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7 Pathway elements

Here we describe some of the commonly used terminology and concepts used in PathVisio, libGPML, GPML, and WikiPathways.

The main components of a pathway model are referred to as Pathway Elements.

PathVisio4 user interface, with open pathway WP4876. In this diagram, we color DataNodes (Purple), States (Orange), Interactions/Graphical Lines (Light Blue), Lables (Red), Shapes (Green), and Groups (Dark Blue).

Figure 0.1: PathVisio4 user interface, with open pathway WP4876. In this diagram, we color DataNodes (Purple), States (Orange), Interactions/Graphical Lines (Light Blue), Lables (Red), Shapes (Green), and Groups (Dark Blue).

  • DataNodes - denotes a biological entity that forms a node in a pathway.
    • Aliases - special data node type.
  • States - represents a specific state of the biological entity (e.g. phosphorylation, genetic variants, etc). A state is linked to a data node.
  • Interactions - represents the biological relation between entities.
  • Graphical Lines - a visual annotation without semantic meaning. It is often used to partition space or connect other pathway elements.
  • Labels - a text field which can be used to annotate any aspect of a pathway
  • Shapes - a visual annotation or graphical element.
  • Groups - a collection of structurally or functionally similar or related pathway elements.