Michael Bada

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 10

Top Topics

Manual Annotation

Machine Translation

Top Venues

ICBO/BioCreative

Publications

Mayla R. Boguslav, Nourah M. Salem, Elizabeth K. White, Katherine J. Sullivan, Michael Bada, Teri L. Hernandez, Sonia M. Leach, Lawrence E. Hunter
Creating an ignorance-base: Exploring known unknowns in the scientific literature. J. Biomed. Informatics 143 (2023)
Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya Bathla Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin T. Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR (2023)
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew H. Brush, Richard M. Bruskiewich, Paul A. Clemons, Vlado Dancík, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim E. Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne T. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall
Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. CoRR (2022)
Mayla Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
Concept recognition as a machine translation problem. BMC Bioinform. 22 (1) (2021)
William A. Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy D. Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter
CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference. BioNLP-OST@EMNLP-IJNCLP (2019)
Tiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter
OWL-NETS: Transforming OWL representations for improved network inference. PSB (2018)
Prabha Yadav, Elisabetta Jezek, Pierrette Bouillon, Tiffany J. Callahan, Michael Bada, Lawrence E. Hunter, K. Bretonnel Cohen
Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. MedInfo (2017)
Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database J. Biol. Databases Curation 2017 (2017)
K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinform. 18 (1) (2017)
Michael Bada, Nicole A. Vasilevsky, Melissa A. Haendel, Lawrence Hunter
Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions. ICBO/BioCreative (2016)
Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinform. 16 (2015)
Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinform. 15 (2014)
Kevin M. Livingston, Michael Bada, Lawrence E. Hunter, Karin Verspoor
Representing annotation compositionality and provenance for the Semantic Web. J. Biomed. Semant. 4 (2013)
Michael Bada, Karen Eilbeck
Efforts toward a More Consistent and Interoperable Sequence Ontology. ICBO (2012)
Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L. Johnson, Christophe Roeder, Jinho D. Choi, Christopher S. Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A. Baumgartner Jr., Michael Bada, Martha Palmer, Lawrence E. Hunter
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinform. 13 (2012)
Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner Jr., K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Lawrence E. Hunter
Concept annotation in the CRAFT corpus. BMC Bioinform. 13 (2012)
Christopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer I. Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax
Cross-product extensions of the Gene Ontology. J. Biomed. Informatics 44 (1) (2011)
Michael Bada, Lawrence Hunter
Desiderata for ontologies to be used in semantic annotation of biomedical documents. J. Biomed. Informatics 44 (1) (2011)
Michael Bada, Miriam Eckert, Martha Palmer, Lawrence Hunter
An Overview of the CRAFT Concept Annotation Guidelines. Linguistic Annotation Workshop (2010)
Michael Bada, Lawrence Hunter
Identification of OBO nonalignments and its implications for OBO enrichment. Bioinform. 24 (12) (2008)
Michael Bada, Chris Mungall, Lawrence Hunter
A Call for an Abductive Reasoning Feature in OWL-Reasoning Tools toward Ontology Quality Control. OWLED (2008)
Michael Bada, Lawrence Hunter
Enrichment of OBO ontologies. J. Biomed. Informatics 40 (3) (2007)
Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. Pacific Symposium on Biocomputing (2006)
Michael Bada, Daniele Turi, Robin McEntire, Robert Stevens
Using Reasoning to Guide Annotation with Gene Ontology Terms in GOAT. SIGMOD Rec. 33 (2) (2004)
Michael Bada, Robert Stevens, Carole A. Goble, Yolanda Gil, Michael Ashburner, Judith A. Blake, J. Michael Cherry, Midori A. Harris, Suzanna Lewis
A short study on the success of the Gene Ontology. J. Web Semant. 1 (2) (2004)
Russ B. Altman, Michael Bada, Xiaoqian J. Chai, Michelle Whirl Carrillo, Richard O. Chen, Neil F. Abernethy
RiboWeb: An Ontology-Based System for Collaborative Molecular Biology. IEEE Intell. Syst. 14 (5) (1999)