Revision 6403
Added by Aaron Marcuse-Kubitza over 11 years ago
test.xml.ref | ||
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1 | 1 |
Put template: |
2 | 2 |
<VegBIEN> |
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<_simplifyPath id="-1"> |
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<next>parent_id</next> |
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<_setDefault id="-1"> |
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<col>source_id</col> |
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<value><source><shortname>TNRS</shortname></source></value> |
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5 | 6 |
<path> |
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<location>
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<locationevent>
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<taxonoccurrence>
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<taxondetermination>
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<taxonverbatim_id>
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<taxonverbatim>
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<taxonlabel_id>
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<taxonlabel>
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<matched_label_id>0</matched_label_id>
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<parent_id>
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<_simplifyPath>
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<next>parent_id</next>
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<path>
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<location>
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<locationevent>
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<taxonoccurrence>
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<taxondetermination>
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<taxonverbatim_id>
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<taxonverbatim>
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<taxonlabel_id>
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<taxonlabel> |
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<rank>$Name_matched_rank</rank> |
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<taxonverbatim><verbatimrank>$Name_matched_rank</verbatimrank></taxonverbatim> |
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<matched_label_id>0</matched_label_id> |
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<parent_id> |
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<taxonlabel> |
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<rank>cultivar</rank> |
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<rank>$Name_matched_rank</rank> |
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<taxonverbatim><verbatimrank>$Name_matched_rank</verbatimrank></taxonverbatim> |
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<parent_id> |
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<taxonlabel> |
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<rank>forma</rank>
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<rank>cultivar</rank>
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25 | 26 |
<parent_id> |
26 | 27 |
<taxonlabel> |
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<rank>variety</rank>
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<rank>forma</rank>
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28 | 29 |
<parent_id> |
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<taxonlabel> |
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<rank>subspecies</rank>
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<rank>variety</rank>
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31 | 32 |
<parent_id> |
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<taxonlabel> |
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<rank>species</rank> |
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<taxonepithet>$Specific_epithet_matched</taxonepithet> |
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<rank>subspecies</rank> |
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35 | 35 |
<parent_id> |
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<taxonlabel> |
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<rank>genus</rank> |
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<matched_label_id> |
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<taxonlabel> |
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<source_id><source><shortname>NCBI</shortname></source></source_id> |
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<taxonomicname>$Genus_matched</taxonomicname> |
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</taxonlabel> |
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</matched_label_id> |
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<taxonepithet>$Genus_matched</taxonepithet> |
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<rank>species</rank> |
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<taxonepithet>$Specific_epithet_matched</taxonepithet> |
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45 | 39 |
<parent_id> |
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<taxonlabel> |
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<rank>family</rank>
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<rank>genus</rank>
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48 | 42 |
<matched_label_id> |
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<taxonlabel> |
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<source_id><source><shortname>NCBI</shortname></source></source_id> |
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<taxonomicname>$Name_matched_accepted_family</taxonomicname>
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<taxonomicname>$Genus_matched</taxonomicname>
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</taxonlabel> |
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</matched_label_id> |
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<taxonepithet>$Name_matched_accepted_family</taxonepithet> |
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<taxonepithet>$Genus_matched</taxonepithet> |
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<parent_id> |
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<taxonlabel> |
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<rank>family</rank> |
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<matched_label_id> |
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<taxonlabel> |
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<source_id><source><shortname>NCBI</shortname></source></source_id> |
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<taxonomicname>$Name_matched_accepted_family</taxonomicname> |
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</taxonlabel> |
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</matched_label_id> |
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<taxonepithet>$Name_matched_accepted_family</taxonepithet> |
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</taxonlabel> |
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</parent_id> |
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55 | 61 |
</taxonlabel> |
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</parent_id> |
57 | 63 |
</taxonlabel> |
... | ... | |
64 | 70 |
</parent_id> |
65 | 71 |
</taxonlabel> |
66 | 72 |
</parent_id> |
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<taxonepithet>$Infraspecific_epithet_matched</taxonepithet> |
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67 | 74 |
</taxonlabel> |
68 | 75 |
</parent_id> |
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<taxonepithet>$Infraspecific_epithet_matched</taxonepithet> |
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</taxonlabel> |
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</parent_id> |
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<rank>$Name_matched_rank</rank> |
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<sourceaccessioncode>$Name_matched_url</sourceaccessioncode> |
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<taxonlabel fkey="matched_label_id"> |
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<matched_label_fit_fraction> |
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<_max> |
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<1>$Family_score</1> |
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<2>$Genus_score</2> |
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<3>$Specific_epithet_score</3> |
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<4>$Overall_score</4> |
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</_max> |
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</matched_label_fit_fraction> |
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<taxonepithet>$Unmatched_terms</taxonepithet> |
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<taxonomicname>$Name_submitted</taxonomicname> |
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<taxonverbatim> |
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<author>$Author_matched</author> |
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<family>$Family_matched</family> |
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<genus>$Genus_matched</genus> |
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<morphospecies>$Unmatched_terms</morphospecies> |
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<specific_epithet>$Specific_epithet_matched</specific_epithet> |
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<taxonname>$Name_matched</taxonname> |
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<verbatimrank>$Infraspecific_rank</verbatimrank> |
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</taxonverbatim> |
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</taxonlabel> |
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<taxonomicname> |
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<_join_words> |
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<1> |
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<_taxon_family_require_std> |
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<family> |
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<_nullIf> |
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<null>$Name_matched</null> |
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<value>$Name_matched_accepted_family</value> |
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</_nullIf> |
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</family> |
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</_taxon_family_require_std> |
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</1> |
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<2> |
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<rank>$Name_matched_rank</rank> |
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<sourceaccessioncode>$Name_matched_url</sourceaccessioncode> |
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<taxonlabel fkey="matched_label_id"> |
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<matched_label_fit_fraction> |
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<_max> |
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<1>$Family_score</1> |
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<2>$Genus_score</2> |
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<3>$Specific_epithet_score</3> |
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<4>$Overall_score</4> |
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</_max> |
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</matched_label_fit_fraction> |
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<taxonepithet>$Unmatched_terms</taxonepithet> |
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<taxonomicname>$Name_submitted</taxonomicname> |
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<taxonverbatim> |
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<author>$Author_matched</author> |
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<family>$Family_matched</family> |
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<genus>$Genus_matched</genus> |
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<morphospecies>$Unmatched_terms</morphospecies> |
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<specific_epithet>$Specific_epithet_matched</specific_epithet> |
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<taxonname>$Name_matched</taxonname> |
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<verbatimrank>$Infraspecific_rank</verbatimrank> |
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</taxonverbatim> |
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</taxonlabel> |
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<taxonomicname> |
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108 | 100 |
<_join_words> |
109 | 101 |
<1> |
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<_alt> |
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<1>$Name_matched</1> |
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<2> |
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<_join_words> |
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<2>$Genus_matched</2> |
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<3>$Specific_epithet_matched</3> |
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<5> |
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<_taxon_family_require_std> |
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<family> |
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<_nullIf> |
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<null>$Name_matched</null> |
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<value>$Name_matched_accepted_family</value> |
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</_nullIf> |
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</family> |
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</_taxon_family_require_std> |
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</1> |
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<2> |
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<_join_words> |
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<1> |
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<_alt> |
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<1>$Name_matched</1> |
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<2> |
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<_join_words> |
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<1> |
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<_if name="if has infraspecificEpithet"> |
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<cond>$Infraspecific_epithet_matched</cond> |
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<then>$Name_matched_rank</then> |
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</_if> |
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</1> |
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<2>$Infraspecific_epithet_matched</2> |
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<2>$Genus_matched</2> |
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<3>$Specific_epithet_matched</3> |
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<5> |
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<_join_words> |
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<1> |
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<_if name="if has infraspecificEpithet"> |
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<cond>$Infraspecific_epithet_matched</cond> |
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<then>$Name_matched_rank</then> |
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</_if> |
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</1> |
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<2>$Infraspecific_epithet_matched</2> |
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</_join_words> |
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</5> |
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</_join_words> |
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</5>
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</_join_words>
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</2>
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</_alt>
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</1>
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<2>$Name_matched_author</2>
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</2>
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</_alt>
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</1>
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<2>$Name_matched_author</2>
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</_join_words>
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</2> |
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</_join_words> |
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</2>
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</_join_words>
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</taxonomicname>
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<taxonstatus>$Taxonomic_status</taxonstatus>
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</taxonlabel>
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</taxonlabel_id>
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<author>$Name_matched_author</author>
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<family>$Name_matched_accepted_family</family>
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<genus>$Genus_matched</genus>
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<specific_epithet>$Specific_epithet_matched</specific_epithet>
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<taxonname>$Name_matched</taxonname>
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<verbatimrank>$Name_matched_rank</verbatimrank>
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</taxonverbatim>
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</taxonverbatim_id>
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</taxondetermination>
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</taxonoccurrence>
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</locationevent>
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</location>
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</taxonomicname>
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<taxonstatus>$Taxonomic_status</taxonstatus>
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</taxonlabel>
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</taxonlabel_id>
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<author>$Name_matched_author</author>
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<family>$Name_matched_accepted_family</family>
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<genus>$Genus_matched</genus>
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<specific_epithet>$Specific_epithet_matched</specific_epithet>
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<taxonname>$Name_matched</taxonname>
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<verbatimrank>$Name_matched_rank</verbatimrank>
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</taxonverbatim>
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</taxonverbatim_id>
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</taxondetermination>
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</taxonoccurrence>
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</locationevent>
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</location>
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</path>
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</_simplifyPath>
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151 | 157 |
</path> |
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</_simplifyPath>
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</_setDefault>
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153 | 159 |
</VegBIEN> |
154 | 160 |
Inserted 18 new rows into database |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()