Acquisition and evaluation of verb subcategorization resources for biomedicine

Journal of Biomedical Informatics

Volumn 46, Issue 2, 2013, Pages 228-237

  Rimell, Laura ^a   Lippincott, Thomas ^a   Verspoor, Karin ^b   Johnson, Helen L ^c   Korhonen, Anna ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b CSIRO   (Australia)

^c UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

Biomedical text processing; Lexical resources; Natural language processing; Verb subcategorization

Indexed keywords

BIOMEDICAL LITERATURE; BIOMEDICAL RESOURCE; BIOMEDICAL TEXT; LEXICAL RESOURCES; LINGUISTIC RESOURCES; NATURAL LANGUAGE PROCESSING; RELATION EXTRACTION; VERB SUBCATEGORIZATION;

GOLD; LINGUISTICS; MERGERS AND ACQUISITIONS; NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS; STANDARDS; TEXT PROCESSING;

QUALITY CONTROL;

ACCURACY; ARTICLE; BIOMEDICINE; GOLD STANDARD; INFORMATION; LANGUAGE PROCESSING; LINGUISTICS; PRIORITY JOURNAL; SEMANTICS;

ABSTRACTING AND INDEXING AS TOPIC; BIOMEDICAL RESEARCH; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PUBLICATIONS; SEMANTICS;

EID: 84875604453     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2013.01.001     Document Type: Article

References (29)

1. Lippincott T, Rimell L, Verspoor K, Korhonen A. Approaches to verb subcategorization for biomedicine. J Biomed Inform, in press.
2. Ananiadou S, Thompson P, Nawaz R. Improving search through event-based biomedical text mining. In: Proceedings o the first international worksho on automated motif discovery in cultural heritage and scientific communication texts (AMICUS 2010), CLARIN/DARIAH 2010. Vienna, Austria; 2010.
3. Rupp C, Thompson P, Black W, McNaught J. A specialised verb lexicon as the basis of fact extraction in the biomedical domain. In: Proceedings of interdisciplinary workshop on verbs: the identification and representation of verb features (Verb 2010). Pisa, Italy; 2010.
4. Sasaki Y, Montemagni S, Pezik P, Rebholz-Schuhmann D, McNaught J, Ananiadou S. BioLexicon: a lexical resource for the biology domain. In: Proc. of the third international symposium on semantic mining in biomedicine (SMBM 2008); 2008.
5. Rebholz-Schuhmann D., Pezik P., Lee V., Kim J.J., del Gratta R., McNaught Y.S.J., et al. Towards a reference terminological resource in the biomedical domain. Proc. of 16th ann. int. conf. on intelligent systems for molecular biology (ISMB-2008) 2008, Oxford University Press, Toronto, Canada.
6. Venturi G., Montemagni S., Marchi S., Sasaki Y., Thompson P., McNaught J., et al. Bootstrapping a verb lexicon for biomedical information extraction. Lecture notes in computer science 2009, vol. 5449:137-148. Springer, Berlin/Heidelberg, doi: 10.1007/978-3-642-00382-0-1, URL http://dx.doi.org/10.1007/978-3-642-00382-0-11. A. Gelbukh (Ed.).
7. Thompson P., McNaught J., Montemagni S., Calzolari N., Gratta R.D., Lee V., et al. The biolexicon: a large-scale terminological resource for biomedical text mining. BMC Bioinformatics 2011, 12. 397-397.
8. Grishman R, Macleod C, Meyers A. COMLEX syntax: building a computational lexicon. In: Proceedings of COLING. Kyoto; 1994.
9. Wattarujeekrit T., Shah P., Collier N. PASBio: predicate-argument structures for event extraction in molecular biology. BMC Bioinformatics 2004, 5.
10. Tsai RTH, Chou WC, Lin YC, Sung CL, Ku W. BIOSMILE: adapting semantic role labeling for biomedical verbs: an exponential model coupled with automatically generated template features. In: Proceedings of the BioNLP'06 workshop on linking natural language processing and biology. Association for Computational Linguistics; 2005. p. 57-64.
11. Tsai R.T.H., Dai H.J., Huang C.H., Hsu W.L. Semi-automatic conversion of BioProp semantic annotation to PASBio annotation. BMC Bioinformatics 2008, 9(Suppl. 12). S18-1.
12. Cohen K.B., Hunter L. A critical review of pasbio's argument structures for biomedical verbs. BMC Bioinformatics 2006, 7(Suppl. 3):S5-1.
13. Preiss J, Briscoe T, Korhonen A. A system for large-scale acquisition of verbal, nominal and adjectival subcategorization frames from corpora. In: Proceedings of the 45th annual meeting of the association for computational linguistics. Prague, Czech Republic; 2007.
14. Boguraev B, Carroll J, Briscoe E, Carter D, Grover C. The derivation of a grammatically-indexed lexicon from the longman dictionary of contemporary english. In: Proceedings of the 25th annual meeting of ACL. Stanford, CA; 1987. p. 193-200.
15. Palmer M., Gildea D., Kingsbury P. The proposition bank: an annotated corpus of semantic roles. Comput Linguist 2005, 31(1):71-106. . 10.1162/0891201053630264.
16. Briscoe E, Carrol J, Watson R. The second release of the RASP system. In: Proceedings of the COLING/ACL 2006 interactive presentation sessions. Sydney, Australia; 2006.
17. Klein D, Manning CD. Accurate unlexicalized parsing. In: Proceedings of ACL; 2003. p. 423-30.
18. Korhonen A. Subcategorization acquisition. Ph.D. thesis, University of Cambridge Computer Laboratory; 2002.
19. NIH. The pubmed central open access subset; 2009a.http://www.pubmedcentral.nih.gov/about/openftlist.html.
20. NIH. Journal publishing tag set; 2009b.http://dtd.nlm.nih.gov/publishing/.
21. Lippincott T., O Seaghdha D., Korhonen A. Exploring subdomain variation in biomedical language. BMC Bioinformatics 2011, 12(1).
22. Verspoor K., Cohen K.B., Hunter L. The textual characteristics of traditional and open access scientific journals are similar. BMC Bioinformatics 2009, 10. 183-1.
23. Miyao Y., Tsujii J. Feature forest models for probabilistic HPSG parsing. Comput Linguist 2008, 34:35-80.
24. Ohta T, Tsuruoka Y, Takeuchi J, Kim JD, Miyao Y, Yakushiji A, et al. An intelligent search engine and gui-based efficient medline search tool based on deep syntactic parsing. In: Proceedings of the COLING/ACL on interactive presentation sessions (COLING-ACL '06). Stroudsburg, PA, USA: Association for Computational Linguistics; 2006. p. 17-20. doi:http://dx.doi.org/10.3115/1225403.1225408.
25. Kim J.D., Ohta T., Tateisi Y., Tsujii J. GENIA corpus - a semantically annotated corpus for bio-textmining. Bioinformatics 2003, 19(Suppl. 1):i180-i182.
26. Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas 1960, 20:37-46.
27. Krippendorff K. Content analysis: an introduction to its methodology 1980, Sage Publications, Beverly Hills, CA.
28. Korhonen A, Krymolowski Y, Briscoe T. A large subcategorization lexicon for natural language processing applications. In: Proceedings of LREC; 2006.
29. Lippincott T, O Seaghdha D, Korhonen A. Learning syntactic verb frames using graphical models. In: Proceedings of the 50th annual meeting of the association for computational linguistics (ACL). Jeju, Korea; 2012.