Data Structure

Every pathway will have a collection of elements that make up its model. This collection will be arranged in the data structure below.

Semantic vs. Graphical

The elements can be described as semantic or graphical. Semantic elements are those elements that will use a pre-defined shape when rendered, regardless of the shape type specified in GPML. The default shape to be used for each semantic element will be defined in Pathvisio.js, but users will be free to set their own defaults. Graphical elements will be rendered exactly as specified in GPML and as rendered in PathVisio (Java).

Groups, Nodes, Edges and Anchors

Groups are containers for nodes, edges and anchors. A node is an element that has a pre-defined set of anchors associated with it, but it cannot be attached to anchors (ie., it cannot be directly associated with any anchor other than the set of pre-defined anchors). Edges are elements with endpoints that can be attached to anchors. Anchors are defined points that can be used to specify the location of an endpoint of an edge.

• Anchors (all currently graphical)
  • Graphical
    • Circle
    • None
• Groups
  • Graphical
    • Group
    • None
  • Semantic
    • Pathway (note there is also a node named "Pathway")
    • Complex (note there is also a node named "Complex")
• Nodes
  • Graphical
    • Label
    • Arc
    • Rectangle
    • Ellipse (called "Oval" in GPML)
    • Rounded rectangle
    • Triangle
    • Pentagon
    • Hexagon
    • Brace
    • MIM degradation
  • Semantic
    • Gene product
    • Complex (note there is also a group named "Complex")
    • Metabolite
    • Pathway (note there is also a group named "Pathway")
    • Protein
    • RNA
    • Unknown
    • Cell
    • Nucleus
    • Nucleolus
    • Endoplasmic reticulum
    • Golgi apparatus
    • Mitochondria
    • Sarcoplasmic reticulum
    • Organelle
    • Vesicle
    • Extracellular region
    • Vacuole
    • Lysosome
    • Cytosol region
    • Membrane region
• Edges
  • Graphical (called "Graphical lines" in GPML)
    • Line
    • Arrow
  • Semantic (called "Interactions" in GPML)
    • Unspecified (called "line" in PathVisio [Java])
    • Indirect unspecified (called "dashedline" in PathVisio [Java])
    • Activity (called "arrow" in PathVisio [Java])
    • Indirect activity (called "dashedarrow" in PathVisio [Java])
    • Inhibitory activity (called "tbar" in PathVisio [Java])
    • MIM necessary stimulation
    • MIM binding
    • MIM conversion
    • MIM stimulation
    • MIM modification
    • MIM catalysis
    • MIM inhibition
    • MIM cleavage
    • MIM covalent bond
    • MIM branching left
    • MIM branching right
    • MIM transcription-translation
    • MIM gap