<opt
  name="organisms"
  date="20051129"
  title="Species abbreviations"
  >

  <!-- perl regex for making file-name abbreviation from genus_species -->
  <species_short_pattern>^(\w)[^_]*_(\w{1,3})</species_short_pattern>
  <!-- alternate .. -->
  <species_short_pattern6>^(\w{1,3})[^_]*_(\w{1,3})</species_short_pattern6>

  <about>
  Table of organism species, abbreviation-id values.
  Cannot assume chado organism table has values we need.
  
  Can optionally add other attributes here.
  Note that species == Genus_species; all spaces are underscored.
  </about>
  
  <!-- 0710: add taxon code for go_association table -->
  <organism id="agam" taxon="0" species="Anopheles_gambiae" />
  <organism id="amel" taxon="0" species="Apis_mellifera" />
  <organism id="atha" taxon="0" species="Arabidopsis_thaliana" />
  <organism id="cbri" taxon="0" species="Caenorhabditis_briggsae" />
  <organism id="cele" taxon="0" species="Caenorhabditis_elegans" />
  <organism id="cfam" taxon="0" species="Canis_familiaris" />
  <organism id="dana" taxon="0" species="Drosophila_ananassae" />
  <organism id="ddis" taxon="0" species="Dictyostelium_discoideum" />
  <organism id="dere" taxon="0" species="Drosophila_erecta" />
  <organism id="dgri" taxon="0" species="Drosophila_grimshawi" />
  <organism id="dmag" taxon="0" species="Daphnia_magna" />
  <organism id="dmel" taxon="0" species="Drosophila_melanogaster" />
  <organism id="dmoj" taxon="0" species="Drosophila_mojavensis" />
  <organism id="dper" taxon="0" species="Drosophila_persimilis" />
  <organism id="dpse" taxon="0" species="Drosophila_pseudoobscura"  />
  <organism id="dpul" taxon="0" species="Daphnia_pulex" />
  <organism id="drer" taxon="0" species="Danio_rerio" />
  <organism id="dsec" taxon="0" species="Drosophila_sechellia" />
  <organism id="dsim" taxon="0" species="Drosophila_simulans" />
  <organism id="dvir" taxon="0" species="Drosophila_virilis" />
  <organism id="dwil" taxon="0" species="Drosophila_willistoni" />
  <organism id="dyak" taxon="0" species="Drosophila_yakuba" />
  <organism id="ecol" taxon="0" species="Escherichia_coli" />
  <organism id="frub" taxon="0" species="Fugu_rubripes" />
  <organism id="ggal" taxon="0" species="Gallus_gallus" />
  <organism id="hsap" taxon="0" species="Homo_sapiens" />
  <organism id="mmus" taxon="0" species="Mus_musculus" />
  <organism id="osat" taxon="0" species="Oryza_sativa" />
  <organism id="pfal" taxon="0" species="Plasmodium_falciparum" />
  <organism id="ptro" taxon="0" species="Pan_troglodytes" />
  <organism id="rnor" taxon="0" species="Rattus_norvegicus" />
  <organism id="scer" taxon="4932" species="Saccharomyces_cerevisiae" />
  <organism id="spom" taxon="0" species="Schizosaccharomyces_pombe" />
  <organism id="tnig" taxon="0" species="Tetraodon_nigroviridi" />

</opt>
