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Revision 10615

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/UNCC/Specimen/map.csv: infrarank: remapped to EQUIV (of usdaRank). usdaRank, infrarank: documented the VegCore term that each would map to.

View differences:

inputs/UNCC/Specimen/map.csv
13 13 
family,family,,
14 14 
genus,genus,,
15 15 
species,specificEpithet,,
16 
usdaRank,taxonRank,/_alt/1,
17 
infrarank,taxonRank,/_alt/2,
16 
usdaRank,taxonRank,,is taxonRank__abbr
17 
infrarank,EQUIV#to:usdaRank#infrarank,,is taxonRank__code
18 18 
infraname,infraspecificEpithet,,
19 19 
SciName,taxonName,,
20 20 
authors,scientificNameAuthorship,,
inputs/UNCC/Specimen/VegBIEN.csv
82 82 
collectno,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
83 83 
cultivated__main,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1/_alt/1",
84 84 
cultivated__campus,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1/_alt/2",
85 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank/_alt/1",
86 
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank/_alt/2",
85 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",is taxonRank__abbr
87 86 
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
88 87 
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
89 88 
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
90 89 
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
91 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank/_alt/1,
92 
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank/_alt/2,
93 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank/_alt/1",
94 
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank/_alt/2",
90 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,is taxonRank__abbr
91 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",is taxonRank__abbr
95 92 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
96 93 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
97 94 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,
98 95 
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
99 96 
infraname,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
100 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then/_alt/1",
101 
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then/_alt/2",
97 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",is taxonRank__abbr
102 98 
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
103 99 
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,
104 100 
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
......
106 102 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
107 103 
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
108 104 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
109 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank/_alt/1,
110 
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank/_alt/2,
105 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,is taxonRank__abbr
111 106 
accession,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then","Globally unique, although occasionally duplicated. [1]
112 107 

  		




  113
  108
  
    
[1] Using the following query:


  		




  ......




  132
  127
  
    
flower,,** No join mapping for flower_verbatim ** 


  		




  133
  128
  
    
fruit,,** No join mapping for fruit_verbatim ** 


  		




  134
  129
  
    
herbarium,,"** No join mapping for specimenDonorInstitution_verbatim ** ""The name or acronym in use by the institution that donated the collection"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/593/UNCC-validation-Peet.xlsx#institutionCode)"


  		




  
  130
  
    
infrarank,,** No join mapping for EQUIV#to:usdaRank#infrarank ** is taxonRank__code


  		




  135
  131
  
    
inorout,,"** No join mapping for *inorout ** values: I, A. only populated in 19 rows."


  		




  136
  132
  
    
leaves,,** No join mapping for *leaves ** 


  		




  137
  133
  
    
loanto,,** No join mapping for *loanto ** only populated in one row


  		












  

    
      inputs/UNCC/Specimen/test.xml.ref
    
  





  111
  111
  
    
                                                <taxonlabel>


  		




  112
  112
  
    
                                                    <parent_id>


  		




  113
  113
  
    
                                                        <taxonlabel>


  		




  114
  
  
    
                                                            <rank>


  		




  115
  
  
    
                                                                <_alt>


  		




  116
  
  
    
                                                                    <1>$usdaRank</1>


  		




  117
  
  
    
                                                                    <2>$infrarank</2>


  		




  118
  
  
    
                                                                </_alt>


  		




  119
  
  
    
                                                            </rank>


  		




  
  114
  
    
                                                            <rank>$usdaRank</rank>


  		




  120
  115
  
    
                                                            <parent_id>


  		




  121
  116
  
    
                                                                <taxonlabel>


  		




  122
  117
  
    
                                                                    <rank>cultivar</rank>


  		




  ......




  158
  153
  
    
                                                            <taxonepithet>$infraname</taxonepithet>


  		




  159
  154
  
    
                                                        </taxonlabel>


  		




  160
  155
  
    
                                                    </parent_id>


  		




  161
  
  
    
                                                    <rank>


  		




  162
  
  
    
                                                        <_alt>


  		




  163
  
  
    
                                                            <1>$usdaRank</1>


  		




  164
  
  
    
                                                            <2>$infrarank</2>


  		




  165
  
  
    
                                                        </_alt>


  		




  166
  
  
    
                                                    </rank>


  		




  
  156
  
    
                                                    <rank>$usdaRank</rank>


  		




  167
  157
  
    
                                                    <taxonomicname>


  		




  168
  158
  
    
                                                        <_merge_prefix>


  		




  169
  159
  
    
                                                            <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>


  		




  ......




  181
  171
  
    
                                                                                            <1>


  		




  182
  172
  
    
                                                                                                <_if name="if has infraspecificEpithet">


  		




  183
  173
  
    
                                                                                                    <cond>$infraname</cond>


  		




  184
  
  
    
                                                                                                    <then>


  		




  185
  
  
    
                                                                                                        <_alt>


  		




  186
  
  
    
                                                                                                            <1>$usdaRank</1>


  		




  187
  
  
    
                                                                                                            <2>$infrarank</2>


  		




  188
  
  
    
                                                                                                        </_alt>


  		




  189
  
  
    
                                                                                                    </then>


  		




  
  174
  
    
                                                                                                    <then>$usdaRank</then>


  		




  190
  175
  
    
                                                                                                </_if>


  		




  191
  176
  
    
                                                                                            </1>


  		




  192
  177
  
    
                                                                                            <2>$infraname</2>


  		




  ......




  208
  193
  
    
                                            <genus>$genus</genus>


  		




  209
  194
  
    
                                            <specific_epithet>$species</specific_epithet>


  		




  210
  195
  
    
                                            <taxonname>$SciName</taxonname>


  		




  211
  
  
    
                                            <verbatimrank>


  		




  212
  
  
    
                                                <_alt>


  		




  213
  
  
    
                                                    <1>$usdaRank</1>


  		




  214
  
  
    
                                                    <2>$infrarank</2>


  		




  215
  
  
    
                                                </_alt>


  		




  216
  
  
    
                                            </verbatimrank>


  		




  
  196
  
    
                                            <verbatimrank>$usdaRank</verbatimrank>


  		




  217
  197
  
    
                                        </taxonverbatim>


  		




  218
  198
  
    
                                    </taxonverbatim_id>


  		




  219
  199
  
    
                                </taxondetermination>


  		












  

    
      inputs/UNCC/Specimen/new_terms.csv
    
  





  1
  1
  
    
herbarium,specimenDonorInstitution_verbatim,,"""The name or acronym in use by the institution that donated the collection"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/593/UNCC-validation-Peet.xlsx#institutionCode)"


  		




  2
  
  
    
usdaRank,taxonRank,/_alt/1,


  		




  3
  
  
    
infrarank,taxonRank,/_alt/2,


  		




  
  2
  
    
usdaRank,taxonRank,,is taxonRank__abbr


  		




  
  3
  
    
infrarank,EQUIV#to:usdaRank#infrarank,,is taxonRank__code


  		




  4
  4
  
    
infraname,infraspecificEpithet,,


  		




  5
  5
  
    
SciName,taxonName,,


  		




  6
  6
  
    
authors,scientificNameAuthorship,,


  		












  

    
      inputs/UNCC/Specimen/unmapped_terms.csv
    
  





  1
  1
  
    
*row_num


  		




  2
  2
  
    
specimenDonorInstitution_verbatim


  		




  
  3
  
    
EQUIV#to:usdaRank#infrarank


  		




  3
  4
  
    
cultivated__campus__verbatim


  		




  4
  5
  
    
*leaves


  		




  5
  6
  
    
flower_verbatim


  		












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