K. Bretonnel Cohen

86 papers B 4C 1Misc 16Journal 30Unranked 29
YearRankTypeTitle / Venue / Authors
2020 — conf
MEDA 2020: The Curative Power of Medical Data.
JCDL
K. Bretonnel Cohen, Daniela Gîfu, Youzhu Li, Anna Ripple, Jingbo Xia
2020 — conf
Reviewing Natural Language Processing Research.
ACL (tutorial)
K. Bretonnel Cohen, Karën Fort, Margot Mieskes, Aurélie Névéol
2020 — conf
Writing about Data Science Research for Digital Libraries.
JCDL
K. Bretonnel Cohen, Daniela Gîfu
2019 Misc conf
Community Perspective on Replicability in Natural Language Processing.
RANLP
Margot Mieskes, Karën Fort, Aurélie Névéol, Cyril Grouin, K. Bretonnel Cohen
2019 J jnl
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem.
Bioinform.
Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J. Callahan, K. Bretonnel Cohen
2019 — conf
P-Hacking Lexical Richness Through Definitions of "Type" and "Token".
MedInfo
K. Bretonnel Cohen, Lawrence E. Hunter, Peter S. Pressman
2018 — conf
A Modular Ontology for Modeling Service Provision in a Communication Network for Coordination of Care.
MIE
Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, Luis Felipe Melo Mora, K. Bretonnel Cohen, Jean Charlet
2018 — conf
De l'intérêt des ontologies modulaires. Application à la modélisation de la prise en charge de la SLA.
IC
Sonia Cardoso, Xavier Aimé, Vincent Meininger, David Grabli, K. Bretonnel Cohen, Jean Charlet
2018 Misc conf
Improving precision in concept normalization.
PSB
Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter
2018 B conf
Three Dimensions of Reproducibility in Natural Language Processing.
LREC
K. Bretonnel Cohen, Jingbo Xia, Pierre Zweigenbaum, Tiffany Callahan, Orin Hargraves, Foster R. Goss, Nancy Ide, Aurélie Névéol, Cyril Grouin, Lawrence E. Hunter
2017 J jnl
A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support.
BMC Bioinform.
Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram, John Pestian
2017 J jnl
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.
BMC Bioinform.
K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter
2017 — conf
Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement.
MedInfo
Prabha Yadav, Elisabetta Jezek, Pierrette Bouillon, Tiffany J. Callahan, Michael Bada, Lawrence E. Hunter, K. Bretonnel Cohen
2017 — conf
Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles.
MedInfo
K. Bretonnel Cohen, Foster R. Goss, Pierre Zweigenbaum, Lawrence E. Hunter
2016 J jnl
Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.
J. Biomed. Semant.
Christopher S. Funk, K. Bretonnel Cohen, Lawrence E. Hunter, Karin M. Verspoor
2016 J jnl
Introduction.
Trait. Autom. des Langues
Karën Fort, Gilles Adda, K. Bretonnel Cohen
2016 B conf
SuperCAT: The (New and Improved) Corpus Analysis Toolkit.
LREC
K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova
2015 — conf
Measuring the readability of medical research journal abstracts.
BioNLP@IJCNLP
Samuel J. Severance, K. Bretonnel Cohen
2014 Misc conf
Combining Heterogenous Data for Prediction of Disease Related and Pharmacogenes.
Pacific Symposium on Biocomputing
Christopher S. Funk, Lawrence E. Hunter, K. Bretonnel Cohen
2014 J jnl
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.
BMC Bioinform.
Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor
2014 C conf
Ontology Translation: A Case Study on Translating the Gene Ontology from English to German.
NLDB
Negacy D. Hailu, K. Bretonnel Cohen, Lawrence E. Hunter
2014 J jnl
Research and applications: Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals.
J. Am. Medical Informatics Assoc.
Brian Connolly, Pawel Matykiewicz, K. Bretonnel Cohen, Shannon M. Standridge, Tracy A. Glauser, Dennis J. Dlugos, Susan Koh, Eric Tham, John Pestian
2014 B conf
Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora.
LREC
Irina P. Temnikova, William A. Baumgartner Jr., Negacy D. Hailu, Ivelina Nikolova, Tony McEnery, Adam Kilgarriff, Galia Angelova, K. Bretonnel Cohen
2013 J jnl
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation
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 G. 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
2013 J jnl
Chapter 16: Text Mining for Translational Bioinformatics.
PLoS Comput. Biol.
K. Bretonnel Cohen, Lawrence E. Hunter
2013 Misc conf
Closure Properties of Bulgarian Clinical Text.
RANLP
Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen
2013 — conf
Evaluation of SPARQL query generation from natural language questions.
SWAIE@RANLP
K. Bretonnel Cohen, Jin-Dong Kim
2013 Misc conf
Measuring Closure Properties of Patent Sublanguages.
RANLP
Irina P. Temnikova, Negacy D. Hailu, Galia Angelova, K. Bretonnel Cohen
2013 — conf
UColorado_SOM: Extraction of Drug-Drug Interactions from Biomedical Text using Knowledge-rich and Knowledge-poor Features.
SemEval@NAACL-HLT
Negacy D. Hailu, Lawrence E. Hunter, K. Bretonnel Cohen
2012 — conf
Assessment of Software Testing and Quality Assurance in Natural Language Processing Applications and a Linguistically Inspired Approach to Improving It.
EternalS@ECAI
K. Bretonnel Cohen, Lawrence E. Hunter, Martha Palmer
2012 J jnl
Concept annotation in the CRAFT corpus.
BMC Bioinform.
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
2012 J jnl
Text mining for the biocuration workflow.
Database J. Biol. Databases Curation
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
2012 J jnl
The state of the art in text mining and natural language processing for pharmacogenomics.
J. Biomed. Informatics
Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman
2011 — conf
A scaleable automated quality assurance technique for semantic representations and proposition banks.
Linguistic Annotation Workshop
K. Bretonnel Cohen, Lawrence Hunter, Martha Palmer
2011 J jnl
Amazon Mechanical Turk: Gold Mine or Coal Mine?
Comput. Linguistics
Karën Fort, Gilles Adda, K. Bretonnel Cohen
2011 — conf
Fast and simple semantic class assignment for biomedical text.
BioNLP@ACL
K. Bretonnel Cohen, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter
2011 J jnl
High-Precision Biological Event Extraction: Effects of System and of Data.
Comput. Intell.
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
2011 — conf
Hypothesis and Evidence Extraction from Full-Text Scientific Journal Articles.
BioNLP@ACL
Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter
2011 — conf
MetaMap is a Superior Baseline to a Standard Document Retrieval Engine for the Task of Finding Patient Cohorts in Clinical Free Text.
TREC
K. Bretonnel Cohen, Tom Christiansen, Lawrence E. Hunter
2011 J jnl
U-Compare bio-event meta-service: compatible BioNLP event extraction services.
BMC Bioinform.
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
2011 J jnl
U-Compare: A modular NLP workflow construction and evaluation system.
IBM J. Res. Dev.
Yoshinobu Kano, Makoto Miwa, K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, Jun'ichi Tsujii
2010 — ch.
BioNLP.
Handbook of Natural Language Processing
K. Bretonnel Cohen
2010 J jnl
Exploring Species-Based Strategies for Gene Normalization.
IEEE ACM Trans. Comput. Biol. Bioinform.
Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
2010 — ed.
Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2010, Uppsala, Sweden, July 15, 2010
BioNLP@ACL
K. Bretonnel Cohen, Dina Demner-Fushman, Sophia Ananiadou, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber
2010 B conf
Test Suite Design for Biomedical Ontology Concept Recognition Systems.
LREC
K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor
2010 J jnl
The structural and content aspects of abstracts versus bodies of full text journal articles are different.
BMC Bioinform.
K. Bretonnel Cohen, Helen L. Johnson, Karin Verspoor, Christophe Roeder, Lawrence Hunter
2010 — conf
Visualization and Language Processing for Supporting Analysis across the Biomedical Literature.
KES (4)
Carsten Görg, Hannah J. Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John T. Stasko, Lawrence Hunter
2009 J jnl
Current issues in biomedical text mining and natural language processing.
J. Biomed. Informatics
Wendy Webber Chapman, K. Bretonnel Cohen
2009 — conf
High-precision biological event extraction with a concept recognizer.
BioNLP@HLT-NAACL (Shared Task)
K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Lawrence Hunter
2009 J jnl
Ontology quality assurance through analysis of term transformations.
Bioinform.
Karin Verspoor, Daniel Dvorkin, K. Bretonnel Cohen, Lawrence Hunter
2009 J jnl
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD).
BMC Bioinform.
Thomas C. Wiegers, Allan Peter Davis, K. Bretonnel Cohen, Lynette Hirschman, Carolyn J. Mattingly
2009 J jnl
The textual characteristics of traditional and Open Access scientific journals are similar.
BMC Bioinform.
Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter
2009 J jnl
U-Compare: share and compare text mining tools with UIMA.
Bioinform.
Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii
2008 J jnl
Getting Started in Text Mining.
PLoS Comput. Biol.
K. Bretonnel Cohen, Lawrence Hunter
2008 Misc conf
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks.
Pacific Symposium on Biocomputing
J. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter
2008 J jnl
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.
Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen
2008 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman
2008 — ed.
Software Engineering, Testing, and Quality Assurance for Natural Language Processing@ACL 2008, Columbus, Ohio, USA, June 20, 2008
SETQALNLP
K. Bretonnel Cohen, Bob Carpenter
2008 — conf
Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing.
SETQALNLP
K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
2008 J jnl
Themes in biomedical natural language processing: BioNLP08.
BMC Bioinform.
Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber
2008 — conf
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology.
BIBM
Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu
2007 Misc conf
A Fault Model for Ontology Mapping, Alignment, and Linking Systems.
Pacific Symposium on Biocomputing
Helen L. Johnson, K. Bretonnel Cohen, Lawrence Hunter
2007 — conf
A shared task involving multi-label classification of clinical free text.
BioNLP@ACL
John P. Pestian, Chris Brew, Pawel Matykiewicz, D. J. Hovermale, Neil Johnson, K. Bretonnel Cohen, Wlodzislaw Duch
2007 — conf
BioNLP.
HLT-NAACL (Tutorial Abstracts)
K. Bretonnel Cohen
2007 — ed.
Biological, translational, and clinical language processing, BioNLP@ACL 2007, Prague, Czech Republic, June 29, 2007
BioNLP@ACL
K. Bretonnel Cohen, Dina Demner-Fushman, Carol Friedman, Lynette Hirschman, John Pestian
2007 Misc conf
Generif Quality Assurance as Summary Revision.
Pacific Symposium on Biocomputing
Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter
2007 — conf
Manual curation is not sufficient for annotation of genomic databases.
ISMB/ECCB (Supplement of Bioinformatics)
William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George K. Acquaah-Mensah, Lawrence Hunter
2007 J jnl
MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinform.
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter
2007 J jnl
Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations.
J. Bioinform. Comput. Biol.
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter
2007 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, K. Bretonnel Cohen
2006 — conf
A critical review of PASBio's argument structures for biomedical verbs.
SMBM
K. Bretonnel Cohen, Lawrence Hunter
2006 J jnl
A critical review of PASBio's argument structures for biomedical verbs.
BMC Bioinform.
K. Bretonnel Cohen, Lawrence Hunter
2006 — conf
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering.
TREC
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
2006 Misc conf
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies.
Pacific Symposium on Biocomputing
Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter
2006 Misc conf
Finding GeneRIFs via Gene Ontology Annotations.
Pacific Symposium on Biocomputing
Zhiyong Lu, K. Bretonnel Cohen, Lawrence Hunter
2006 — conf
Refactoring Corpora.
BioNLP@NAACL-HLT
Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter
2006 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
K. Bretonnel Cohen, Olivier Bodenreider, Lynette Hirschman
2005 J jnl
BioCreAtIvE Task1A: entity identification with a stochastic tagger.
BMC Bioinform.
Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, Lawrence Hunter
2005 — conf
Concept Recognition and the TREC Genomics Tasks.
TREC
J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter
2005 — conf
Corpus Design for Biomedical Natural Language Processing.
LBLODMBS@IDMB
K. Bretonnel Cohen, Lynne M. Fox, Philip V. Ogren, Lawrence Hunter
2005 Misc conf
Empirical data on corpus design and usage in biomedical natural language processing.
AMIA
K. Bretonnel Cohen, Philip V. Ogren, Lynne M. Fox, Lawrence Hunter
2005 Misc conf
Implications of Compositionality in the Gene Ontology for Its Curation and Usage .
Pacific Symposium on Biocomputing
Philip V. Ogren, K. Bretonnel Cohen, Lawrence Hunter
2005 — ed.
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics@ISMB 2005, Detroit, MI, USA June 24, 2005
LBLODMBS@ISMB
K. Bretonnel Cohen, Lynette Hirschman, Hagit Shatkay, Christian Blaschke
2004 — ch.
Natural Language Processing and Systems Biology.
Artificial Intelligence Methods And Tools For Systems Biology
K. Bretonnel Cohen, Lawrence Hunter
2004 Misc conf
The Compositional Structure of Gene Ontology Terms.
Pacific Symposium on Biocomputing
Philip V. Ogren, K. Bretonnel Cohen, George K. Acquaah-Mensah, Jens Eberlein, Lawrence Hunter
2002 — conf
Contrast and variability in gene names.
ACL Workshop on Natural Language Processing in the Biomedical Domain
K. Bretonnel Cohen, Andrew Dolbey, George K. Acquaah-Mensah, Lawrence Hunter