Lynette Hirschman

Summary

Affiliation: The MITRE Corporation
Country: USA

Publications

  1. 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
  2. pmc BioCreative III interactive task: an overview
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S4. 2011
  3. pmc Text mining for the biocuration workflow
    Lynette Hirschman
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    Database (Oxford) 2012:bas020. 2012
  4. pmc Text mining for biology--the way forward: opinions from leading scientists
    Russ B Altman
    Stanford University, Stanford, California, 94305 5444, USA
    Genome Biol 9:S7. 2008
  5. pmc Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S1. 2008
  6. pmc Overview of BioCreative II gene normalization
    Alexander A Morgan
    Biomedical Informatics, Stanford University, Stanford, CA, 94305, USA
    Genome Biol 9:S3. 2008
  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 Overview of BioCreAtIvE: critical assessment of information extraction for biology
    Lynette Hirschman
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    BMC Bioinformatics 6:S1. 2005
  9. pmc Overview of BioCreAtIvE task 1B: normalized gene lists
    Lynette Hirschman
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    BMC Bioinformatics 6:S11. 2005
  10. ncbi request reprint Rutabaga by any other name: extracting biological names
    Lynette Hirschman
    The MITRE Corporation, MS K312, 202 Burlington Rd, Bedford, MA 01730, USA
    J Biomed Inform 35:247-59. 2002

Collaborators

Detail Information

Publications25

  1. 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...
  2. pmc BioCreative III interactive task: an overview
    Cecilia N Arighi
    Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
    BMC Bioinformatics 12:S4. 2011
    ..To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested...
  3. pmc Text mining for the biocuration workflow
    Lynette Hirschman
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    Database (Oxford) 2012:bas020. 2012
    ..These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community...
  4. pmc Text mining for biology--the way forward: opinions from leading scientists
    Russ B Altman
    Stanford University, Stanford, California, 94305 5444, USA
    Genome Biol 9:S7. 2008
    ....
  5. pmc Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge
    Martin Krallinger
    Structural Biology and Biocomputing Programme, Spanish Nacional Cancer Research Centre CNIO, Madrid, Spain
    Genome Biol 9:S1. 2008
    ....
  6. pmc Overview of BioCreative II gene normalization
    Alexander A Morgan
    Biomedical Informatics, Stanford University, Stanford, CA, 94305, USA
    Genome Biol 9:S3. 2008
    ..Inter-annotator agreement was measured at over 90%...
  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 Overview of BioCreAtIvE: critical assessment of information extraction for biology
    Lynette Hirschman
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    BMC Bioinformatics 6:S1. 2005
    ..The articles collected in this BMC Bioinformatics supplement entitled "A critical assessment of text mining methods in molecular biology" describe the BioCreAtIvE tasks, systems, results and their independent evaluation...
  9. pmc Overview of BioCreAtIvE task 1B: normalized gene lists
    Lynette Hirschman
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    BMC Bioinformatics 6:S11. 2005
    ..The task was to produce the correct list of unique gene identifiers for the genes and gene products mentioned in sets of abstracts from three model organisms (Yeast, Fly, and Mouse)...
  10. ncbi request reprint Rutabaga by any other name: extracting biological names
    Lynette Hirschman
    The MITRE Corporation, MS K312, 202 Burlington Rd, Bedford, MA 01730, USA
    J Biomed Inform 35:247-59. 2002
    ..We conclude by outlining a research agenda to raise performance of named entity tagging to a level where it can be used to perform tasks of biological importance...
  11. 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...
  12. ncbi request reprint Accomplishments and challenges in literature data mining for biology
    Lynette Hirschman
    The MITRE Corporation, USA
    Bioinformatics 18:1553-61. 2002
    ..To encourage participation and accelerate progress in this expanding field, we propose creating challenge evaluations, and we describe two specific applications in this context...
  13. ncbi request reprint Gene name identification and normalization using a model organism database
    Alexander A Morgan
    MITRE Corporation, 202 Burlington Road, Mail Stop K325, Bedford, MA 01730 1420, USA
    J Biomed Inform 37:396-410. 2004
    ....
  14. ncbi request reprint Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup
    Alexander S Yeh
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    Bioinformatics 19:i331-9. 2003
    ..We report on the evaluation results and describe the techniques used by the top performing groups...
  15. doi request reprint The MITRE Identification Scrubber Toolkit: design, training, and assessment
    John Aberdeen
    The MITRE Corporation, 202 Burlington Rd, Bedford, MA 01730, United States
    Int J Med Inform 79:849-59. 2010
    ....
  16. pmc BioCreAtIvE task 1A: gene mention finding evaluation
    Alexander Yeh
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    BMC Bioinformatics 6:S2. 2005
    ..Finding mentions" is a basic task, which can be used as a building block for other text mining tasks. The task makes use of data and evaluation software provided by the (US) National Center for Biotechnology Information (NCBI)...
  17. pmc Data preparation and interannotator agreement: BioCreAtIvE task 1B
    Marc E Colosimo
    The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
    BMC Bioinformatics 6:S12. 2005
    ..We did this by careful assessment of interannotator agreement and the use of answer pooling of participant results to improve the quality of the final testing dataset...
  18. pmc MITRE system for clinical assertion status classification
    Cheryl Clark
    The MITRE Corporation, Bedford, Massachusetts 01730 1420, USA
    J Am Med Inform Assoc 18:563-7. 2011
    ....
  19. pmc Nephele: genotyping via complete composition vectors and MapReduce
    Marc E Colosimo
    The MITRE Corporation, 202 Burlington Rd, Bedford MA 01730, USA
    Source Code Biol Med 6:13. 2011
    ..abstract:..
  20. pmc Rapidly retargetable approaches to de-identification in medical records
    Ben Wellner
    The MITRE Corporation, Bedford, MA, USA
    J Am Med Inform Assoc 14:564-73. 2007
    ..This paper describes a successful approach to de-identification that was developed to participate in a recent AMIA-sponsored challenge evaluation...
  21. doi request reprint Meeting report: the fourth Genomic Standards Consortium (GSC) workshop
    Dawn Field
    NERC Centre for Ecology and Hydrology, Mansfield Road, Oxford, OX1 3SR United Kingdom
    OMICS 12:101-8. 2008
    ..g., compliant with MIGS/MIMS), but also be extended to include a variety of data processing and calculations. Further information about the Genomic Standards Consortium and its range of activities can be found at http://gensc.org...
  22. ncbi request reprint Do you do text?
    Christian Blaschke
    Centro Nacional de Biotecnologia, CNB CSIC Cantoblanco, Madrid, Spain
    Bioinformatics 21:4199-200. 2005
  23. ncbi request reprint Information extraction in molecular biology
    Christian Blaschke
    Protein Design Group, National Center for Biotechnology, CNB CSIC, Cantoblanco, Madrid, Spain
    Brief Bioinform 3:154-65. 2002
    ....
  24. doi request reprint Toward a standards-compliant genomic and metagenomic publication record
    George M Garrity
    Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
    OMICS 12:157-60. 2008
    ....
  25. doi request reprint Meeting report: the fifth Genomic Standards Consortium (GSC) workshop
    Dawn Field
    NERC Center for Ecology and Hydrology, Oxford, United Kingdom
    OMICS 12:109-13. 2008
    ..Further information about the GSC and its range of activities can be found at http://gensc.org...