K. Bretonnel Cohen

Publication Activity (10 Years)

Years Active: 2002-2020
Publications (10 Years): 17

Top Topics

Closure Properties

Natural Language

Journal Articles

Query Generation

Top Venues

Publications

K. Bretonnel Cohen, Daniela Gîfu, Youzhu Li, Anna Ripple, Jingbo Xia
MEDA 2020: The Curative Power of Medical Data. JCDL (2020)
K. Bretonnel Cohen, Daniela Gîfu
Writing about Data Science Research for Digital Libraries. JCDL (2020)
K. Bretonnel Cohen, Karën Fort, Margot Mieskes, Aurélie Névéol
Reviewing Natural Language Processing Research. ACL (tutorial) (2020)
Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J. Callahan, K. Bretonnel Cohen
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. Bioinform. 35 (21) (2019)
Margot Mieskes, Karën Fort, Aurélie Névéol, Cyril Grouin, K. Bretonnel Cohen
Community Perspective on Replicability in Natural Language Processing. RANLP (2019)
K. Bretonnel Cohen, Lawrence E. Hunter, Peter S. Pressman
P-Hacking Lexical Richness Through Definitions of "Type" and "Token". MedInfo (2019)
K. Bretonnel Cohen, Jingbo Xia, Pierre Zweigenbaum, Tiffany Callahan, Orin Hargraves, Foster R. Goss, Nancy Ide, Aurélie Névéol, Cyril Grouin, Lawrence E. Hunter
Three Dimensions of Reproducibility in Natural Language Processing. LREC (2018)
Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter
Improving precision in concept normalization. PSB (2018)
Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, K. Bretonnel Cohen, Jean Charlet
De l'intérêt des ontologies modulaires. Application à la modélisation de la prise en charge de la SLA. IC (2018)
Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, Luis Felipe Melo Mora, K. Bretonnel Cohen, Jean Charlet
A Modular Ontology for Modeling Service Provision in a Communication Network for Coordination of Care. MIE (2018)
Prabha Yadav, Elisabetta Jezek, Pierrette Bouillon, Tiffany J. Callahan, Michael Bada, Lawrence E. Hunter, K. Bretonnel Cohen
Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. MedInfo (2017)
K. Bretonnel Cohen, Foster R. Goss, Pierre Zweigenbaum, Lawrence E. Hunter
Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles. MedInfo (2017)
Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram, John Pestian
A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support. BMC Bioinform. 18 (1) (2017)
K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinform. 18 (1) (2017)
Karën Fort, Gilles Adda, K. Bretonnel Cohen
Introduction. Trait. Autom. des Langues 57 (2) (2016)
K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova
SuperCAT: The (New and Improved) Corpus Analysis Toolkit. LREC (2016)
Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter, Karin M. Verspoor
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition. J. Biomed. Semant. 7 (2016)
Samuel J. Severance, K. Bretonnel Cohen
Measuring the readability of medical research journal abstracts. BioNLP@IJCNLP (2015)
Negacy D. Hailu, K. Bretonnel Cohen, Lawrence E. Hunter
Ontology Translation: A Case Study on Translating the Gene Ontology from English to German. NLDB (2014)
Irina P. Temnikova, William A. Baumgartner Jr., Negacy D. Hailu, Ivelina Nikolova, Tony McEnery, Adam Kilgarriff, Galia Angelova, K. Bretonnel Cohen
Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora. LREC (2014)
Christopher S. Funk, Lawrence E. Hunter, K. Bretonnel Cohen
Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes. Pacific Symposium on Biocomputing (2014)
Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinform. 15 (2014)
Brian Connolly, Pawel Matykiewicz, K. Bretonnel Cohen, Shannon M. Standridge, Tracy A. Glauser, Dennis J. Dlugos, Susan Koh, Eric Tham, John Pestian
Research and applications: Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals. J. Am. Medical Informatics Assoc. 21 (5) (2014)
Negacy D. Hailu, Lawrence E. Hunter, K. Bretonnel Cohen
UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features. SemEval@NAACL-HLT (2013)
Irina P. Temnikova, Negacy D. Hailu, Galia Angelova, K. Bretonnel Cohen
Measuring Closure Properties of Patent Sublanguages. RANLP (2013)
K. Bretonnel Cohen, Lawrence E. Hunter
Chapter 16: Text Mining for Translational Bioinformatics. PLoS Comput. Biol. 9 (4) (2013)
K. Bretonnel Cohen, Jin-Dong Kim
Evaluation of SPARQL query generation from natural language questions. SWAIE@RANLP (2013)
Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013)
Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen
Closure Properties of Bulgarian Clinical Text. RANLP (2013)
Lynette Hirschman, Gully A. P. C. Burns, Martin Krallinger, Cecilia N. Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert S. Nash, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter
Text mining for the biocuration workflow. Database J. Biol. Databases Curation 2012 (2012)
Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman
The state of the art in text mining and natural language processing for pharmacogenomics. J. Biomed. Informatics 45 (5) (2012)
K. Bretonnel Cohen, Lawrence E. Hunter, Martha Palmer
Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It. EternalS@ECAI (2012)
Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner Jr., K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Lawrence E. Hunter
Concept annotation in the CRAFT corpus. BMC Bioinform. 13 (2012)
K. Bretonnel Cohen, Lawrence Hunter, Martha Palmer
A scaleable automated quality assurance technique for semantic representations and proposition banks. Linguistic Annotation Workshop (2011)
Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter
Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles. BioNLP@ACL (2011)
Karën Fort, Gilles Adda, K. Bretonnel Cohen
Amazon Mechanical Turk: Gold Mine or Coal Mine? Comput. Linguistics 37 (2) (2011)
K. Bretonnel Cohen, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter
Fast and simple semantic class assignment for biomedical text. BioNLP@ACL (2011)
K. Bretonnel Cohen, Tom Christiansen, Lawrence E. Hunter
MetaMap is a Superior Baseline to a Standard Document Retrieval Engine for the Task of Finding Patient Cohorts in Clinical Free Text. TREC (2011)
K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Hannah J. Tipney, Lawrence Hunter
High-Precision Biological Event Extraction: Effects of System and of Data. Comput. Intell. 27 (4) (2011)
Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12 (2011)
Yoshinobu Kano, Makoto Miwa, K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, Jun'ichi Tsujii
U-Compare: A modular NLP workflow construction and evaluation system. IBM J. Res. Dev. 55 (3) (2011)
Carsten Görg, Hannah J. Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John T. Stasko, Lawrence Hunter
Visualization and Language Processing for Supporting Analysis across the Biomedical Literature. KES (4) (2010)
K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor
Test Suite Design for Biomedical Ontology Concept Recognition Systems. LREC (2010)
Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
Exploring Species-Based Strategies for Gene Normalization. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (3) (2010)
K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor, Christophe Roeder, Lawrence Hunter
The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinform. 11 (2010)
Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii
U-Compare: share and compare text mining tools with UIMA. Bioinform. 25 (15) (2009)
Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter
The textual characteristics of traditional and Open Access scientific journals are similar. BMC Bioinform. 10 (2009)
Wendy Webber Chapman, K. Bretonnel Cohen
Current issues in biomedical text mining and natural language processing. J. Biomed. Informatics 42 (5) (2009)
Thomas C. Wiegers, Allan Peter Davis, K. Bretonnel Cohen, Lynette Hirschman, Carolyn J. Mattingly
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD). BMC Bioinform. 10 (2009)
Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, Lawrence Hunter
Ontology quality assurance through analysis of term transformations. Bioinform. 25 (12) (2009)
K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Lawrence Hunter
High-precision biological event extraction with a concept recognizer. BioNLP@HLT-NAACL (Shared Task) (2009)
K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing. SETQALNLP (2008)
K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman
Session Introduction. Pacific Symposium on Biocomputing (2008)
J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing (2008)
Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinform. 9 (2008)
K. Bretonnel Cohen, Lawrence Hunter
Getting Started in Text Mining. PLoS Comput. Biol. 4 (1) (2008)
Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM (2008)
Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber
Themes in biomedical natural language processing: BioNLP08. BMC Bioinform. 9 (S-11) (2008)
Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter
Generif Quality Assurance as Summary Revision. Pacific Symposium on Biocomputing (2007)
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter
MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinform. 23 (14) (2007)
Helen L. Johnson, K. Bretonnel Cohen, Lawrence Hunter
A Fault Model for Ontology Mapping, Alignment, and Linking Systems. Pacific Symposium on Biocomputing (2007)
William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George K. Acquaah-Mensah, Lawrence Hunter
Manual curation is not sufficient for annotation of genomic databases. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, K. Bretonnel Cohen
Session Introduction. Pacific Symposium on Biocomputing (2007)
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter
Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations. J. Bioinform. Comput. Biol. 5 (6) (2007)
K. Bretonnel Cohen
BioNLP. HLT-NAACL (Tutorial Abstracts) (2007)
John P. Pestian, Chris Brew, Pawel Matykiewicz, D. J. Hovermale, Neil Johnson, K. Bretonnel Cohen, Wlodzislaw Duch
A shared task involving multi-label classification of clinical free text. BioNLP@ACL (2007)
Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter
Refactoring Corpora. BioNLP@NAACL-HLT (2006)
K. Bretonnel Cohen, Lawrence Hunter
A critical review of PASBio's argument structures for biomedical verbs. BMC Bioinform. 7 (S-3) (2006)
J. Gregory Caporaso, William A. Baumgartner Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne M. Fox, Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering. TREC (2006)
K. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman
Session Introduction. Pacific Symposium on Biocomputing (2006)
Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. Pacific Symposium on Biocomputing (2006)
K. Bretonnel Cohen, Lawrence Hunter
A critical review of PASBio's argument structures for biomedical verbs. SMBM (2006)
Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter
Finding GeneRIFs via Gene Ontology Annotations. Pacific Symposium on Biocomputing (2006)
K. Bretonnel Cohen, Philip V. Ogren, Lynne M. Fox, Lawrence Hunter
Empirical data on corpus design and usage in biomedical natural language processing. AMIA (2005)
J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter
Concept Recognition and the TREC Genomics Tasks. TREC (2005)
Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, Lawrence Hunter
BioCreAtIvE Task1A: entity identification with a stochastic tagger. BMC Bioinform. 6 (S-1) (2005)
K. Bretonnel Cohen, Lynne M. Fox, Philip V. Ogren, Lawrence Hunter
Corpus Design for Biomedical Natural Language Processing. LBLODMBS@IDMB (2005)
Philip V. Ogren, K. Bretonnel Cohen, Lawrence Hunter
Implications of Compositionality in the Gene Ontology for Its Curation and Usage . Pacific Symposium on Biocomputing (2005)
Philip V. Ogren, K. Bretonnel Cohen, George K. Acquaah-Mensah, Jens Eberlein, Lawrence Hunter
The Compositional Structure of Gene Ontology Terms. Pacific Symposium on Biocomputing (2004)
K. Bretonnel Cohen, Andrew Dolbey, George K. Acquaah-Mensah, Lawrence Hunter
Contrast and variability in gene names. ACL Workshop on Natural Language Processing in the Biomedical Domain (2002)