M
Michael Bada
Researcher at University of Colorado Denver
Publications - 43
Citations - 1473
Michael Bada is an academic researcher from University of Colorado Denver. The author has contributed to research in topics: Ontology (information science) & Open Biomedical Ontologies. The author has an hindex of 19, co-authored 40 publications receiving 1315 citations. Previous affiliations of Michael Bada include Anschutz Medical Campus & Case Western Reserve University.
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Journal ArticleDOI
Concept annotation in the CRAFT corpus
Michael Bada,Miriam R. Eckert,Donald Evans,Kristin Garcia,Krista Shipley,Dmitry Sitnikov,William A. Baumgartner,K. Bretonnel Cohen,Karin Verspoor,Judith A. Blake,Lawrence Hunter +10 more
TL;DR: The concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems.
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Cross-product extensions of the Gene Ontology
Christopher J. Mungall,Michael Bada,Tanya Z. Berardini,Jennifer I. Deegan,Amelia Ireland,Midori A. Harris,David P. Hill,Jane Lomax +7 more
TL;DR: Preliminary results of an ongoing effort to normalize the Gene Ontology by explicitly stating the definitions of compositional classes in a form that can be used by reasoners are presented.
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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,Kevin Bretonnel Cohen,Arrick Lanfranchi,Colin Warner,Helen L. Johnson,Christophe Roeder,Jinho D. Choi,Christopher S. Funk,Yuriy Malenkiy,Miriam R. Eckert,Nianwen Xue,William A. Baumgartner,Michael Bada,Martha Palmer,Lawrence Hunter +14 more
TL;DR: The finding that some systems were able to train high-performing models based on this corpus is additional evidence, beyond high inter-annotator agreement, that the quality of the CRAFT corpus is high.
Journal ArticleDOI
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters
Christopher S. Funk,William A. Baumgartner,Benjamin J. Garcia,Christophe Roeder,Michael Bada,K. Bretonnel Cohen,Lawrence Hunter,Karin Verspoor +7 more
TL;DR: ConceptMapper is generally the best-performing system; it produces the highest F-measure of seven out of eight ontologies, and suggestions for choosing the best parameters based on ontology characteristics are presented.
Journal ArticleDOI
A short study on the success of the Gene Ontology
Michael Bada,Robert Stevens,Carole Goble,Yolanda Gil,Michael Ashburner,Judith A. Blake,J. Michael Cherry,Midori A. Harris,Suzanna E. Lewis +8 more
TL;DR: The Gene Ontology (GO), an evolving structured controlled vocabulary of nearly 16,000 terms in the domain of biological functionality, has been widely used for annotation of biological-database entries and in biomedical research.