BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Tsai, Richard ^a   Chou, Wen Chi ^a   Su, Ying Shan ^a,b   Lin, Yu Chun ^a   Sung, Cheng Lung ^a   Dai, Hong Jie ^a   Yeh, Irene Tzu Hsuan ^a,c   Ku, Wei ^a   Sung, Ting Yi ^a   Hsu, Wen Lian ^a  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^b Howard Hughes Medical Institute   (United States)

^c CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC PROCESSING; AUTOMATICALLY GENERATED; BIOMEDICAL LITERATURE; CLASSIFICATION ACCURACY; INFORMATION EXTRACTION SYSTEMS; LARGE SCALE EXPERIMENTS; NATURAL LANGUAGE PROCESSING; SEMANTIC ROLE LABELING;

BIOINFORMATICS; EXPERIMENTS; LINGUISTICS; PROTEINS; SEMANTICS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

ARTICLE; COMPUTER PROGRAM; EXTRACTION; GRAMMAR; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INFORMATION SYSTEM; LANGUAGE PROCESSING; MACHINE LEARNING; PROTEIN PROTEIN INTERACTION; SEMANTICS; ARTIFICIAL INTELLIGENCE; BIOLOGY; COMPUTER SIMULATION; LINGUISTICS; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PUBLICATION; THEORETICAL MODEL;

NES;

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; INFORMATION STORAGE AND RETRIEVAL; MODELS, THEORETICAL; NATURAL LANGUAGE PROCESSING; PERIODICALS AS TOPIC; SEMANTICS; VOCABULARY, CONTROLLED;

EID: 36048934274     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-325     Document Type: Article

References (39)

1. Manning CD Schütze H Foundations of Statistical Natural Language Processing Cambridge, MA, MIT Press 1999.
2. Lee I Date SV Adai AT Marcotte EM A probabilistic functional network of yeast genes Science 2004, 306(5701):1555-1558. 10.1126/science.1099511 15567862
3. Ramani AK Bunescu RC Mooney RJ Marcotte EM Consolidating the set of know human proteinprotein interactions in preparation for large-scale mapping of the human interactome Genome Biology 2005, 6(5):r40. 1175952 15892868 10.1186/gb-2005-6-5-r40
4. Wren JD Extending the mutual information measure to rank inferred literature relationships BMC Bioinformatics 2004, 5(145):. 526381 15471547
5. Chen H Sharp BM Content-rich biological network constructed by mining PubMed abstracts BMC Bioinformatics 2004, 5(147):.
6. Donaldson I Martin J Bruijn B Wolting C Lay V Tuekam B Zhang S Baskin B Bader GD Michalickova K Pawson T Hogue CWV PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine BMC Bioinformatics 2003, 4(11):. 153503 12689350
7. Ray S Craven M Representing sentence structure in hidden Markov models for information extraction 2001.
8. Zhao S Grishman R Extracting relations with integrated information using kernel methods: Arbor, Michigan. 2005.
9. Bunescu RC Mooney RJ Subsequence kernels for relation extraction: Vancouver, BC. 2005.
10. Hacioglu K Pradhan S WayneWard Martin JH Jurafsky D Shallow Semantic Parsing using Support Vector Machines 2003.
11. Hörnig R Rauh R Strube G EVENTS-II: Modeling event recognition The cognitive psychology of knowledge Amsterdam, Elsevier Science Publishers Strube G, Wender KF 1993:113-138.
12. Gildea D Palmer M The Necessity of Parsing for Predicate Argument Recognition 2002.
13. Gildea D Jurafsky D Automatic labeling of semantic roles Computational Linguistics 2002, 28(3):.
14. Xue N Palmer M Calibrating Features for Semantic Role Labeling 2004.
15. Punyakanok V Roth D Yih W Zimak D Semantic Role Labeling via Integer Linear Programming Inference 2004.
16. Morarescu P Bejan C Harabagiu S Shallow Semantics for Relation Extraction 2005.
17. Pradhan S Hacioglu K Kruglery V Ward W Martin JH Jurafsky D Support Vector Learning for Semantic Argument Classification Journal of Machine Learning 2004.
18. Punyakanok V Roth D Yih W The Necessity of Syntactic Parsing for Semantic Role Labeling 2005.
19. Tsai TH Wu CW Lin YC Hsu WL Exploiting Full Parsing Information to Label Semantic Roles Using an Ensemble of ME and SVM via Integer Linear Programming. 2005.
20. Palmer M Gildea D Kingsbury P The Proposition Bank: An Annotated Corpus of Semantic Roles Computational Linguistics 2005, 31(1):.
21. Chou WC Tsai RTH Su YS Ku W Sung TY Hsu WL A Semi-Automatic Method for Annotating a Biomedical Proposition Bank 2006.
22. Kim JD Ohta T Tateisi Y Tsujii J GENIA corpus - semantically annotated corpus for bio-textmining Bioinformatics 2003, 19 Suppl 1:i180-2. 10.1093/bioinformatics/btg1023 12855455
23. Kim JD Ohta T Tsuruoka Y Tateisi Y Collier N Introduction to the Bio-Entity Task at JNLPBA 2004.
24. Tateisi Y Yakushiji A Ohta T Tsujii J Syntax Annotation for the GENIA corpus 2005 Companion volume pp. 222 -227
25. Bies A Ferguson M Katz K MacIntyre R Tredinnick V Kim G Marcinkiewicz MA Schasberger B Bracketing Guidelines for Treebank II Style Penn Treebank Project 1995.
26. Wattarujeekrit T Shah PK Collier N PASBio: Predicate-argument structures for event extraction in molecular biology BMC Bioinformatics 2004, 5:155. 535924 15494078 10.1186/1471-2105-5-155
27. Carreras X Màrquez L Introduction to the CoNLL-2005 Shared Task: Semantic Role Labeling 2005.
28. Dowty DR Thematic proto-roles and argument selection Language 1991, 67(3):547-619. 10.2307/415037
29. Yuan X Hu ZZ Wu HT Torii M Narayanaswamy M Ravikumar KE Vijay-Shanker K Wu CH An online literature mining tool for protein phosphorylation Bioinformatics 2006, 22(13):1668-1669. 10.1093/bioinformatics/btl159 16644790
30. Siegel S Castellan JN Nonparametric statistics for the behavioral sciences Boston, MA, McGraw Hill 1988.
31. Shah PK Bork P LSAT: Learning about alternative transcripts in MEDLINE BMC Bioinformatics 2006, 22(7):857-865.
32. Cohen KB Hunter L Natural Language Processing and Systems Biology Artificial Intelligence and Systems Biology Springer Dubitzky W, Azuaje F Springer Series on Computational Biology 2005.
33. Kogan Y Collier N Pakhomov S Krauthammer M Towards semantic role labeling & IE in the medical literature 2005:410-414. 1560806 16779072
34. Tsai RTH Chou WC Lin YC Ku W Su YS Sung TY Hsu WL BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs: An Exponential Model Coupled with Automatically Generated Template Features: New York. 2006.
35. Smith TF Waterman MS Identification of common molecular subsequences Journal of Molecular Biology 1981, 147:195-197. 10.1016/ 0022-2836(81)90087-5 7265238
36. Hacioglu K Pradhan S Ward W Martin JH Jurafsky D Semantic Role Labeling by Tagging Syntactic Chunks 2004. 14996672
37. Darroch JN Ratcliff D Generalized Iterative Scaling for Log-Linear Models The Annals of Mathematical Statistics 1972.
38. Nocedal J Wright SJ Numerical Optimization Springer 1999.
39. Surdeanu M Harabagiu SM Williams J Aarseth P Using Predicate-Argument Structures for Information Extraction 2003:8-15.