Scientific Explanation and Computation. - James A. Overton (ExaCt, 2011)

Philosophy, Ontology, and Scientific Explanation. - James A. Overton (ICBO, 2011)

Open Biomedical Ontologies applied to prostate cancer. - James A. Overton; Cesare Romagnoli; Rethy Chhem (Appl. Ontology, 2011)

A Taxonomy for Immunologists. - James A. Overton; Randi Vita; Jason Greenbaum; Heiko Dietze; Alessandro Sette; Bjoern Peters (ICBO, 2013)

Query enhancement through the practical application of ontology: the IEDB and OBI. - Randi Vita; James A. Overton; Jason Greenbaum; Alessandro Sette; Björn Peters (J. Biomed. Semant., 2013)

"Explain" in scientific discourse. - James A. Overton (Synth., 2013)

EDN-LD: A simple linked data tool. - James A. Overton (ICBO, 2015)

ROBOT: A command-line tool for ontology development. - James A. Overton; Heiko Dietze; Shahim Essaid; David Osumi-Sutherland; Christopher J. Mungall (ICBO, 2015)

The immune epitope database (IEDB) 3.0. - Randi Vita; James A. Overton; Jason A. Greenbaum; Julia V. Ponomarenko; Jason D. Clark; Jason R. Cantrell; Daniel K. Wheeler; Joseph L. Gabbard; Deborah Hix; Alessandro Sette; Bjoern Peters (Nucleic Acids Res., 2015)

Humane OWL: RDF and OWL for Humans. - James A. Overton (ICBO/BioCreative, 2016)

An ontology for major histocompatibility restriction. - Randi Vita; James A. Overton; Emily Seymour; John Sidney; Jim Kaufman; Rebecca L. Tallmadge; Shirley Ellis; John Hammond; Geoff W. Butcher; Alessandro Sette; Bjoern Peters (J. Biomed. Semant., 2016)

Semantic representation of reported measurements in radiology. - Heiner Oberkampf; Sonja Zillner; James A. Overton; Bernhard Bauer 001; Alexander Cavallaro; Michael Uder; Matthias Hammon (BMC Medical Informatics Decis. Mak., 2016)

Semantic Modeling for Accelerated Immune Epitope Database (IEDB) Biocuration. - Gully A. Burns; Randi Vita; James A. Overton; Ward Fleri; Bjoern Peters (K-CAP Workshops, 2017)

Better living through ontologies at the Immune Epitope Database. - Randi Vita; James A. Overton; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2017)

Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. - Metin N. Gurcan; John Tomaszewski 001; James A. Overton; Scott Doyle; Alan Ruttenberg; Barry Smith 001 (J. Biomed. Informatics, 2017)

Standardizing Ontology Workflows Using ROBOT. - Rebecca Tauber; James P. Balhoff; Eric Douglass; Chris Mungall; James A. Overton (ICBO, 2018)

Formalizing the Representation of Immune Exposures for Human Immunology Studies. - Randi Vita; Bjoern Peters; James A. Overton; Kei-Hoi Cheung; Steven H. Kleinstein (ICBO, 2018)

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. - Randi Vita; James A. Overton; Christopher J. Mungall; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2018)

Identification of errors in the IEDB using ontologies. - Randi Vita; James A. Overton; Bjoern Peters (Database J. Biol. Databases Curation, 2018)

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. - Yongqun He; Zuoshuang Xiang; Jie Zheng 001; Yu Lin; James A. Overton; Edison Ong (J. Biomed. Semant., 2018)

ROBOT: A Tool for Automating Ontology Workflows. - Rebecca C. Jackson; James P. Balhoff; Eric Douglass; Nomi L. Harris; Christopher J. Mungall; James A. Overton (BMC Bioinform., 2019)

Reporting and connecting cell type names and gating definitions through ontologies. - James A. Overton; Randi Vita; Patrick Dunn; Julie G. Burel; Syed Ahmad Chan Bukhari; Kei-Hoi Cheung; Steven H. Kleinstein; Alexander D. Diehl; Bjoern Peters (BMC Bioinform., 2019)

The Immune Epitope Database (IEDB): 2018 update. - Randi Vita; Swapnil Mahajan; James A. Overton; Sandeep Kumar Dhanda; Sheridan Martini; Jason R. Cantrell; Daniel K. Wheeler; Alessandro Sette; Bjoern Peters (Nucleic Acids Res., 2019)

A structured model for immune exposures. - Randi Vita; James A. Overton; Patrick Dunn; Kei-Hoi Cheung; Steven H. Kleinstein; Alessandro Sette; Bjoern Peters (Database J. Biol. Databases Curation, 2020)

String of PURLs - frugal migration and maintenance of persistent identifiers. - James A. Overton; Michael Cuffaro; Christopher J. Mungall (Data Sci., 2020)

An immunologically friendly classification of non-peptidic ligands. - Lindy Edwards; Rebecca C. Jackson; James A. Overton; Randi Vita; Nina Blazeska; Bjoern Peters; Alessandro Sette (Database J. Biol. Databases Curation, 2021)

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. - Rebecca C. Jackson; Nicolas Matentzoglu; James A. Overton; Randi Vita; James P. Balhoff; Pier Luigi Buttigieg; Seth Carbon; Mélanie Courtot; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Nomi L. Harris; et al. (Database J. Biol. Databases Curation, 2021)

Standardization of assay representation in the Ontology for Biomedical Investigations. - Randi Vita; Jie Zheng 001; Rebecca C. Jackson; Damion M. Dooley; James A. Overton; Mark A. Miller; Daniel C. Berrios; Richard H. Scheuermann; Yongqun He; Hande Küçük-McGinty; Mathias Brochhausen; Aisyah Yu Lin; et al. (Database J. Biol. Databases Curation, 2021)

Building an Application Ontology and Knowledge Graph for Rare Disease Patient-Level Data. - Emily Hartley; Daniel Olson; Ian Braun; Nicolas Matentzoglu; James A. Overton; Ramona L. Walls (ICBO, 2022)

The OntoDev Suite of Ontology and Data Integration Tools. - James A. Overton (ICBO, 2022)

COB: A Core Ontology for Biology and Biomedicine. - James A. Overton; Rebecca C. Jackson; Nicolas Matentzoglu; William D. Duncan; Randi Vita; Nomi L. Harris; Christopher J. Mungall; Bjoern Peters (ICBO, 2022)

OBO Academy: Training Materials for Bioontologists. - James A. Overton; Rebecca C. Jackson; Sabrina Toro; Shawn Zheng Kai Tan; Bradley Varner; David Osumi-Sutherland; Nicolas Matentzoglu; Nicole A. Vasilevsky (ICBO, 2022)

A Simple Standard for Sharing Ontological Mappings (SSSOM). - Nicolas Matentzoglu; James P. Balhoff; Susan M. Bello; Chris Bizon; Matthew H. Brush; Tiffany J. Callahan; Christopher G. Chute; William D. Duncan; Chris T. A. Evelo; Davera Gabriel; John B. Graybeal; Alasdair J. G. Gray; et al. (Database J. Biol. Databases Curation, 2022)

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (Database J. Biol. Databases Curation, 2022)

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (CoRR, 2022)

Coronavirus Immunotherapeutic Consortium Database. - Jarjapu Mahita; Brendan Ha; Anais Gambiez; Sharon L. Schendel; Haoyang Li; Kathryn M. Hastie; S. Moses Dennison; Kan Li; Natalia Kuzmina; Sivakumar Periasamy; Alexander Bukreyev; Jennifer E. Munt; et al. (Database J. Biol. Databases Curation, 2023)

Horned-OWL: Flying Further and Faster with Ontologies. - Phillip Lord; Björn Gehrke; Martin Larralde; Janna Hastings; Filippo De Bortoli; James A. Overton; James P. Balhoff; Jennifer D. Warrender (TGDK, 2024)

Horned-OWL. - Phillip Lord; Björn Gehrke; Martin Larralde; Janna Hastings; Filippo De Bortoli; James A. Overton; James P. Balhoff; Jennifer D. Warrender (DROPS Artifacts, 2024)

A change language for ontologies and knowledge graphs. - Harshad Hegde; Jennifer Vendetti; Damien Goutte-Gattat; J. Harry Caufield; John B. Graybeal; Nomi L. Harris; Naouel Karam; Christian Kindermann; Nicolas Matentzoglu; James A. Overton; Mark A. Musen; Christopher J. Mungall (Database J. Biol. Databases Curation, 2025)

Putting computational models of immunity to the test - An invited challenge to predict B.pertussis vaccination responses. - Pramod Shinde; Lisa Willemsen; Michael Anderson; Minori Aoki; Saonli Basu; Julie G. Burel; Peng Cheng; Souradipto Ghosh Dastidar; Aidan Dunleavy; Tal Einav; Jamie Forschmiedt; Slim Fourati; et al. (PLoS Comput. Biol., 2025)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)

Standardizing free-text data exemplified by two fields from the Immune Epitope Database. - Sebastian Duesing; Jason Bennett; James A. Overton; Randi Vita; Bjoern Peters (J. Biomed. Semant., 2025)