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more species added
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Sat, 19 Oct 2013 00:03:43 +0000 (00:03 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Sat, 19 Oct 2013 00:03:43 +0000 (00:03 +0000)
forester/data/tol_151.xml patch | blob | history

diff --git a/forester/data/tol_151.xml b/forester/data/tol_151.xml
index 0284e8d..e28a3af 100644 (file)
--- a/forester/data/tol_151.xml
+++ b/forester/data/tol_151.xml
@@ -1259,8 +1259,6 @@
                               </taxonomy>\r
                               <clade>\r
                                 <name>Onychophora &amp; Arthropoda</name>\r
-                                <taxonomy>\r
-                                </taxonomy>\r
                                 <reference doi="10.1073/pnas.1105499108">\r
                                   <desc>MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda</desc>\r
                                 </reference>\r
@@ -4429,13 +4427,14 @@
                             </clade>\r
                             <clade>\r
                               <taxonomy>\r
-                                <id provider="uniprot">4641</id>\r
-                                <code>MUSAC</code>\r
-                                <scientific_name>Musa acuminata</scientific_name>\r
-                                <common_name>Banana</common_name>\r
-                                <synonym>Musa cavendishii</synonym>\r
-                                <rank>species</rank>\r
-                                <uri>http://upload.wikimedia.org/wikipedia/commons/f/fd/Musa_acuminata1.jpg</uri>\r
+                                <id provider="uniprot">214687</id>\r
+                                <code>MUSAM</code>\r
+                                <scientific_name>Musa acuminata subsp. malaccensis</scientific_name>\r
+                                <authority>(Ridl.) N.W.Simmonds</authority>\r
+                                <common_name>Wild banana</common_name>\r
+                                <synonym>Musa malaccensis</synonym>\r
+                                <rank>subspecies</rank>\r
+                                <uri>http://farm5.staticflickr.com/4009/4572831376_07ca3089d1_z.jpg</uri>\r
                               </taxonomy>\r
                             </clade>\r
                           </clade>\r
@@ -5003,10 +5002,6 @@
                   </taxonomy>\r
                   <clade>\r
                     <name>Labyrinthulomycetes &amp; Ochrophyta &amp; Oomycetes</name>\r
-                    <taxonomy>\r
-                    </taxonomy>\r
-                    <sequence>\r
-                    </sequence>\r
                     <clade>\r
                       <name>Ochrophyta &amp; Oomycetes</name>\r
                       <reference doi="10.1016/j.protis.2008.11.004">\r
@@ -5083,8 +5078,6 @@
                         </clade>\r
                         <clade>\r
                           <name>Pelagophyceae &amp; Phaeophyceae</name>\r
-                          <taxonomy>\r
-                          </taxonomy>\r
                           <reference doi="10.1128/AEM.06952-11">\r
                             <desc>Distribution patterns and phylogeny of marine stramenopiles in the north pacific ocean</desc>\r
                           </reference>\r
@@ -5315,11 +5308,34 @@
                 </clade>\r
                 <clade>\r
                   <taxonomy>\r
-                    <id provider="uniprot">5664</id>\r
-                    <code>LEIMA</code>\r
-                    <scientific_name>Leishmania major</scientific_name>\r
-                    <rank>species</rank>\r
+                    <id provider="uniprot">5658</id>\r
+                    <scientific_name>Leishmania</scientific_name>\r
+                    <rank>genus</rank>\r
                   </taxonomy>\r
+                  <clade>\r
+                    <taxonomy>\r
+                      <id provider="uniprot">5664</id>\r
+                      <code>LEIMA</code>\r
+                      <scientific_name>Leishmania major</scientific_name>\r
+                      <rank>species</rank>\r
+                    </taxonomy>\r
+                  </clade>\r
+                  <clade>\r
+                    <taxonomy>\r
+                      <id provider="uniprot">5671</id>\r
+                      <code>LEIIN</code>\r
+                      <scientific_name>Leishmania infantum</scientific_name>\r
+                      <rank>species</rank>\r
+                    </taxonomy>\r
+                  </clade>\r
+                  <clade>\r
+                    <taxonomy>\r
+                      <id provider="uniprot">5660</id>\r
+                      <code>LEIBR</code>\r
+                      <scientific_name>Leishmania braziliensis</scientific_name>\r
+                      <rank>species</rank>\r
+                    </taxonomy>\r
+                  </clade>\r
                 </clade>\r
               </clade>\r
               <clade>\r
@@ -5581,10 +5597,10 @@
                   </clade>\r
                   <clade>\r
                     <taxonomy>\r
-                      <id provider="uniprot">2234</id>\r
+                      <id provider="uniprot">224325</id>\r
                       <code>ARCFU</code>\r
-                      <scientific_name>Archaeoglobus fulgidus</scientific_name>\r
-                      <rank>species</rank>\r
+                      <scientific_name>Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)</scientific_name>\r
+                      <rank>strain</rank>\r
                     </taxonomy>\r
                   </clade>\r
                 </clade>\r
@@ -5917,8 +5933,9 @@
                       <taxonomy>\r
                         <id provider="uniprot">2287</id>\r
                         <code>SULSO</code>\r
-                        <scientific_name>Sulfolobus solfataricus</scientific_name>\r
-                        <rank>species</rank>\r
+                        <scientific_name>Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)</scientific_name>\r
+                        <synonym>Sulfolobus solfataricus P2</synonym>\r
+                        <rank>strain</rank>\r
                       </taxonomy>\r
                     </clade>\r
                   </clade>\r
@@ -6887,17 +6904,18 @@
                                     <name>b_136</name>\r
                                     <clade>\r
                                       <taxonomy>\r
-                                        <id provider="uniprot">1172</id>\r
-                                        <code>ANAVA</code>\r
-                                        <scientific_name>Anabaena variabilis</scientific_name>\r
-                                        <rank>species</rank>\r
+                                        <id provider="uniprot">240292</id>\r
+                                        <code>ANAVT</code>\r
+                                        <scientific_name>Anabaena variabilis (strain ATCC 29413 / PCC 7937)</scientific_name>\r
+                                        <synonym>Anabaena flos-aquae (strain IUCC 1444)</synonym>\r
+                                        <rank>strain</rank>\r
                                       </taxonomy>\r
                                     </clade>\r
                                     <clade>\r
                                       <taxonomy>\r
                                         <id provider="uniprot">28072</id>\r
                                         <code>NOSS7</code>\r
-                                        <scientific_name>Nostoc sp. (strain PCC 7524)</scientific_name>\r
+                                        <scientific_name>Nostoc sp. (strain ATCC 29411 / PCC 7524)</scientific_name>\r
                                         <rank>species</rank>\r
                                       </taxonomy>\r
                                     </clade>\r
@@ -6907,15 +6925,16 @@
                                       <id provider="uniprot">63737</id>\r
                                       <code>NOSP7</code>\r
                                       <scientific_name>Nostoc punctiforme (strain ATCC 29133 / PCC 73102)</scientific_name>\r
+                                      <rank>strain</rank>\r
                                     </taxonomy>\r
                                   </clade>\r
                                 </clade>\r
                                 <clade>\r
                                   <taxonomy>\r
-                                    <id provider="uniprot">155978</id>\r
-                                    <code>ACAMR</code>\r
-                                    <scientific_name>Acaryochloris marina</scientific_name>\r
-                                    <rank>species</rank>\r
+                                    <id provider="uniprot">329726</id>\r
+                                    <code>ACAM1</code>\r
+                                    <scientific_name>Acaryochloris marina (strain MBIC 11017</scientific_name>\r
+                                    <rank>strain</rank>\r
                                   </taxonomy>\r
                                 </clade>\r
                               </clade>\r
@@ -6952,10 +6971,9 @@
                             </clade>\r
                             <clade>\r
                               <taxonomy>\r
-                                <id provider="uniprot">1148</id>\r
+                                <id provider="uniprot">1111708</id>\r
                                 <code>SYNY3</code>\r
-                                <scientific_name>Synechocystis sp. (strain PCC 6803)</scientific_name>\r
-                                <rank>species</rank>\r
+                                <scientific_name>Synechocystis sp. (strain PCC 6803 / Kazusa)</scientific_name>\r
                               </taxonomy>\r
                             </clade>\r
                           </clade>\r
@@ -7784,10 +7802,10 @@
       </clade>\r
       <clade>\r
         <taxonomy>\r
-          <id provider="uniprot">63363</id>\r
+          <id provider="uniprot">224324</id>\r
           <code>AQUAE</code>\r
-          <scientific_name>Aquifex aeolicus</scientific_name>\r
-          <rank>species</rank>\r
+          <scientific_name>Aquifex aeolicus (strain VF5)</scientific_name>\r
+          <rank>strain</rank>\r
         </taxonomy>\r
       </clade>\r
     </clade>\r