James A. Overton

Resumé

James A. Overton

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.

Education

• Degrees
  • Doctor of Philosophy. The University of Western Ontario 2007 - 2012. Thesis: "Explanation in Science"
  • Bachelor of Mathematics (Honours), with Highest Honours. Carleton University 2004 - 2005. Thesis: "Categories and their Algebra"
  • Master of Arts in Philosophy, with Distinction. Carleton University 2002 - 2004. Thesis: "Toward a Foundation for Interdisciplinary Science: A Model of Special Sciences and Levels of Complexity."
  • Bachelor of Humanities (Honours), with Highest Honours and a Specialization in English Literature. Carleton University 1998 - 2002.
• Grants, Awards, and Scholarships
  • 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.
  • 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.

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.

Work History

• Owner Knocean Inc. (Toronto, Ontario, Canada), 2016 - Present.
  • consulting and development services at the intersection of philosophy, science, and software
• Owner Knocean (Toronto, Ontario, Canada), 2012 - 2016.
  • consulting and development services at the intersection of philosophy, science, and software
• 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
• 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
• Contractor Jool.nl (Bodegraven, The Netherlands), 2012.
  • design and development of a custom semantic web prototype
• Web Developer Self-Employed (Various Locations), 2001 - 2012.
  • design and implementation of custom websites and web-based applications
• Open Source Software Developer Mozile Project (http://mozile.mozdev.org), 2003 - 2008.
  • development of a WYSIWYG X/HTML and XML editor using Mozilla technologies such as XUL and XBL, and web technologies such as JavaScript, DOM, and CSS
  • software design, implementation, testing, and documentation
  • lead developer and project leader since June 2004, including responsibility for all releases
• Instructor for Bioethics The University of Western Ontario (London, Ontario, Canada), January to April 2010.
  • course design and teaching for a class of 45
  • design and evaluation of term work and exams
• Teaching Assistant for Introduction to Philosophy The University of Western Ontario (London, Ontario, Canada), September 2008 to April 2009.
  • weekly tutorials for 25 students
  • some lecturing for a class of 100
  • grading of term work and exams
• Contractor Jool.nl (Bodegraven, The Netherlands), Summer 2007.
  • design and development of custom web applications
• Teaching Assistant Carleton University (Ottawa, Ontario, Canada), Periodic between Fall 2001 and Summer 2004.
  • individual tutoring of students to improve writing skills
  • grading of term work and exams
  • some teaching
• Contractor Marktek Business Development Group (Cobourg, Ontario, Canada), Summer 2000.
  • design, development, and maintenance of several web sites, using tools such as Perl, MySQL, Flash, and Photoshop
  • development of WAP and WML based cell phone applications
• Contractor G.C. Piano Company (Toronto, Ontario, Canada), Periodic between Summer 1999 and Summer 2003.
  • manufacture of custom piano bass strings

Skills