Appendix A. The yWays XML Format

Table of Contents

Topology Layer
Layout Layer

In this appendix gives a short overview over the yWays XML format. Files in the yWays format are recommended to have the extension .xml. The DTD of the yWays XML format has the following URI:

http://pathways.informatik.uni-tuebingen.de/dtds/ReactionNetDiagram.dtd.

A file in the yWays XML format must begin with the following header:

<?xml version="1.0"?>
<!DOCTYPE PathwayDiagram SYSTEM 
     "http://pathways.informatik.uni-tuebingen.de/dtds/PathwayDiagram.dtd">
	
The yWays XML format follows the layered approach of the yWays library. Currrently the topological layer and the layout layer are supported. The global structure of an yWays XML file is as follows:
<ReactioNetDiagram id="id" style="KEGG">
  <!-- Topology Layer -->
  <ReactionNet>
          ... 
  </ReactionNet>
  <!-- Layout Layer -->
  <ReactionNetLayout>
          ... 
  </ReactionNetLayout>
<ReactionNetDiagram>    
	

Topology Layer

The topology layer consists of two lists, one containing the compounds of the reaction net, and one containing the reactions.

<ReactionNet>
  <CompoundList>
          ... 
  </CompoundList>
  <ReactionList>
        ... 
  </ReactionList>
</ReactionNet>
	  

Each compound in the compound list must have a unique id and a name. The id of the compound must begin with a letter. The following fragment shows an example:

<Compound id="C4">
  <Name>Benzylalcohol</Name>
</Compound>    
	  

Each reaction in the reaction list may have a unique id and lists of substrates, compounds, co-substrates, co-compounds and catalysts. Each entry in the lists refers to the definition of the compound by its id. The id of the reaction must begin with a letter. The following fragment shows an example:

<Reaction id="R233">
  <Substrat ref="C274"/>
  <Substrat ref="C276"/>
  <Product ref="C278"/>
  <Product ref="C279"/>
  <Catalyst ref="C280"/>
</Reaction id="R233">