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. 0.7.2 -->

<!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       "0.7.2"
  appVersion            CDATA       "0.7.2"
>

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

<!-- =================================================================== -->
<!-- Diagram structural model                                            -->
<!--                                                                     -->
<!-- General comments:                                                   -->
<!--   All diagram elements (compartmentInfo, node and edge) have kernel -->
<!--   and id attributes:                                                -->
<!--                                                                     -->
<!--   kernel - this attribute contains complete path for data element   -->
<!--            used as kernel; currently path is relative module.       -->
<!--   id     - generally diagram element name is kernel name,           -->
<!--            but if diagram element name differs from kernel name,    -->
<!--            then it should be stored as id attribute.                -->
<!--                                                                     -->
<!-- =================================================================== -->

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

<!ELEMENT compartmentInfo (image?)>
<!--  
   "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
  id                    CDATA
  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?)>
<!-- Currently background attributes are used only for notes. -->
<!ATTLIST node 
  kernel                CDATA       #REQUIRED 
  kernel_type           CDATA
  id                    CDATA
  title                 CDATA       
  comment               CDATA
  x                     CDATA       #IMPLIED
  y                     CDATA       #IMPLIED
  width                 CDATA       
  height                CDATA       
  background_visible    CDATA       "false"
  background_color      CDATA        
>


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

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

<!ENTITY % segmentType "(moveTo|lineTo|quadTo|cubicTo|close)">

<!-- DML path concept is based on Java java.awt.geom.GeneralPath concept.
  Path represents a geometric path constructed from straight lines, 
  and quadratic and cubic (Bézier) curves. 
  Currently only straight lines (segment types moveTo and lineTo) 
  are supported. -->
<!ELEMENT path (segment)+>
<!ELEMENT segment>
<!ATTLIST segment
  type                  segmentType  #REQUIRED 
  x0                    CDATA       
  y0                    CDATA       
  x1                    CDATA       
  y1                    CDATA       
  x2                    CDATA       
  y2                    CDATA       
>

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

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

<!ELEMENT parameter>
<!ATTLIST parameter 
  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
>