Universal-particular distinction in biomedical ontologies –
                         Abstract
                         Steven Chun Tak Wong1,2,∗ , Vojtěch Svátek1
                         1
                           Department of Information and Knowledge Engineering, Prague University of Economics and Business, nám. Winstona
                         Churchilla 1938/4, 130 67, Prague, Czech Republic
                         2
                           First Faculty of Medicine, Charles University, Kateřinská 1660/32, Prague, Czech Republic


                                      Abstract
                                      Biomedical ontologies are essential frameworks for organizing life science knowledge, from simple molecules
                                      to complex biological processes. However, the philosophical distinction between universals (concepts) and
                                      particulars (individuals) poses significant challenges. Standard ontology languages like OWL struggle to capture
                                      this subtlety, as object properties are intended to associate individuals. Consequently, universal concepts like
                                      phosphorylation — a pervasive process where a phosphate group is added to a molecule—are forced into the
                                      category of individuals to utilize properties. This leads to misuse of annotations; for example, in the BioPax
                                      Ontology, although phosphorylation is neither an explicit class nor an individual, the class ModificationFeature
                                      is annotated with rdfs:comment to provide instances like “A phosphorylation on a protein.” These restrictions
                                      may disconnect the ontology from the underlying reality, hindering expressiveness and reasoning capabilities.
                                      Ontology Design Patterns (ODPs) have been developed to overcome certain limitations of languages like OWL,
                                      which support binary but not n-ary relations. One proposed ODP involves reifying numerical values with different
                                      aspects to represent n-ary relationships. For instance, standard_water_boiling_point can be decomposed into
                                      magnitudes and units of temperature and pressure. While standard_water_boiling_point is intended as a particular,
                                      it also demonstrates universal aspects. The notion of “standard” is arbitrary and context-dependent, varying
                                      with different definitions of standard pressure by organizations like IUPAC, EU REACH, and the EPA. How these
                                      differences can be represented, whether standard_water_boiling_point should be modeled as a universal or a
                                      particular, and whether reasoning can provide correct information remain open questions. This research aims to
                                      address this gap by exploring alternative approaches to representing universals and particulars in biomedical
                                      ontologies. Limitations of workarounds like annotation and punning in OWL warrant further investigation.
                                      Logical consistency checking might be emulated through instance-level constraint checking in languages like
                                      SHACL or ShEx. New conceptual modeling languages like ML2 or PURO, designed to accommodate this distinction,
                                      deserve assessment within the biomedical domain. Examining how ontologies represent entities in biological
                                      processes can provide insights into the universals-particulars distinction. By investigating these alternatives,
                                      this research can contribute to designing more refined ontologies. Accurate representation of universals and
                                      particulars will enable ontologies to better reflect reality and advance biomedicine. Enhanced expressiveness will
                                      support robust reasoning capabilities, leading to new predictions and discoveries that deepen our understanding
                                      of health.

                                      Keywords
                                      biomedical ontologies, universals, particulars, ODPs, entity representation, expressiveness, logical consistency




                          15th International Conference on Biomedical Ontologies 2024, July 17-19, 2024, Enschede, The Netherlands
                         ∗
                              Corresponding author.
                          Envelope-Open wongchu@o365.cuni.cz (S. C. T. Wong); svatek@vse.cz (V. Svátek)
                          Orcid 0000-0001-6706-1914 (S. C. T. Wong); 0000-0002-2256-2982 (V. Svátek)
                                     © 2024 Copyright for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).


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