forester/test_data/gsdi_test_species_tree.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                     <code>HUMAN</code>
  39                     <scientific_name>Homo sapiens</scientific_name>
  40                     <common_name>Human</common_name>
  41                     <rank>species</rank>
  42                   </taxonomy>
  43                 </clade>
  44                 <clade>
  45                   <taxonomy>
  46                     <id provider="uniprot">10090</id>
  47                     <code>MOUSE</code>
  48                     <scientific_name>Mus musculus</scientific_name>
  49                     <common_name>Mouse</common_name>
  50                     <rank>species</rank>
  51                   </taxonomy>
  52                 </clade>
  53               </clade>
  54               <clade>
  55                 <taxonomy>
  56                   <id provider="uniprot">7757</id>
  57                   <code>PETMA</code>
  58                   <scientific_name>Petromyzon marinus</scientific_name>
  59                   <common_name>Sea lamprey</common_name>
  60                   <rank>species</rank>
  61                 </taxonomy>
  62               </clade>
  63             </clade>
  64             <clade>
  65               <taxonomy>
  66                 <id provider="uniprot">45351</id>
  67                 <code>NEMVE</code>
  68                 <scientific_name>Nematostella vectensis</scientific_name>
  69                 <common_name>Starlet sea anemone</common_name>
  70                 <rank>species</rank>
  71               </taxonomy>
  72             </clade>
  73           </clade>
  74           <clade>
  75             <name>Pezizomycotina_Saccharomycetales</name>
  76             <clade>
  77               <taxonomy>
  78                 <id provider="uniprot">41254</id>
  79                 <scientific_name>Mycosphaerella</scientific_name>
  80                 <rank>genus</rank>
  81               </taxonomy>
  82               <clade>
  83                 <taxonomy>
  84                   <id provider="uniprot">54734</id>
  85                   <code>MYCGR</code>
  86                   <scientific_name>Mycosphaerella graminicola</scientific_name>
  87                   <common_name>Speckled leaf blotch fungus</common_name>
  88                   <synonym>Septoria tritici</synonym>
  89                   <rank>species</rank>
  90                 </taxonomy>
  91               </clade>
  92               <clade>
  93                 <taxonomy>
  94                   <id provider="uniprot">64363</id>
  95                   <code>MYCPJ</code>
  96                   <scientific_name>Mycosphaerella pini</scientific_name>
  97                   <common_name>Red band needle blight disease fungus</common_name>
  98                   <synonym>Dothistroma septosporum</synonym>
  99                   <synonym>Dothistroma pini</synonym>
 100                   <rank>species</rank>
 101                 </taxonomy>
 102               </clade>
 103             </clade>
 104             <clade>
 105               <taxonomy>
 106                 <id provider="uniprot">4932</id>
 107                 <code>YEAST</code>
 108                 <scientific_name>Saccharomyces cerevisiae</scientific_name>
 109                 <common_name>Baker&apos;s yeast</common_name>
 110                 <rank>species</rank>
 111               </taxonomy>
 112             </clade>
 113           </clade>
 114         </clade>
 115         <clade>
 116           <taxonomy>
 117             <id provider="uniprot">5820</id>
 118             <scientific_name>Plasmodium</scientific_name>
 119             <rank>genus</rank>
 120           </taxonomy>
 121           <clade>
 122             <taxonomy>
 123               <id provider="uniprot">5825</id>
 124               <code>PLACH</code>
 125               <scientific_name>Plasmodium chabaudi</scientific_name>
 126               <rank>species</rank>
 127             </taxonomy>
 128           </clade>
 129           <clade>
 130             <taxonomy>
 131               <id provider="uniprot">5833</id>
 132               <code>PLAFA</code>
 133               <scientific_name>Plasmodium falciparum</scientific_name>
 134               <rank>species</rank>
 135             </taxonomy>
 136           </clade>
 137           <clade>
 138             <taxonomy>
 139               <id provider="uniprot">73239</id>
 140               <code>PLAYO</code>
 141               <scientific_name>Plasmodium yoelii yoelii</scientific_name>
 142               <rank>subspecies</rank>
 143             </taxonomy>
 144           </clade>
 145         </clade>
 146       </clade>
 147       <clade>
 148         <clade>
 149           <taxonomy>
 150             <id provider="uniprot">53953</id>
 151             <code>PYRHO</code>
 152             <scientific_name>Pyrococcus horikoshii</scientific_name>
 153             <rank>species</rank>
 154           </taxonomy>
 155         </clade>
 156         <clade>
 157           <name>i have no species!</name>
 158         </clade>
 159       </clade>
 160     </clade>
 161     <clade>
 162       <name>b_193</name>
 163       <clade>
 164         <name>b_115</name>
 165         <clade>
 166           <name>KINRD</name>
 167           <taxonomy>
 168             <id provider="uniprot">266940</id>
 169             <code>KINRD</code>
 170             <scientific_name>Kineococcus radiotolerans (strain ATCC BAA-149 / DSM 14245 / SRS30216)</scientific_name>
 171           </taxonomy>
 172         </clade>
 173         <clade>
 174           <name>KOCRD</name>
 175           <taxonomy>
 176             <id provider="uniprot">378753</id>
 177             <code>KOCRD</code>
 178             <scientific_name>Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201)</scientific_name>
 179           </taxonomy>
 180         </clade>
 181         <clade>
 182           <name>STRCO</name>
 183           <taxonomy>
 184             <id provider="uniprot">1902</id>
 185             <code>STRCO</code>
 186             <scientific_name>Streptomyces coelicolor</scientific_name>
 187             <rank>species</rank>
 188           </taxonomy>
 189         </clade>
 190         <clade>
 191           <name>THEFY</name>
 192           <taxonomy>
 193             <id provider="uniprot">269800</id>
 194             <code>THEFY</code>
 195             <scientific_name>Thermobifida fusca (strain YX)</scientific_name>
 196           </taxonomy>
 197         </clade>
 198         <clade>
 199           <taxonomy>
 200             <id provider="uniprot">1032480</id>
 201             <code>MICPN</code>
 202             <scientific_name>Microlunatus phosphovorus (strain ATCC 700054 / DSM 10555 / JCM 9379 / NBRC 101784 / NCIMB 13414 / VKM Ac-1990 / NM-1)</scientific_name>
 203             <common_name>Microlunatus phosphovorus NM-1</common_name>
 204             <rank>strain</rank>
 205           </taxonomy>
 206         </clade>
 207       </clade>
 208       <clade>
 209         <name>BACTN</name>
 210         <taxonomy>
 211           <id provider="uniprot">818</id>
 212           <code>BACTN</code>
 213           <scientific_name>Bacteroides thetaiotaomicron</scientific_name>
 214           <rank>species</rank>
 215         </taxonomy>
 216       </clade>
 217     </clade>
 218   </clade>
 219 </phylogeny>
 220 </phyloxml>