Formalizing a General Disease Module

Disease is of vital importance in the biomedical domain. A proper understanding of disease would help to provide a general conceptual framework for the integration of biological and biomedical data. This paper aims to elaborate upon the recent view that, on closer examination of existing ontological models of disease, a disease is generally characterized as a dependent continuant of a clinically abnormal causal pattern. This work will constitute a further step towards the development of an ontological module for generic disease representation.

[1]  Nicola Guarino,et al.  BFO and DOLCE: So Far, So Close… , 2017 .

[2]  Ludger Jansen,et al.  The Identity of Dispositions , 2018, FOIS.

[3]  George Hripcsak,et al.  Methodological Review: A review of causal inference for biomedical informatics , 2011 .

[4]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[5]  S. Mumford,et al.  Evidence based on what? , 2015, Journal of evaluation in clinical practice.

[6]  Gary H. Merrill,et al.  Ontological realism: Methodology or misdirection? , 2010, Appl. Ontology.

[7]  Werner Ceusters,et al.  Malaria Diagnosis and the Plasmodium Life Cycle: The BFO Perspective , 2010 .

[8]  Kazuhiko Ohe,et al.  River Flow Model of Diseases , 2011, ICBO.

[9]  Adrien Barton,et al.  A Formal Representation of Affordances as Reciprocal Dispositions , 2018, TriCoLore.

[10]  Kazuhiko Ohe,et al.  Disease Compass– a navigation system for disease knowledge based on ontology and linked data techniques , 2017, Journal of Biomedical Semantics.

[11]  Richard W. Taylor Action and Purpose , 1967 .

[12]  S. Mumford,et al.  Getting Causes from Powers , 2011 .

[13]  Ludger Jansen,et al.  Tendencies and Other Realizables in Medical Information Sciences , 2007 .

[14]  Mitsuru Ikeda,et al.  Causation: A functional perspective , 2019, Appl. Ontology.

[15]  A. Bird Overpowering: How the Powers Ontology Has Overreached Itself , 2016 .

[16]  Werner Ceusters,et al.  Foundations for a realist ontology of mental disease , 2010, J. Biomed. Semant..

[17]  Vinay K. Chaudhri,et al.  Representing States in a Biology Textbook , 2015, AAAI Spring Symposia.

[18]  Riichiro Mizoguchi,et al.  Causality and the ontology of disease , 2015, Appl. Ontology.

[19]  Stefano Borgo,et al.  A unifying definition for artifact and biological functions , 2016, Appl. Ontology.

[20]  Anita Burgun-Parenthoine,et al.  The Cardiovascular Disease Ontology , 2014, FOIS.

[21]  J. Wakefield,et al.  The concept of mental disorder. On the boundary between biological facts and social values. , 1992, The American psychologist.

[22]  Johannes Röhl,et al.  Representing dispositions , 2011, J. Biomed. Semant..

[23]  Barry Smith,et al.  Dispositions and the Infectious Disease Ontology , 2010, FOIS.

[24]  Neil E. Williams The Factory Model of Disease , 2007 .

[25]  Marie I. Kaiser,et al.  Potentiality in Biology , 2018 .

[26]  Adrien Barton,et al.  The Identity and Mereology of Pathological Dispositions , 2018, ICBO.

[27]  Gary H. Merrill,et al.  Realism and reference ontologies: Considerations, reflections and problems , 2010, Appl. Ontology.

[28]  Riichiro Mizoguchi,et al.  YAMATO: Yet Another More Advanced Top-Level Ontology with Analysis of Five Examples of Change , 2021, JOWO.

[29]  Werner Ceusters,et al.  Ontological realism: A methodology for coordinated evolution of scientific ontologies , 2010, Appl. Ontology.

[30]  Antony Galton,et al.  The water falls but the waterfall does not fall: New perspectives on objects, processes and events , 2009, Appl. Ontology.

[31]  Maël Lemoine,et al.  Defining disease beyond conceptual analysis: an analysis of conceptual analysis in philosophy of medicine , 2013, Theoretical Medicine and Bioethics.

[32]  James E. Tomberlin,et al.  On the Plurality of Worlds. , 1989 .

[33]  Werner Ceusters,et al.  Toward an Ontological Treatment of Disease and Diagnosis , 2009, Summit on translational bioinformatics.

[34]  Rani Lill Anjum,et al.  Causation and evidence-based practice: an ontological review. , 2012, Journal of evaluation in clinical practice.

[35]  Robert Arp,et al.  Building Ontologies with Basic Formal Ontology , 2015 .

[36]  Kazuhiko Ohe,et al.  An ontological modeling approach for abnormal states and its application in the medical domain , 2014, Journal of Biomedical Semantics.

[37]  J. Wakefield The biostatistical theory versus the harmful dysfunction analysis, part 1: is part-dysfunction a sufficient condition for medical disorder? , 2014, The Journal of medicine and philosophy.

[38]  Christopher Boorse,et al.  On the Distinction between Disease and Illness , 1999 .

[39]  C. Martin Mind in Nature , 2023 .

[40]  Mitsuru Ikeda,et al.  Causation and the River Flow Model of Diseases , 2017, ICBO.

[41]  Pascal Hitzler,et al.  Some Open Issues After Twenty Years of Formal Ontology , 2018, Formal Ontology in Information Systems.

[42]  Jon Williamson,et al.  Interpreting Causality in the Health Sciences , 2007 .

[43]  John Heil,et al.  Dispositions , 2005, Synthese.

[44]  Laure Vieu,et al.  Graph-Based Approaches to Structural Universals and Complex States of Affairs , 2018, FOIS.

[45]  Lawrie Reznek,et al.  The Nature of Disease , 1987 .

[46]  Fumiaki Toyoshima,et al.  Linking Temporal Parts in Processual Biological Ontology , 2019, JOWO.

[47]  S. Goodman,et al.  Causal inference in public health. , 2013, Annual review of public health.

[48]  Fumiaki Toyoshima,et al.  How Do Processes Work? , 2019, JOWO.