CIDO: The Community-Based Coronavirus Infectious Disease Ontology. - Yongqun He; Hong Yu 014; Edison Ong; Yang Wang; Yingtong Liu; Anthony Huffman; Hsin-Hui Huang; John Beverley; Asiyah Yu Lin; William D. Duncan; Sivaram Arabandi; Jiangan Xie; et al. (ICBO/ODLS, 2020)

A Community Effort for COVID-19 Ontology Harmonization. - Asiyah Yu Lin; Yuki Yamagata; William D. Duncan; Leigh C. Carmody; Tatsuya Kushida; Hiroshi Masuya; John Beverley; Biswanath Dutta; Michael DeBellis; Zoë May Pendlington; Paola Roncaglia; Yongqun He (ICBO, 2021)

The Infectious Disease Ontology in the age of COVID-19. - Shane Babcock; John Beverley; Lindsay G. Cowell; Barry Smith 001 (J. Biomed. Semant., 2021)

Coordinating Coronavirus Research: The Virus Infectious Disease Ontology. - John Beverley; Yongqun He; Barry Smith 001; Shane Babcock; Eric Merrell; Lindsay G. Cowell; Regina Hurley; Sebastian Deusing (ICBO, 2022)

Toward an Occupation Ontology, OccO. - Sam Smith; Damion M. Dooley; Eric Merrell; John Beverley; Yongqun He (ICBO, 2022)

BFO: Basic Formal Ontology. - J. Neil Otte; John Beverley; Alan Ruttenberg (Appl. Ontology, 2022)

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. - Yongqun He; Hong Yu 014; Anthony Huffman; Asiyah Yu Lin; Darren A. Natale; John Beverley; Ling Zheng; Yehoshua Perl; Zhigang Wang; Yingtong Liu; Edison Ong; Yang Wang; et al. (J. Biomed. Semant., 2022)

Ontology Development Strategies and the Infectious Disease Ontology Ecosystem. - Giacomo De Colle; Ali Hasanzadeh; John Beverley (ICBO, 2023)

The Occupation Ontology (OccO): Building a Bridge between Global Occupational Standards. - John Beverley; Sam Smith; Matthew Diller; William D. Duncan; Jie Zheng 001; John W. Judkins; William R. Hogan; Robin McGill; Damion M. Dooley; Yongqun He (JOWO, 2023)

Evaluation and Design of Generalist Systems (EDGeS). - John Beverley; Amanda Hicks (AI Mag., 2023)

The Common Core Ontologies. - Mark Jensen; Giacomo De Colle; Sean Kindya; Cameron More; Alexander P. Cox; John Beverley (FOIS, 2024)

Credentials in the Occupation Ontology. - John Beverley; Robin McGill; Sam Smith; Jie Zheng 001; Giacomo De Colle; Finn Wilson; Matthew Diller; William D. Duncan; William R. Hogan; Yongqun He (ICBO, 2024)

Grounding Realizable Entities. - Michael Rabenberg; Carter Benson; Federico Donato; Yongqun He; Anthony Huffman; Shane Babcock; John Beverley (ICBO, 2024)

Middle architecture criteria. - John Beverley; Giacomo De Colle; Mark Jensen; Carter-Beau Benson; Barry Smith 001 (JOWO, 2024)

Ontologies, arguments, and large-language models (short paper). - John Beverley; Francesco Franda; Mohammed Hedi Karray; Dan Maxwell; Carter-Beau Benson; Barry Smith 001 (JOWO, 2024)

Capabilities: An ontology. - John Beverley; David Limbaugh; Eric Merrell; Peter Koch 008; Barry Smith 001 (JOWO, 2024)

Towards a cyber information ontology. - David Limbaugh; Mark Jensen; John Beverley (JOWO, 2024)

Foundations for digital twins. - Finn Wilson; Regina Hurley; Daniel Maxwell; Jon McLellan; John Beverley (JOWO, 2024)

Editorial: Special Issue on Ontologies and Large-Language Models. - John Beverley (Appl. Ontology, 2024)

Capabilities. - John Beverley; Peter Koch 008; David Limbaugh; Barry Smith 001 (CoRR, 2024)

Foundations for Digital Twins. - Regina Hurley; Dan Maxwell; Jon McLellan; Finn Wilson; John Beverley (CoRR, 2024)

My Ontologist: Evaluating BFO-Based AI for Definition Support. - Carter Benson; Alec Sculley; Austin Liebers; John Beverley (CoRR, 2024)

Mapping the Provenance Ontology to Basic Formal Ontology. - Tim Prudhomme; Giacomo De Colle; Austin Liebers; Alec Sculley; Peihong Xie; Sydney Cohen; John Beverley (CoRR, 2024)

Concretizing plan specifications as realizables within the OBO foundry. - William D. Duncan; Matthew Diller; Damion M. Dooley; William R. Hogan; John Beverley (J. Biomed. Semant., 2024)

Editorial: Volume II Special Issue on Ontologies and Large Language Models. - John Beverley (Appl. Ontology, 2025)

Extending the design space of ontologization practices: Using bCLEARer as an example. - Chris Partridge; Andrew Mitchell; Sergio de Cesare; John Beverley (CoRR, 2025)

How Group Lives Go Well. - John Beverley; Regina Hurley (CoRR, 2025)

A Path to Loving. - John Beverley; Regina Hurley (CoRR, 2025)

Unreal Patterns. - John Beverley; Jim Logan; Barry Smith 001 (CoRR, 2025)

From over-reliance to smart integration: using Large-Language Models as translators between specialized modeling and simulation tools. - Philippe J. Giabbanelli; John Beverley; Istvan David; Andreas Tolk (CoRR, 2025)

Ontology Enabled Hybrid Modeling and Simulation. - John Beverley; Andreas Tolk (CoRR, 2025)

Ontological Foundations of State Sovereignty. - John Beverley; Danielle Limbaugh (CoRR, 2025)

A fourfold pathogen reference ontology suite. - John Beverley; Shane Babcock; Carter Benson; Giacomo De Colle; Sydney Cohen; Alexander D. Diehl; Ram A. N. R. Challa; Ray Mavrovich; Joshua Billig; Anthony Huffman; Yongqun He (J. Biomed. Semant., 2025)