BioCreAtIvE task1A: entity identification with a stochastic taggerShuhei 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...
- 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
- 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...
- 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...
- 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
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- 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...
- 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...
- 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...
Rapid pattern development for concept recognition systems: application to point mutationsJ 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/)...
- 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...
- 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...
- 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
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- 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...
- 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...
- 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
..Implementations, source code and unit tests are available in Python, Perl and Java. MutationFinder can be used as a stand-alone script, or imported by other applications. PROJECT URL: http://bionlp.sourceforge.net...
- 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...
- 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...
- 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
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- 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
- 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...
- 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
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- Chapter 16: text mining for translational bioinformatics
K Bretonnel Cohen
Computational Bioscience Program, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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...
Habitat-Lite: a GSC case study based on free text terms for environmental metadataLynette 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...
