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1

Natural Language Processing for Online Applications: Text Retrieval, Extraction and Categorization (review)

Cohen, Kevin Bretonnel

Journal:

Year:

2004

Language:

english

File:

PDF, 254 KB

english, 2004

2

A Machine Learning Approach to Identifying the Thought Markers of Suicidal Subjects: A Prospective Multicenter Trial

Pestian, John P., Sorter, Michael, Connolly, Brian, Bretonnel Cohen, Kevin, McCullumsmith, Cheryl, Gee, Jeffry T., Morency, Louis-Philippe, Scherer, Stefan, Rohlfs, Lesley

Journal:

Suicide and Life-Threatening Behavior

Year:

2016

Language:

english

File:

PDF, 117 KB

english, 2016

3

[untitled]

Review by: K. Bretonnel Cohen

Journal:

Year:

2004

Language:

english

File:

PDF, 217 KB

english, 2004

4

[untitled]

Review by: K. Bretonnel Cohen

Journal:

Year:

2004

Language:

english

File:

PDF, 232 KB

english, 2004

5

Replicability and reproducibility of research results for human language technology: introducing anLREspecial section

António Branco,Kevin Bretonnel Cohen,Piek Vossen…

Journal:

Language Resources and Evaluation

Year:

2017

Language:

english

File:

PDF, 363 KB

english, 2017

6

[ACM Press the 18th ACM/IEEE - Fort Worth, Texas, USA (2018.06.03-2018.06.07)] Proceedings of the 18th ACM/IEEE on Joint Conference on Digital Libraries - JCDL '18 - The Curative Power of Medical Data

Gifu, Daniela, Trandabat, Diana, Cohen, Kevin Bretonnel, Xia, Jigbo

Year:

2018

Language:

english

File:

PDF, 564 KB

english, 2018

7

Spanish/English Contrasts: A Course in Spanish Linguistics (review)

Cohen, K. Bretonnel

Journal:

Year:

2004

Language:

english

File:

PDF, 191 KB

english, 2004

8

[IEEE 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI) - Beijing, China (2018.10.13-2018.10.15)] 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI) - Guideline Design of an Active Gene Annotation Corpus for the Purpose of Drug Repurposing

Wang, Yuxing, Yao, Xinzhi, Zhou, Kaiyin, Qin, Xuan, Kim, Jin-Dong, Cohen, Kevin Bretonnel, Xia, Jingbo

Year:

2018

Language:

english

File:

PDF, 8 KB

english, 2018

9

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA

K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Chris Roeder, Philip V. Ogren, William A. Baumgartner Jr, Elizabeth White, Hannah Tipney, Lawr

Journal:

Computational Intelligence

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

10

Current issues in biomedical text mining and natural language processing

Wendy W. Chapman, K. Bretonnel Cohen

Journal:

Journal of Biomedical Informatics

Year:

2009

Language:

english

File:

PDF, 128 KB

english, 2009

11

The textual characteristics of traditional and Open Access scientific journals are similar

Karin Verspoor, K Bretonnel Cohen, Lawrence Hunter

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 472 KB

english, 2009

12

Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)

Thomas C Wiegers, Allan Peter Davis, K Bretonnel Cohen, Lynette Hirschman, Carolyn J Mattingly

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 736 KB

english, 2009

13

The structural and content aspects of abstracts versus bodies of full text journal articles are different

K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder, Lawrence E Hunter

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 306 KB

english, 2010

14

Integrating text mining into high-throughput assay analysis

K Bretonnel Cohen

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 139 KB

english, 2010

15

U-Compare bio-event meta-service: compatible BioNLP event extraction services

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 V

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 257 KB

english, 2011

16

BioCreAtIvE Task1A: entity identification with a stochastic tagger

Shuhei Kinoshita, K Bretonnel Cohen, Philip V Ogren, Lawrence Hunter

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 257 KB

english, 2005

17

A critical review of PASBio's argument structures for biomedical verbs

K Bretonnel Cohen, Lawrence Hunter

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 269 KB

english, 2006

18

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

Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner, Helen L Johnson, Philip V Ogren, K Bretonnel Cohen

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 543 KB

english, 2008

19

Themes in biomedical natural language processing: BioNLP08

Dina Demner-Fushman, Sophia Ananiadou, K Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie Webber

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 182 KB

english, 2008

20

Biomedical Language Processing: What's Beyond PubMed?

Lawrence Hunter, K. Bretonnel Cohen

Journal:

Year:

2006

Language:

english

File:

PDF, 210 KB

english, 2006

21

The state of the art in text mining and natural language processing for pharmacogenomics

Adrien Coulet, K. Bretonnel Cohen, Russ B. Altman

Journal:

Journal of Biomedical Informatics

Year:

2012

Language:

english

File:

PDF, 133 KB

english, 2012

22

Concept annotation in the CRAFT corpus

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

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 442 KB

english, 2012

23

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A Baumga

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 383 KB

english, 2012

24

Getting Started in Text Mining

Cohen, K. Bretonnel, Hunter, Lawrence

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 193 KB

english, 2008

25

[IEEE 2008 IEEE International Conference on Bioinformatics and Biomedicine - Philadelphia, PA, USA (2008.11.3-2008.11.5)] 2008 IEEE International Conference on Bioinformatics and Biomedicine - iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology

Hu, Zhang-Zhi, Cohen, K. Bretonnel, Hirschman, Lynette, Valencia, Alfonso, Liu, Hongfang, Giglio, Michelle G., Wu, Cathy H.

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

26

Methods in Biomedical Informatics || Biomedical Natural Language Processing and Text Mining

Cohen, Kevin Bretonnel

Year:

2014

Language:

english

File:

PDF, 619 KB

english, 2014

27

Amazon Mechanical Turk: Gold Mine or Coal Mine?

Fort, Karën, Adda, Gilles, Cohen, K. Bretonnel

Journal:

Computational Linguistics

Year:

2011

Language:

english

File:

PDF, 96 KB

english, 2011

28

Exploring Species-Based Strategies for Gene Normalization

Verspoor, Karin, Roeder, Christophe, Johnson, Helen L, Cohen, Kevin Bretonnel, Baumgartner, William A, Hunter, Lawrence E

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.93 MB

english, 2010

29

Habitat-Lite: A GSC Case Study Based on Free Text Terms for Environmental Metadata

Hirschman, Lynette, Clark, Cheryl, Cohen, K. Bretonnel, Mardis, Scott, Luciano, Joanne, Kottmann, Renzo, Cole, James, Markowitz, Victor, Kyrpides, Nikos, Morrison, Norman, Schriml, Lynn M., Field, Daw

Journal:

Omics A Journal of Integrative Biology

Year:

2008

Language:

english

File:

PDF, 189 KB

english, 2008

30

RAPID PATTERN DEVELOPMENT FOR CONCEPT RECOGNITION SYSTEMS: APPLICATION TO POINT MUTATIONS

CAPORASO, J. GREGORY, BAUMGARTNER, WILLIAM A., RANDOLPH, DAVID A., COHEN, K. BRETONNEL, HUNTER, LAWRENCE

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2007

Language:

english

File:

PDF, 405 KB

english, 2007

31

Corpus Refactoring: a Feasibility Study

Johnson, Helen L, Baumgartner, William A, Krallinger, Martin, Cohen, K Bretonnel, Hunter, Lawrence

Journal:

Journal of Biomedical Discovery and Collaboration

Year:

2007

Language:

english

File:

PDF, 303 KB

english, 2007

32

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

Baumgartner, William A, Cohen, K Bretonnel, Hunter, Lawrence

Journal:

Journal of Biomedical Discovery and Collaboration

Year:

2008

Language:

english

File:

PDF, 670 KB

english, 2008

33

War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

Rzhetsky, Andrey, Evans, James A., Cohen, Kevin Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 89 KB

english, 2011

34

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis

Divoli, Anna, Mendonça, Eneida A., Evans, James A., Rzhetsky, Andrey, Cohen, Kevin Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.14 MB

english, 2011

35

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy

Blair, David R., Wang, Kanix, Nestorov, Svetlozar, Evans, James A., Rzhetsky, Andrey, Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.24 MB

english, 2014

36

Predicting the Extension of Biomedical Ontologies

Pesquita, Catia, Couto, Francisco M., Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 999 KB

english, 2012

37

Chapter 16: Text Mining for Translational Bioinformatics

Cohen, K. Bretonnel, Hunter, Lawrence E., Lewitter, Fran, Kann, Maricel

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 193 KB

english, 2013

38

Benchmarking Ontologies: Bigger or Better?

Yao, Lixia, Divoli, Anna, Mayzus, Ilya, Evans, James A., Rzhetsky, Andrey, Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.32 MB

english, 2011

39

Assessing the similarity of surface linguistic features related to epilepsy across pediatric hospitals

Connolly, B., Matykiewicz, P., Bretonnel Cohen, K., Standridge, S. M., Glauser, T. A., Dlugos, D. J., Koh, S., Tham, E., Pestian, J.

Journal:

Journal of the American Medical Informatics Association

Year:

2014

Language:

english

File:

PDF, 240 KB

english, 2014

40

Survey of the State of the Art in Human Language Technologyby Giovanni Varile; Antonio Zampolli; Ronald Cole; Joseph Mariani; Hans Uszkoreit; Annie Zaenen; Victor Zue

Review by: K. Bretonnel Cohen

Journal:

Year:

2000

Language:

english

File:

PDF, 683 KB

english, 2000

41

A Controlled Trial Using Natural Language Processing to Examine the Language of Suicidal Adolescents in the Emergency Department

Pestian, John P., Grupp-Phelan, Jacqueline, Bretonnel Cohen, Kevin, Meyers, Gabriel, Richey, Linda A., Matykiewicz, Pawel, Sorter, Michael T.

Journal:

Suicide and Life-Threatening Behavior

Year:

2016

Language:

english

File:

PDF, 96 KB

english, 2016

42

[untitled]

Review by: K. Bretonnel Cohen and Andrew Dolbey

Journal:

Year:

2002

Language:

english

File:

PDF, 174 KB

english, 2002

43

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - EVALUATION OF LEXICAL METHODS FOR DETECTING RELATIONSHIPS BETWEEN CONCEPTS FROM MULTIPLE ONTOLOGIES

JOHNSON, HELEN L., COHEN, K. BRETONNEL, BAUMGARTNER, WILLIAM A., LU, ZHIYONG, BADA, MICHAEL, KESTER, TODD, KIM, HYUNMIN, HUNTER, LAWRENCE

Language:

english

File:

PDF, 670 KB

english

44

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

LU, ZHIYONG, COHEN, K. BRETONNEL, HUNTER, LAWRENCE

Language:

english

File:

PDF, 832 KB

english

45

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Maui, Hawaii (3 – 7 January 2006)] Biocomputing 2006 - LINKING BIOMEDICAL INFORMATION THROUGH TEXT MINING: SESSION INTRODUCTION

COHEN, K. BRETONNEL, BODENREIDER, OLIVIER, HIRSCHMAN, LYNETTE

Language:

english

File:

PDF, 186 KB

english

46

Crowdsourcing and curation: perspectives from biology and natural language processing

Hirschman, Lynette, Fort, Karën, Boué, Stéphanie, Kyrpides, Nikos, Islamaj Doğan, Rezarta, Cohen, Kevin Bretonnel

Journal:

Year:

2016

Language:

english

File:

PDF, 1.01 MB

english, 2016

47

Erratum to: Replicability and reproducibility of research results for human language technology: introducing anLREspecial section

António Branco,Kevin Bretonnel Cohen,Piek Vossen…

Journal:

Language Resources and Evaluation

Year:

2017

Language:

english

File:

PDF, 312 KB

english, 2017

48

PubAnnotation-query: a search tool for corpora with multi-layers of annotation

Jin-Dong Kim,Kevin Bretonnel Cohen,Jung-jae Kim

Journal:

BMC Proceedings

Year:

2015

Language:

english

File:

PDF, 350 KB

english, 2015

49

Introduction to the Biomedical Linked Annotation Hackathon (BLAH) 2015 Symposium

Jin-Dong Kim,Kevin Bretonnel Cohen,Nigel Collier,Zhiyong Lu…

Journal:

BMC Proceedings

Year:

2015

Language:

english

File:

PDF, 200 KB

english, 2015

50

Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition

Christopher S. Funk,K. Bretonnel Cohen…

Journal:

Journal of Biomedical Semantics

Year:

2016

Language:

english

File:

PDF, 729 KB

english, 2016