Abstract
BackgroundWith the emergence of high-throughput technologies, Big Data and eScience, the use of online data repositories and the establishment of new data standards that require data to be computer-parsable become increasingly important. As a consequence, there is an increasing need for an integrated system of hierarchies of levels of different types of material entities that helps with organizing, structuring and integrating data from disparate sources to facilitate data exploration, data comparison and analysis. Theories of granularity provide such integrated systems.ResultsOn the basis of formal approaches to theories of granularity authored by information scientists and ontology researchers, I discuss the shortcomings of some applications of the concept of levels and argue that the general theory of granularity proposed by Keet circumvents these problems. I introduce the concept of building blocks, which gives rise to a hierarchy of levels that can be formally characterized by Keet’s theory. This hierarchy functions as an organizational backbone for integrating various other hierarchies that I briefly discuss, resulting in a domain granularity framework for the life sciences. I also discuss the consequences of this granularity framework for the structure of the top-level category of ‘material entity’ in Basic Formal Ontology.ConclusionsThe domain granularity framework suggested here is meant to provide the basis on which a more comprehensive information framework for the life sciences can be developed, which would provide the much needed conceptual framework for representing domains that cover multiple granularity levels. This framework can be used for intuitively structuring data in the life sciences, facilitating data exploration, and it can be employed for reasoning over different granularity levels across different hierarchies. It would provide a methodological basis for establishing comparability between data sets and for quantitatively measuring their degree of semantic similarity.
Highlights
Compositional Building Block (CBB) Granular Perspective Based on the abovementioned characterization of general building blocks one can identify the following prototypical building blocks: 'atom' < 'molecule'32 < 'singlemembrane-enclosed entity' (= most organelles and all prokaryotic cells) < 'membranewithin-membrane entity' (= eukaryotic cell) < 'epithelially-delimited compartment' (= some, but not all of the entities that are commonly referred to as organs) < 'epitheliallydelimited multi-cellular organism' (= organisms with an epidermis)
When considering that actual material entities can be composed of a multiplicity of different possible combinations (= aggregates) of those building blocks, comparable to constructions made from lego-bricks, the diversity of possible types of material entities increases even more with each newly evolved* general building block
The framework provides a meta-layer that (i) defines the relations between entities that belong to different granularity levels of the same granular perspective and between entities across different granular perspectives; (ii) integrates various frames of reference within a single framework, all of which are essential for the life sciences, ranging from purely spatiostructural frames of reference, to functional, developmental, ecological, and evolutionary frames of reference; (iii) improves searching and navigating through large complex
Summary
The question of how molecules make up cells and cells make up organisms resulted in the publication of various compositional hierarchies of different levels of biological organization of living systems and their component parts (e.g., Woodger, 1929; Novikoff, 1945; Wimsatt, 1976, 1994; MacMahon et al, 1978; Mayr, 1982; genealogical hierarchy, Eldredge & Salthe, 1984; somatic hierarchy, Eldredge, 1985; scalar hierarchy, Salthe, 1985, 1993; Theorie des Schichtenbaus der Welt, Riedl, 1985, 1997, 2000; ecological hierarchy, Levinton, 1988; homological hierarchy, Striedter & Northcutt, 1991; cumulative constitutive hierarchy, genetic hierarchy, Valentine & May, 1996; building block systems, Jagers op Akkerhuis & van Straalen, 1998; Heylighen, 2000; McShea, 2001; Valentine, 2003; Korn, 2005). By understanding the levels of complexity as a result of evolution* and that with higher building block levels the complexity and diversity exponentially increases, it reflects some ideas of Wimsatt's prototypical account of levels of organization With their definition of an operator, Jagers op Akkerhuis and Van Straalen (1998) are more specific about how levels are distinguished and what is required for a new level to evolve*. Whereas the taxonomy relates all resources of the ontology in a single subsumption hierarchy, the formalized descriptions often result in several disconnected partonomies These partonomies provide only locally applicable granularity schemes, as opposed to a single globally and universally applicable scheme of granularity levels, like for instance the abovementioned operatorbased hierarchy of building block systems. It is an aggregate of molecules, cells and epithelially-delimited compartment building blocks (see discussion below)
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