Formal definition of graphic notation

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Graphic notation can be defined formally as XML document.

 

Main XML tags and properties are summarized in Table 1. It should be noted that XML document includes JavaScript function to generate images for nodes and edges.

 

See also

· http://www.biouml.org/sbgn.shtml - more detailed description of graphic notation concept, XML format and implementation details
· http://www.biouml.org/_sbgn/graphic%20notation.dtd - DTD for XML document that defines graphic notation
· http://www.biouml.org/_sbgn/SBGN%20-%20formal%20definition.doc � description of main concepts and SBGN implementation

 

Table 1 .

Formal definition of graphic notation as XML document

Graphic notation components

(XML tag)

Main properties

(XML attributes)

JavaScript

Comment

properties

  property

name

type

short description

controlled vocabulary

-

formal definition of properties that can be used as properties of nodes and edges (for example, title, multimer, etc.)

nodes

 node

name

icon

properties

short description

function to generate node view

definition of node types

edges

 edge

name

icon

properties

short description

function to generate edge view

definition of edge types

reactions

 reactions

name

icon

properties

short description

function to generate reaction view

definition of reaction types

semanticController


o canAccept
o isResizable
o move

defines rules for semantic control of diagram integrity. For this purpose it defines corresponding JavaScript  functions.

viewOptions

 property

name

type

short description


view options to generate node or edge view

examples

  dml



a set of diagrams that can be used as test cases, legend and examples for the graphic notation.
DML - Diagram Markup Language � is used for this purpose.