Dear Monks,

I have recently been working with a network that has a flat file format something like:


!autogenerated-by:     DAG-Edit version 1.314
!saved-by:             gwg
!date:                 Mon Dec 23 13:11:22 GMT 2002
!version: $Revision: 2.649 $
!type: % ISA Is a
!type: < PARTOF Part of
!note:     file automatically generated by GO-Editor
$Gene_Ontology ; GO:0003673
 <biological_process ; GO:0008150
  %behavior ; GO:0007610
   %adult behavior ; GO:0030534
    %adult behavior (sensu Insecta) ; GO:0008044
     %response to cocaine (sensu Insecta) ; GO:0008341 % response to c
+ocaine ; GO:0042220
     %response to ethanol (sensu Insecta) ; GO:0045473 % response to e
+thanol ; GO:0045471
     %response to ether (sensu Insecta) ; GO:0045474 % response to eth
+er ; GO:0045472
    %adult feeding behavior ; GO:0008343 % feeding behavior ; GO:00076
+31
     %adult feeding behavior (sensu Insecta) ; GO:0030535
    %adult locomotory behavior ; GO:0008344 % locomotory behavior ; GO
+:0007626
     %adult walking behavior ; GO:0007628
     %flight behavior ; GO:0007629
     %jump response ; GO:0007630
   %behavioral fear response ; GO:0001662
   %chemosensory behavior ; GO:0007635

[download]
The full flat file for this can be found here:

http://www.geneontology.org/ontology/process.ontology

And background info here :

http://www.geneontology.org/

Does anyone know if this is a standard format that is used beyond Gene Ontology (GO). If so, are there perl modules that work with this format? And does anyone have experience in using the XML or MySQL versions of GO which seem to me not so clear to the eye. Maybe some generous people here have beautiful pieces of code that they would like to share by way of example.

Thank you Monks

In reply to Network format for Gene Ontology by matth

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