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Fig. 6 | Journal of Biomedical Semantics

Fig. 6

From: Levels and building blocks—toward a domain granularity framework for the life sciences

Fig. 6

Top-Level Subclasses of ‘material entity’ and ‘spatio-structural entity’. The labeled grey boxes represent classes. The class ‘spatio-structural entity’ is characterized in reference to causal unity via internal physical forces, ‘functional entity’ in reference to causal unity via bearing a specific function, and ‘historical/evolutionary entity’ in reference to causal unity via common historical/evolutionary origin. As a consequence of the perspective-dependence of bona fideness, these three classes are not disjoint. The functional and historical/evolutionary entities are further differentiated according to disjoint categories of bona fide units and fiat unit parts. Spatio-structural entities are further differentiated in correspondence with the granularity levels of the compositional building block granular perspective (see discussion in text), ranging from ‘atom level entity’ to ‘epithelially-delimited multi-cellular organism level entity’, but include not only the respective bona fide entities of that level, but also their corresponding object aggregate and fiat object part entities. Because bona fideness is not only perspective-dependent, but also granularity-dependent, each building block level has its own spatio-structural frame of reference and thus its own perspective. Due to the cumulative-constitutive organization of biological entities, entities from finer spatio-structural frames of reference (e.g., molecules) must be represented in coarser frames of reference (e.g., eukaryotic cell) as fiat portions of matter. These representations are covered through the ‘portion of matter entity’ class (see also Fig. 8)

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