James A. Overton

Thoughts on philosophy, science, and software.

Curriculum Vitae

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James A. Overton

(Updated 2025-06-24)

Apt. 2 - 107 Quebec Ave.

Toronto, Ontario, Canada

M6P 2T3

james@overton.ca

1 (416) 318-1112

Citizenship: Canadian

Languages: English (mother tongue), French (reading knowledge)

Education

  • Degrees

  • Grants and Fellowships

    • Cesare Romagnoli, Gillian Barker, and James A. Overton. "The Ontology and Epistemology of Medical Imaging." Joseph L. Rotman Institute of Science and Values Graduate Research Assistantship, April 2014.
    • Cesare Romagnoli and James A. Overton. "Structured Reporting of Prostate Cancer." Image Guidance for Prostate Cancer Management Project Grant, January 2012.
    • Visiting Fellowship at the Tilburg Center for Logic and Philosophy of Science (TiLPS), 2011.
    • Gillian Barker, Cesare Romagnoli, and James A. Overton. "The Interdisciplinary Prostate Ontology Project -- Stage Two." Joseph L. Rotman Institute of Science and Values Seed Grant, July 2009.
    • Cesare Romagnoli and James A. Overton. "The Interdisciplinary Prostate Ontology Project." London Health Sciences Centre Department of Medical Imaging Project Grant, September 2008.

  • Scholarships and Awards

    • Canada Graduate Scholarships -- Michael Smith Foreign Study Supplement, Social Sciences and Humanities Research Council of Canada ($6000), 2009.
    • Canada Graduate Scholarships -- Doctoral Award, Social Sciences and Humanities Research Council of Canada ($105 000 over 3 years), 2007-2010.
    • The University of Western Ontario Department of Philosophy Entrance Scholarship ($4000), 2007.
    • University Medal in Mathematics, Carleton University, 2005.
    • Doctoral Fellowship, Social Sciences and Humanities Research Council of Canada ($80 000 over 4 years, declined to pursue employment), 2005.
    • Ontario Graduate Scholarships ($15 000 each, awarded twice), 2002-2003, 2003-2004.
    • Carleton University Dean of Graduate Studies Entrance Scholarship for Academic Excellence ($2000), 2002.
    • Carleton University Senate Medal for Outstanding Academic Achievement, 2002.
    • Carleton University Deans' Honour List, 1999-2002, 2004 (all years of eligibility).
    • Carleton University Entrance Scholarship ($3200 per annum, renewed three times), 1998-2002.

Current Occupation

My company Knocean Inc. offers consulting and development services at the intersection of philosophy, science, and software. I specialize in scientific database integration using biomedical ontologies. Examples include ontology development and deployment, building semantic web tools, and developing custom web applications for scientific and medical projects.

  • Consultant La Jolla Institute (San Diego, California, USA), 2012 - Present: ontology development, software development, and database integration for: Immune Epitope Database; Coronavirus Immunotherapy Consortium Database; Immunophenotyping assessment in a COVID-19 cohort project; Computational Models of Immunology: Pertussis Boost; ImmuneSpace; Adaptive Immune Receptor Repertoire Knowledge Commons
  • Consultant ASRC Federal (Reston, Virginia, USA), 2012 - Present: ontology development, software development, and database integration for the Chemical Effects on Biological Systems project and Division of Translational Toxicology data dictionary
  • Technical Working Group Member OBO Operations Committee, 2014 - Present: collaborative development of policies, tools, and infrastructure for the maintenance of the OBO Foundry
  • Release Manager Ontology for Biomedical Investigations (http://obi-ontology.org), 2014 - Present: development and coordination of OBI review and release processes, and supporting tools

Recent Engagements

  • Consultant Wellcome Sanger Institute (Hinxton, Cambridgeshire, UK), 2024-2025: software development for the BRAIN Initiative Cell Atlas Network (BICAN) Taxonomy Development Tools project
  • Consultant University of Florida (Gainesville, Florida, USA), 2023-2024: software and ontology development for the Drug Ontology
  • Consultant European Bioinformatics Institute (Hinxton, Cambridgeshire, UK), 2023: software development and data integration for the BRAIN Initiative Cell Atlas Network (BICAN)
  • Consultant Critical Path Institute (Tucson, Arizona, USA), 2021, 2022: ontology development training; ontology development and data integration
  • Consultant Lawrence Berkeley National Laboratory (Berkeley, California, USA), 2015, 2016, 2021: software development for Gene Ontology; software development for Knowledge Graph Change Language
  • Consultant European Bioinformatics Institute (Hinxton, Cambridgeshire, UK), 2020 - 2021: software development and data integration for the International Hundred+ Cohorts Consortium

Research Interests

Scientific explanation and science informatics are at the centre of my research. Scientific explanations help us to understand our world better. Science informatics multiplies the power and reach of science by helping us to collect, manage, and analyze vast quantities of data. More data and more analytical power mean that we explain more, but also that we explain differently. I use tools from epistemology, ontology, mathematics, and computer science to better understand the changing nature of scientific explanation and build better science informatics systems.

Publications

  • Refereed Papers

    • Shawn Zheng Kai Tan, Aleix Puig-Barbe, Damien Goutte-Gattat, Caroline Eastwood, Brian Aevermann, Alida Avola, James P Balhoff, Ismail Ugur Bayindir, Jasmine Belfiore, Anita Reane Caron, David S Fischer, Nancy George, Benjamin M Gyori, Melissa A Haendel, Charles Tapley Hoyt, Huseyin Kir, Tiago Lubiana, Nicolas Matentzoglu, James A Overton, Beverly Peng, Bjoern Peters, Ellen M Quardokus, Patrick L Ray, Paola Roncaglia, Andrea D Rivera, Ray Stefancsik, Wei Kheng Teh, Sabrina Toro, Nicole Vasilevsky, Chuan Xu, Yun Zhang, Richard H Scheuermann, Chirstopher J Mungall, Alexander D Diehl, David Osumi-Sutherland. "The Cell Ontology in the age of single-cell omics." arXiv preprint arXiv:2506.10037. 2025.
    • 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, Javier Garcia, William Gibson, Jason A Greenbaum, Leying Guan, Weikang Guan, Jeremy P Gygi, Brendan Ha, Joe Hou, Jason Hsiao, Yunda Huang, Rick Jansen, Bhargob Kakoty, Zhiyu Kang, James J Kobie, Mari Kojima, Anna Konstorum, Jiyeun Lee, Sloan A Lewis, Aixin Li, Eric F Lock, Jarjapu Mahita, Marcus Mendes, Hailong Meng, Aidan Neher, Somayeh Nili, Lars Rønn Olsen, Shelby Orfield, James A Overton, Nidhi Pai, Cokie Parker, Brian Qian, Mikkel Rasmussen, Joaquin Reyna, Eve Richardson, Sandra Safo, Josey Sorenson, Aparna Srinivasan, Nicola Thrupp, Rashmi Tippalagama, Raphael Trevizani, Steffen Ventz, Jiuzhou Wang, Cheng-Chang Wu, Ferhat Ay, Barry Grant, Steven H Kleinstein, Bjoern Peters. "Putting computational models of immunity to the test—An invited challenge to predict B. pertussis vaccination responses." PLoS computational biology. 21(3), 2025.
    • Randi Vita, Nina Blazeska, Daniel Marrama, IEDB Curation Team Members Shackelford Deborah Zalman Leora Foos Gabriele Zarebski Laura Chan Kenneth Reardon Brian Fitzpatrick Sidne Busse Matthew Coleman Sara Sedwick Caitlin Edwards Lindy MacFarlane Catriona Ennis Marcus, Sebastian Duesing, Jason Bennett, Jason Greenbaum, Marcus De Almeida Mendes, Jarjapu Mahita, Daniel K Wheeler, Jason R Cantrell, James A Overton, Darren A Natale, Alessandro Sette, Bjoern Peters. "The Immune Epitope Database (IEDB): 2024 update." Nucleic Acids Research. 53(D1):D436-D443, 2025.
    • 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. "A change language for ontologies and knowledge graphs." Database. 2025.
    • Duesing, Sebastian and Bennett, Jason and Overton, James A and Vita, Randi and Peters, Bjoern. "Standardizing Free-Text Data Exemplified by Age and Data-Location Fields in the Immune Epitope Database." Journal of Biomedical Semantics. 16(1):5, 2025.
    • Phillip Lord, Björn Gehrke, Martin Larralde, Janna Hastings, Filippo De Bortoli, James A Overton, James P Balhoff, Jennifer Warrender. "Horned-OWL: Flying Further and Faster with Ontologies." Transactions on Graph Data and Knowledge. 2(2):1-9, 2024.
    • Kerstin Westendorf, James Overton, Randi Vita, Brendan Ha, Anais Gambiez, Pramod Shinde, Robert McDougal, Mari Kojima, Jason Greenbaum, Steven Kleinstein, Bjoern Peters. "ImmuneSpace: Enhanced curation of immunological study data for the HIPC consortium." The Journal of Immunology. 212(1 Supplement):0586.5245, 2024.
    • Scott Christley, Felix Breden, Kevin Burns, Brian Corrie, William Lees, James Overton, Bjoern Peters, Eve Richardson, Krishna Roskin, Randi Vita, Corey Watson, Gur Yaari, Lindsay Cowell. "Adaptive Immune Receptor Repertoire Knowledge Commons: large-scale knowledge for research and innovation (https://airr-knowledge. org)." The Journal of Immunology. 212(1 Supplement):1522.5717, 2024.
    • Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason A Greenbaum, James A Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P Gygi, Ricardo da Silva Antunes, Alessandro Sette, Barry Grant, Lars Rønn Olsen, Anna Konstorum, Leying Guan, Ferhat Ay, Steven H Kleinstein, Bjoern Peters. "A multi-omics systems vaccinology resource to develop and test computational models of immunity." Cell Reports Methods. 4(3): 2024.
    • Pramod Shinde, Ferran Soldevila, Joaquin Reyna, Minori Aoki, Mikkel Rasmussen, Lisa Willemsen, Mari Kojima, Brendan Ha, Jason A Greenbaum, James A Overton, Hector Guzman-Orozco, Somayeh Nili, Shelby Orfield, Jeremy P Gygi, Ricardo da Silva Antunes, Alessandro Sette, Barry Grant, Lars Rønn Olsen, Anna Konstorum, Leying Guan, Ferhat Ay, Steven H Kleinstein, Bjoern Peters. "A systems vaccinology resource to develop and test computational models of immunity." bioRxiv. 2023.
    • Joann Diray-Arce, Slim Fourati, Naresh Doni Jayavelu, Ravi Patel, Cole Maguire, Ana C Chang, Ravi Dandekar, Jingjing Qi, Brian H Lee, Patrick van Zalm, Andrew Schroeder, Ernie Chen, Anna Konstorum, Anderson Brito, Jeremy P Gygi, Alvin Kho, Jing Chen, Shrikant Pawar, Ana Silvia Gonzalez-Reiche, Annmarie Hoch, Carly E Milliren, James A Overton, Kerstin Westendorf, James Abraham, Michael Adkisson, Marisa Albert, Luz Torres Altamirano, Bonny Alvarenga, Matthew L Anderson, Evan J Anderson, Azlann Arnett, Hiromitsu Asashima, Mark A Atkinson, Lindsey R Baden, Brenda Barton, Katherine Beach, Elizabeth Beagle, Patrice M Becker, Matthew R Bell, Mariana Bernui, Christian Bime, Arun Kumar Boddapati, J Leland Booth, Brittney Borresen, Scott C Brakenridge, Laurel Bristow, Robert Bryant, Carolyn S Calfee, Juan Manuel Carreño, Sidney Carrillo, Suzanna Chak, Iris Chang, Jennifer Connors, Michelle Conway, David B Corry, David Cowan, Brett Croen, Charles S Dela Cruz, Gina Cusimano, Lily Eaker, Carolyn Edwards, Lauren IR Ehrlich, David Elashoff, Heidi Erickson, David J Erle, Shelli Farhadian, Keith Farrugia, Benoit Fatou, Andrea Fernandes, Ana Fernandez-Sesma, Gabriela K Fragiadakis, Sara Furukawa, Janelle N Geltman, Rajani Ghale, Maria Carolina Bermúdez González, I Michael Goonewardene, Estella Sanchez Guerrero, Faheem W Guirgis, David A Hafler, Sydney Hamilton, Paul Harris, Arash Nemati Hayati, Carolyn M Hendrickson, Nelson I Agudelo Higuita, Thomas Hodder, Steven M Holland, Catherine L Hough, Christopher Huerta, Kerin C Hurley, Scott R Hutton, Akiko Iwasaki, Alejandra Jauregui, Meenakshi Jha, Brandi Johnson, David Joyner, Kirsten N Kangelaris, Geoffrey Kelly, Zain Khalil, Zenab Khan, Farrah Kheradmand, James N Kim, Hiroki Kimura, Albert I Ko, Bernard Kohr, Monica Kraft, Matthew Krummel, Michele A Kutzler, Jessica Lasky-Su, Serena Lee, Deanna Lee, Michael Leipold, Claudia Lentucci, Carolyn Leroux, Edward Lin, Shanshan Liu, Christina Love, Zhengchun Lu, Lenka Maliskova, Brittany Roth Manning, Monali Manohar, Mark Martens, Grace A McComsey, Kerry McEnaney, Renee McLin, Esther Melamed, Nataliya Melnyk, Kevin Mendez, William B Messer, Jordan P Metcalf, Gregory Michelotti, Eran Mick, Subhasis Mohanty, Jarrod Mosier, Lubbertus CF Mulder, Maimouna Murphy, Kari RC Nadeau, Ebony Nelson, Allison Nelson, Viet Nguyen, Jordan Oberhaus, Bernadine Panganiban, Kathryn L Pellegrini, Harry C Pickering, Debra L Powell, Scott Presnell, Bali Pulendran, Adeeb H Rahman, Ahmad Sadeed Rashid, Ariel Raskin, Elaine F Reed. "Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients." Cell Reports Medicine. 4(6): 2023.
    • 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. 2023.
    • Al Ozonoff, Joanna Schaenman, Naresh Doni Jayavelu, Carly E Milliren, Carolyn S Calfee, Charles B Cairns, Monica Kraft, Lindsey R Baden, Albert C Shaw, Florian Krammer, Harm Van Bakel, Denise A Esserman, Shanshan Liu, Ana Fernandez Sesma, Viviana Simon, David A Hafler, Ruth R Montgomery, Steven H Kleinstein, Ofer Levy, Christian Bime, Elias K Haddad, David J Erle, Bali Pulendran, Kari C Nadeau, Mark M Davis, Catherine L Hough, William B Messer, Nelson I Agudelo Higuita, Jordan P Metcalf, Mark A Atkinson, Scott C Brakenridge, David Corry, Farrah Kheradmand, Lauren IR Ehrlich, Esther Melamed, Grace A McComsey, Rafick Sekaly, Joann Diray-Arce, Bjoern Peters, Alison D Augustine, Elaine F Reed, Matthew C Altman, Patrice M Becker, Nadine Rouphael, Chris Bime, Mark M Davis, Kerry McEnaney, Brenda Barton, Claudia Lentucci, Mehmet Saluvan, Ana C Chang, Annmarie Hoch, Marisa Albert, Tanzia Shaheen, Alvin T Kho, Sanya Thomas, Jing Chen, Maimouna D Murphy, Mitchell Cooney, Scott Presnell, Gabriela K Fragiadakis, Ravi Patel, Leying Guan, Jeremy Gygi, Shrikant Pawar, Anderson Brito, Zain Khalil, Cole Maguire, Slim Fourati, James A Overton, Randi Vita, Kerstin Westendorf, Ramin Salehi-Rad, Aleksandra Leligdowicz, Michael A Matthay, Jonathan P Singer, Kirsten N Kangelaris, Carolyn M Hendrickson, Matthew F Krummel, Charles R Langelier, Prescott G Woodruff, Debra L Powell, James N Kim, Brent Simmons, I Michael Goonewardene, Cecilia M Smith, Mark Martens, Jarrod Mosier, Hiroki Kimura, Amy C Sherman, Stephen R Walsh, Nicolas C Issa, Charles Dela Cruz, Shelli Farhadian, Akiko Iwasaki, Albert I Ko, Sharon Chinthrajah, Neera Ahuja, Angela J Rogers, Maja Artandi, Sarah AR Siegel, Zhengchun Lu, Douglas A Drevets, Brent R Brown, Matthew L Anderson, Faheem W Guirgis, Rama V Thyagarajan, Justin F Rousseau, Dennis Wylie, Johanna Busch, Saurin Gandhi, Todd A Triplett, George Yendewa, Olivia Giddings, Evan J Anderson, Aneesh K Mehta, Jonathan E Sevransky, Bernard Khor, Adeeb Rahman, Daniel Stadlbauer, Jayeeta Dutta, Hui Xie, Seunghee Kim-Schulze, Ana Silvia Gonzalez-Reiche, Adriana van de Guchte, Keith Farrugia, Zenab Khan, Holden T Maecker, David Elashoff, Jenny Brook, Estefania Ramires-Sanchez, Megan Llamas, Adreanne Rivera, Claudia Perdomo, Dawn C Ward, Clara E Magyar, Jennifer A Fulcher, Yumiko Abe-Jones, Saurabh Asthana, Alexander Beagle, Sharvari Bhide, Sidney A Carrillo, Suzanna Chak, Rajani Ghale, Ana Gonzalez, Alejandra Jauregui, Norman Jones, Tasha Lea, Deanna Lee, Raphael Lota. "Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study." EBioMedicine. 83: 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 Haendel, Nomi L Harris, William R Hogan, Charles Tapley Hoyt, Rebecca C Jackson, HyeongSik Kim, Huseyin Kir, Martin Larralde, Julie A McMurry, James A Overton, Bjoern Peters, Clare Pilgrim, Ray Stefancsik, Sofia MC Robb, Sabrina Toro, Nicole A Vasilevsky, Ramona Walls, Christopher J Mungall, David Osumi-Sutherland. "Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies." Database. 2022.
    • Randi Vita, Apurva Mody, James A Overton, Soren Buus, Stephen T Haley, Alessandro Sette, Vamsee Mallajosyula, Mark M Davis, Dale L Long, Richard A Willis, Bjoern Peters, John D Altman. "Minimal Information about MHC Multimers (MIAMM)." The Journal of Immunology. 208(3): 531-537, 2022.
    • Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, 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 Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher J Mungall. "A simple standard for sharing ontological mappings (SSSOM)." Database. 2022.
    • Ferran C Soldevila, Pramod Shinde, Mari Kojima, James A Overton, Brendan Ha, Jason Greenbaum, Ferhat Ay, Steven H Kleinstein, Barry J Grant, Bjoern Peters. "Computational models of Immunity--Pertussis Boost (CMI-PB): Engaging the broader scientific community to develop predictive models of Tdap booster vaccination.." The Journal of Immunology. 206(1 Supplement):59.22, 2021.
    • Randi Vita, Jie Zheng, Rebecca Jackson, Damion 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. 2021.
    • Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie 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. 2021.
    • Lindy Edwards, Rebecca Jackson, James A Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette. "An immunologically friendly classification of non-peptidic ligands." Database. 2021.
    • Randi Vita, James A Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H Kleinstein, Alessandro Sette, Bjoern Peters. "A structured model for immune exposures." Database. 2020.
    • James A Overton, Michael Cuffaro, OBO Foundry Operations Committee Technical Working Group c, Christopher J Mungall. "String of PURLs--frugal migration and maintenance of persistent identifiers." Data Science. 3(1):3-13, 2020.
    • Jackson, Rebecca C and Balhoff, James P and Douglass, Eric and Harris, Nomi L and Mungall, Christopher J and Overton, James Rebecca C Jackson, James P Balhoff, Eric Douglass, Nomi L Harris, Christopher J Mungall, James A OvertonA. "ROBOT: a tool for automating ontology workflows." BMC Bioinformatics. 20:1-10, 2019.
    • Nima Salimi, 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 enables and accelerates research." The Journal of Immunology. 202(1 Supplement):130.20, 2019.
    • Randi J Vita, James A Overton, Kei-Hoi Cheung, Patrick Dunn, Julie Burel, Syed Ahmad Chan, Alexander D Diehl, Steven H Kleinstein, Alessandro Sette, Bjoern Peters. "Formal representation of immunology related data with ontologies." The Journal of Immunology. 202(1 Supplement):130.26, 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 Bioinformatics. 20: 259-264, 2019.
    • 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 Research. 47(D1): D339-D343, 2019.
    • Randi Vita, James A Overton, Bjoern Peters. "Identification of errors in the IEDB using ontologies." Database. 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. 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." Journal of Biomedical Semantics. 9:1-10, 2018.
    • Randi Vita, James A Overton, Alessandro Sette, Bjoern Peters. "Better living through ontologies at the Immune Epitope Database." Database. 2017.
    • 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." Journal of Biomedical Informatics. 66:129-135, 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." Journal of Biomedical Semantics. 7:1-7, 2016.
    • Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H Brush, Bill Bug, Marcus C Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Daniel Schober, Barry Smith, Larisa N Soldatova, Christian J Stoeckert Jr, Chris F Taylor, Carlo Torniai, Jessica A Turner, Randi Vita, Patricia L Whetzel, Jie Zheng. "The Ontology for Biomedical Investigations." PLoS One. 11(4), 2016.
    • Heiner Oberkampf, Sonja Zillner, James A Overton, Bernhard Bauer, Alexander Cavallaro, Michael Uder, and Matthias Hammon. "Semantic representation of reported measurements in radiology." BMC Medical Informatics and Decision Making. 16(1):1, 2016.
    • Randi Vita, James A Overton, Emily Seymour, John Sidney, Jim Kaufman, Rebecca L Tallmadge, Shirley Ellis, John Hammond, Geoff W Butcher, Alessandro Sette, and Bjoern Peters. "An ontology for major histocompatibility restriction." Journal of Biomedical Semantics. 7(1):1, 2016.
    • Barry Smith, Sivaram Arabandi, Mathias Brochhausen, Michael Calhoun, Paolo Ciccarese, Scott Doyle, Bernard Gibaud, Ilya Goldberg, Charles E Kahn, James A Overton, John Tomaszewski, and Metin Gurcan. "Biomedical imaging ontologies: A survey and proposal for future work." Journal of Pathology Informatics. 6(1):37, 2015.
    • Randi Vita, James A Overton, Jason A Greenbaum, Julia 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 Research. 43(D1):D405–D412, 2015.
    • Randi Vita, James A Overton, Jason A Greenbaum, Alessandro Sette, and Bjoern Peters. "Query enhancement through the practical application of ontology: the IEDB and OBI." Journal of Biomedical Semantics. 4(1):1–10, 2013.
    • James A Overton. "`Explain' in Scientific Discourse." Synthese. 190(8): 2013.
    • James A Overton. "Mechanisms, Types, and Abstractions." Philosophy of Science. 78(5): 2011.
    • James A Overton, Cesare Romagnoli, and Rethy K. Chhem. "Open Biomedical Ontologies Applied to Prostate Cancer." Applied Ontology. 6(1): 35-51, 2011.

  • Book Chapters

    • James A Overton and Cesare Romagnoli. "Radiology, Philosophy, and Ontology." In Rethy K. Chhem, Heiner Fangerau, Irmgard Müller, and Shih-chang Wang, editors, Medical Imaging and Philosophy. Franz Steiner Verlag, Stuggart, 2012.
    • Cesare Romagnoli, James A Overton, and Rethy K. Chhem. "Philosophy of radiology: The ontological challenge." In Teresa Van Deven, Kathryn M. Hibbert, and Rethy K. Chhem, editors, The Practice of Radiology Education. Springer, New York, 2010.
    • Robert Arp, Cesare Romagnoli, Rethy K. Chhem, and James A Overton. "Radiological and Biomedical Knowledge Integration: The Ontological Way." In Rethy K. Chhem, Kathryn M. Hibbert, and Teresa Van Deven, editors, Radiology Education: The Scholarship of Teaching and Learning. Springer, New York, 2009.

Presentations

  • Papers Presented

    • Gary Berg-Cross, James A Overton. "Helping Scientific Researchers Make Better Use of Ontologies." Ontolog Forum. 2023.
    • Nicole Vasilevsky, James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, Nicolas Matentzoglu. "OBO Academy: Training materials for bio-ontologists." ISMB Bio-Ontologies Community. 273:10.5281, 2022.
    • Randi Vita, Bjoern Peters, James A Overton, Kei-Hoi Cheung, Steven H Kleinstein. "Formalizing the Representation of Immune Exposures for Human Immunology Studies." International Conference on Biomedical Ontology. Corvallis, Oregon. 2018.
    • Rebecca Tauber, James P Balhoff, Eric Douglass, Chris Mungall, James A Overton. "Standardizing Ontology Workflows Using ROBOT.." International Conference on Biomedical Ontology. Corvallis, Oregon. 2018.
    • 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.
    • James A Overton, Barry Smith, Christopher J Mungall, Christian J Stoeckert Jr, Randi Vita, and Melissa Haendel. "OBO Tutorial: Open Biological and Biomedical Ontologies in Action." 6th International Conference on Biomedical Ontology. Corvallis, Oregon. August 1, 2016.
    • Spencer Hey and James A Overton. "Explanatory Agnosticism in Translational Medicine." Society for Philosphy of Science in Practice. Glassboro, New Jersey. June 17, 2016.
    • James A Overton, Alan Ruttenberg, Barry Smith, and Jie Zheng. "OBO Tutorial: Best Practises for Ontology Use." 5th International Conference on Biomedical Ontology. Lisbon, Portugal. July 28, 2015.
    • James A Overton. "Linked Data for Toxicology." National Institute for Environmental Health Sciences. Durham, North Carolina. April 13, 2015.
    • James A Overton. "Explanation in Science." Philosophy of Science Association. Chicago, Illinois. November 7, 2014.
    • Heiner Oberkampf, James A Overton, Sonja Zillner, Bernhard Bauer, and Matthias Hammon. "Expressing Medical Image Measurements using Ontologies of the OBO Library." CrEDIBLE Thematic Working Days. Sophia Antipolis, France. October 10, 2014.
    • Melanie Courtot, Melissa Haendel, James A Overton, Bjoern Peters, Alan Ruttenberg, and Jie Zheng. "OBO Technical Workshop: Hands-On with Open Biological and Biomedical Ontologies." 4th International Conference on Biomedical Ontology. Houston, Texas. October 7, 2014.
    • Melanie Courtot, Melissa Haendel, James A Overton, Bjoern Peters, Alan Ruttenberg, Barry Smith, and Jie Zheng. "OBO Tutorial: Getting Things Done with Open Biological and Biomedical Ontologies." 4th International Conference on Biomedical Ontology. Houston, Texas. October 6, 2014.
    • James A Overton, Nick Nash, and Cesare Romagnoli. "C.S. Peirce and the Philosophy of Medical Imaging." Charles S. Peirce Centennial Congress. Lowell, Massachusetts. July 17, 2014.
    • Heiner Oberkampf and James A Overton. "Expressing Medical Image Measurements using the Ontology for Biomedical Investigations." Ontology and Imaging Informatics: Third Clinical and Translational Science Ontology Workshop. Buffalo, New York. June 24, 2014.
    • James A Overton. "Representing Scientific Investigations." Society for Philosophy of Science in Practice, Fourth Biennial Conference. Institute for the History and Philosophy of Science and Technology, Victoria College, The University of Toronto. June 28, 2013.
    • James A Overton, Randi Vita, Jason A Greenbaum, Heiko Dietze, Alessandro Sette and Bjoern Peters. "A Taxonomy for Immunologists." Bio-Ontologies SIG. Berlin, Germany. July 20, 2013.
    • James A Overton. "The Ontology for Biomedical Investigations and the Philosophy of Science." Ontology Research Group. State University of New York at Buffalo. July 9, 2012.
    • James A Overton. "`Explanation' in Scientific Discourse." Canadian Philosophical Association. The University of Waterloo. May 29, 2012.
    • James A Overton. "`Explanation' in Scientific Discourse." Formal Epistemology Meets Experimental Philosophy. Tilburg University. September 30, 2011.
    • James A Overton. "Philosophy, Ontology, and Scientific Explanation." Doctoral and Post-Doctoral Colloquium, International Conference on Biomedical Ontology. Buffalo, New York. July 27, 2011.
    • James A Overton. "Scientific Explanation and Computation." Explanation Aware Computing Workshop, International Joint Conference on Artificial Intelligence. Barcelona, Spain. July 17, 2011.
    • James A Overton. "Informatics, Philosophy, and Ontology." The Society for the Philosophy of Science in Practice. Exeter, UK. June 24, 2011.
    • James A Overton. "Effective Explanation." Tilburg Institute for Logic and Philosophy of Science: Research Seminar in Epistemology and Philosophy of Science. Tilburg University. February 8, 2011.
    • James A Overton. "Mechanisms, Types, and Abstractions." Philosophy of Science Association. Montréal, Canada. November 4, 2010.
    • James A Overton. "Rethinking Scientific Explanation." The University of Western Ontario Philosophy Graduate Student Association Colloquium Series. The University of Western Ontario. October 6, 2010.
    • James A Overton and Cesare Romagnoli. "Philosophy of Radiology: The Ontological Challenge." 1st International Conference on Medical Imaging and Philosophy. Ulm, Germany. May 22, 2010.
    • James A Overton. "Rethinking Medical Imaging Artifacts." History and Philosophy of Science and Technology (HAPSAT) Graduate Conference. The University of Toronto. April 25, 2010.
    • James A Overton and Cesare Romagnoli. "Structured Reporting and Ontologies." Digital Imaging Group of London, 6th Project Review Meeting. London, Ontario. September 10, 2009.
    • James A Overton, Cesare Romagnoli, and Rethy K. Chhem. "Open Biomedical Ontologies Applied to Prostate Cancer." International Conference on Biomedical Ontology. The State University of New York at Buffalo. July 24, 2009.
    • "Domain Ontologies and Philosophy of Science." Canadian Society for the History and Philosophy of Science. Carleton University. May 28, 2009.
    • James A Overton. "Biomedical Ontologies and Scientific Explanation." Philosophy Graduate Student Association Colloquium Series. The University of Western Ontario. January 28, 2009.
    • James A Overton and Cesare Romagnoli. "The Interdisciplinary Prostate Ontology Project." Italian Association of Telemedicine and Medical Informatics. Ottawa, Ontario. October 6, 2008.
    • James A Overton and Cesare Romagnoli. "Applications of Ontologies to Radiology." Digital Imaging Group, London Health Sciences Centre. The University of Western Ontario. July 23, 2008.
    • James A Overton. "Limits to Abstraction: Software and Science." North American Computation and Philosophy Conference. The University of Indiana, Bloomington. July 12, 2008.
    • James A Overton. "Building Better Bridge Laws with Category Theory." Canadian Society for the History and Philosophy of Science. The University of British Columbia. June 4, 2008.
    • James A Overton. "Higher Isomorphism: Philosophical Issues in the Definition of Weak n-Categories." Canadian Society for the History and Philosophy of Mathematics. The University of British Columbia. June 2, 2008.
    • James A Overton. "The Philosophy of Interdisciplinary Science." Western Research Forum. The University of Western Ontario. March 29, 2008.
    • James A Overton. "Unity and Diversity Among Sciences." Essays of Significance Graduate Conference. The University of Windsor. March 15, 2008.
    • James A Overton. "Complexity and Interdisciplinary Sciences." Philosophy Graduate Student Association Colloquium Series. The University of Western Ontario. October 17, 2007.
    • James A Overton. "An Alternative to the Hierarchy of Sciences." Philosophy Graduate Student Association Conference. The University of Waterloo. March 4, 2005.

  • Invited Comments

    • Roger White, "Evidential Symmetry and Mushy Credence." Formal Epistemology Workshop, The University of Wisconsin -- Madison. May 17, 2008.

  • Posters Presented

    • James A Overton. "Humane OWL: RDF and OWL for Humans." 6th International Conference on Biomedical Ontology. Corvallis, Oregon. August 2, 2016.
    • James A Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland, and Christopher J Mungall. "ROBOT: A command-line tool for ontology development." 5th International Conference on Biomedical Ontology. Lisbon, Portugal. July 29, 2015.
    • James A Overton. "EDN-LD: A simple linked data tool." 5th International Conference on Biomedical Ontology. Lisbon, Portugal. July 29, 2015.
    • James A Overton, Randi Vita, Jason A Greenbaum, Matthew Maybeno, Alessandro Sette, and Bjoern Peters. "Providing a standardized nomenclature and intuitive hierarchy for protein records from different databases." Seventh International Biocuration Conference. Toronto, Ontario. April 7, 2014.
    • James A Overton, Randi Vita, Jason A Greenbaum, Heiko Dietze, Alessandro Sette and Bjoern Peters. "A Taxonomy for Immunologists." Fourth International Conference on Biomedical Ontologies. Montreal, Canada. July 8, 2013.
    • James A Overton, Randi Vita, Jason A Greenbaum, Heiko Dietze, Alessandro Sette and Bjoern Peters. "A Taxonomy for Immunologists." 6th International Biocuration Conference. Cabridge, UK. April 8, 2013.
    • James A Overton and Cesare Romagnoli. "A Tool for Effective Structured Reporting of Prostate Ultrasound." Radiological Society of North America. Chicago, Illinois. December 1, 2011.
    • James A Overton and Cesare Romagnoli. "Structured Reporting for Ultrasound of the Prostate." The University of Western Ontario: Research Day. London, Ontario. March 24, 2010.
    • James A Overton and Cesare Romagnoli. "Structured Reporting for Ultrasound of the Prostate." Imaging Applications in Prostate Cancer Workshop. London, Ontario. November 9, 2009.

Academic Work Experience

  • Service

    • Steering Committee Student Representative for the Joseph L. Rotman Institute of Science and Values. December 2008 - August 2009.
    • Secretary for the Philosophy Graduate Student Association, The University of Western Ontario. 2008 - 2009.
    • Referee for the Logic, Math, and Physics Graduate Philosophy Conference, The University of Western Ontario. 2008 - 2010.
    • Referee for the Philosophy, Language, Mind, and Cognition (PhilMiLCog) Graduate Philosophy Conference, The University of Western Ontario. 2008 - 2011.

  • Instructor

    • Bioethics (PHIL2071). Department of Philosophy, The University of Western Ontario, January 2010 - April 2010.

  • Teaching Assistant

    • Introduction to Philosophy (PHIL1300), John Thorp. Department of Philosophy, The University of Western Ontario, September 2008 - April 2009. Duties: Tutorial leader; some lecturing; grading.
    • Truth and Propaganda (PHIL 2900), Randal Marlin. Department of Philosophy, Carleton University, June - August 2005. Duties: Grading of term work and exams.
    • Ancient Philosophy (PHIL 2006), Diane Dubrule. Department of Philosophy, Carleton University, May - July 2005. Duties: Grading of term work and exams.
    • Informal Reasoning (PHIL 2003), Nadine Faulkner. Department of Philosophy, Carleton University, January - April 2004. Duties: Grading of term work and exams.
    • Ancient Philosophy (PHIL 2006), Diane Dubrule. Department of Philosophy, Carleton University, September - December 2003. Duties: Grading of term work and exams.
    • Philosophy of Mind (PHIL 1301), Paul Raymont. Department of Philosophy, Carleton University, January - April 2003. Duties: Grading of term work and exams, student support.
    • Language and Communication (32.254), Corinne Iten. Department of Philosophy, Carleton University, September - December 2002. Duties: Grading of term work and exams, student support.
    • Writing Tutorial Service, Jen Gilbert. School of Linguistics and Applied Language Studies, Carleton University, September 2001 - April 2002. Duties: Individual tutoring of students to improve writing skills.

References

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