Clinical Information Extraction at the CLEF eHealth Evaluation lab 2016

CEUR Workshop Proceedings

Volumn 1609, Issue , 2016, Pages 28-42

  Névéol, Aurélie ^a   Cohen, K Bretonnel ^a,b   Grouin, Cyril ^a   Hamon, Thierry ^a,c   Lavergne, Thomas ^a,d   Kelly, Liadh ^e   Goeuriot, Lorraine ^f   Rey, Grégoire ^g   Robert, Aude ^g   Tannier, Xavier ^a,d   Zweigenbaum, Pierre ^a  

^a UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

^b UNIVERSITY OF COLORADO   (United States)

^c UNIVERSITÉ PARIS 13   (France)

^d UNIVERSITÉ PARIS SACLAY   (France)

^e TRINITY COLLEGE DUBLIN   (Ireland)

^f UNIV GRENOBLE ALPES   (France)

^g INSERM   (France)

Author keywords

Biomedical Text; Entity Linking; French; Named Entity Recognition; Natural Language Processing; Text Classification; UMLS

Indexed keywords

ARTIFICIAL INTELLIGENCE; CLASSIFICATION (OF INFORMATION); INFORMATION ANALYSIS; INFORMATION RETRIEVAL; LABORATORIES; LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS; TEXT PROCESSING;

BIOMEDICAL TEXT; ENTITY LINKING; FRENCH; NAMED ENTITY RECOGNITION; NATURAL LANGUAGE PROCESSING; TEXT CLASSIFICATION; UMLS;

CHARACTER RECOGNITION;

EID: 85019624486     PISSN: 16130073     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (29)

1. Jones KS, Galliers JR. Evaluating natural language processing systems: An analysis and review. 1995. Springer Science & Business Media:1083
2. Voorhees EM, Harman DK and others. TREC: Experiment and evaluation in information retrieval, vol 1. 2005. MIT press Cambridge.
3. Suominen H, Salantera S, Velupillai S, Chapman WW, Savova G, Elhadad N, Pradhan S, South BR, Mowery DL, Jones GJF, Leveling J, Kelly L, Goeuriot L, Martinez D, Zuccon G. Overview of the ShARe/CLEF eHealth Evaluation Lab 2013. In: Forner P, Müller H, Paredes R, Rosso P, Stein B (eds), Information Access Evaluation. Multilinguality, Multimodality, and Visualization. LNCS (vol. 8138):212-231. Springer, 2013
4. Goeuriot L, Kelly L, Suominen H, Hanlen L, Névéol A, Grouin C, Palotti J, Zuccon G. Overview of the CLEF eHealth Evaluation Lab 2015. In: Information Access Evaluation. Multilinguality, Multimodality, and Interaction. Springer, 2015
5. Kelly L, Goeuriot L, Suominen H, Schreck T, Leroy G, Mowery DL, Velupillai S, Chapman WW, Martinez D, Zuccon G, Palotti J. Overview of the ShARe/CLEF eHealth Evaluation Lab 2014. In: Kanoulas E, Lupu M, Clough P, Sanderson M, Hall M, Hanbury A, Toms E (eds), Information Access Evaluation. Multilinguality, Multimodality, and Interaction. LNCS (vol. 8685):172-191. Springer, 2014
6. Névéol A, Grouin C, Tannier X, Hamon T, Kelly L, Goeuriot L, Zweigenbaum P (2015). CLEF eHealth Evaluation Lab 2015 Task 1b: clinical named entity recognition. CLEF 2015, Online Working Notes, CEUR-WS 1391.
7. Chapman WW, Nadkarni PM, Hirschman L, D'Avolio LW, Savova GK, Uzuner O (2011). Overcoming barriers to NLP for clinical text: The role of shared tasks and the need for additional creative solutions. J Am Med Inform Assoc, 18(5):540-3
8. Huang CC, Lu Z (2015). Community challenges in biomedical text mining over 10 years: success, failure and the future. Brief Bioinform, 2015 May 1. pii: bbv024.
9. Yeh A, Morgan A, Colosimo M, Hirschman L. BioCreAtIvE task 1A: gene mention finding evaluation. BMC Bioinformatics. 2005;6 Suppl 1:S2.
10. Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, Hsu CN, Lin YS, Klinger R, Friedrich CM, Ganchev K, Torii M, Liu H, Haddow B, Struble CA, Povinelli RJ, Vlachos A, Baumgartner WA Jr, Hunter L, Carpenter B, Tsai RT, Dai HJ, Liu F, Chen Y, Sun C, Katrenko S, Adriaans P, Blaschke C, Torres R, Neves M, Nakov P, Divoli A, Maña-Lopez M, Mata J, Wilbur WJ. Overview of BioCreative II gene mention recognition. Genome Biol. 2008;9 Suppl 2:S2
11. Arighi CN, Wu CH, Cohen KB, Hirschman L, Krallinger M, Valencia A, Lu Z, Wilbur JW, Wiegers TC. BioCreative-IV virtual issue. Database (Oxford). 2014 May 22;2014. pii: bau039.
12. Uzuner O, South BR, Shen S, DuVall SL. 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. J Am Med Inform Assoc. 2011 Sep-Oct;18(5):552-6.
13. Hirschman L, Colosimo M, Morgan A, Yeh A. Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics. 2005;6 Suppl 1:S11.
14. , Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, Divoli A, Fundel K, Leaman R, Hakenberg J, Sun C, Liu HH, Torres R, Krauthammer M, Lau WW, Liu H, Hsu CN, Schuemie M, Cohen KB, Hirschman L. Overview of BioCreative II gene normalization. Genome Biol. 2008;9 Suppl 2:S3.
15. Lu Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai RT, Dai HJ, Okazaki N, Cho HC, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston KM, Wilbur WJ. The gene normalization task in BioCreative III. BMC Bioinformatics. 2011 Oct 3;12 Suppl 8:S2.
16. Uzuner O, South BR, Shen S, DuVall SL. 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. J Am Med Inform Assoc. 2011 Sep-Oct;18(5):552-6.
17. Névéol A, Grosjean J, Darmoni SJ, Zweigenbaum P (2014). Language Resources for French in the Biomedical Domain. In: Proc of LREC, p. 2146-2151
18. Névéol A, Grouin C, Leixa J, Rosset S, Zweigenbaum P (2014). The QUAERO French Medical Corpus: A Ressource for Medical Entity Recognition and Normalization. In: Proc of Bio TextM, p. 24-30
19. Pavillon G., Laurent F (2003). Certification et codification des causes médicales de décés. Bulletin Epidémiologique Hebdomadaire-BEH:134-138. http://opac.invs.sante.fr/doc-num.php?explnum-id=2065 (accessed: 2016-06-06)
20. Verspoor K, Jimeno Yepes A, Cavedon L, McIntosh T, Herten-Crabb H, Thomas Z, Plazzer JP (2013). Annotating the Biomedical Literature for the Human Variome. Database (Oxford), virtual issue for BioCuration 2013 meeting
21. Mottin L, Gobeill J, Mottaz A, Pasche E, Gaudinat A, Ruch P (2016). BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction CLEF 2016 Online Working Notes. CEUR-WS
22. Dermouche M, Looten V, Flicoteaux R, Chevret S, Velcin J and Taright N (2016). ECSTRA-INSERM @ CLEF eHealth2016-Task 2: ICD10 Code Extraction from Death Certificates. CLEF 2016 Online Working Notes. CEUR-WS
23. Van Mulligen E, Afzal Z, Akhondi SA, Vo D, Kors JA (2016). Erasmus MC at CLEF eHealth 2016: Concept Recognition and Coding in French Texts. CLEF 2016 Online Working Notes, CEUR-WS
24. Afzal Z, Akhondi SA, van Haagen H, Van Mulligen E and Kors JA (2015). Biomedical Concept Recognition in French Text Using Automatic Translation of English Terms. CLEF 2015 Online Working Notes. CEUR-WS
25. Ho-Dac LM, Tanguy L, Grauby C, Hnub N, Heu Mby A, Malosse J, Riviére L, Veltz-Mauclair A and Wauquier M (2015). LITL at CLEF eHealth2016: recognizing entities in French biomedical documents. CLEF 2016 Online Working Notes. CEUR-WS
26. Urieli A (2013). Robust French syntax analysis: reconciling statistical methods and linguistic knowledge in the Talismane toolkit. PhD thesis. Université de Toulouse II-Le Mirail
27. Zweigenbaum P and Lavergne T (2016). LIMSI ICD10 coding experiments on CepiDC death certificate statements. CLEF 2016 Online Working Notes. CEURWS
28. Cabot C, Soualmia LF, Dahamna B and Darmoni SJ (2016). SIBM at CLEF eHealth Evaluation Lab 2016: Extracting Concepts in French Medical Texts with ECMT and CIMIND. CLEF 2016 Online Working Notes. CEUR-WS
29. Vivaldi J, Rodriguez H and Cotik V (2016). Semantic tagging and normalization of French medical entities. CLEF 2016 Online Working Notes. CEUR-WS