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Figure 4 | BMC Bioinformatics

Figure 4

From: Ultra-Structure database design methodology for managing systems biology data and analyses

Figure 4

Basic BioEntity Network and Relationship ruleforms. Panel A: The BioEntity Network ruleform (simplified for clarity) exemplifies network ruleforms by defining relationships between BioEntities. Here, "Subject" and "Object" both refer to BioEntities, while "Relationship" refers to rules defined in the "Relationship" ruleform (Panel B). Each rule specifies a single binary relationship. The "Distance" consideration reflects how far away from each other in the network the two BioEntities are. In the rules shown, "Glycine" is two steps away from "Amino Acid", going first through "Non-Polar Amino Acid". Rules of distance greater than 1 are generated automatically via logical deduction. Panel B: The Relationship ruleform specifies all valid binary relationships that can exist between entities in the system. The "Inverse" consideration indicates the Relationship to use in the reverse formulation of a rule; for example, if "Carbon is-a Element", then "Element includes Carbon". The "Preferred" consideration is a Boolean flag that indicates Relationships that are to be used when entering original (as opposed to automatically deduced) rules.

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