Linking Temporal Parts in Processual Biological Ontology

There are two conflicting foundational approaches to biological reality. Substantialism says that objects are more fundamental than processes, whereas processualism argues for the converse: processes are more basic than objects. It is of practical significance to harmonize a substantialist framework for biological data with a processual one. This short paper aims to propose that temporal parts of biological objects in processual ontology be linked in a dispositionally causal way.

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

[2]  Duško Sekulić,et al.  The concept of identity , 2010 .

[3]  Joost Breuker,et al.  Towards principled core ontologies , 1996 .

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

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

[6]  A. Burgun,et al.  Towards Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets , 2009 .

[7]  Till Mossakowski,et al.  A Categorical Approach to Networks of Aligned Ontologies , 2017, Journal on Data Semantics.

[8]  Theodore Sider,et al.  Arguments Against Four‐Dimensionalism , 2001 .

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

[10]  H. Herre.  General Formal Ontology (GFO): A Foundational Ontology for Conceptual Modelling , 2010 .

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

[12]  Alan Ruttenberg,et al.  The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability , 2016, J. Biomed. Semant..

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

[14]  Heinrich Herre,et al.  Persistence, Change, and the Integration of Objects and Processes in the Framework of the General Formal Ontology , 2013, ArXiv.

[15]  T. Sider,et al.  Against Parthood* , 2020 .

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

[17]  Todd Rogers,et al.  Persistence , 2014 .

[18]  Maureen Donnelly.  Endurantist and perdurantist accounts of persistence , 2011 .

[19]  Ringo Baumann,et al.  Axiomatic theories of the ontology of time in GFO , 2014, Appl. Ontology.

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

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

[22]  Hannes Michalek,et al.  A formal ontological approach to causality embedded in the top level ontology of GFO (General Formal Ontology) , 2009 .

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

[24]  Yuri Balashov.  Persistence and Spacetime , 2010 .

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

[26]  C. Maria Keet,et al.  ROMULUS: The Repository of Ontologies for MULtiple USes Populated with Mediated Foundational Ontologies , 2016, Journal on Data Semantics.

[27]  Robert Hoehndorf,et al.  GFO-Bio: A biological core ontology , 2008, Appl. Ontology.

[28]  S Schulz,et al.  Formal Ontologies in Biomedical Knowledge Representation , 2013, Yearbook of Medical Informatics.

[29]  J. Dupré,et al.  Everything Flows : Towards a Processual Philosophy of Biology , 2018 .

[30]  Thomas M. Crisp,et al.  ‘Wholly Present’ Defined , 2005 .

[31]  Thomas Sattig,et al.  The language and reality of time , 2006 .