The biomedical discourse relation bank

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Prasad, Rashmi ^a   McRoy, Susan ^d   Frid, Nadya ^c   Joshi, Aravind ^a,b   Yu, Hong ^c,d  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

^d University of Wisconsin Milwaukee   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL DOMAIN; BIOMEDICAL TEXT; CLASSIFIER PERFORMANCE; DISCOURSE PROCESSING; EVALUATING METHOD; HIGH RELIABILITY; NEWS ARTICLES; POOR PERFORMANCE;

EXPERIMENTS; SEMANTICS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; DATA MINING; HUMAN; METHODOLOGY; NATURAL LANGUAGE PROCESSING; SEMANTICS;

COMPUTATIONAL BIOLOGY; DATA MINING; HUMANS; NATURAL LANGUAGE PROCESSING; SEMANTICS; SOFTWARE;

EID: 79956216619     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-188     Document Type: Article

References (102)

1. Jensen L, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nature Reviews Genetics 2006, 7:119-129. 10.1038/nrg1768, 16418747.
2. Krallinger M, Valencia A. Text-mining and information-retrieval services for molecular biology. Genome Biol 2005, 6:224. 10.1186/gb-2005-6-7-224, 1175978, 15998455.
3. Shatkay H, Feldman R. Mining the biomedical literature in the genomic era: an overview. J Comput Biol 2003, 10:821-855. 10.1089/106652703322756104, 14980013.
4. Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. Frontiers of biomedical text mining: current progress. Briefings in Bioinformatics 2007, 8:358-375. 10.1093/bib/bbm045, 2516302, 17977867.
5. Fukuda K, Tamura A, Tsunoda T, Takagi T. Toward information extraction: identifying protein names from biological papers. Proceedings of the Pacific Symposium on Biocomputing 1998, 707-718.
6. McDonald R, Pereira F. Identifying gene and protein mentions in text using conditional random fields. BMC Bioinformatics 2005, 6(Suppl 1):S6. 10.1186/1471-2105-6-S1-S6, 1866379, 16351755.
7. Liu J, Huang M, Zhu X. Recognizing Biomedical Named Entities Using Skip-Chain Conditional Random Fields. Proceedings of the Workshop on Biomedical Natural Language Processing, Uppsala, Sweden 2010, 10-18.
8. Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics 2001, 17(Suppl 1):S74-82. 10.1093/bioinformatics/17.suppl_1.S74, 11472995.
9. Li Z, Liu F, Antieau L, Yu H. Lancet: a high precision medication event extraction system for clinical text. Journal of the American Medical Informatics Association (JAMIA) 2010, 17(5):563-567.
10. Wilbur WJ. A thematic analysis of the AIDS literature. Proceedings of Pacific Symposium on Biocomputing 2002, 386-397.
11. Cao Y, Li Z, Liu F, Agarwal S, Zhang Q, Yu H. An IR-aided machine learning framework for the BioCreative II.5 Challenge. IEEE/ACM Transactions on Computational Biololgy and Bioinformatics 2010, 7(3):454-461.
12. Srinivasan P, Libbus B. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 2004, 20(Suppl 1):I290-I296. 10.1093/bioinformatics/bth914, 15262811.
13. Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B. Automatically generating gene summaries from biomedical literature. Proceedings of the Pacific Symposium on Biocomputing, Maui, Hawaii 2006, 40-51.
14. Agarwal S, Yu H. FigSum: automatically generating structured text summaries for figures in biomedical literature. Proceedings of the 2009 AMIA Annual Symposium, San Francisco, CA 2009, 6-10.
15. Naderi N, Witte R. Ontology-Based Extraction and Summarization of Protein Mutation Impact Information. Proceedings of the ACL Workshop on Biomedical Natural Language Processing, Uppsala, Sweden 2010, 128-129.
16. Plaza L, Stevenson M, Diaz A. Improving Summarization of Biomedical Documents Using Word Sense Disambiguation. Proceedings of the ACL Workshop on Biomedical Natural Language Processing, Uppsala, Sweden 2010, 55-63.
17. Chen SC, Zhao T, Gordon GJ, Murphy RF. Automated image analysis of protein localization in budding yeast. Bioinformatics 2007, 23(13):i66-171. 10.1093/bioinformatics/btm206, 17646347.
18. Shatkay H, Chen N, Blostein D. Integrating image data into biomedical text categorization. Bioinformatics 2006, 22:e446-453. 10.1093/bioinformatics/btl235, 16873506.
19. Yu H, Lee M. Accessing bioscience images from abstract sentences. Bioinformatics 2006, 22:e547-556. 10.1093/bioinformatics/btl261, 16873519.
20. Yu H, Agarwal S, Johnston M, Cohen A. Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension. Journal of Biomedical Discovery and Collaboration 2009, 4:1. 10.1186/1747-5333-4-1, 2631451, 19126221.
21. Yu H, Liu F, Ramesh BP. Automatic Figure Ranking and User Interfacing for Intelligent Figure Search. PLoS ONE 2010, 5(10):e12983. 10.1371/journal.pone.0012983, 2951344, 20949102.
22. Yu H, Lee M, Kaufman D, Ely J, Oshero JA, Hripcsak G, Cimino J. Development, implementation, and a cognitive evaluation of a definitional question answering system for physicians. Journal of Biomedical Informatics 2007, 40:236-251. 10.1016/j.jbi.2007.03.002, 17462961.
23. Cao YG, Cimino JJ, Ely J, Yu H. Automatically extracting information needs from complex clinical questions. Journal of Biomedical Informatics 2010, 43:962-971. 10.1016/j.jbi.2010.07.007, 20670693.
24. Garzone M. Automated classification of citations using linguistic semantic grammars. PhD thesis 1996, The University of Western Ontario, Ontario, Canada.
25. Garzone M, Mercer R. Towards an automated citation classifier. Proceedings on 13th Biennial Conference of the Canadian Society for Computational Studies of Intelligence 2000, 337-346.
26. DiMarco C, Mercer R. Toward a catalogue of citation-related rhetorical cues in scientific texts. Proceedings of Pacific Association for Computational Linguistics (PACLING 2003), Halifax, Canada 2003,
27. Light M, Qiu X, Srinivasan P. The language of bioscience: fact, speculations, and statements in between. Proceedings of the HLT-NAACL 2004 Workshop: BioLINK, Linking Biological Literature, Ontologies and Databases, Boston, MA 2004, 17-24.
28. Shatkay H, Pan F, Rzhetsky A, Wilbur WJ. Multi-Dimensional Classification Of Biomedical Text: Toward Automated, Practical Provision of High-Utility Text to Diverse Users. Bioinformatics 2008, 24(18):2086-2093. 10.1093/bioinformatics/btn381, 2530883, 18718948.
29. Wilbur WJ, Rzhetsky A, Shatkay H. New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinformatics 2006, 7:356. 10.1186/1471-2105-7-356, 1559725, 16867190.
30. Mullen T, Mizuta Y, Collier N. A baseline feature set for learning rhetorical zones using full articles in the biomedical domain. ACM SIGKDD Explorations Newsletter 2005, 7:52-58.
31. Agarwal S, Yu H. Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion. Bioinformatics 2009, 25(23):3174-3180. 10.1093/bioinformatics/btp548, 2913661, 19783830.
32. Biber D, Jones JK. Merging corpus linguistic and discourse analytic research goals: Discourse units in biology research articles. Corpus Linguistics and Linguistic Theory 2005, 1(2):151-182.
33. Hearst MA. TextTiling: Segmenting text into multi-paragraph subtopic passages. Computational Linguistics 1997, 23:33-64.
34. jae Kim J, Zhang Z, Park JC, Ng SK. BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature. Bioinformatics 2006, 22(5):597-605. 10.1093/bioinformatics/btk016, 16368768.
35. Castano J, Zhang J, Pustejovsky J. Anaphora resolution in biomedical literature. International Symposium on Reference Resolution 2002,
36. Szarvas G, Vincze V, Farkas R, Csirik J. The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts. Proceedings of BioNLP 2008: Current Trends in Biomedical Natural Language Processing, Columbus, Ohio 2008, 38-45.
37. Agarwal S, Yu H. Detecting Hedge Cues and their Scope in Biomedical Literature with Conditional Random Fields. Journal of Biomedical Informatics 2010, 43(6):953-961. 10.1016/j.jbi.2010.08.003, 20709188.
38. Agarwal S, Yu H. Biomedical Negation Scope Detection with Conditional Random Fields. Journal of the Americian Medical Informatics Association (JAMIA) 2010, 17:696-701.
39. Kim J, Ohta T, Tateisi Y, Tsujii J. GENIA corpus - semantically annotated corpus for bio-textmining. Bioinformatics 2003, 19(Suppl 1):i180-182. 10.1093/bioinformatics/btg1023, 12855455.
40. Liakata M, Soldatova L. Guidelines for the annotation of General Scientific Concepts. 2008, [JISC Project Report]., http://ie-repository.jisc.ac.uk
41. Liakata M, Q C, Soldatova LN. Semantic Annotation of Papers: Interface & Enrichment Tool (SAPIENT). Proceedings of the BioNLP 2009 Workshop, Boulder, Colorado: Association for Computational Linguistics 2009, 193-200., http://www.aclweb.org/anthology/W09-1325
42. Tarassishin L, Yin YI, Bassit B, Li YM. Processing of Notch and amyloid precursor protein by gamma-secretase is spatially distinct. Proceedings of the National Academy of Sciences USA 2004, 101(49):17050-17055.
43. Verpy E, Leibovici M, Petit C. Characterization of otoconin-95, the major protein of murine otoconia, provides insights into the formation of these inner ear biominerals. Proceedings of the National Academy of Sciences USA 1999, 96(2):529-534.
44. Pitler E, Nenkova A. Using Syntax to Disambiguate Explicit Discourse Connectives in Text. Proceedings of the 47th Annual Meeting of the ACL and the 4th IJCNLP of the AFNLP (ACL-IJCNLP 2009: Short Papers), Suntec, Singapore 2009, 13-16.
45. Ramesh BP, Yu H. Identifying Discourse Connectives in Biomedical Text. Proceedings of the AMIA 2010 Symposium, Washington, D.C 2010, 657-661.
46. Dinesh N, Lee A, Miltsakaki E, Prasad R, Joshi A, Webber B. Attribution and the (Non)-Alignment of Syntactic and Discourse Arguments of Connectives. Proceedings of the ACL Workshop on Frontiers in Corpus Annotation II: Pie in the Sky, Ann Arbor, MI 2005, 29-36.
47. Wellner B, Pustejovsky J. Automatically Identifying the Arguments of Discourse Connectives. Proceedings of EMNLP-CoNLL, Prague, Czech Republic 2007, 92-101.
48. Elwell R, Baldridge J. Discourse connective argument identification with connective specific rankers. Proceedings of the IEEE International Conference on Semantic Computing (ICSC), Santa Clara, CA 2008, 198-205.
49. Prasad R, Dinesh N, Lee A, Miltsakaki E, Robaldo L, Joshi A, Webber B. The Penn Discourse TreeBank 2.0. Proceedings of 6th International Conference on Language Resources and Evaluation (LREC), Marrackech, Morocco 2008,
50. Prasad R, Joshi A, Webber B. Exploiting Scope for Shallow Discourse Parsing. Proceedings of the Seventh International Conference on Language Resources and their Evaluation (LREC), Valletta, Malta 2010, 2076-2083.
51. Miltsakaki E, Dinesh N, Prasad R, Joshi A, Webber B. Experiments on Sense Annotation and Sense Disambiguation of Discourse Connectives. Proceedings of the Fourth Workshop on Treebanks and Linguistic Theories (TLT), Barcelona, Spain 2005,
52. Pitler E, Raghupathy M, Mehta H, Nenkova A, Lee A, Joshi A. Easily Identifiable Discourse Relations. Proceedings of the 22nd International Conference on Computational Linguistics (COLING 2008: Posters), Manchester, U.K 2008, 87-90.
53. Marcu D, Echihabi A. An Unsupervised Approach to Recognizing Discourse Relations. Proceedings of the 40th Annual Meeting of the Association for Computational Linguistics, Philadelphia, PA 2002, 368-375.
54. Lin Z, Kan MY, Ng HT. Recognizing Implicit Discourse Relations in the Penn Discourse Treebank. Proceedings of the Conference on Empirical Methods in Natural Language Processing, Suntec, Singapore 2009, 343-351.
55. Pitler E, Louis A, Nenkova A. Automatic sense prediction for implicit discourse relations in text. Proceedings of the 47th Annual Meeting of the ACL and the 4th IJCNLP of the AFNLP, Suntec, Singapore 2009, 683-691.
56. Wellner B. Sequence Models and Re-ranking Methods for Discourse Parsing. PhD thesis, Brandeis University, Boston, MA 2009,
57. Zhi-Min Z, Man L, Yu X, Zheng-Yu N, Jian S. Predicting Discourse Connectives for Implicit Discourse Relation Recognition. Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010: Posters), Beijing, China 2010, 1507-1514.
58. Louis A, Joshi A, Prasad R, Nenkova A. Using Entity Features to Classify Implicit Discourse Relations. Proceedings of the SIGDIAL Conference, Tokyo, Japan 2010, 59-62.
59. Marcu D. The rhetorical parsing, summarization and generation of natural language texts. PhD thesis, University of Toronto 1997,
60. Marcus MP, Santorini B, Marcinkiewicz MA. Building a Large Annotated Corpus of English: The Penn Treebank. Computational Linguistics 1993, 19(2):313-330.
61. Agarwal S, Choubey L, Yu H. Automatically Classifying the Role of Citations in Biomedical Articles. Proceedings of American Medical Informatics Association Fall Symposium (AMIA), Washington, D.C 2010, 11-15.
62. Webber B, Joshi A. Anchoring a Lexicalized Tree-Adjoining Grammar for Discourse. Discourse Relations and Discourse Markers: Proceedings of the Conference 1998, 86-92. Somerset, New Jersey: Association for Computational Linguistics, Stede M, Wanner L, Hovy E.
63. Webber B, Joshi A, Stone M, Knott A. Anaphora and Discourse Structure. Computational Linguistics 2003, 29(4):545-587.
64. Asher N. Reference to Abstract Objects 1993, Dordrecht: Kluwer.
65. Knott A. Review of 'coherence in natural language: data structures and applications'. Computational Linguistics 2007, 33:591-595.
66. Mann W, Thompson S. Rhetorical Structure Theory. Toward a Functional Theory of Text Organization. Text 1988, 8(3):243-281.
67. Polanyi L. The Linguistic Discourse Model: Towards a Formal Theory of Discourse Structure. 1987, Tech. Rep. 6409, Bolt Beranek and Newman, Inc., Cambridge, Mass.
68. Clegg A, Shepherd A. Evaluating and integrating treebank parsers on a biomedical corpus. Proceedings of the Workshop on Software, Ann Arbor, Michigan 2005, 14-33.
69. Asher N, Lascarides A. Logics of conversation 2003, Cambridge University Press.
70. Wolf F, Gibson E. Representing Discourse Coherence: A corpus-based study. Computational Linguistics 2005, 31(2):249-288.
71. Lee A, Prasad R, Joshi A, Dinesh N, Webber B. Complexity of Dependencies in Discourse: Are Dependencies in Discourse More Complex Than in Syntax?. Proceedings of the 5th International Workshop on Treebanks and Linguistic Theories (TLT), Prague, Czech Republic 2006,
72. Lee A, Prasad R, Joshi A, Webber B. Departures from Tree Structures in Discourse: Shared Arguments in the Penn Discourse Treebank. Proceedings of the Constraints in Discourse III Workshop, Potsdam, Germany 2008,
73. Miltsakaki E, Prasad R, Joshi A, Webber B. Annotating discourse connectives and their arguments. Proceedings of the HLT/NAACL Workshop on Frontiers in Corpus Annotation, Boston, MA 2004, 9-16.
74. Yu H, Frid N, McRoy S, Prasad R, Lee A, Joshi A. A Pilot Annotation to Investigate Discourse Connectivity in Biomedical Text. Proceedings of the ACL:HLT 2008 BioNLP Workshop, Columbus, Ohio 2008, 92-93.
75. Yu H, Frid N, McRoy S, Simpson P, Prasad R, Lee A, Joshi A. Exploring Discourse Connectivity in Biomedical Text for Text Mining. Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology BioLINK SIG Meeting, Toronto, Canada 2008,
76. Blair-Goldensohn S, McKeown KR, Rambow O. Building and Refining Rhetorical-Semantic Relation Models. Proceedings of NAACL-HLT, Rochester, NY 2007, 428-435.
77. Webber B, Prasad R. Sentence-Initial Discourse Connectives, Discourse Structure and Semantics. Proceedings of the Workshop on Formal and Experimental Approaches to Discourse Particles and Modal Adverbs, Hamburg, Germany 2008,
78. Webber B. Genre distinctions for discourse in the Penn TreeBank. Proceedings of the 47th Annual Meeting of the ACL and the 4th IJCNLP of the AFNLP, Suntec, Singapore 2009, 674-682.
79. Prasad R, Joshi A. A Discourse-based Approach to Generating Why-Questions from Texts. Proceedings of the Workshop on the Question Generation Shared Task and Evaluation Challenge, Arlington, VA 2008,
80. Robaldo L, Miltsakaki E, Hobbs J. Refining the Meaning of Sense Labels in PDTB: "Concession". Proceedings of Symposium on Semantics in Text Processing (STEP), Venice, Italy 2008, 207-219.
81. Prasad R, Joshi A, Webber B. Realization of Discourse Relations by Other Means: Alternative Lexicalizations. Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010: Posters), Beijing, China 2010, 1023-1031.
82. Hernault H, Bollegala D, Ishizuka M. A Semi-Supervised Approach to Improve Classification of Infrequent Discourse Relations Using Feature Vector Extension. Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP-2010), Cambridge, MA 2010, 399-409.
83. Louis A, Joshi A, Nenkova A. Discourse Indicators for Content Selection in Summarization. Proceedings of the SIGDIAL Conference, Tokyo, Japan 2010, 147-156.
84. Lin Z, Ng HT, Kan MY. A PDTB-Styled End-to-End Discourse Parser. Tech. Rep. TRB8/10, School of Computing, National University of Singapore 2010,
85. Zeyrek D, Webber B. A Discourse Resource for Turkish: Annotating Discourse Connectives in the METU Corpus. Proceedings of the 6th Workshop on Asian Language Resources, Hyderabad, India 2008, 65-71.
86. Oza U, Prasad R, Kolachina S, Sharma DM, Joshi A. The Hindi Discourse Relation Bank. Proceedings of the Third Linguistic Annotation Workshop (LAW-III), ACL-IJCNLP-2009, Suntec, Singapore 2009, 158-161.
87. Oza U, Prasad R, Kolachina S, Meena S, Sharma DM, Joshi A. Experiments with Annotating Discourse Relations in the Hindi Discourse Relation Bank. Proceedings of the 7th International Conference on Natural Language Processing (ICON-2009), Hyderabad, India 2009,
88. Xue N. Annotating Discourse Connectives in the Chinese Treebank. Proceedings of the ACL Workshop on Frontiers in Corpus Annotation II: Pie in the Sky, Ann Arbor, MI 2005, 84-91.
89. Mladova L, Zikanova S, Hajicova E. From Sentence to Discourse: Building an Annotation Scheme for Discourse Based on Prague Dependency Treebank. Proceedings of the Sixth International Language Resources and Evaluation (LREC'08) 2008,
90. Tonelli S, Riccardi G, Prasad R, Joshi A. Annotation of Discourse Relations for Conversational Spoken Dialogs. Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC 2010), Valletta, Malta 2010, 2084-2090.
91. Prasad R, Mcroy S, Frid N, Yu H. The Biomedical Discourse Relation Bank (BioDRB) Annotation Guidelines. 2010, Http://spring.ims.uwm.edu/uploads/biodrb_guidelines.pdf
92. Karttunen L. Presupposition and Linguistic Context. Theoretical Linguistics 1974, 1:181-94.
93. Miltsakaki E, Robaldo L, Lee A, Joshi A. Sense Annotation in the Penn Discourse Treebank. Computational Linguistics and Intelligent Text Processing, Lecture Notes in Computer Science 2008, 4919:275-286.
94. Verspoor K, Cohen KB, Hunter L. The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinformatics 2009, 10:183. 10.1186/1471-2105-10-183, 2714574, 19527520.
95. Cohen WW, Singer Y. A simple, fast, and effective rule learner. Proceedings of the sixteenth national conference on Artificial intelligence and the eleventh Innovative applications of artificial intelligence conference innovative applications of artificial intelligence (AAAI '99/IAAI '99), Orlando, FL 1999, 335-342.
96. Harris Z. A Grammar of English on mathematical principles 1982, New York: Wiley.
97. Harris Z. A theory of language and information: a mathematical approach 1991, Oxford: Clarendon Press.
98. Friedman C, Kra P, Rzhetsky A. Two biomedical sublanguages: A description based on the theories of Zellig. Journal of Biomedical Informatics 2002, 35(4):222-235. 10.1016/S1532-0464(03)00012-1, 12755517.
99. Gabbay I, Sutcliffe R. A qualitative comparison of scientific and journalistic texts from the perspective of extracting definitions. Proceedings of the ACL Workshop on Question Answering in Retricted Domains, Barcelona, Spain 2004, 16-22.
100. Salanger-Meyer F. Discoursal movements in medical English abstracts and their linguistic exponents: A genre analysis study. INTERFACE: Journal of Applied Linguistics 1990, 4(2):107-124.
101. Swales J. Genre Analysis: English in Academic and Research Settings 1990, Cambridge, England: Cambridge University Press.
102. Sollaci LB, Pereira MG. The introduction, methods, results, and discussion (IMRAD) structure: a fifty-year survey. Journal of the Medical Library Association 2004, 92(3):364-371. 442179, 15243643.