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Revision 10617

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/UNCC/Specimen/map.csv: usdaRank, infrarank: documented that they should actually be mapped to infraspecificRank*. it is better to map them to taxonRank for now because infraspecificRank is now mapped to VegBIEN.

View differences:

inputs/UNCC/Specimen/map.csv
13 13 
family,family,,
14 14 
genus,genus,,
15 15 
species,specificEpithet,,
16 
usdaRank,taxonRank,,is taxonRank__abbr
17 
infrarank,EQUIV#to:usdaRank#infrarank,,is taxonRank__code
16 
usdaRank,taxonRank,,is infraspecificRank__abbr
17 
infrarank,EQUIV#to:usdaRank#infrarank,,is infraspecificRank__abbr__verbatim
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",is taxonRank__abbr
85 
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",is infraspecificRank__abbr
86 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",
87 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",
88 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",
89 89 
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
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
90 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,is infraspecificRank__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 infraspecificRank__abbr
92 92 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
93 93 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
94 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,
95 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,
96 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",
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
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 infraspecificRank__abbr
98 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,
99 99 
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,
100 100 
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
......
102 102 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
103 103 
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
104 104 
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
105 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,is taxonRank__abbr
105 
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,is infraspecificRank__abbr
106 106 
accession,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then","Globally unique, although occasionally duplicated. [1]
107 107 

  		




  108
  108
  
    
[1] Using the following query:


  		




  ......




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


  		




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


  		




  129
  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 non-empty join mapping for EQUIV#to:usdaRank#infrarank ** is taxonRank__code


  		




  
  130
  
    
infrarank,,** No non-empty join mapping for EQUIV#to:usdaRank#infrarank ** is infraspecificRank__abbr__verbatim


  		




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


  		




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


  		




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


  		












  

    
      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,,is taxonRank__abbr


  		




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


  		




  
  2
  
    
usdaRank,taxonRank,,is infraspecificRank__abbr


  		




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


  		




  4
  4
  
    
infraname,infraspecificEpithet,,


  		




  5
  5
  
    
SciName,taxonName,,


  		




  6
  6
  
    
authors,scientificNameAuthorship,,


  		












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