That module link is interesting (readmore below). It shows how GO can be passed into XML format. Is this often done? Is the XML format here easy to work with? And can anyone give examples of code with which this XML format is used? I expect that most people work with the flat files. I previously used simple but long perl scripts to pick up network paths and then did the rest of the analysis in Excel.

<readmore>

eg format: go-text for storing graphs and metadata:

  !version: $Revision: 1.19 $
  !date: $Date: 2002/12/11 01:15:01 $
  !editors: Michael Ashburner (FlyBase), Midori Harris (SGD), Judy Bla
+ke (MGD)
  $Gene_Ontology ; GO:0003673
   $cellular_component ; GO:0005575
    %extracellular ; GO:0005576
     <fibrinogen ; GO:0005577
      <fibrinogen alpha chain ; GO:0005972
      <fibrinogen beta chain ; GO:0005973

this is the following file parsed with events turned directly into XML
+:

<subgraph>
 <term>
  <acc>GO:0003673</acc>
  <name>Gene_Ontology</name>
  <is_root>1</is_root>
 </term>
 <term>
  <acc>GO:0005575</acc>
  <name>cellular_component</name>
  <rel>
   <type>isa</type>
   <obj>GO:0003673</obj>
  </rel>
 </term>
 <term>
  <acc>GO:0005576</acc>
  <name>extracellular</name>
  <rel>
   <type>isa</type>
   <obj>GO:0005575</obj>
  </rel>
 </term>
 <term>
  <acc>GO:0005577</acc>
  <name>fibrinogen</name>
  <rel>
   <type>partof</type>
   <obj>GO:0005576</obj>
  </rel>
 </term>
 <term>
  <acc>GO:0005972</acc>
  <name>fibrinogen alpha chain</name>
  <rel>
   <type>partof</type>
   <obj>GO:0005577</obj>
  </rel>
 </term>
 <term>
  <acc>GO:0005973</acc>
  <name>fibrinogen beta chain</name>
  <rel>
   <type>partof</type>
   <obj>GO:0005577</obj>
  </rel>
 </term>
</subgraph>
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