Abstract
BackgroundApplication oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them.Methodology/Principal FindingsBy systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: ‘fiat object part aggregate’ and ‘object with fiat object part aggregate’. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity.Conclusions/SignificanceWe suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our result, however, depends on the premise that all material entities are organized according to a constitutive granularity.
Highlights
Biomedical databases are becoming increasingly important and more and more researchers and health professionals use them on a daily basis for storing, annotating, managing, sharing, and analyzing their data and metadata
Suggestions for Extending the Basic Formal Ontology The different types of material entity presented above are differentiated along three distinct lines of thought: 1) Given that the distinction between bona fide and fiat boundary is absolute and exhaustive for any given particular level of object granularity of constitutively organized material entities, it follows that: a) ‘Object’ and ‘fiat object part’ represent primary building blocks for all top-level types of material entity, and no other type of material entity has this role
This results in five basic types of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’, ‘fiat object part aggregate’, ‘object with fiat object part aggregate’; Fig. 3, 7)
Summary
Biomedical databases are becoming increasingly important and more and more researchers and health professionals use them on a daily basis for storing, annotating, managing, sharing, and analyzing their data and metadata. Many biomedical ontologies fail to live up to these claims, since their definitions are not comparable and/or compatible among each other This is partly due to the fact that most ontologies are application oriented and have been developed with a particular practical purpose in mind. Application oriented ontologies are important for reliably communicating and managing data in databases They often differ in the definitions they use and do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them
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