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Revision 5092

mappings/VegCore-VegBIEN.csv: Don't forward scientificName to taxonoccurrence.authortaxoncode when importing just taxonpaths, as for TNRS

View differences:

inputs/XAL/Specimen/VegBIEN.csv
19 19
darwin:CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
20 20
darwin:InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
21 21
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
22
darwin:ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
23 23
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
24 24
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
25 25
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
inputs/NY/Specimen/VegBIEN.csv
23 23
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
24 24
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
25 25
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,Usage inconsistent with DwC definition
26
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
27 27
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
28 28
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
29 29
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
inputs/Madidi/Organism/VegBIEN.csv
26 26
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
27 27
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
28 28
Tag number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
29
Specie+autor,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/2,
30
Species and morphotypes,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,"Contains less than ""Specie+autor"""
29
Specie+autor,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2",
30
Species and morphotypes,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3","Contains less than ""Specie+autor"""
31 31
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
32 32
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
33 33
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
inputs/UNCC/Specimen/VegBIEN.csv
31 31
HAVING count(*) > 1
32 32
-----"
33 33
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
34
SciName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
34
SciName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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cultivated,/location/locationevent/taxonoccurrence/iscultivated/_alt/1,Ignore other values
36 36
accession,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,"Globally unique, although occasionally duplicated. [1]
37 37

  
inputs/ACAD/Specimen/VegBIEN.csv
17 17
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
18 18
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
19 19
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
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scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/2,
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scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2",
21 21
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
22 22
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
23 23
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
inputs/CVS/Organism/VegBIEN.csv
8 8
authorObsCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/authorlocationcode",
9 9
obsStartDate,/location/locationevent/obsstartdate/_*/date/_alt/1,
10 10
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value,
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currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
11
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
13 13
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_alt/2/_join_words/1/_alt/1,
14 14
county,/location/locationplace/*_id/placepath/county,
inputs/.TNRS/tnrs/VegBIEN.csv
1 1
TNRS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2
Accepted_name,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
2
Name_submitted,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/cond/_exists",
3
Accepted_name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
3 4
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/author,
4 5
Accepted_name_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
5 6
Accepted_name_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
inputs/.TNRS/tnrs/test.xml.ref
6 6
            <location>
7 7
                <locationevent>
8 8
                    <taxonoccurrence>
9
                        <authortaxoncode>$Accepted_name</authortaxoncode>
10 9
                        <taxondetermination>
11 10
                            <taxonpath_id>
12 11
                                <taxonpath>
......
40 39
        </path>
41 40
    </_simplifyPath>
42 41
</VegBIEN>
43
Inserted 8 new rows into database
42
Inserted 7 new rows into database
inputs/ARIZ/Specimen/VegBIEN.csv
26 26
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
27 27
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
28 28
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
29
ScientificNameAuthor,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/2,Contains the binomial in addition to the authority
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ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2",Contains the binomial in addition to the authority
30
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
31 31
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
32 32
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
33 33
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
inputs/GBIF/Specimen/VegBIEN.csv
11 11
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
12 12
CollectionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
13 13
InstitutionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
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ScientificNameOriginal,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/1,
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ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
14
ScientificNameOriginal,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/1",
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ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
17 17
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
18 18
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
inputs/NCU-NCSC/Specimen/VegBIEN.csv
11 11
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
12 12
SeriesName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
13 13
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
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Full Taxon Name,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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Full Taxon Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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Cultivated?,/location/locationevent/taxonoccurrence/iscultivated/_alt/1,
16 16
Accession Number,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
17 17
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
inputs/SpeciesLink/Specimen/VegBIEN.csv
89 89
-----"
90 90
conceptual_darwin_2003_1_0_CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/3,
91 91
dwc_curatorial_CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/3,
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conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
93
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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dwc_terms_scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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conceptual_darwin_2003_1_0_ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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dwc_dwcore_ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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dwc_terms_scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
95 95
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
96 96
conceptual_darwin_2003_1_0_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
97 97
dwc_curatorial_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
inputs/MO/Specimen/VegBIEN.csv
18 18
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
19 19
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
20 20
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
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ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
22 22
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
23 23
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
24 24
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
inputs/VegBank/taxonobservation_/VegBIEN.csv
7 7
collectiondate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1/_*/date,
8 8
notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
9 9
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
10
authorplantname,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/1,
10
authorplantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/1",
11 11
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,
12 12
Class,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/class,
13 13
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
inputs/QMOR/Specimen/VegBIEN.csv
24 24
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
25 25
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
26 26
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
27
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
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scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
28 28
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
29 29
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
30 30
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
mappings/VegCore-VegBIEN.csv
113 113
locationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
114 114
plotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
115 115
tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
116
originalScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/1,
117
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/2,
118
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
116
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/cond/_exists",
117
originalScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/1",
118
scientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2",
119
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
119 120
growthForm,/location/locationevent/taxonoccurrence/growthform,
120 121
verbatimGrowthForm,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
121 122
cultivated,/location/locationevent/taxonoccurrence/iscultivated/_alt/1,
mappings/for_review/VegCore-VegBIEN.csv
113 113
locationID,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/cond/_exists",
114 114
plotName,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/cond/_exists",
115 115
tag,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/then",
116
originalScientificName,//taxonoccurrence/authortaxoncode,
117
scientificNameWithAuthorship,//taxonoccurrence/authortaxoncode,
118
scientificName,//taxonoccurrence/authortaxoncode,
116
verbatimScientificNameWithAuthorship,"//taxonoccurrence/authortaxoncode/_if[@name=""if is taxonpath only""]/cond/_exists",
117
originalScientificName,"//taxonoccurrence/authortaxoncode/_if[@name=""if is taxonpath only""]/else",
118
scientificNameWithAuthorship,"//taxonoccurrence/authortaxoncode/_if[@name=""if is taxonpath only""]/else",
119
scientificName,"//taxonoccurrence/authortaxoncode/_if[@name=""if is taxonpath only""]/else",
119 120
growthForm,//taxonoccurrence/growthform,
120 121
verbatimGrowthForm,//taxonoccurrence/growthform,"According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
121 122
cultivated,//taxonoccurrence/iscultivated,

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