James A. Overton

According to our database, James A. Overton authored at least 31 papers between 2011 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2023

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, Mary Osei-Twum, Caroline Atyeo, James A. Overton, Randi Vita, Hector Guzman-Orozco, Marcus Mendes, Mari Kojima, Peter J. Halfmann, Yoshihiro Kawaoka, Galit Alter, Luc Gagnon, Ralph S. Baric, Georgia D. Tomaras, Tim Germann, Daniel Bedinger, Jason A. Greenbaum, Erica Ollmann Saphire, Bjoern Peters

Database J. Biol. Databases Curation, February, 2023

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, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland

CoRR, 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, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland

Database J. Biol. Databases Curation, 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 Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall

Database J. Biol. Databases Curation, 2022

2021

Standardization of assay representation in the Ontology for Biomedical Investigations.

Randi Vita, Jie Zheng, 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, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.

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, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters

Database J. Biol. Databases Curation, 2021

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

2020

String of PURLs - frugal migration and maintenance of persistent identifiers.

James A. Overton, Michael Cuffaro, Christopher J. Mungall

Data Sci., 2020

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

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

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

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

2018

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong

J. Biomed. Semant., 2018

Identification of errors in the IEDB using ontologies.

Randi Vita, James A. Overton, Bjoern Peters

Database J. Biol. Databases Curation, 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

Formalizing the Representation of Immune Exposures for Human Immunology Studies.

Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

Standardizing Ontology Workflows Using ROBOT.

Rebecca Tauber, James P. Balhoff, Eric Douglass, Chris Mungall, James A. Overton

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem.

Metin N. Gurcan, John Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith

J. Biomed. Informatics, 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

Semantic Modeling for Accelerated Immune Epitope Database (IEDB) Biocuration.

Gully A. Burns, Randi Vita, James A. Overton, Ward Fleri, Bjoern Peters

Proceedings of Workshops and Tutorials of the 9th International Conference on Knowledge Capture (K-CAP2017), 2017

2016

Semantic representation of reported measurements in radiology.

Heiner Oberkampf, Sonja Zillner, James A. Overton, Bernhard Bauer, Alexander Cavallaro, Michael Uder, Matthias Hammon

BMC Medical Informatics Decis. Mak., 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

Humane OWL: RDF and OWL for Humans.

James A. Overton

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

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

ROBOT: A command-line tool for ontology development.

James A. Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontology, 2015

EDN-LD: A simple linked data tool.

James A. Overton

Proceedings of the International Conference on Biomedical Ontology, 2015

2013

"Explain" in scientific discourse.

James A. Overton

Synth., 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

A Taxonomy for Immunologists.

James A. Overton, Randi Vita, Jason Greenbaum, Heiko Dietze, Alessandro Sette, Bjoern Peters

Proceedings of the 4th International Conference on Biomedical Ontology, 2013

2011

Open Biomedical Ontologies applied to prostate cancer.

James A. Overton, Cesare Romagnoli, Rethy Chhem

Appl. Ontology, 2011

Philosophy, Ontology, and Scientific Explanation.

James A. Overton

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011