The GLAIR Cognitive Architecture. - Stuart C. Shapiro; Jonathan P. Bona (AAAI Fall Symposium: Biologically Inspired Cognitive Architectures, 2009)

The agent takes the stage. - Josephine Anstey; A. Patrice Seyed; Sarah Bay-Cheng; Dave Pape; Stuart C. Shapiro; Jonathan P. Bona; Stephen Hibit (Int. J. Arts Technol., 2009)

Modality in the MGLAIR Architecture. - Jonathan P. Bona; Stuart C. Shapiro (BICA, 2012)

Ontology Based Annotation of Contextualized Vital Signs. - Albert Goldfain; Min Xu; Jonathan P. Bona; Barry Smith 001 (ICBO, 2013)

An Ontology-Based Symbol Grounding System for Human-Robot Interaction. - Patrick Beeson; David Kortenkamp; R. Peter Bonasso; Andreas Persson; Amy Loutfi; Jonathan P. Bona (AAAI Fall Symposia, 2014)

Representing Modification Sites in PRO. - Jonathan P. Bona; Alan Ruttenberg; Jenny Rouleau (ICBO, 2014)

Applications of OBI 'assay'. - Mark Jensen; Alexander P. Cox; Jonathan P. Bona; William D. Duncan; Patrick L. Ray; Alexander D. Diehl (ICBO, 2014)

An Ontology-Driven Patient History Questionnaire System. - Jonathan P. Bona (AMIA, 2015)

Replacing EHR structured data with explicit representations. - Jonathan P. Bona; Werner Ceusters (ICBO, 2015)

Ontology-driven patient history questionnaires. - Jonathan P. Bona; Gunther Kohn; Alan Ruttenberg (ICBO, 2015)

Comparing Small Graph Retrieval Performance for Ontology Concepts in Medical Texts. - Daniel R. Schlegel; Jonathan P. Bona; Peter L. Elkin (Big-O(Q)/DMAH@VLDB, 2015)

Identifying Missing Finding Site Relations in SNOMED CT. - Jonathan P. Bona; Werner Ceusters (AMIA, 2016)

Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities. - Werner Ceusters; Jonathan P. Bona (AMIA, 2016)

Ontologies of Dynamical Systems and Verifiable Ontology-Based Computation: Towards a Haskell-Based Implementation of Referent Tracking. - Thomas Bittner; Jonathan P. Bona; Werner Ceusters (FOIS, 2016)

Representing SNOMED CT Concept Evolutions using Process Profiles. - Werner Ceusters; Jonathan P. Bona (JOWO@FOIS, 2016)

Analysis of SNOMED "Bleeding" Concepts & Terms. - Jonathan P. Bona; Selja Seppälä; Werner Ceusters (ICBO/BioCreative, 2016)

The ImmPort Antibody Ontology. - William D. Duncan; Travis Allen; Jonathan P. Bona; Olivia Helfer; Barry Smith 001; Alan Ruttenberg; Alexander D. Diehl (ICBO/BioCreative, 2016)

Does Semantic Tag Usage in SNOMED CT Match its Concept Hierarchy? - Jonathan P. Bona (AMIA, 2017)

Creating RDF Data on Trauma Care Organizations from Questionnaires. - Joseph R. Utecht; Jonathan P. Bona; Mathias Brochhausen (AMIA, 2017)

Scrutinizing the Relationships Between SNOMED CT Concepts and Semantic Tags. - Jonathan P. Bona; Werner Ceusters (ICBO, 2017)

Toward Using Ontologies to Improve Results in Searches for Mental Health Information. - Jonathan P. Bona; John Grohol; Meredith N. Zozus; Robert Zozus; Mathias Brochhausen (ICBO, 2017)

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Jonathan P. Bona; Chuming Chen; Sheng-Chih Chen; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; William D. Duncan; et al. (Nucleic Acids Res., 2017)

Ontologies Enabling Non-image Data Queries in The Cancer Imaging Archive. - Jonathan P. Bona; Tracy S. Nolan; Dillon Gibson; Mathias Brochhausen (AMIA, 2018)

Ontology-Enhanced Representations of Non-Image Data in The Cancer Image Archive. - Jonathan P. Bona; Tracy S. Nolan; Mathias Brochhausen (ICBO, 2018)

Towards the Development of an Opioid Misuse Ontology. - Corey J. Hayes; Jonathan P. Bona; Mathias Brochhausen (ICBO, 2018)

The Role of Axiomatically-Rich Ontologies in Transforming Medical Data to Knowledge. - Mathias Brochhausen; Jonathan P. Bona; Bernd Blobel (pHealth, 2018)

Mismatches between major subhierarchies and semantic tags in SNOMED CT. - Jonathan P. Bona; Werner Ceusters (J. Biomed. Informatics, 2018)

Providing a User-oriented Interface to Enable Semantic Queries in PRISM. - Jonathan P. Bona; Joseph Utecht; Mathias Brochhausen (AMIA, 2019)

Using Semantic Representations for Urine Drug Tests in the Veterans Health Administration. - Corey J. Hayes; Jonathan P. Bona; Mathias Brochhausen (AMIA, 2019)

Semantic Representations of Multi-Modal Data, NeuroInformatic Processing Pipelines, and Derived Neuroimaging Results in the Arkansas Image Enterprise System (ARIES). - Aaron S. Kemp; Jonathan P. Bona; Tracy S. Nolan; Linda J. Larson-Prior; Tuhin Virmani; Lakshmi R. Pillai; Mathias Brochhausen; Lawrence Tarbox; Fred W. Prior (AMIA, 2019)

Semantic Integration of Neuroinformatics Data in the Arkansas Image Enterprise System with Open Biomedical Ontologies. - Jonathan P. Bona; Aaron S. Kemp; Tracy S. Nolan; Linda J. Larson-Prior; Aparna Das; Tuhin Virmani; Lakshmi R. Pillai; Mathias Brochhausen; Fred W. Prior (ICBO, 2019)

Building a Shared Ontology Use Patterns Repository. - Jonathan P. Bona; Joseph Utecht; Sarah Bost; Corey J. Hayes; Mathias Brochhausen (ICBO, 2019)

Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers. - Jonathan P. Bona; Mathias Brochhausen; William R. Hogan (BMC Bioinform., 2019)

A Python Utility for Working with OBO Foundry Terms (short paper). - Jonathan P. Bona (ICBO/ODLS, 2020)

Recent Refinements of the NeuroPsychological Testing Ontology. - Alexander P. Cox; Kiernan L. Johnson; Lauren Wishnie; Aaron S. Kemp; Jonathan P. Bona; Alexander D. Diehl (ICBO, 2021)

Semantic Integration of Multi-Modal Data and Derived Neuroimaging Results Using the Platform for Imaging in Precision Medicine (PRISM) in the Arkansas Imaging Enterprise System (ARIES). - Jonathan P. Bona; Aaron S. Kemp; Carli Cox; Tracy S. Nolan; Lakshmi R. Pillai; Aparna Das; James E. Galvin; Linda Larson-Prior; Tuhin Virmani; Fred W. Prior (Frontiers Artif. Intell., 2021)

Reddit Caregiver Support Forums: NLP and Visualization for Digestion of Complex Themes. - Catherine C. Shoults; Michael W. Rutherford; Aaron S. Kemp; Merideth Addicott; Aliza Brown; Carolyn Greene; Corey J. Hayes; Jennifer Gan; Linda Larson-Prior; Jonathan P. Bona (AMIA, 2022)

Enhancing Childhood Nutrition Data with Open Biomedical Ontologies. - Jonathan P. Bona; Alexander D. Diehl; Alexander P. Cox; Aaron S. Kemp; Linda Larson-Prior (ICBO, 2022)

Building a Radiation Therapy Ontology. - Mark Phillips; Andre Dekker; Charles Mayo; Peter Gabriel; Jonathan P. Bona (ICBO, 2022)

Expanding the Ontology of Organizational Structures of Trauma Centers and Trauma Systems. - Diya Mehta; Justin M. Whorton; Reza Shahriari; Eric D. Ragan; Jonathan P. Bona; William R. Hogan; Kevin W. Sexton; Mathias Brochhausen (ICBO, 2024)