|
Formal definition of graphic notation |
  
|
|
Formal definition of graphic notation |
|
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 |
|
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. |