Diagram type

To take into account different diagram types and problem domain specificity we have introduced the diagram type concept.
Diagram type defines:

o	types of biological components and their interactions that can be shown on the diagram;

o	diagram view builder � it generates view (image) for each graph element taking into account the problem domain peculiarities. For example, biological pathway diagram view builder displays proteins as circles, genes as rectangles and substances as squares;

o	semantic controller - provides semantic integrity of the diagram during its editing. It takes into account problem domain constraints, for example if some substance is removed on biological pathway diagram, all related reactions should be removed too.

Diagram type can be defined (created) by two ways:

1.	programmatically - as Java class implementing special interface. There are 5 predefined diagram types that allows to describe complex biological systems on cellular level with different level of details and formality;

2.	declaratively - as XML document. BioUML workbench provides Graphic Notation Editor that allows advanced user to create and edit diagram types. By this way diagram types for SBGN (Le Novère et al, 2009) and KEGG/Pathways database were created (Figure 1.4).

BioUML workbench provides 3 main diagram types for modeling metabolic pathways, signal transduction pathways and gene networks:

1.	Semantic network - this diagram type is used to describe semantic relationships between system components, system states, and related problem domain concepts. This diagram type is also convenient as overview.

2.	Pathway - is used for formalized description of biological pathway structure (metabolic pathway or gene network).

3.	Pathway simulation - is extension of pathway, where variables are associated with graph nodes and differential equations with graph edges. This allows to BioUML workbench automatically generate mathematical model of the system and simulate its dynamics.