This is DTD for BioUML diagrams markup language.

This format is used by BioUML workbench to store diagrams. Diagram structure description is divided into two parts:

1. diagram structure model - it describes the graph structure, location of diagram elements and database objects ('kernels') that are associated with diagram elements.
2.  executable model - stores mathematical model associated with graph.

<!-- BioUML diagrams markup language (DML) v. 0.9.2 -->

<!ELEMENT dml (diagramInfo?, diagram, executableModel?)>
<!-- 
  "version" attribute contains version of the language
  "appVersion" attribute contains version of BioUML that has created this file -->
<!ATTLIST dml
  version               CDATA 		"0.9.2"
  appVersion            CDATA 		"0.7.0"
>


<!ELEMENT diagramInfo>
<!ATTLIST diagramInfo 
  value                 CDATA     
>

<!-- =================================================================== -->
<!-- Diagram structural model                                            -->
<!-- =================================================================== -->

<!ELEMENT diagram (compartmentInfo, nodes, edges)>
<!-- 
  "diagramType" attribute contains name of Java class
->
<!ATTLIST diagram
  diagramType           CDATA		#REQUIRED 
>

<!ELEMENT compartmentInfo (image?)>
<!-- 
"kernel" attribute contains complete path for data element used as kernel;
         currently path is relative module/Data  
  "shape" attribute possible values are: 0-rectangle; 1-round_rectangle; 2-oval
-->
<!ATTLIST compartmentInfo 
  kernel                CDATA		#REQUIRED
  x                     CDATA		#REQUIRED
  y                     CDATA		#REQUIRED 
  width                 CDATA		#REQUIRED
  height                CDATA		#REQUIRED
  title                 CDATA		
  comment               CDATA
  shape                 CDATA		"0"
  color                 CDATA		"255, 255, 255"
>

<!ELEMENT nodes (compartment|equivalentNodeGroup|node)*>
<!ELEMENT edges (edge)*>


<!ELEMENT compartment (compartmentInfo, nodes, edges)>
<!ATTLIST compartment
>

<!ELEMENT equivalentNodeGroup (compartmentInfo, nodes, edges)>
<!-- 
  "representative" attribute contains name of kernel used as representative
-->
<!ATTLIST compartment
  representative        CDATA		#REQUIRED 
>

<!ELEMENT node (image?)>
<!ATTLIST node 
  kernel                CDATA		#REQUIRED 
  title                 CDATA		
  comment               CDATA
  x                     CDATA
  y                     CDATA
>

<!ELEMENT edge>
<!ATTLIST edge 
  kernel                CDATA		#REQUIRED 
  in                    CDATA		#REQUIRED 
  out                   CDATA		#REQUIRED 
  title                 CDATA		 
  comment               CDATA
  inPort                CDATA
  outPort               CDATA
>

<!ELEMENT image>
<!ATTLIST image 
  src                   CDATA		#REQUIRED 
  width                 CDATA	
  height                CDATA
  hideTitle             CDATA		"false"
>	 

<!-- =================================================================== -->
<!-- Executable model                                                    -->
<!-- =================================================================== -->

<!ELEMENT executableModel (constant*, variable*, equation*)>
<!ATTLIST executableModel
  class                 CDATA		#REQUIRED 
  initialTime           CDATA		#REQUIRED
  completionTime        CDATA		#REQUIRED
  comment               CDATA
>

<!ELEMENT constant>
<!ATTLIST constant 
  name                  CDATA		#REQUIRED 
  value                 CDATA		#REQUIRED 
  units                 CDATA
  comment               CDATA
>

<!ELEMENT variable>
<!-- "diagramElement" attribute - diagram element name (relative Diagram) -->
<!ATTLIST variable 
  diagramElement        CDATA		#REQUIRED
  initialValue          CDATA		"0.0"
  boundaryCondition     CDATA       	"false"
  showInPlot            CDATA		"true"
  plotLineSpec          CDATA		"-"
  units                 CDATA
  comment               CDATA
>

<!ELEMENT equation>
<!-- 
  "diagramElement" attribute - diagram element name (relative Diagram) 
  "type" attribute - equation type. Possible values are: algebraic, rate or scalar. 
-->
<!ATTLIST equation
  diagramElement        CDATA		#REQUIRED
  variable              CDATA		#REQUIRED
  formula               CDATA		#REQUIRED 
  type                  CDATA		"rate"
  units                 CDATA
  comment               CDATA
>

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