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Figure 2 | Journal of Biomedical Semantics

Figure 2

From: Using ontologies to study cell transitions

Figure 2

Outline of an ontology of cell mechanisms and its use to describe cell transitions. The figure shows a structure by which mechanism changes can be formally represented, using entity terms (shown on the left hand side) and quality modifiers (shown on the right hand side). The colour code follows the code used in Figure 3: Occurrents relevant for cell phenotypes are indicated in yellow, occurrents relevant for ultrastructures in blue, and occurrents directly involving molecules in green. 'Up’ and 'down’ are intended to indicate relative changes: 'Interaction Occludin-JAM Up’ states that there is a development in the cell to feature more interactions of this kind, no matter how many of them there have been before. With the exception of “is_a”, all relations are meant to have an all-some syntax (cf. Figure 1).

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