AU - Jelinek, F. AU - Klavans, J. AU - Liberman, M. PY - 1991 DA - 1991// TI - Procedure for quantitatively comparing the syntactic coverage of English grammars BT - Proceedings of the workshop on Speech and Natural Language PB - Association for Computational Linguistics CY - Morristown, NJ, USA ID - Abney1991 ER -