Annotation of specialized corpora using a comprehensive entity and relation scheme

Proceedings of the 9th International Conference on Language Resources and Evaluation, LREC 2014

Volumn , Issue , 2014, Pages 1267-1274

  Deléger, Louise ^a   Ligozat, Anne Laure ^a,b   Grouin, Cyril ^a   Zweigenbaum, Pierre ^a   Névéol, Aurélie ^a  

^a CNRS   (France)

^b ENSIIE   (France)

Author keywords

Annotation; Clinical Texts; Natural Language Processing

Indexed keywords

NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS;

ANNOTATION; ANNOTATION SCHEME; AUTOMATIC TOOLS; BIOMEDICAL DOMAIN; CLINICAL TEXTS; HIGH QUALITY; SPECIALIZED CORPORA; SUBFIELDS;

LINGUISTICS;

EID: 85021715801     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. Bada, M., Eckert, M., Evans, D., Garcia, K., Shipley, K., Sitnikov, D., Baumgartner, W. A., and Cohen., K. B., Verspoor, K., Blake, J. A., and Hunter, L. E. (2012). Concept annotation in the CRAFT corpus. BMC Bioinformatics, 13(161).
2. Bodenreider, O. and McCray, A. T. (2003). Exploring semantic groups through visual approaches. J Biomed Inform, 36(6):414-32.
3. Chapman, W. W., and Savova., G. K., Zheng, J., Tharp, M., and Crowley, R. (2012). Anaphoric reference in clinical reports: characteristics of an annotated corpus. J Biomed Inform, 45(3):507-21.
4. Deléger, L., Li, Q., Lingren, T., Kaiser, M., Molnar, K., Stoutenborough, L., Kouril, M., Marsolo, K., and Solti, I. (2012). Building gold standard corpora for medical natural language processing tasks. In AMIA Annu Symp Proc, pages 144-53.
5. Doǧan, R. I. and Lu, Z. (2012). An improved corpus of disease mentions in PubMed citations. In Proc of BioNLP, pages 91-9.
6. Hripcsak, G. and Rothschild, A. S. (2005). Agreement, the f-measure, and reliability in information retrieval. J Am Med Inform Assoc, 12(3):296-8.
7. Kim, J.-D., Ohta, T., Tateisi, Y., and Tsujii, J. (2003). GENIA corpus - a semantically annotated corpus for biotextmining. BMC Bioinformatics, 19(Suppl 1):i180-2.
8. McCray, A. T., Burgun, A., and Bodenreider, O. (2001). Aggregating UMLS semantic types for reducing conceptual complexity. In Proc of MedInfo, Volume 10, pages 216-20.
9. Névéol, A., Doǧan, R. I., and Lu, Z. (2011). Semiautomatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. J Biomed Inform, 44(2):310-8.
10. Ohta, T., Pyysalo, S., Tsujii, J., and Ananiadou, S. (2012). Open-domain anatomical entity mention detection. In Proc of Workshop on Detecting Structure in Scholarly Discourse, pages 27-36.
11. Osman, D., Yearwood, J., and Vamplew, P. (2010). Automated opinion detection: Implications of the level of agreement between human raters. Inf Process Manage, 46(3):331-42.
12. Savova, G., Styler, W., Albright, D., Palmer, M., Harris, D., Zaramba, G., Haug, P., Clark, C., Wu, S., and Ihrke, D. (2012). SHARP template annotations: Guidelines. Technical report, Mayo Clinic.
13. Smith, L. H., and Rindflesch., T. C., and Wilbur, W. J. (2004). MedPost: a part of speech tagger for biomedical text. BMC Bioinformatics, 20(14):2320-21.
14. South, B. R., Shen, S., Jones, M., Garvin, J., and Samore., M. H., Chapman, W. W., and Gundlapalli, A. V. (2009). Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease. BMC Bioinformatics, 10(Suppl 9):S12.
15. Stenetorp, P., Pyysalo, S., Topić, G., Ohta, T., Ananiadou, S., and Tsujii, J. (2012). Brat: a web-based tool for NLP-assisted text annotation. In Proc of EACL Demo Session, pages 102-7.
16. Uzuner, O., Solti, I., and Cadag, E. (2010). Extracting medication information from clinical text. J Am Med Inform Assoc, 17(5):514-8.
17. Verspoor, K., and Yepes., A. J., Cavedon, L., McIntosh, T., Herten-Crabb, A., Thomas, Z., and Plazzer, J.-P. (2013). Annotating the biomedical literature for the human variome. Database.