Abstract
BackgroundWith the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.ResultsThe above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the compositional object perspective as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities.ConclusionsThe here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different views on its content (i.e. data, knowledge), each organized into different levels of detail.
Highlights
With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important
It is often claimed that entities belonging to the same level of granularity should have roughly the same size. While such requirements have been identified to be problematic, size relations still seem to be important to theories of granularity (Kumar et al.'s fifth principle: grains in a given level must be smaller in size than those entities on the higher level of which they are parts [13])
7 Conclusions The most important consequence from accepting the existence of cumulative-constitutively organized material entities is that all their parts of one granularity level do not always exhaustively sum to the whole in a granularity tree - not all entities belonging to one level of granularity always form parts of entities of the higher level of granularity. This has far reaching consequences for any theory of granularity, which have been discussed in detail above. Another problem of most commonly used granularity schemes is that they commit to a granularity framework that does not allow the integration of different granularity perspectives within a common framework
Summary
The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatiostructural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the compositional object perspective as an integrating backbone This granularity framework allows to consistently assign structural granularity values to all different types of material entities
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