forester/test_data/gsdi_test_species_tree_ids.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd" xmlns="http://www.phyloxml.org">
   3 <phylogeny rooted="true" rerootable="false">
   4   <clade>
   5     <name>cellular_organisms</name>
   6     <clade>
   7       <taxonomy>
   8         <scientific_name>Neomura</scientific_name>
   9       </taxonomy>
  10       <clade>
  11         <taxonomy>
  12           <id provider="uniprot">2759</id>
  13           <scientific_name>Eukaryota</scientific_name>
  14           <rank>superkingdom</rank>
  15         </taxonomy>
  16         <clade>
  17           <taxonomy>
  18             <id provider="uniprot">33154</id>
  19             <scientific_name>Opisthokonta</scientific_name>
  20             <common_name>Fungi/Metazoa group</common_name>
  21           </taxonomy>
  22           <clade>
  23             <name>Bilateria_Cnidaria</name>
  24             <clade>
  25               <taxonomy>
  26                 <id provider="uniprot">7742</id>
  27                 <scientific_name>Vertebrata</scientific_name>
  28               </taxonomy>
  29               <clade>
  30                 <taxonomy>
  31                   <id provider="uniprot">314146</id>
  32                   <scientific_name>Euarchontoglires</scientific_name>
  33                   <rank>superorder</rank>
  34                 </taxonomy>
  35                 <clade>
  36                   <taxonomy>
  37                     <id provider="uniprot">9606</id>
  38                     <common_name>Human</common_name>
  39                   </taxonomy>
  40                 </clade>
  41                 <clade>
  42                   <taxonomy>
  43                     <id provider="uniprot">10090</id>
  44                     <common_name>Mouse</common_name>
  45                   </taxonomy>
  46                 </clade>
  47               </clade>
  48               <clade>
  49                 <taxonomy>
  50                   <id provider="uniprot">7757</id>
  51                   <common_name>Sea lamprey</common_name>
  52                 </taxonomy>
  53               </clade>
  54             </clade>
  55             <clade>
  56               <name>NEMVE</name>
  57               <taxonomy>
  58                 <id provider="uniprot">45351</id>
  59                 <common_name>Starlet sea anemone</common_name>
  60               </taxonomy>
  61             </clade>
  62           </clade>
  63           <clade>
  64             <name>Pezizomycotina_Saccharomycetales</name>
  65             <clade>
  66               <taxonomy>
  67                 <id provider="uniprot">41254</id>
  68                 <scientific_name>Mycosphaerella</scientific_name>
  69                 <rank>genus</rank>
  70               </taxonomy>
  71               <clade>
  72                 <name>MYCGR</name>
  73                 <taxonomy>
  74                   <id provider="uniprot">54734</id>
  75                   <common_name>Speckled leaf blotch fungus</common_name>
  76                 </taxonomy>
  77               </clade>
  78               <clade>
  79                 <name>MYCPJ</name>
  80                 <taxonomy>
  81                   <id provider="uniprot">64363</id>
  82                   <common_name>Red band needle blight disease fungus</common_name>
  83                 </taxonomy>
  84               </clade>
  85             </clade>
  86             <clade>
  87               <clade>
  88                 <name>YEAST</name>
  89                 <taxonomy>
  90                   <id provider="uniprot">4932</id>
  91                   <common_name>Baker&apos;s yeast</common_name>
  92                 </taxonomy>
  93               </clade>
  94               <clade>
  95                 <name>ihave no species information!</name>
  96               </clade>
  97             </clade>
  98           </clade>
  99         </clade>
 100         <clade>
 101           <taxonomy>
 102             <id provider="uniprot">5820</id>
 103             <scientific_name>Plasmodium</scientific_name>
 104             <rank>genus</rank>
 105           </taxonomy>
 106           <clade>
 107             <taxonomy>
 108               <id provider="uniprot">5825</id>
 109               <code>PLACH</code>
 110               <scientific_name>Plasmodium chabaudi</scientific_name>
 111               <rank>species</rank>
 112             </taxonomy>
 113           </clade>
 114           <clade>
 115             <taxonomy>
 116               <id provider="uniprot">5833</id>
 117             </taxonomy>
 118           </clade>
 119           <clade>
 120             <taxonomy>
 121               <id provider="uniprot">73239</id>
 122               <code>PLAYO</code>
 123               <scientific_name>Plasmodium yoelii yoelii</scientific_name>
 124               <rank>subspecies</rank>
 125             </taxonomy>
 126           </clade>
 127         </clade>
 128       </clade>
 129       <clade>
 130         <clade>
 131           <taxonomy>
 132             <id provider="uniprot">53953</id>
 133             <code>PYRHO</code>
 134             <scientific_name>Pyrococcus horikoshii</scientific_name>
 135             <rank>species</rank>
 136           </taxonomy>
 137         </clade>
 138         <clade>
 139           <taxonomy>
 140             <code>WOAMI</code>
 141           </taxonomy>
 142         </clade>
 143       </clade>
 144     </clade>
 145     <clade>
 146       <name>b_193</name>
 147       <clade>
 148         <name>b_115</name>
 149         <clade>
 150           <taxonomy>
 151             <id provider="uniprot">266940</id>
 152             <code>KINRD</code>
 153           </taxonomy>
 154         </clade>
 155         <clade>
 156           <taxonomy>
 157             <id provider="uniprot">378753</id>
 158             <code>KOCRD</code>
 159           </taxonomy>
 160         </clade>
 161         <clade>
 162           <taxonomy>
 163             <id provider="uniprot">1902</id>
 164             <code>STRCO</code>
 165             <rank>species</rank>
 166           </taxonomy>
 167         </clade>
 168         <clade>
 169           <taxonomy>
 170             <id provider="uniprot">269800</id>
 171             <code>THEFY</code>
 172             <scientific_name>Thermobifida fusca (strain YX)</scientific_name>
 173           </taxonomy>
 174         </clade>
 175         <clade>
 176           <taxonomy>
 177             <id provider="uniprot">1032480</id>
 178             <code>MICPN</code>
 179             <common_name>Microlunatus phosphovorus NM-1</common_name>
 180             <rank>strain</rank>
 181           </taxonomy>
 182         </clade>
 183       </clade>
 184       <clade>
 185         <taxonomy>
 186           <id provider="uniprot">818</id>
 187           <code>BACTN</code>
 188         </taxonomy>
 189       </clade>
 190     </clade>
 191   </clade>
 192 </phylogeny>
 193 </phyloxml>