Affiliation: University of Colorado Denver
- Mapping of biomedical text to concepts of lexicons, terminologies, and ontologiesMichael 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....
- Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontologyDavid P Hill
Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
BMC Genomics 14:513. 2013....
- Concept annotation in the CRAFT corpusMichael 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...
- Desiderata for ontologies to be used in semantic annotation of biomedical documentsMichael 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....
- Identification of OBO nonalignments and its implications for OBO enrichmentMichael 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...
- Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parametersChristopher 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...
- A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing toolsKarin 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...
- Enrichment of OBO ontologiesMichael 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...
- KaBOB: ontology-based semantic integration of biomedical databasesKevin M Livingston
Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
BMC Bioinformatics 16:126. 2015....