forester/test_data/gsdi_test_species_tree_codes.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                     <code>HUMAN</code>
  38                   </taxonomy>
  39                 </clade>
  40                 <clade>
  41                   <taxonomy>
  42                     <code>MOUSE</code>
  43                   </taxonomy>
  44                 </clade>
  45               </clade>
  46               <clade>
  47                 <taxonomy>
  48                   <code>PETMA</code>
  49                 </taxonomy>
  50               </clade>
  51             </clade>
  52             <clade>
  53               <clade>
  54                 <taxonomy>
  55                   <code>NEMVE</code>
  56                 </taxonomy>
  57               </clade>
  58               <clade>
  59                 <taxonomy>
  60                   <common_name>nemve sister</common_name>
  61                 </taxonomy>
  62               </clade>
  63             </clade>
  64           </clade>
  65           <clade>
  66             <name>Pezizomycotina_Saccharomycetales</name>
  67             <clade>
  68               <taxonomy>
  69                 <id provider="uniprot">41254</id>
  70                 <scientific_name>Mycosphaerella</scientific_name>
  71                 <rank>genus</rank>
  72               </taxonomy>
  73               <clade>
  74                 <taxonomy>
  75                   <code>MYCGR</code>
  76                 </taxonomy>
  77               </clade>
  78               <clade>
  79                 <taxonomy>
  80                   <code>MYCPJ</code>
  81                 </taxonomy>
  82               </clade>
  83             </clade>
  84             <clade>
  85               <clade>
  86                 <name>YEAST</name>
  87                 <taxonomy>
  88                   <code>YEAST</code>
  89                 </taxonomy>
  90               </clade>
  91               <clade>
  92                 <taxonomy>
  93                   <code>WOAMI</code>
  94                 </taxonomy>
  95               </clade>
  96             </clade>
  97           </clade>
  98         </clade>
  99         <clade>
 100           <clade>
 101             <taxonomy>
 102               <code>PLACH</code>
 103             </taxonomy>
 104           </clade>
 105           <clade>
 106             <name>PLAFA</name>
 107             <taxonomy>
 108               <code>PLAFA</code>
 109             </taxonomy>
 110           </clade>
 111           <clade>
 112             <taxonomy>
 113               <code>PLAYO</code>
 114             </taxonomy>
 115           </clade>
 116         </clade>
 117       </clade>
 118       <clade>
 119         <clade>
 120           <taxonomy>
 121             <code>PYRHO</code>
 122           </taxonomy>
 123         </clade>
 124         <clade>
 125           <name>i have no species information!</name>
 126         </clade>
 127       </clade>
 128     </clade>
 129     <clade>
 130       <name>b_193</name>
 131       <clade>
 132         <name>b_115</name>
 133         <clade>
 134           <name>KINRD</name>
 135           <taxonomy>
 136             <id provider="uniprot">266940</id>
 137             <code>KINRD</code>
 138           </taxonomy>
 139         </clade>
 140         <clade>
 141           <name>KOCRD</name>
 142           <taxonomy>
 143             <id provider="uniprot">378753</id>
 144             <code>KOCRD</code>
 145             <scientific_name>Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)</scientific_name>
 146           </taxonomy>
 147         </clade>
 148         <clade>
 149           <name>STRCO</name>
 150           <taxonomy>
 151             <id provider="uniprot">1902</id>
 152             <code>STRCO</code>
 153             <scientific_name>Streptomyces coelicolor</scientific_name>
 154             <rank>species</rank>
 155           </taxonomy>
 156         </clade>
 157         <clade>
 158           <name>THEFY</name>
 159           <taxonomy>
 160             <id provider="uniprot">269800</id>
 161             <code>THEFY</code>
 162             <scientific_name>Thermobifida fusca (strain YX)</scientific_name>
 163           </taxonomy>
 164         </clade>
 165         <clade>
 166           <taxonomy>
 167             <id provider="uniprot">1032480</id>
 168             <code>MICPN</code>
 169             <common_name>Microlunatus phosphovorus NM-1</common_name>
 170             <rank>strain</rank>
 171           </taxonomy>
 172         </clade>
 173       </clade>
 174       <clade>
 175         <name>BACTN</name>
 176         <taxonomy>
 177           <id provider="uniprot">818</id>
 178           <code>BACTN</code>
 179           <scientific_name>Bacteroides thetaiotaomicron</scientific_name>
 180           <rank>species</rank>
 181         </taxonomy>
 182       </clade>
 183     </clade>
 184   </clade>
 185 </phylogeny>
 186 </phyloxml>