K Bretonnel Cohen

Summary

Publications

  1. pmc BioCreAtIvE task1A: entity identification with a stochastic tagger
    Shuhei Kinoshita
    Center for Computational Pharmacology, University of Colorado School of Medicine, Denver, Colorado, USA
    BMC Bioinformatics 6:S4. 2005
  2. pmc Getting started in text mining
    K Bretonnel Cohen
    University of Colorado School of Medicine, Center for Computational Pharmacology, UCHSC at Fitzsimons, Department of Pharmacology, Aurora, Colorado, United States of America
    PLoS Comput Biol 4:e20. 2008
  3. pmc Chapter 16: text mining for translational bioinformatics
    K Bretonnel Cohen
    Computational Bioscience Program, University of Colorado School of Medicine, Aurora, Colorado, USA
    PLoS Comput Biol 9:e1003044. 2013
  4. pmc 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
    Computational Bioscience Program, U, Colorado School of Medicine, 12801 E 17th Ave, Aurora, MS 8303, CO 80045, USA
    BMC Bioinformatics 13:207. 2012
  5. pmc U-Compare bio-event meta-service: compatible BioNLP event extraction services
    Yoshinobu Kano
    Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama, 332 0012, Japan
    BMC Bioinformatics 12:481. 2011
  6. pmc Overview of the BioCreative III Workshop
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S1. 2011
  7. pmc Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD)
    Thomas C Wiegers
    Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
    BMC Bioinformatics 10:326. 2009
  8. pmc A critical review of PASBio's argument structures for biomedical verbs
    K Bretonnel Cohen
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    BMC Bioinformatics 7:S5. 2006
  9. pmc Nominalization and alternations in biomedical language
    K Bretonnel Cohen
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 3:e3158. 2008
  10. pmc The structural and content aspects of abstracts versus bodies of full text journal articles are different
    K Bretonnel Cohen
    Department of Pharmacology, Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
    BMC Bioinformatics 11:492. 2010

Collaborators

Detail Information

Publications26

  1. pmc BioCreAtIvE task1A: entity identification with a stochastic tagger
    Shuhei Kinoshita
    Center for Computational Pharmacology, University of Colorado School of Medicine, Denver, Colorado, USA
    BMC Bioinformatics 6:S4. 2005
    ..We participated in both the open and the closed divisions; for the open division, we made use of data from NCBI...
  2. pmc Getting started in text mining
    K Bretonnel Cohen
    University of Colorado School of Medicine, Center for Computational Pharmacology, UCHSC at Fitzsimons, Department of Pharmacology, Aurora, Colorado, United States of America
    PLoS Comput Biol 4:e20. 2008
  3. pmc Chapter 16: text mining for translational bioinformatics
    K Bretonnel Cohen
    Computational Bioscience Program, University of Colorado School of Medicine, Aurora, Colorado, USA
    PLoS Comput Biol 9:e1003044. 2013
    ..Like all translational bioinformatics software, text mining software for translational bioinformatics can be considered health-critical and should be subject to the strictest standards of quality assurance and software testing...
  4. pmc 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
    Computational Bioscience Program, U, Colorado School of Medicine, 12801 E 17th Ave, Aurora, MS 8303, CO 80045, USA
    BMC Bioinformatics 13:207. 2012
    ..We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus...
  5. pmc U-Compare bio-event meta-service: compatible BioNLP event extraction services
    Yoshinobu Kano
    Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4 1 8 Honcho, Kawaguchi, Saitama, 332 0012, Japan
    BMC Bioinformatics 12:481. 2011
    ..While such systems provide useful services individually, there is a need for a meta-service to enable comparison and ensemble of such services, offering optimal solutions for various purposes...
  6. pmc Overview of the BioCreative III Workshop
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S1. 2011
    ..This special issue contains overview papers for the three tasks of BioCreative III...
  7. pmc Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD)
    Thomas C Wiegers
    Department of Bioinformatics, The Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
    BMC Bioinformatics 10:326. 2009
    ....
  8. pmc A critical review of PASBio's argument structures for biomedical verbs
    K Bretonnel Cohen
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    BMC Bioinformatics 7:S5. 2006
    ..Here, we quantitatively evaluate several dimensions of the initial PASBio propositional structure repository...
  9. pmc Nominalization and alternations in biomedical language
    K Bretonnel Cohen
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
    PLoS ONE 3:e3158. 2008
    ..The data is used to assess the implications of alternations for biomedical text mining systems and to test the fit of the sublanguage model to biomedical texts...
  10. pmc The structural and content aspects of abstracts versus bodies of full text journal articles are different
    K Bretonnel Cohen
    Department of Pharmacology, Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
    BMC Bioinformatics 11:492. 2010
    ..However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research...
  11. ncbi request reprint Rapid pattern development for concept recognition systems: application to point mutations
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, Center for Computational Pharmacology, University of Colorado Health Sciences Center, Aurora, CO, USA
    J Bioinform Comput Biol 5:1233-59. 2007
    ..Both MutationFinder and the complete corpus are publicly available at (http://mutationfinder.sourceforge.net/)...
  12. pmc Concept recognition for extracting protein interaction relations from biomedical text
    William A Baumgartner
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Genome Biol 9:S9. 2008
    ..The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing...
  13. pmc Exploring species-based strategies for gene normalization
    Karin Verspoor
    Center for Computational Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
    IEEE/ACM Trans Comput Biol Bioinform 7:462-71. 2010
    ..5 tasks...
  14. pmc 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
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 9:78. 2008
    ....
  15. pmc Ontology quality assurance through analysis of term transformations
    Karin Verspoor
    Center for Computational Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
    Bioinformatics 25:i77-84. 2009
    ..However, in practice terms are not always expressed consistently, and we must develop methods for identifying terms that are not univocal so that they can be corrected...
  16. pmc MutationFinder: a high-performance system for extracting point mutation mentions from text
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA
    Bioinformatics 23:1862-5. 2007
    ..We present an open-source, rule-based system, MutationFinder, for extracting point mutation mentions from text. On blind test data, it achieves nearly perfect precision and a markedly improved recall over a baseline...
  17. pmc Concept annotation in the CRAFT corpus
    Michael Bada
    Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
    BMC Bioinformatics 13:161. 2012
    ..Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text...
  18. pmc The textual characteristics of traditional and Open Access scientific journals are similar
    Karin Verspoor
    Center for Computational Pharmacology, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 10:183. 2009
    ..If this assumption is wrong, the cost to the community will be large, including not just wasted resources, but also flawed science. This paper examines that assumption...
  19. pmc Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters
    Christopher Funk
    Computational Bioscience Program, U, of Colorado School of Medicine, Aurora, CO 80045, USA
    BMC Bioinformatics 15:59. 2014
    ..There are many recognizers for specific ontologies, but a general approach for concept recognition is an open problem...
  20. pmc Parenthetically speaking: classifying the contents of parentheses for text mining
    K Bretonnel Cohen
    Computational Bioscience Program, University of Colorado School of Medicine, Aurora, CO, USA
    AMIA Annu Symp Proc 2011:267-72. 2011
    ..It performs at a micro-averaged accuracy of 68% and a macro-averaged accuracy of 60% on an annotated corpus. The application is available as a Java class and as a Perl module...
  21. pmc Corpus refactoring: a feasibility study
    Helen L Johnson
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 2:4. 2007
    ..We tracked the total time expended and the success rates of the automated steps...
  22. pmc Manual curation is not sufficient for annotation of genomic databases
    William A Baumgartner
    Center for Computational Pharmacology, University of Colorado School of Medicine, USA
    Bioinformatics 23:i41-8. 2007
    ....
  23. pmc Biomedical language processing: what's beyond PubMed?
    Lawrence Hunter
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, 80045, USA
    Mol Cell 21:589-94. 2006
  24. pmc An open-source framework for large-scale, flexible evaluation of biomedical text mining systems
    William A Baumgartner
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
    J Biomed Discov Collab 3:1. 2008
    ....
  25. pmc Combining heterogenous data for prediction of disease related and pharmacogenes
    Christopher S Funk
    Computational Bioscience Program, University of Colorado School of Medicine, Aurora, CO 80045, USA
    Pac Symp Biocomput 19:328-39. 2014
    ..Performance of F=0.86, AUC=0.860 is achieved. The top 10 predicted genes are analyzed. Additionally, a set of enriched pharmacogenic Gene Ontology concepts is produced. ..
  26. doi request reprint Habitat-Lite: a GSC case study based on free text terms for environmental metadata
    Lynette Hirschman
    Information Technology Center, The MITRE Corporation, Bedford, Massachusetts 01730, USA
    OMICS 12:129-36. 2008
    ..We invite the community's feedback on its further development to provide a minimum list of terms to capture high-level habitat information and to provide classification bins needed for future studies...