James A. Overton

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 24

Top Topics

Ontology Development

Domain Ontology

Top Venues

Database J. Biol. Databases Curation

J. Biomed. Semant.

Publications

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
Coronavirus Immunotherapeutic Consortium Database. Database J. Biol. Databases Curation 2023 (2023)
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
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. CoRR (2022)
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 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
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022 (2022) (2022)
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
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database J. Biol. Databases Curation 2022 (2022) (2022)
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
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR (2021)
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
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)
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.
Standardization of assay representation in the Ontology for Biomedical Investigations. Database J. Biol. Databases Curation 2021 (2021)
Lindy Edwards, Rebecca C. Jackson, James A. Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette
An immunologically friendly classification of non-peptidic ligands. Database J. Biol. Databases Curation 2021 (2021)
James A. Overton, Michael Cuffaro, Christopher J. Mungall
String of PURLs - frugal migration and maintenance of persistent identifiers. Data Sci. 3 (1) (2020)
Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters
A structured model for immune exposures. Database J. Biol. Databases Curation 2020 (2020)
Randi Vita, Swapnil Mahajan, James A. Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R. Cantrell, Daniel K. Wheeler, Alessandro Sette, Bjoern Peters
The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 47 (Database-Issue) (2019)
Rebecca C. Jackson, James P. Balhoff, Eric Douglass, Nomi L. Harris, Christopher J. Mungall, James A. Overton
ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinform. 20 (1) (2019)
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
Reporting and connecting cell type names and gating definitions through ontologies. BMC Bioinform. (5) (2019)
Rebecca Tauber, James P. Balhoff, Eric Douglass, Chris Mungall, James A. Overton
Standardizing Ontology Workflows Using ROBOT. ICBO (2018)
Randi Vita, James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. Database J. Biol. Databases Curation 2018 (2018)
Randi Vita, Bjoern Peters, James A. Overton, Kei-Hoi Cheung, Steven H. Kleinstein
Formalizing the Representation of Immune Exposures for Human Immunology Studies. ICBO (2018)
Randi Vita, James A. Overton, Bjoern Peters
Identification of errors in the IEDB using ontologies. Database J. Biol. Databases Curation 2018 (2018)
Yongqun He, Zuoshuang Xiang, Jie Zheng, Yu Lin, James A. Overton, Edison Ong
The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability. J. Biomed. Semant. 9 (1) (2018)
Metin N. Gurcan, John Tomaszewski, James A. Overton, Scott Doyle, Alan Ruttenberg, Barry Smith
Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem. J. Biomed. Informatics 66 (2017)
Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters
Better living through ontologies at the Immune Epitope Database. Database J. Biol. Databases Curation 2017 (2017)
Gully A. Burns, Randi Vita, James A. Overton, Ward Fleri, Bjoern Peters
Semantic Modeling for Accelerated Immune Epitope Database (IEDB) Biocuration. K-CAP Workshops (2017)
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
An ontology for major histocompatibility restriction. J. Biomed. Semant. 7 (2016)
James A. Overton
Humane OWL: RDF and OWL for Humans. ICBO/BioCreative (2016)
Heiner Oberkampf, Sonja Zillner, James A. Overton, Bernhard Bauer, Alexander Cavallaro, Michael Uder, Matthias Hammon
Semantic representation of reported measurements in radiology. BMC Medical Informatics Decis. Mak. 16 (2016)
James A. Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland, Christopher J. Mungall
ROBOT: A command-line tool for ontology development. ICBO (2015)
James A. Overton
EDN-LD: A simple linked data tool. ICBO (2015)
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
The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 43 (Database-Issue) (2015)
Randi Vita, James A. Overton, Jason Greenbaum, Alessandro Sette, Björn Peters
Query enhancement through the practical application of ontology: the IEDB and OBI. J. Biomed. Semant. 4 (S-1) (2013)
James A. Overton, Randi Vita, Jason Greenbaum, Heiko Dietze, Alessandro Sette, Bjoern Peters
A Taxonomy for Immunologists. ICBO (2013)
James A. Overton
"Explain" in scientific discourse. Synth. 190 (8) (2013)
James A. Overton, Cesare Romagnoli, Rethy Chhem
Open Biomedical Ontologies applied to prostate cancer. Appl. Ontology 6 (1) (2011)
James A. Overton
Philosophy, Ontology, and Scientific Explanation. ICBO (2011)