Purdue University Purdue e-Pubs Open Access Dissertations Theses and Dissertations 4-2016 A black art: Ontology, data, and the Tower of Babel problem Andrew J. Iliadis Purdue University Follow this and additional works at: https://docs.lib.purdue.edu/open_access_dissertations Part of the Communication Commons, Library and Information Science Commons, and the Metaphysics Commons Recommended Citation Iliadis, Andrew J., "A black art: Ontology, data, and the Tower of Babel problem" (2016). Open Access Dissertations. 663. https://docs.lib.purdue.edu/open_access_dissertations/663 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. i A BLACK ART: ONTOLOGY, DATA, AND THE TOWER OF BABEL PROBLEM A Dissertation Submitted to the Faculty of Purdue University by Andrew J Iliadis In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2016 Purdue University West Lafayette, Indiana ii For my parents iii ACKNOWLEDGEMENTS I would like to acknowledge the support of the Brian Lamb School of Communication and the Department of Philosophy at Purdue University. I would also like to thank my co- advisors and committee members, including Dr. Ashley R. Kelly, Dr. Daniel W. Smith, Dr. Sorin A. Matei, and Dr. Daniel R. Kelly. A special thank you to my parents, Cathy and Jim, and to my brother, Michael. I could not have done this without your support. iv TABLE OF CONTENTS Page LIST OF TABLES ............................................................................................................. vi LIST OF FIGURES .......................................................................................................... vii LIST OF ABBREVIATIONS ............................................................................................ ix ABSTRACT ........................................................................................................................ x CHAPTER 1. THE TOWER OF BABEL PROBLEM .................................................... 1 1.1 Introduction ............................................................................................................... 1 1.2 Philosophical and Computational Ontology ............................................................. 5 1.3 Ontology as Communication ................................................................................... 11 1.4 Ontologies of Life and Death .................................................................................. 14 1.5 A Theory of Informational Ontology and Technologies of Individuation .............. 18 1.6 The Tower of Babel Problem .................................................................................. 23 1.7 Computational Ontology and Science and Technology Studies ............................. 29 1.8 Informational Ontology as a Realism of Relations ................................................. 36 1.9 Method and Framework .......................................................................................... 50 CHAPTER 2. PHILOSOPHICAL ONTOLOGY .......................................................... 52 2.1 Chapter Summary .................................................................................................... 52 2.2 Philosophy’s Influence on Applied Ontology ......................................................... 52 2.3 Realism, Conceptualism, Nominalism .................................................................... 57 2.4 Realism-Based Applied Ontology is a Method ....................................................... 60 2.5 Aristotle’s Ontological Square ................................................................................ 61 2.6 Husserl’s Formal Ontology – Formal Logic Distinction ........................................ 65 2.7 Ingarden’s Ontological Essence of Time ................................................................ 70 2.8 Ontological Realism in Modern Applied Ontology ................................................ 74 v Page CHAPTER 3. SCIENTIFIC ONTOLOGY AS COMMUNICATION .......................... 78 3.1 Chapter Summary .................................................................................................... 78 3.2 Ontology as a Community Practice ......................................................................... 78 3.3 Realism-Based Ontology Groups and their Institutions .......................................... 82 3.4 The Data Smiths ...................................................................................................... 87 3.5 Communities in Ontology History: Conferences, Email Lists, Organizations ....... 96 CHAPTER 4. BASIC FORMAL ONTOLOGY AND THE FOUNDRY ................... 104 4.1 Chapter Summary .................................................................................................. 104 4.2 The Basic Formal Ontology Discuss Group ......................................................... 105 4.3 I’d Rather Share My Toothbrush (Referent Tracking) .......................................... 115 4.4 The Method of Individuation: SNAP and SPAN .................................................. 121 4.5 Basic Formal Ontology, Upper Ontologies, and Domain Ontologies ................... 128 4.6 The Open Biological and Biomedical Ontologies Foundry .................................. 146 CHAPTER 5. CRITICAL DATA STUDIES, ONTOLOGY, AND ETHICS ............. 152 5.1 Chapter Summary .................................................................................................. 152 5.2 Critical Data Studies .............................................................................................. 153 5.3 Ontology in Context and Social Ontology ............................................................ 162 5.4 Military Ontology .................................................................................................. 167 5.5 Virtual Science ...................................................................................................... 175 5.6 Final Remarks ....................................................................................................... 178 REFERENCES ............................................................................................................... 180 APPENDICES Appendix A Interview Questions .................................................................................... 200 Appendix B BFO Ontologies and their Contexts............................................................ 202 VITA ............................................................................................................................... 209 PUBLICATIONS ............................................................................................................ 224 vi LIST OF TABLES Table .............................................................................................................................. Page 1 Ethics Matrix ................................................................................................................ 161 Appendix Table BFO Ontologies and their Contexts ................................................................................ 202 vii LIST OF FIGURES Figure ............................................................................................................................. Page 1.1 Tagged Scientific Article ............................................................................................ 22 1.2 Google Ngram Search Results for “Ontology” ........................................................... 33 1.3 Ontology as a Specification of a Conceptualization ................................................... 37 1.4 Example of Referent Tracking Confusion .................................................................. 39 1.5 Floridi’s SLMS Scheme with Ontological Commitment............................................ 46 1.6 Floridi’s SLMS Scheme with Ordered Ontological Commitment ............................. 48 1.7 Transparent Partitions of One and the Same Reality .................................................. 49 2.1 Aristotle’s Ontological Square .................................................................................... 63 2.2 Poli’s Logical-Formal and Ontological-Formal Concepts .......................................... 68 2.3 First-Order Logic with Universal Terms .................................................................... 76 3.1 Ontology vs. Controlled Vocabulary in PubMed/MEDLINE .................................... 81 4.1 BFO Discuss – the Basic Formal Ontology Google Group ...................................... 107 4.2 Debate in the BFO Discuss Google Group ............................................................... 112 4.3 Military Referent Tracking ....................................................................................... 119 4.4 SPAN and SPAN Entities ......................................................................................... 124 4.5 Cuts of Meat and a Map of the United States ........................................................... 126 4.6 Taxonomy of Fiat and Bona Fide Entities ................................................................ 127 4.7 Blood Ontology Website........................................................................................... 131 4.8 Basic Formal Ontology Website ............................................................................... 133 4.9 Information Artifact Ontology