RiboWeb: An Ontology-Based System for Collaborative Molecular Biology. - Russ B. Altman; Michael Bada; Xiaoqian J. Chai; Michelle Whirl Carrillo; Richard O. Chen; Neil F. Abernethy (IEEE Intell. Syst., 1999)

Using Reasoning to Guide Annotation with Gene Ontology Terms in GOAT. - Michael Bada; Daniele Turi; Robin McEntire; Robert Stevens 001 (SIGMOD Rec., 2004)

A short study on the success of the Gene Ontology. - Michael Bada; Robert Stevens 001; Carole A. Goble; Yolanda Gil; Michael Ashburner; Judith A. Blake; J. Michael Cherry; Midori A. Harris; Suzanna Lewis (J. Web Semant., 2004)

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. - Helen L. Johnson 001; K. Bretonnel Cohen; William A. Baumgartner Jr.; Zhiyong Lu; Michael Bada; Todd Kester; Hyunmin Kim; Lawrence Hunter (Pacific Symposium on Biocomputing, 2006)

Enrichment of OBO ontologies. - Michael Bada; Lawrence Hunter (J. Biomed. Informatics, 2007)

A Call for an Abductive Reasoning Feature in OWL-Reasoning Tools toward Ontology Quality Control. - Michael Bada; Chris Mungall; Lawrence Hunter (OWLED, 2008)

Identification of OBO nonalignments and its implications for OBO enrichment. - Michael Bada; Lawrence Hunter (Bioinform., 2008)

An Overview of the CRAFT Concept Annotation Guidelines. - Michael Bada; Miriam Eckert; Martha Palmer; Lawrence Hunter (Linguistic Annotation Workshop, 2010)

Desiderata for ontologies to be used in semantic annotation of biomedical documents. - Michael Bada; Lawrence Hunter (J. Biomed. Informatics, 2011)

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 (J. Biomed. Informatics, 2011)

Efforts toward a More Consistent and Interoperable Sequence Ontology. - Michael Bada; Karen Eilbeck (ICBO, 2012)

Concept annotation in the CRAFT corpus. - 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 (BMC Bioinform., 2012)

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 001; Christophe Roeder; Jinho D. Choi; Christopher S. Funk; Yuriy Malenkiy; Miriam Eckert; Nianwen Xue; William A. Baumgartner Jr.; et al. (BMC Bioinform., 2012)

Representing annotation compositionality and provenance for the Semantic Web. - Kevin M. Livingston; Michael Bada; Lawrence E. Hunter; Karin Verspoor (J. Biomed. Semant., 2013)

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. - Christopher S. Funk; William A. Baumgartner Jr.; Benjamin Garcia; Christophe Roeder; Michael Bada; K. Bretonnel Cohen; Lawrence E. Hunter; Karin Verspoor (BMC Bioinform., 2014)

KaBOB: ontology-based semantic integration of biomedical databases. - Kevin M. Livingston; Michael Bada; William A. Baumgartner Jr.; Lawrence E. Hunter (BMC Bioinform., 2015)

Gold-Standard Ontology-Based Annotation of Concepts in Biomedical Text in the CRAFT Corpus: Updates and Extensions. - Michael Bada; Nicole A. Vasilevsky; Melissa A. Haendel; Lawrence Hunter (ICBO/BioCreative, 2016)

Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement. - Prabha Yadav; Elisabetta Jezek; Pierrette Bouillon; Tiffany J. Callahan; Michael Bada; Lawrence E. Hunter; K. Bretonnel Cohen (MedInfo, 2017)

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. - Michael Bada; Nicole A. Vasilevsky; William A. Baumgartner Jr.; Melissa A. Haendel; Lawrence E. Hunter (Database J. Biol. Databases Curation, 2017)

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. - K. Bretonnel Cohen; Arrick Lanfranchi; Miji Joo-young Choi; Michael Bada; William A. Baumgartner Jr.; Natalya Panteleyeva; Karin Verspoor; Martha Palmer; Lawrence E. Hunter (BMC Bioinform., 2017)

OWL-NETS: Transforming OWL representations for improved network inference. - Tiffany J. Callahan; William A. Baumgartner Jr.; Michael Bada; Adrianne L. Stefanski; Ignacio Tripodi; Elizabeth K. White; Lawrence E. Hunter (PSB, 2018)

CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference. - William A. Baumgartner Jr.; Michael Bada; Sampo Pyysalo; Manuel R. Ciosici; Negacy D. Hailu; Harrison Pielke-Lombardo; Michael Regan; Lawrence Hunter (BioNLP-OST@EMNLP-IJNCLP, 2019)

Concept recognition as a machine translation problem. - Mayla Boguslav; Negacy D. Hailu; Michael Bada; William A. Baumgartner Jr.; Lawrence E. Hunter (BMC Bioinform., 2021)

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science. - 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; et al. (CoRR, 2022)

An Open-Source Knowledge Graph Ecosystem for the Life Sciences. - 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; et al. (CoRR, 2023)

Creating an ignorance-base: Exploring known unknowns in the scientific literature. - Mayla R. Boguslav; Nourah M. Salem; Elizabeth K. White; Katherine J. Sullivan; Michael Bada; Teri L. Hernandez; Sonia M. Leach; Lawrence E. Hunter (J. Biomed. Informatics, 2023)