cdmlib-io/src/test/resources/eu/etaxonomy/cdm/io/specimen/abcd206/in/db6.xml

   1 <?xml version='1.0' encoding='UTF-8'?>
   2 <abcd21:DataSets>
   3   <abcd21:DataSet>
   4     <abcd21:Units>
   5       <abcd21:Unit>
   6         <abcd21:SourceInstitutionID>BGBM</abcd21:SourceInstitutionID>
   7         <abcd21:SourceID>DNA Bank</abcd21:SourceID>
   8         <abcd21:UnitID>DB 6</abcd21:UnitID>
   9         <abcd21:Identifications>
  10           <abcd21:Identification>
  11             <abcd21:Result>
  12               <abcd21:TaxonIdentified>
  13                 <abcd21:HigherTaxa>
  14                   <abcd21:HigherTaxon>
  15                     <abcd21:HigherTaxonName>COMPOSITAE</abcd21:HigherTaxonName>
  16                     <abcd21:HigherTaxonRank>familia</abcd21:HigherTaxonRank>
  17                   </abcd21:HigherTaxon>
  18                 </abcd21:HigherTaxa>
  19                 <abcd21:ScientificName>
  20                   <abcd21:FullScientificNameString>Cichorium intybus L.</abcd21:FullScientificNameString>
  21                   <abcd21:NameAtomised>
  22                     <abcd21:Botanical>
  23                       <abcd21:GenusOrMonomial>Cichorium</abcd21:GenusOrMonomial>
  24                       <abcd21:FirstEpithet>intybus</abcd21:FirstEpithet>
  25                     </abcd21:Botanical>
  26                   </abcd21:NameAtomised>
  27                 </abcd21:ScientificName>
  28               </abcd21:TaxonIdentified>
  29             </abcd21:Result>
  30             <abcd21:PreferredFlag>1</abcd21:PreferredFlag>
  31           </abcd21:Identification>
  32         </abcd21:Identifications>
  33         <abcd21:RecordBasis>MaterialSample</abcd21:RecordBasis>
  34         <abcd21:KindOfUnit>DNA</abcd21:KindOfUnit>
  35         <abcd21:SpecimenUnit>
  36           <abcd21:Preparations>
  37             <abcd21:preparation>
  38               <abcd21:preparationType>gDNA</abcd21:preparationType>
  39               <abcd21:preparationMaterials>DNeasy Plant Mini Spin Kit
  40                 Qiagen</abcd21:preparationMaterials>
  41               <abcd21:preparationAgent>
  42                 <abcd21:Person>
  43                   <abcd21:FullName>Bansemer, Jana</abcd21:FullName>
  44                 </abcd21:Person>
  45               </abcd21:preparationAgent>
  46               <abcd21:preparationDate>2002-08-13T00:00:00</abcd21:preparationDate>
  47             </abcd21:preparation>
  48           </abcd21:Preparations>
  49           <abcd21:Preservations>
  50             <abcd21:preservation>
  51               <abcd21:preservationType>TE buffer</abcd21:preservationType>
  52               <abcd21:preservationTemperature>-80</abcd21:preservationTemperature>
  53             </abcd21:preservation>
  54           </abcd21:Preservations>
  55         </abcd21:SpecimenUnit>
  56         <abcd21:MultiMediaObjects>
  57           <abcd21:MultiMediaObject>
  58             <abcd21:fileURI>http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=7475</abcd21:fileURI>
  59           </abcd21:MultiMediaObject>
  60           <abcd21:MultiMediaObject>
  61             <abcd21:fileURI>http://ww2.bgbm.org/herbarium/images/B/10/00/66/57/thumbs/B_10_0066577.jpg</abcd21:fileURI>
  62           </abcd21:MultiMediaObject>
  63         </abcd21:MultiMediaObjects>
  64         <abcd21:Associations>
  65           <abcd21:UnitAssociation>
  66             <abcd21:SourceInstitutionCode>BGBM</abcd21:SourceInstitutionCode>
  67             <abcd21:SourceName>Herbarium Berolinense</abcd21:SourceName>
  68             <abcd21:UnitID>B 10 0066577</abcd21:UnitID>
  69             <abcd21:AssociationType>DNA and specimen from the same
  70               population</abcd21:AssociationType>
  71             <abcd21:DatasetAccessPoint>http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar_BiNHum</abcd21:DatasetAccessPoint>
  72           </abcd21:UnitAssociation>
  73         </abcd21:Associations>
  74         <abcd21:Gathering>
  75           <abcd21:Agents>
  76             <abcd21:GatheringAgent>
  77               <abcd21:Person>
  78                 <abcd21:FullName>B. Valdés, S. Talavera, G. Alziar, D.
  79                   Jeanmonod, N. Galland, U. MatthÃ¤s, V. Stevanovic, P.
  80                   Minissale, S. Fici, B. Foggi, M. Watson, P. Hinz &amp;
  81                   J. M. Romero</abcd21:FullName>
  82               </abcd21:Person>
  83             </abcd21:GatheringAgent>
  84           </abcd21:Agents>
  85           <abcd21:LocalityText>Bailén Prov. Jaen.</abcd21:LocalityText>
  86         </abcd21:Gathering>
  87         <abcd21:CollectorsFieldNumber>Rec.It2993/88</abcd21:CollectorsFieldNumber>
  88         <abcd21:UnitExtensions>
  89           <abcd21:UnitExtension>
  90             <ggbn:GGBN>
  91               <ggbn:ratioOfAbsorbance260_280>1,38</ggbn:ratioOfAbsorbance260_280>
  92               <ggbn:ratioOfAbsorbance260_230>0,77</ggbn:ratioOfAbsorbance260_230>
  93               <ggbn:concentration Unit="ng/µl">17,14</ggbn:concentration>
  94               <ggbn:qualityCheckDate>2008-04-15T00:00:00</ggbn:qualityCheckDate>
  95               <ggbn:Amplifications>
  96                 <ggbn:amplification>
  97                   <ggbn:marker>ITS (ITS1, 5.8S rRNA, ITS2)</ggbn:marker>
  98                   <ggbn:Sequencings>
  99                     <ggbn:sequencing>
 100                       <ggbn:SingleSequencings>
 101                         <ggbn:singleSequencing>
 102                           <ggbn:sequencingDirection>forward</ggbn:sequencingDirection>
 103                           <ggbn:chromatogramFileURI>http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&amp;path=%2FCAM385_GM312-petD_F.ab1</ggbn:chromatogramFileURI>
 104                           <ggbn:SequencingPrimers>
 105                             <ggbn:sequencingPrimer>
 106                               <ggbn:primerSequence
 107                                 Direction="forward">5´-GCCGTMTTTATGTTAATGC-3´</ggbn:primerSequence>
 108                               <ggbn:primerName>PIpetB1411F</ggbn:primerName>
 109                               <ggbn:primerReferenceCitation>Löhne &amp;
 110                                 Borsch 2005</ggbn:primerReferenceCitation>
 111                             </ggbn:sequencingPrimer>
 112                           </ggbn:SequencingPrimers>
 113                         </ggbn:singleSequencing>
 114                         <ggbn:singleSequencing>
 115                           <ggbn:sequencingDirection>reverse</ggbn:sequencingDirection>
 116                           <ggbn:chromatogramFileURI>http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&amp;path=%2FCAM385_GM312-petD_R.ab1</ggbn:chromatogramFileURI>
 117                           <ggbn:SequencingPrimers>
 118                             <ggbn:sequencingPrimer>
 119                               <ggbn:primerSequence
 120                                 Direction="reverse">5´-AATTTAGCYCTTAATACAGG-3´</ggbn:primerSequence>
 121                               <ggbn:primerName>PIpetD738R</ggbn:primerName>
 122                               <ggbn:primerReferenceCitation>Löhne &amp;
 123                                 Borsch 2005</ggbn:primerReferenceCitation>
 124                             </ggbn:sequencingPrimer>
 125                           </ggbn:SequencingPrimers>
 126                         </ggbn:singleSequencing>
 127                       </ggbn:SingleSequencings>
 128                       <ggbn:consensusSequence>
 129                       TTTCGGGTCC TTTATAGTGA AGATATAGCA TAGATAGTTG
 130                       TAATCCATTA TGTATCATTG GGGAAGGAAG GAGAATATTT
 131                       TTTTGATAGA ATACAAGTAT GGATTATTGA AACTAATACG
 132                       CCATGTATTT GGATATTTCC CTTGAACTGC ATAATATTCT
 133                       TTATTTTCCA TGAATAGTGT AAGGGAATTT TTCGAAGAGA
 134                       AAATGGATTA TGGGAGTGTG TGACTTGAGC TATTGATTGG
 135                       TCTGTGCAGA TACGGGCTTT TATCTATCTG CCACATTGTA
 136                       ATTCACAAAC CAATGTGTCT TTGTTCCAAC CATCGCGTAA
 137                       GCCCCATACA GAAGATAGGC TGGTTCGCTT GAAGAGAATC
 138                       TTTTCTATGA TCAGATCCGA ATTATGTCGT ACATGAGCAG
 139                       GCTCCGTAAG ATCTAGTTGA CTTAAGTCAA ACTTCAATAG
 140                       TATAAAAATG CACTCATTTC CTCTGCATTG ACACGAGCTA
 141                       TGAGACTATC GGAGTGAAAG AAAGGGTCTA AAGAAGAAGA
 142                       AAGCTTGGGC TAGATTAGTA ACAAGTAAAT CCTTTGTGTG
 143                       TGTGTTTGTA ATTAGTAAAT GGGCTCTCAA TATTTTGGGG
 144                       CTAATTACTG ATCCTAAGGT TTGAGACGAC CCAGAAAGCA
 145                       CTTGATCATA TCACGATTGA CTTTGTAAGC CTACTTGGGT
 146                       ATTGAGTATT TACTTGTAAG AACCGAATTC TTTGGGGGAT
 147                       AGTTGCAAAA AGAATCCAGT CAATTGTTCT TACGTAAAAC
 148                       CATTCATATC TCGTATATGG ATATGTCTAG ATAGGCTATC
 149                       GATTTTCGAT GGATTCGTTT GGTTCTTTTG ATTATTGCTC
 150                       GAGCTGGATG ATGAAAAATT ATCATGTCCG GTTCCTTCG</ggbn:consensusSequence>
 151                       <ggbn:consensusSequenceLength>912</ggbn:consensusSequenceLength>
 152                       <ggbn:consensusSequenceChromatogramFileURI>http://ww2.biocase.org/websvn/filedetails.php?repname=campanula&amp;path=%2FCAM385_Campa_drabifolia.pde</ggbn:consensusSequenceChromatogramFileURI>
 153                       <ggbn:geneticAccession>
 154                         <ggbn:geneticAccessionNumber>AJ746397</ggbn:geneticAccessionNumber>
 155                         <ggbn:geneticAccessionNumberURI>http://www.ncbi.nlm.nih.gov/nuccore/56310613</ggbn:geneticAccessionNumberURI>
 156                       </ggbn:geneticAccession>
 157                       <ggbn:References>
 158                         <ggbn:Reference>
 159                           <ggbn:ReferenceCitation>Gemeinholzer,B.,
 160                             Bachmann,K. (2005): Examining morphological
 161                             and molecular diagnostic character states in
 162                             Cichorium intybus L. (Asteraceae) and
 163                             Cichorium spinosum L. Plant Systematics and
 164                             Evolution 253 (1-3): 105-123.</ggbn:ReferenceCitation>
 165                         </ggbn:Reference>
 166                       </ggbn:References>
 167                     </ggbn:sequencing>
 168                   </ggbn:Sequencings>
 169                 </ggbn:amplification>
 170               </ggbn:Amplifications>
 171             </ggbn:GGBN>
 172           </abcd21:UnitExtension>
 173         </abcd21:UnitExtensions>
 174       </abcd21:Unit>
 175     </abcd21:Units>
 176   </abcd21:DataSet>
 177 </abcd21:DataSets>