Biomedical Natural Language Processing
| University of Colorado, School of Medicine
| National Library of Medicine
Biomedical Natural Language Processing is a comprehensive tour through the classic and current work in the field. It discusses all subjects from both a rule-based and a machine learning approach, and also describes each subject from the perspective of both biological science and clinical medicine. The intended audience is readers who already have a background in natural language processing, but a clear introduction makes it accessible to readers from the fields of bioinformatics and computational biology, as well. The book is suitable as a reference, as well as a text for advanced courses in biomedical natural language processing and text mining.
[Natural Language Processing, 11] 2014. xi, 160 pp.
Publishing status: Available
© K. Bretonnel Cohen & Dina Demner-Fushman
Table of Contents
Acknowledgments
|
v
|
List of figures
|
xi
|
1. Introduction to natural language processing
|
1–6
|
2. Historical background
|
7–20
|
3. Named entity recognition
|
21–30
|
4. Relation extraction
|
31–50
|
5. Information retrieval/document classification
|
51–62
|
6. Concept normalization
|
63–76
|
7. Ontologies and computational lexical semantics
|
77–86
|
8. Summarization
|
87–94
|
9. Question-answering
|
95–116
|
10. Software engineering
|
117–130
|
11. Corpus construction and annotation
|
131–140
|
References
|
141–154
|
Index
|
155–160
|
“[...] impressive book.”
Jun’ichi Tsujii, University of Tokyo & University of Manchester
“[…] the perfect resource especially for new NLP investigators. It is an easy read, quite insightful, and filled with lots of valuable “between the studies” truisms.”
Peter White, Children's Hospital of Philadelphia
“I enjoyed reading the book!”
Zhiyong Lu, National Center for Biotechnology Information
“[…] a great job of distilling a huge amount of work!”
Karin Verspoor, National ICT Australia
“This looks like a great book and I am looking forward to seeing it published!”
Preslav Nakov, Qatar Computing Research Institute, Qatar Foundation
Cited by
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Campillos, Leonardo, Louise Deléger, Cyril Grouin, Thierry Hamon, Anne-Laure Ligozat & Aurélie Névéol
Casillas, Arantza, Koldo Gojenola, Alicia Perez & Maite Oronoz
Deléger, Louise, Leonardo Campillos, Anne-Laure Ligozat & Aurélie Névéol
Gaudet-Blavignac, Christophe, Vasiliki Foufi, Mina Bjelogrlic & Christian Lovis
Green, Nancy L.
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Kim, Jin-Dong, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J Callahan, K Bretonnel Cohen & Jonathan Wren
Leaman, Robert, Ritu Khare & Zhiyong Lu
Li, Qi, Xuan Wang, Yu Zhang, Fei Ling, Cathy H. Wu & Jiawei Han
Luo, Yuan, William K. Thompson, Timothy M. Herr, Zexian Zeng, Mark A. Berendsen, Siddhartha R. Jonnalagadda, Matthew B. Carson & Justin Starren
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Navathe, Amol S., Feiran Zhong, Victor J. Lei, Frank Y. Chang, Margarita Sordo, Maxim Topaz, Shamkant B. Navathe, Roberto A. Rocha & Li Zhou
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Sakhaee, Neda & Mark C. Wilson
Santiso, Sara, Arantza Casillas, Alicia Pérez & Maite Oronoz
Santiso, Sara, Arantza Casillas & Alicia Pérez
Santiso, Sara, Alicia Pérez, Arantza Casillas & Maite Oronoz
Valenzuela-Escárcega, Marco A, Özgün Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir & Clayton T Morrison
Wang, Xuan, Yu Zhang, Qi Li, Yinyin Chen & Jiawei Han
Weissman, Gary E., Michael O. Harhay, Ricardo M. Lugo, Barry D. Fuchs, Scott D. Halpern & Mark E. Mikkelsen
Zhu, Hongyin, Yi Zeng, Dongsheng Wang & Cunqing Huangfu
This list is based on CrossRef data as of 14 january 2021. Please note that it may not be complete. Sources presented here have been supplied by the respective publishers. Any errors therein should be reported to them.
References
References
Afantenos, S.; Karkaletsis, V.; and Stamatopoulos, P.
Agarwal, S., and Yu, H.
Ahlers, C. B.; Fiszman, M.; Demner-Fushman, D.; Lang, F.-M.; and Rindflesch, T. C.
AHRQ
Alex, B.; Grover, C.; Haddow, B.; Kabadjov, M.; Klein, E.; Matthews, M.; Roebuck, S.; Tobin, R.; and Wang, X.
Ando, R. K.; Dredze, M.; and Zhang, T.
2006 Trec 2005 genomics track experiments at ibm Watson. In
Proceedings of TREC 2005
.
Aronson, A. R., and Lang, F.-M.
Aronson, A. R., and Rindflesch, T. C.
1997 Query expansion using the umls Metathesaurus. In
Proceedings of the 1997 Annual Symposium of the American Medical Informatics Association (AMIA 1997)
, 485–489.
Aronson, A. R.; Mork, J. G.; Gay, C. W.; Humphrey, S. M.; and Rogers, W. J.
2004 The nlm indexing initiative’s Medical Text Indexer. In
Proceedings of the 11th World Congress on Medical Informatics (MEDINFO 2004)
, 268–272.
Aronson, A. R.; Demner-Fushman, D.; Humphrey, S. H.; Lin, J.; Liu, H.; Ruch, P.; Ruiz, M. E.; Smith, L. H.; Tanabe, L. K.; and Wilbur, W. J.
2005 Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents. In Voorhees, E. M., and Buckland, L. P., eds.,
Proceedings of the Fourteenth Text REtrieval Conference (TREC 2005)
, November 2005, Gaithersburg, Maryland. National Institute of Standards and Technology, pp. 36–45.
Aronson, A. R.
2001 Effective mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program. In
Proceeding of the 2001 Annual Symposium of the American Medical Informatics Association (AMIA 2001)
, 17–21.
Bada, M., and Hunter, L.
Bada, M.; Eckert, M.; Evans, D.; Garcia, K.; Shipley, K.; Sitnikov, D.; Baumgartner Jr., W. A.; Cohen, K. B.; Verspoor, K.; Blake, J. A.; and Hunter, L. E.
Baeza-Yates, R., and Ribeiro-Neto, B.
Bathia, N.; Shah, N.; Rubin, D.; Chiang, A.; and Mussen, M.
Baumgartner Jr., W. A.; Lu, Z.; Johnson, H. L.; Caporaso, J. G.; Paquette, J.; Lindemann, A.; White, E. K.; Medvedeva, O.; Cohen, K. B.; and Hunter, L.
Bekhuis, T., and Demner-Fushman, D.
2010 Towards automating the initial screening phase of a systematic review. In
Proceedings of the 13th World Congress on Medical and Health Informatics (MEDINFO 2010)
.
Biber, D.; Johansson, S.; Leech, G.; Conrad, S.; and Finegan, E.
Blake, J. B.
Blaschke, C., and Valencia, A.
Blaschke, C.; Andrade, M. A.; Ouzounis, C.; and Valencia, A.
Bmj Clinical Evidence
Booth, A., and O’Rourke, A.
Browne, A. C.; Divita, G.; Aronson, A. R.; and McCray, A. T.
2003 Umls language and vocabulary tools. In
Proceedings of the 2003 Annual Symposium of the American Medical Informatics Association (AMIA 2003)
, 798.
Bunescu, R.; Ge, R.; Kate, R. J.; Marcotte, E. M.; Mooney, R. J.; Ramani, A. K.; and Wong, Y. W.
Caporaso, J. G.; Baumgartner Jr., W. A.; Cohen, K. B.; Johnson, H. L.; Paquette, J.; and Hunter, L.
2005 Concept recognition and the TREC Genomics tasks. In
The Fourteenth Text REtrieval Conference (TREC 2005) Proceedings
.
Caporaso, J. G.; Baumgartner Jr., W. A.; Randolph, D. A.; Cohen, K. B.; and Hunter, L.
Card, S. K.; Mackinlay, J. D.; and Shneiderman, B.
Chang, G.; Roth, C. R.; Reyes, C. L.; Pornillos, O.; Chen, Y.-J.; and Chen, A. P.
Chapman, W. W.; Bridewell, W.; Hanbury, P.; Cooper, G. F.; and Buchanan, B. G.
Chatr-aryamontri, A.; Ceol, A.; Palazzi, L. M.; Nardelli, G.; Schneider, M. V.; Castagnoli, L.; and Cesareni, G.
Chen, L., and Friedman, C.
Chen, E. S.; Hripcsak, G.; Xu, H.; and Friedman, C.
Chun, H.-W.; Tsuruoka, Y.; Kim, J.-D.; Shiba, R.; Nagata, N.; Hishiki, T.; and Tsujii, J.
Cimino, J. J.; Aguirre, A.; Johnson, S. B.; and Peng, P.
Cohen, K. B., and Hunter, L.
Cohen, K. B.; Baumgartner Jr., W. A.; and Hunter, L.
Cohen, K. B.; Dolbey, A.; Acquaah-Mensah, G.; and Hunter, L.
Cohen, K. B.; Tanabe, L.; Kinoshita, S.; and Hunter, L.
2004 A resource for constructing customized test suites for molecular biology entity identification systems. In
HLT-NAACL 2004 Workshop: BioLINK 2004, Linking Biological Literature, Ontologies and Databases
, 1–8. Association for Computational Linguistics.
Cohen, K. B.; Fox, L.; Ogren, P.; and Hunter, L.
Cohen, K. B.; Fox, L.; Ogren, P. V.; and Hunter, L.
Cohen, K. B.; Hunter, L.; and Palmer, M.
2014a Assessment of software testing and quality assurance in natural language processing applications and a linguistically inspired approach to improving it. EternalS 2013, Springer, Lecture Notes in Computer Science.
Cohen, K. B.; Johnson, H. L.; Verspoor, K.; Roeder, C.; and Hunter, L. E.
Cohen, K. B.; Lanfranchi, A.; Corvey, W.; Baumgartner Jr., W. A.; Roeder, C.; Ogren, P. V.; Palmer, M.; and Hunter, L. E.
2010 Annotation of all coreference in biomedical text: Guideline selection and adaptation. In
BioTxtM 2010: 2nd workshop on building and evaluating resources for biomedical text mining
, 37–41.
Cohen, K. B.; Roeder, C.; Baumgartner Jr., W. A.; Hunter, L.; and Verspoor, K.
2010. Test suite design for biomedical ontology concept recognition systems. In
Proceedings of the Language Resources and Evaluation Conference
.
Cohen, K. B.; Christiansen, T.; and Hunter, L. E.
2011 Parenthetically speaking: Classifying the contents of parentheses for text mining. In
Proceeding of the 2011 Annual Symposium of the American Medical Informatics Association (AMIA 2011)
, 267–272.
Cohen, K. B.; Verspoor, K.; Bada, M.; Palmer, M.; and Hunter, L. E.
Collier, N.; Park, H. S.; Ogata, N.; Tateishi, Y.; Nobata, C.; Ohta, T.; Sekimizu, T.; Imai, H.; Ibushi, K.; and Tsujii, J.
Consortium, T. G. O.
Corbett, P.; Batchelor, C.; and Teufel, S.
Craven, M., and Kumlien, J.
1999 Constructing biological knowledge bases by extracting information from text sources. In Intelligent Systems for Molecular Biology, 77–86.
Czarnecki, J.; Nobeli, I.; Smith, A. M.; and Shepherd, A. J.
Damianos, L.; Day, D.; Hirschman, L.; Kozierok, R.; Mardis, S.; McEntee, T.; McHenry, C.; Miller, K.; Ponte, J.; Reeder, F.; van Guilder, L.; Wellner, B.; Wilson, G.; and Wohlever, S.
2002 Real users, real data, real problems: the MiTAP system for monitoring bio events. In
Proceedings of BTR2002: unified science and technology for reducing biological threats and countering terrorism
.
Demner-Fushman, D., and Lin, J.
2006a Answer extraction, semantic clustering, and extractive summarization for clinical question answering. In
Proceedings of the 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics (COLING/ACL 2006)
.
2006b Situated question answering in the clinical domain: Selecting the best drug treatment for diseases. In
Proceedings of COLING/ACL 2006 Workshop on Task-Focused Summarization and Question Answering
.
Demner-Fushman, D.; Mork, J. G.; Shooshan, S. E.; and Aronson, A. R.
Demner-Fushman, D.; Abhyankar, S.; Jimeno-Yepes, A.; Loane, R. F.; Rance, B.; Lang, F.-M.; Ide, N. C.; Apostolova, E.; and Aronson, A. R.
Demner-Fushman, D.; Chapman, W. W.; and McDonald, C. J.
Denny, J. C.; Smithers, J. D.; Spickard, A.; and Miller, R. A.
2002 A new tool to identify key biomedical concepts in text documents, with special application to curriculum content. In
Proceedings of the 1997 Annual Symposium of the American Medical Informatics Association (AMIA 1997)
, 1007.
Divoli, A.; Wooldridge, M.; and Hearst, M.
Donaldson, I.; Martin, J.; de Bruijn, B.; Wolting, C.; Lay, V.; Tuekam, B.; Zhang, S.; Baskin, B.; Bader, G.; Michalickova, K.; Pawson, T.; and Hogue, C.
Dowell, K.; McAndrews-Hill, M.; Hill, D.; Drabkin, H.; and Blake, J.
Du, X.-J.; Bathgate, R. A.; Samuel, C. S.; Dart, A. M.; and Summers, R. J.
Ebell, M. H.; Siwek, J.; Weiss, B. D.; Woolf, S. H.; Susman, J.; Ewigman, B.; and Bowman, M.
Elhadad, N.; Kan, M.-Y.; Klavans, J. L.; and McKeown, K. R.
Elhadad, N.
Ely, J. W.; Osheroff, J. A.; Gorman, P. N.; Ebell, M. H.; Chambliss, M. L.; Pifer, E. A.; and Stavri, P. Z.
Ely, J. W.; Osheroff, J. A.; Chambliss, M. L.; Ebell, M. H.; and Rosenbaum, M. E.
Exchange, P.
2010 Parkhurst exchange. Available from: http://www.parkhurstexchange.com/searchQA. Canadian monthly GP/FP journal, accessed 2010.
Fang, H.; Murphy, K.; Jin, Y.; Kim, J.; and White, P.
Flaherty, R. J.
Florance, V.
Fox, E. A., and Shaw, J. A.
1994 Combination of multiple searches. In
Proceedings of the 2nd Text REtrieval Conference (TREC-2)
, 243–252.
Friedman, C.; Sager, N.; Chi, E. C.; Marsh, E.; Christenson, C.; and Lyman, M. S.
1983 Computer structuring of free-text patient data. In
Proceedings of the Annual Symposium on Computer Application in Medical Care
, 688–691.
Friedman, C.; Alderson, P. O.; Austin, J. H.; Cimino, J. J.; and Johnson, S. B.
Friedman, C.; Liu, H.; Shagina, L.; Johnson, S.; and Hripcsak, G.
2001 Evaluating the umls as a source of lexical knowledge for medical language processing. In
Proc. AMIA Annual Symposium
, 189–193.
Friedman, C.
Fukuda, K.; Tamura, A.; Tsunoda, T.; and Takagi, T.
Gabow, A.; Leach, S. M.; Baumgartner Jr., W. A.; Hunter, L. E.; and Goldberg, D. S.
Gaizauskas, R.; Herring, P.; Oakes, M.; Beaulieu, M.; Willett, P.; Fowkes, H.; and Jonsson, A.
2001 Intelligent access to text: integrating information extraction technology into text browsers. In
Proceedings of the human language technology conference (HLT 2001)
, 189–193.
Gao, Q., and Vogel, S.
Garten, Y., and Altman, R. B.
Gasperin, C.; Karamanis, N.; and Seal, R.
2007 Annotation of anaphoric relations in biomedical full-text articles using a domain-relevant scheme. In
Proceedings of DAARC 2007
.
Gasperin, C.
Guyatt, G. H.; Sackett, D.; and Cook, D. J.
Hafner, C.; Baclawski, K.; Futrelle, R.; Fridman, N.; and Sampath, S.
1994 Creating a knowledge base of biological research papers. In
2nd International Conference on Intelligent Systems for Molecular Biology
, 147–155.
Hakenberg, J.; Plake, C.; Leaman, R.; Schroeder, M.; and Gonzalez, G.
Hakenberg, J.; Gerner, M.; Haeussler, M.; Solt, I.; Plake, C.; Schroeder, M.; Gonzalez, G.; Nenadic, G.; and Bergman, C. M.
Hanisch, D.; Fundel, K.; Mevissen, H.-T.; Zimmer, R.; and Fluck, J.
Hatzivassiloglou, V.; Duboué, P. A.; and Rzhetsky, A.
Haynes, R. B.; Wilczynski, N.; McKibbon, K. A.; Walker, C. J.; and Sinclair, J. C.
Hearst, M.; Divoli, A.; Buturu, H.; Ksikes, A.; Nakov, P.; and Wooldridge, M.
Hearst, M.; Divoli, A.; Jerry, Y.; and Wooldridge, M.
Hearst, M. A.
Hersh, W. R., and Greenes, R. A.
Hersh, W. R., and Voorhees, E. M.
Hersh, W. R.; Hickam, D. H.; Haynes, R. B.; and McKibbon, K. A.
Herskovic, J. R.; Tanaka, L. Y.; Hersh, W.; and Bernstam, E. V.
Hoffmann, R., and Valencia, A.
Horn, F.; Lau, A. L.; and Cohen, F. E.
Hripcsak, G.; Bakken, S.; Stetson, P. D.; and Patel, V. L.
Hu, Z.; Narayanaswami, M.; Ravikumar, K.; Vijay-Shanker, K.; and Wu, C.
Huang, M.; Zhu, X.; Hao, Y.; Payan, D. G.; Qu, K.; and Li, M.
Humphrey, S. M.; Rogers, W. J.; Kilicoglu, H.; Demner-Fushman, D.; and Rindflesch, T. C.
Humphreys, B. L., and Lindberg, D. A.
Hunter, L., and Cohen, K. B.
Hunter, L.; Lu, Z.; Firby, J.; Baumgartner Jr., W. A.; Johnson, H. L.; Ogren, P. V.; and Cohen, K. B.
Ide, N. C.; Loane, R. F.; and Demner-Fushman, D.
Jackson, P., and Moulinier, I.
Jacquemart, P., and Zweigenbaum, P.
2003 Towards a medical question-answering system: A feasibility study. In Baud, R.; Fieschi, M.; Beux, P. L.; and Ruch, P., eds., The New Navigators: From Professionals to Patients, volume 95 of Actes Medical Informatics Europe, Studies in Health Technology and Informatics, 463–468. Amsterdam: IOS Press.
Jaeschke, R.; Guyatt, G. H.; and Sackett, D. L.
Jenssen, T.-K.; Lægreid, A.; Komorowski, J.; and Hovig, E.
JFP
2010 Clinical inquiries. The Journal of Family Practice. Available from: http://www.jfponline.com. accessed 2010.
Jiang, J., and Zhai, C.
Jimeno-Yepes, A., and Aronson, A. R.
Jin, Y.; McDonald, R. T.; Lerman, K.; Mandel, M. A.; Carroll, S.; Liberman, M. Y.; Pereira, F. C.; Winters, R. S.; and White, P. S.
Jin, F.; Huang, M.; Lu, Z.; and Zhu, X.
Joachims, T.
Johnson, D.; Zou, Q.; Dionisio, J.; Liu, V.; and Chu, W.
Johnson, H. L.; Cohen, K. B.; Baumgartner Jr., W. A.; Lu, Z.; Bada, M.; Kester, T.; Kim, H.; and Hunter, L.
2006 Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.
Pac Symp Biocomput
, 28–39.
Johnson, S. B.
Jurafsky, D., and Martin, J. H.
Kan, M.-Y.; McKeown, K. R.; and Klavans, J. L.
2001b Domain-specific informative and indicative summarization for information retrieval. In
Proceedings of the Document Understanding Workshop (DUC 2001)
, New Orleans.
Kaner, C.; Bach, J.; and Pettichord, B.
Kaner, C.; Nguyen, H. Q.; and Falk, J.
Kann, M.; Ofran, Y.; Punta, M.; and Radivojac, P.
Katz, B.; Lin, J.; and Felshin, S.
2001 Gathering knowledge for a question answering system from heterogeneous information sources. In
Proceedings of the ACL 2001 Workshop on Human Language Technology and Knowledge Management
.
Kerrien, S.; Alam-Faruque, Y.; Aranda, B.; Bancarz, I.; Bridge, A.; Derow, C.; Dimmer, E.; Feuermann, M.; Friedrichsen, A.; Huntley, R.; Kohler, C.; Khadake, J.; Leroy, C.; Liban, A.; Lieftink, C.; Montecchi-Palazzi, L.; Orchard, S.; Risse, J.; Robbe, K.; Roechert, B.; Thorneycroft, D.; Zhang, Y.; Apweiler, R.; and Hermjakob, H.
Kilicoglu, H., and Bergler, S.
2009 Syntactic dependency based heuristics for biological event extraction. In
BioNLP ’09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
, 119–127.
Kim, J.-D.; Ohta, T.; Tateisi, Y.; and Tsujii, J.
Kim, J.-D.; Ohta, T.; Pyysalo, S.; Kano, Y.; and Tsujii, J.
2009 Overview of BioNLP’09 shared task on event extraction. In
BioNLP 2009 Companion Volume: Shared Task on Entity Extraction
, 1–9.
Kipper-Schuler, K.
Kogan, Y.; Collier, N.; Pakhomov, S.; and Krauthammer, M.
2005 Towards semantic role labeling & IE in the medical literature. In
AMIA 2005 Symposium Proceedings
, 410–414.
Krallinger, M.; Leitner, F.; Rodriguez-Penagos, C.; and Valencia, A.
Krallinger, M.; Leitner, F.; and Valencia, A.
2007 Assessment of the second BioCreative PPI task: automatic extraction of protein–protein interactions. In
Proceedings of the Second BioCreative Challenge Evaluation Workshop
.
Kucera, H.; Francis, W. N.; and Carroll, J. B.
Lancaster, F. W.
Laupacis, A.; Wells, G.; Richardson, W. S.; and Tugwell, P.
Lesk, M.
Levine, M.; Walter, S.; Lee, H.; Haines, T.; Holbrook, A.; and Moyer, V.
Lin, J.
Liu, H.; Christiansen, T.; Baumgartner Jr., W. A.; and Verspoor, K.
Lu, Z.; Cohen, B. K.; and Hunter, L.
Marcus, M. P.; Marcinkiewicz, M. A.; and Santorini, B.
McCray, A. T.; Burgun, A.; and Bodenreider, O.
2001 Aggregating UMLS semantic types for reducing conceptual complexity. In
Proceedings of 10th World Congress on Medical Informatics (MEDINFO 2001)
, 216–220.
Müller, H.-M.; Kenny, E. E.; and Sternberg, P. W.
Miller, G.
Morgan, A. A.; Hirschman, L.; Colosimo, M.; Yeh, A. S.; and Colombe, J. B.
Narayanaswamy, M.; Ravikumar, K. E.; and Shanker, V. K.
Neves, M. L.; Carazo, J.-M.; and Pascual-Montano, A.
Ng, S.-K.
Nielsen, J.
1989 Usability engineering at a discount. In
Proceedings of the third international conference on human-computer interaction
, 394–401.
Ogren, P.; Cohen, K.; and Hunter, L.
2005 Implications of compositionality in the Gene Ontology for its curation and usage. In
Pacific Symposium on Biocomputing
, 174–185.
OLDMEDLINE
Olsson, F.; Eriksson, G.; Franzén, K.; Asker, L.; and Lidén, P.
2002 Notions of correctness when evaluating protein name taggers. In
Proceedings of the 19th international conference on computational linguistics (COLING 2002)
, 765–771.
Ono, T.; Hishigaki, H.; Tanigami, A.; and Takagi, T.
Palmer, M.; Kingsbury, P.; and Gildea, D.
Pestian, J. P.; Brew, C.; Matykiewicz, P.; Hovermale, D.; Johnson, N.; Cohen, K. B.; and Duch, W.
2007 A shared task involving multi-label classification of clinical free text. In
Proceedings of BioNLP 2007
. Association for Computational Linguistics.
Pratt, A. W., and Pacak, M. G.
Pratt, W., and Yetisgen-Yildiz, M.
2003 A study of biomedical concept identification: MetaMap vs. people. In
Proceeding of the 2003 Annual Symposium of the American Medical Informatics Association (AMIA 2003)
, 529–533.
Pyysalo, S.; Ohta, T.; Kim, J.-D.; and Tsujii, J.
Regev, Y.; Finkelstein-Landau, M.; Feldman, R.; Gorodetsky, M.; Zheng, X.; Levy, S.; Charlab, R.; Lawrence, C.; Lippert, R. A.; Zhang, Q.; and Shatkay, H.
Richardson, W. S., and Wilson, M. C.
Richardson, W. S.; Wilson, M. C.; Nishikawa, J.; and Hayward, R. S.
Rindflesch, T.; Tanabe, L.; Weinstein, J.; and Hunter, L.
2000 EDGAR: extraction of drugs, genes and relations from the biomedical literature. In
Pacific Symposium on Biocomputing
, 515–524.
Rosario, B., and Hearst, M. A.
2004 Classifying semantic relations in bioscience texts. In
Proceedings of ACL 2004
, 430–437.
Rosario, B., and Hearst, M.
2005 Multi-way Relation Classification: Application to Protein–protein Interactions. In
Proceedings of the HLT-NAACL
, volume 5.
Rosenberg, W., and Donald, A.
Rzhetsky, A.; Iossifov, I.; Koike, T.; Krauthammer, M.; Kra, P.; Morris, M.; Yu, H.; Duboué, P. A.; Weng, W.; Wilbur, W. J.; Hatzivassiloglou, V.; and Friedman, C.
Sackett, D. L.; Straus, S. E.; Richardson, W. S.; Rosenberg, W.; and Haynes, R. B.
Saeed, M.; Villarroel, M.; Reisner, A. T.; Clifford, G.; Lehman, L.; Moody, G.; Heldt, T.; Kyaw, T. H.; Moody, B.; and Mark, R. G.
Sandusky, R., and Tenopir, C.
Schuemie, M. J.; Kors, J. A.; and Mons, B.
Schwartz, A., and Hearst, M.
Settles, B.
Shah, P. K.; Jensen, L. J.; Boué, S.; and Bork, P.
Shapiro, A. R.
1980 A system for conceptual analysis of medical practices. In
Proceedings of the Annual Symposium on Computer Application in Medical Care
, 867–872.
Shatkay, H.; Chen, N.; and Blostein, D.
Siadaty, M. S.; Shu, J.; and Knaus, W. A.
Sibanda, T., and Uzuner, O.
Smalheiser, N. R., and Swanson, D. R.
Smith, R., and Chalmers, I.
Srinivasan, P.
Stetson, P. D.; Johnson, S. B.; Scotch, M.; and Hripcsak, G.
2002 The sublanguage of cross-coverage. In
Proc. AMIA 2002 Annual Symposium
, 742–746.
Stevenson, M.; Guo, Y.; Gaizauskas, R.; and Martinez, D.
Sundheim, B. M.
Tanabe, L.; Scherf, U.; Smith, L. H.; Lee, J. K.; Hunter, L.; and Weinstein, J. N.
Tateisi, Y.; Yakushiji, A.; Ohta, T.; and Tsujii, J.
2005 Syntax annotation for the GENIA corpus. In
Second international joint conference on natural language processing: Companion volume
, 220–225.
The Gene Ontology Consortium
Ting, K. M., and Witten, I. H.
US-Congress
Uzuner, O.; South, B. R.; Shen, S.; and DuVall, S. L.
Uzuner, O.; Luo, Y.; and Szolovits, P.
Varadan, R.; Assfalg, M.; Raasi, S.; Pickart, C.; and Fushman, D.
Verspoor, K.; Dvorkin, D.; Cohen, K. B.; and Hunter, L.
Verspoor, K.; Cohen, K. B.; Lanfranchi, A.; Warner, C.; Johnson, H. L.; Roeder, C.; Choi, J. D.; Funk, C.; Malenkiy, Y.; Eckert, M.; Xue, N.; Baumgartner Jr., W. A.; Bada, M.; Palmer, M.; and Hunter, L. E.
Verspoor, C.; Joslyn, C.; and Papcun, G.
2003 The Gene Ontology as a source of lexical semantic knowledge for a biological natural language processing application. In
Proceedings of the SIGIR’03 Workshop on Text Analysis and Search for Bioinformatics
.
Voorhees, E. M., and Harman, D. K.
Voorhees, E. M.
Wang, P.; Morgan, A. A.; Zhang, Q.; Sette, A.; and Peters, B.
Wattarujeekrit, T.; Shah, P. K.; and Collier, N.
Weeber, M.; Mork, J.; and Aronson, A.
Weizenbaum, J.
Wiegers, T. C.; Davis, A. P.; Cohen, K. B.; Hirschman, L.; and Mattingly, C. J.
Wilczynski, N.; McKibbon, K. A.; and Haynes, R. B.
2001 Enhancing retrieval of best evidence for health care from bibliographic databases: Calibration of the hand search of the literature. In
Proceedings of 10th World Congress on Medical Informatics (MEDINFO 2001)
, 390–393.
Xenarios, I.; Salwinski, L.; Duan, X. J.; Higney, P.; Kim, S.-M.; and Eisenberg, D.
Xu, H.; Anderson, K.; Grann, V. R.; and Friedman, C.
Xu, R.; Supekar, K.; Morgan, A.; Das, A.; and Garber, A.
2008 Unsupervised method for automatic construction of a disease dictionary from a large free text collection. In
AMIA Annu Symp Proc
, 820–824.
Yang, X. F.; Su, J.; Zhou, G. D.; and Tan, C. L.
Yang, X.; Zhou, G.; Su, J.; and Tan, C. L.
2004b Improving noun phrase coreference resolution by matching strings. In
IJCNLP04
, 326–333.
Yeh, A.; Morgan, A.; Colosimo, M.; and Hirschman, L.
Yuan, X.; Hu, Z.; Wu, H.; Torii, M.; Narayanaswami, M.; Ravikumar, K.; Vijay-Shanker, K.; and Wu, C.
Zhang, J.; Ga, J.; Zhou, M.; and Wang, J.
Zieman, Y. L., and Bleich, H. L.
1997 Conceptual mapping of user’s queries to medical subject headings. In
Proceedings of the 1997 Annual Symposium of the American Medical Informatics Association (AMIA 1997)
, 519–522.
Zou, Q.; Chu, W. W.; Morioka, C.; Leazer, G. H.; and Kangarloo, H.
2003 Indexfinder: A method of extracting key concepts from clinical texts for indexing. In
Proceedings of the 2003 Annual Symposium of the American Medical Informatics Association (AMIA 2003)
, 763–767.
Subjects
BIC Subject: CFX – Computational linguistics
BISAC Subject: LAN009000 – LANGUAGE ARTS & DISCIPLINES / Linguistics / General