Figure 3

Using EQ syntax to represent cellular dynamics. The diagram shows how the two ontologies for cell phenotypes (PHEN) and mechanism changes (MECH) work together with the EQ syntax in order to represent the dynamics of cellular processes. It shows fictive annotation profiles for three cell types (A, B, C) and for two macroscale changes (from type A to B, and from type B to C). Each of the cell type profiles is time-stamped: A is the phenotype of the cell in question before a certain intervention, B the phenotype after 1 hour and C the phenotype after 2 hours. In each annotation profile we use, e.g., terms for molecular entities together with modifiers like 'present’ and 'absent’ to represent the participants of the microscale mechanisms that are actively ongoing in a cell at a certain point of time. The phenotypic profile of a cell will normally vary through time, and such a series of profiles can be used to adequately describe the history of a cell in an experiment. Here, we use terms for mechanisms together with modifiers like 'up’ and 'down’ in order to describe the macroscale changes of the microscale mechanism going on within the cell.