Michael Bada

Summary

Affiliation: University of Colorado Denver
Country: USA

Publications

  1. ncbi request reprint Mapping of biomedical text to concepts of lexicons, terminologies, and ontologies
    Michael Bada
    Computational Bioscience Program, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, RC1S L18 6103, Aurora, CO, 80045 0511, USA
    Methods Mol Biol 1159:33-45. 2014
  2. pmc Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Genomics 14:513. 2013
  3. 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
  4. doi request reprint Desiderata for ontologies to be used in semantic annotation of biomedical documents
    Michael Bada
    Department of Pharmacology, University of Colorado Denver, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6400, P O Box 6511, Aurora, CO 80045, USA
    J Biomed Inform 44:94-101. 2011
  5. pmc Identification of OBO nonalignments and its implications for OBO enrichment
    Michael Bada
    Department of Pharmacology, University of Colorado at Denver, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6400A, PO Box 6511, Aurora, CO 80045, USA
    Bioinformatics 24:1448-55. 2008
  6. doi request reprint 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
  7. 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
  8. pmc Enrichment of OBO ontologies
    Michael Bada
    University of Colorado at Denver and Health Sciences Center, Department of Pharmacology, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6101, P O Box 6511, Aurora, CO 80045, USA
    J Biomed Inform 40:300-15. 2007

Collaborators

  • Karin Verspoor
  • LAWRENCE E HUNTER
  • K Bretonnel Cohen
  • Christophe Roeder
  • Christopher Funk
  • David P Hill
  • William Baumgartner
  • Benjamin Garcia
  • Rebecca E Foulger
  • Nico Adams
  • Janna Hastings
  • Jane Lomax
  • Paula de Matos
  • Steve Turner
  • Harold J Drabkin
  • Paola Roncaglia
  • Namrata S Kale
  • Midori A Harris
  • Colin Batchelor
  • Marcus Ennis
  • Tanya Z Berardini
  • Heiko Dietze
  • Christopher J Mungall
  • Christoph Steinbeck
  • Gareth Owen

Detail Information

Publications8

  1. ncbi request reprint Mapping of biomedical text to concepts of lexicons, terminologies, and ontologies
    Michael Bada
    Computational Bioscience Program, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E 17th Ave, RC1S L18 6103, Aurora, CO, 80045 0511, USA
    Methods Mol Biol 1159:33-45. 2014
    ....
  2. pmc Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
    David P Hill
    Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
    BMC Genomics 14:513. 2013
    ....
  3. 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...
  4. doi request reprint Desiderata for ontologies to be used in semantic annotation of biomedical documents
    Michael Bada
    Department of Pharmacology, University of Colorado Denver, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6400, P O Box 6511, Aurora, CO 80045, USA
    J Biomed Inform 44:94-101. 2011
    ....
  5. pmc Identification of OBO nonalignments and its implications for OBO enrichment
    Michael Bada
    Department of Pharmacology, University of Colorado at Denver, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6400A, PO Box 6511, Aurora, CO 80045, USA
    Bioinformatics 24:1448-55. 2008
    ..If such definitions cannot be added, the reasoners cannot point to the nonalignments through the suggestion of new inferences...
  6. doi request reprint 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...
  7. 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...
  8. pmc Enrichment of OBO ontologies
    Michael Bada
    University of Colorado at Denver and Health Sciences Center, Department of Pharmacology, MS 8303, RC 1 South, 12801 East 17th Avenue, L18 6101, P O Box 6511, Aurora, CO 80045, USA
    J Biomed Inform 40:300-15. 2007
    ..Furthermore, this methodology programmatically integrates assertions into an ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels...