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Revision 5012

mappings/VegCore-VegBIEN.csv: Taxonomic terms: Also join terms together in taxonomicnamewithauthor if scientificNameWithAuthorship is not provided, for use by TNRS

View differences:

inputs/NCU-NCSC/Specimen/test.xml.ref
64 64
                        <authortaxoncode>$Full Taxon Name</authortaxoncode>
65 65
                        <iscultivated>$Cultivated?</iscultivated>
66 66
                        <sourceaccessioncode>$Accession Number</sourceaccessioncode>
67
                        <taxondetermination><taxonpath_id><taxonpath><taxonomicname>$Full Taxon Name</taxonomicname></taxonpath></taxonpath_id></taxondetermination>
67
                        <taxondetermination>
68
                            <taxonpath_id>
69
                                <taxonpath>
70
                                    <taxonomicname>$Full Taxon Name</taxonomicname>
71
                                    <taxonomicnamewithauthor>$Full Taxon Name</taxonomicnamewithauthor>
72
                                </taxonpath>
73
                            </taxonpath_id>
74
                        </taxondetermination>
68 75
                    </taxonoccurrence>
69 76
                </locationevent>
70 77
                <locationplace>
inputs/MO/Specimen/VegBIEN.csv
29 29
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
30 30
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
31 31
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
32
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
33
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
34
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
35
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
36
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
37
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
32 38
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
33 39
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
34 40
Locality,/location/locationnarrative/_merge/1,
inputs/VegBank/taxonobservation_/test.xml.ref
26 26
                                    <order>$Order</order>
27 27
                                    <species>$Species</species>
28 28
                                    <subspecies>$Subspecies</subspecies>
29
                                    <taxonomicnamewithauthor>
30
                                        <_join_words>
31
                                            <1>$Family</1>
32
                                            <2>$Genus</2>
33
                                            <3>$Species</3>
34
                                            <4>$Subspecies</4>
35
                                            <6>
36
                                                <_join_words>
37
                                                    <1>var.</1>
38
                                                    <2>$Variety</2>
39
                                                </_join_words>
40
                                            </6>
41
                                            <7>
42
                                                <_join_words>
43
                                                    <1>fm.</1>
44
                                                    <2>$Forma</2>
45
                                                </_join_words>
46
                                            </7>
47
                                        </_join_words>
48
                                    </taxonomicnamewithauthor>
29 49
                                    <variety>$Variety</variety>
30 50
                                </taxonpath>
31 51
                            </taxonpath_id>
inputs/FIA/Organism/test.xml.ref
64 64
                                <taxonpath>
65 65
                                    <genus>$Genus</genus>
66 66
                                    <species>$SpecificEpithet</species>
67
                                    <taxonomicnamewithauthor>
68
                                        <_join_words>
69
                                            <2>$Genus</2>
70
                                            <3>$SpecificEpithet</3>
71
                                        </_join_words>
72
                                    </taxonomicnamewithauthor>
67 73
                                </taxonpath>
68 74
                            </taxonpath_id>
69 75
                        </taxondetermination>
inputs/SALVIAS/plotObservations/test.xml.ref
128 128
                                            <last>$infra_ep_1</last>
129 129
                                        </_name>
130 130
                                    </subspecies>
131
                                    <taxonomicnamewithauthor>
132
                                        <_join_words>
133
                                            <1>
134
                                                <_join_words>
135
                                                    <1>$Family</1>
136
                                                    <2>$Genus</2>
137
                                                    <3>$Species</3>
138
                                                    <5>
139
                                                        <_join_words>
140
                                                            <1>$infra_rank_1</1>
141
                                                            <2>$infra_ep_1</2>
142
                                                        </_join_words>
143
                                                    </5>
144
                                                </_join_words>
145
                                            </1>
146
                                            <2>$auth</2>
147
                                        </_join_words>
148
                                    </taxonomicnamewithauthor>
131 149
                                </taxonpath>
132 150
                            </taxonpath_id>
133 151
                            <taxonfit>$cfaff</taxonfit>
inputs/U/Specimen/test.xml.ref
77 77
                                <taxonpath>
78 78
                                    <family>$Family</family>
79 79
                                    <genus>$Genus</genus>
80
                                    <taxonomicnamewithauthor>
81
                                        <_join_words>
82
                                            <1>$Family</1>
83
                                            <2>$Genus</2>
84
                                        </_join_words>
85
                                    </taxonomicnamewithauthor>
80 86
                                </taxonpath>
81 87
                            </taxonpath_id>
82 88
                            <determinationdate>
inputs/GBIF/Specimen/VegBIEN.csv
22 22
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
23 23
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
24 24
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
25
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
26
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
27
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
28
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
29
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
30
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
25 31
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,
26 32
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus,
27 33
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicname,
inputs/NCU-NCSC/Specimen/VegBIEN.csv
15 15
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,
18
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
18 19
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
19 20
Country,/location/locationplace/*_id/placepath/country,
20 21
County,/location/locationplace/*_id/placepath/county,
inputs/SpeciesLink/Specimen/test.xml.ref
346 346
                                            <2>$dwc_terms_scientificName</2>
347 347
                                        </_alt>
348 348
                                    </taxonomicname>
349
                                    <taxonomicnamewithauthor>
350
                                        <_join_words>
351
                                            <1>
352
                                                <_alt>
353
                                                    <0>$conceptual_darwin_2003_1_0_ScientificName</0>
354
                                                    <1>$dwc_dwcore_ScientificName</1>
355
                                                    <2>$dwc_terms_scientificName</2>
356
                                                </_alt>
357
                                            </1>
358
                                            <2>
359
                                                <_alt>
360
                                                    <1>$dwc_terms_scientificNameAuthorship</1>
361
                                                    <2>$conceptual_darwin_2003_1_0_ScientificNameAuthor</2>
362
                                                    <3>$dwc_dwcore_AuthorYearOfScientificName</3>
363
                                                </_alt>
364
                                            </2>
365
                                        </_join_words>
366
                                    </taxonomicnamewithauthor>
349 367
                                </taxonpath>
350 368
                            </taxonpath_id>
351 369
                            <determinationdate>
inputs/VegBank/taxonobservation_/VegBIEN.csv
17 17
Order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/order,
18 18
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
19 19
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
20
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
21
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
22
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
23
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
24
Variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/6/_join_words:[1=var.]/2,
25
Forma,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/7/_join_words:[1=fm.]/2,
20 26
Variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/variety,
21 27
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
22 28
taxonfit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
inputs/MT/Specimen/VegBIEN.csv
13 13
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
14 14
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
15 15
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
16
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
17
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
16 18
locality,/location/locationnarrative/_merge/1,
17 19
continent,/location/locationplace/*_id/placepath/continent,
18 20
basisOfRecord,,** No join mapping for basisOfRecord ** 
inputs/MT/Specimen/test.xml.ref
44 44
                                <taxonpath>
45 45
                                    <family>$family</family>
46 46
                                    <genus>$genus</genus>
47
                                    <taxonomicnamewithauthor>
48
                                        <_join_words>
49
                                            <1>$family</1>
50
                                            <2>$genus</2>
51
                                        </_join_words>
52
                                    </taxonomicnamewithauthor>
47 53
                                </taxonpath>
48 54
                            </taxonpath_id>
49 55
                        </taxondetermination>
inputs/XAL/Specimen/VegBIEN.csv
33 33
darwin:Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
34 34
darwin:Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
35 35
darwin:ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
36
darwin:ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
37
darwin:Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
38
darwin:Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
39
darwin:Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
40
darwin:Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
41
darwin:ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
36 42
darwin:DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
37 43
darwin:MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
38 44
darwin:YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
inputs/TEAM/VL/VegBIEN.csv
23 23
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
24 24
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
25 25
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
26
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
27
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
28
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
26 29
Names of Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname,
27 30
Comments,,** No join mapping for *Comments ** 
28 31
Condition Codes,,** No join mapping for *Condition Codes ** 
inputs/TEAM/VL/test.xml.ref
47 47
                                    <family>$Family</family>
48 48
                                    <genus>$Genus</genus>
49 49
                                    <species>$Species</species>
50
                                    <taxonomicnamewithauthor>
51
                                        <_join_words>
52
                                            <1>$Family</1>
53
                                            <2>$Genus</2>
54
                                            <3>$Species</3>
55
                                        </_join_words>
56
                                    </taxonomicnamewithauthor>
50 57
                                </taxonpath>
51 58
                            </taxonpath_id>
52 59
                        </taxondetermination>
inputs/TEAM/VT/VegBIEN.csv
23 23
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
24 24
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
25 25
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
26
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
27
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
28
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
26 29
Names of Collectors,/location/locationevent/taxonoccurrence/verbatimcollectorname,
27 30
Comments,,** No join mapping for *Comments ** 
28 31
Condition Codes,,** No join mapping for *Condition Codes ** 
inputs/TEAM/VT/test.xml.ref
47 47
                                    <family>$Family</family>
48 48
                                    <genus>$Genus</genus>
49 49
                                    <species>$Species</species>
50
                                    <taxonomicnamewithauthor>
51
                                        <_join_words>
52
                                            <1>$Family</1>
53
                                            <2>$Genus</2>
54
                                            <3>$Species</3>
55
                                        </_join_words>
56
                                    </taxonomicnamewithauthor>
50 57
                                </taxonpath>
51 58
                            </taxonpath_id>
52 59
                        </taxondetermination>
inputs/NY/Specimen/VegBIEN.csv
38 38
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
39 39
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
40 40
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
41
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
42
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
43
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
44
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
45
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
46
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
41 47
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
42 48
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
43 49
YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
inputs/NY/Specimen/test.xml.ref
126 126
                                    <species>$Species</species>
127 127
                                    <subspecies>$Subspecies</subspecies>
128 128
                                    <taxonomicname>$ScientificName</taxonomicname>
129
                                    <taxonomicnamewithauthor>
130
                                        <_join_words>
131
                                            <1>$ScientificName</1>
132
                                            <2>$ScientificNameAuthor</2>
133
                                        </_join_words>
134
                                    </taxonomicnamewithauthor>
129 135
                                </taxonpath>
130 136
                            </taxonpath_id>
131 137
                            <determinationdate>
inputs/Madidi/Organism/VegBIEN.csv
37 37
Genera,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
38 38
Specific epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
39 39
Species and morphotypes,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,"Contains less than ""Specie+autor"""
40
Specie+autor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor,
40
Specie+autor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/1,
41
Species and morphotypes,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,"Contains less than ""Specie+autor"""
42
Family (revised),/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
43
Genera,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
44
Specific epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
45
Autor (revised),/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
41 46
Qualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
42 47
Field family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,
43 48
Field name,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus,Often = Genera
inputs/UNCC/Specimen/VegBIEN.csv
50 50
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first/_alt/2,
51 51
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
52 52
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
53
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
54
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
55
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
56
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
57
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1/_alt/1,
58
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1/_alt/2,
59
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
60
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
53 61
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
54 62
collector1,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/2,
55 63
collector2,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/3,
inputs/UNCC/Specimen/test.xml.ref
89 89
                                        </_name>
90 90
                                    </subspecies>
91 91
                                    <taxonomicname>$SciName</taxonomicname>
92
                                    <taxonomicnamewithauthor>
93
                                        <_join_words>
94
                                            <1>$SciName</1>
95
                                            <2>$authors</2>
96
                                        </_join_words>
97
                                    </taxonomicnamewithauthor>
92 98
                                </taxonpath>
93 99
                            </taxonpath_id>
94 100
                        </taxondetermination>
mappings/VegCore-VegBIEN.csv
141 141
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
142 142
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
143 143
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
144
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor,
144
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/1,
145
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
146
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
147
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
148
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
149
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
150
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
151
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
152
variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/6/_join_words:[1=var.]/2,
153
forma,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/7/_join_words:[1=fm.]/2,
154
cultivar,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/8/_join_words:[1=cult.]/2,
155
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
145 156
variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/variety,
146 157
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
147 158
dayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
inputs/QMOR/Specimen/test.xml.ref
115 115
                                        </_name>
116 116
                                    </subspecies>
117 117
                                    <taxonomicname>$scientificName</taxonomicname>
118
                                    <taxonomicnamewithauthor>
119
                                        <_join_words>
120
                                            <1>$scientificName</1>
121
                                            <2>$scientificNameAuthorship</2>
122
                                        </_join_words>
123
                                    </taxonomicnamewithauthor>
118 124
                                </taxonpath>
119 125
                            </taxonpath_id>
120 126
                            <determinationdate><_date><date><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></date></_date></determinationdate>
mappings/for_review/VegCore-VegBIEN.csv
142 142
infraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/subspecies,
143 143
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicname,
144 144
scientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
145
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
146
family,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
147
genus,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
148
specificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
149
subspecies,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
150
taxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
151
infraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
152
variety,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
153
forma,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
154
cultivar,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
155
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/taxonomicnamewithauthor,
145 156
variety,//taxonoccurrence/taxondetermination[]/*_id/taxonpath/variety,
146 157
dateIdentified,//taxonoccurrence/taxondetermination[]/determinationdate/_*/date,
147 158
dayIdentified,//taxonoccurrence/taxondetermination[]/determinationdate,
inputs/ACAD/Specimen/VegBIEN.csv
33 33
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
34 34
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
35 35
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
36
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
37
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
38
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
39
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
40
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
41
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
42
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
36 43
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
37 44
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,
38 45
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
inputs/ACAD/Specimen/test.xml.ref
91 91
                                        </_name>
92 92
                                    </subspecies>
93 93
                                    <taxonomicname>$scientificName</taxonomicname>
94
                                    <taxonomicnamewithauthor>
95
                                        <_join_words>
96
                                            <1>$scientificName</1>
97
                                            <2>$scientificNameAuthorship</2>
98
                                        </_join_words>
99
                                    </taxonomicnamewithauthor>
94 100
                                </taxonpath>
95 101
                            </taxonpath_id>
96 102
                            <determinationdate><_date><date><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></date></_date></determinationdate>
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
70 70
specific_epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
71 71
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
72 72
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
73
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
74
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
75
specific_epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
76
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
77
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
78
specific_authority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,Brad: This is the author of the scientificName.
73 79
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
74 80
orig_family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,Brad: OMIT
75 81
orig_species,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,Brad: OMIT
inputs/SALVIAS-CSV/Organism/test.xml.ref
157 157
                                            <last>$infra_ep_1</last>
158 158
                                        </_name>
159 159
                                    </subspecies>
160
                                    <taxonomicnamewithauthor>
161
                                        <_join_words>
162
                                            <1>
163
                                                <_join_words>
164
                                                    <1>$family</1>
165
                                                    <2>$genus</2>
166
                                                    <3>$specific_epithet</3>
167
                                                    <5>
168
                                                        <_join_words>
169
                                                            <1>$infra_rank_1</1>
170
                                                            <2>$infra_ep_1</2>
171
                                                        </_join_words>
172
                                                    </5>
173
                                                </_join_words>
174
                                            </1>
175
                                            <2>$specific_authority</2>
176
                                        </_join_words>
177
                                    </taxonomicnamewithauthor>
160 178
                                </taxonpath>
161 179
                            </taxonpath_id>
162 180
                            <taxonfit>$cf_aff</taxonfit>
inputs/CVS/Organism/VegBIEN.csv
10 10
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value,
11 11
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3,
12 12
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
13
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
13 14
county,/location/locationplace/*_id/placepath/county,
14 15
state,/location/locationplace/*_id/placepath/stateprovince,
15 16
confidentialityStatus,,** No join mapping for *confidentialityStatus ** 
inputs/CVS/Organism/test.xml.ref
28 28
                    <taxonoccurrence>
29 29
                        <aggregateoccurrence><cover_fraction><_percent_to_fraction><value>$%cover</value></_percent_to_fraction></cover_fraction></aggregateoccurrence>
30 30
                        <authortaxoncode>$currentTaxonName sec Weakley 2006</authortaxoncode>
31
                        <taxondetermination><taxonpath_id><taxonpath><taxonomicname>$currentTaxonName sec Weakley 2006</taxonomicname></taxonpath></taxonpath_id></taxondetermination>
31
                        <taxondetermination>
32
                            <taxonpath_id>
33
                                <taxonpath>
34
                                    <taxonomicname>$currentTaxonName sec Weakley 2006</taxonomicname>
35
                                    <taxonomicnamewithauthor>$currentTaxonName sec Weakley 2006</taxonomicnamewithauthor>
36
                                </taxonpath>
37
                            </taxonpath_id>
38
                        </taxondetermination>
32 39
                    </taxonoccurrence>
33 40
                </locationevent>
34 41
                <locationplace>
inputs/REMIB/Specimen/VegBIEN.csv
36 36
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
37 37
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
38 38
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
39
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
40
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
41
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
39 42
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,
40 43
accession_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
41 44

  
inputs/REMIB/Specimen/test.xml.ref
67 67
                                    <family>$family</family>
68 68
                                    <genus>$genus</genus>
69 69
                                    <species>$specificEpithet</species>
70
                                    <taxonomicnamewithauthor>
71
                                        <_join_words>
72
                                            <1>$family</1>
73
                                            <2>$genus</2>
74
                                            <3>$specificEpithet</3>
75
                                        </_join_words>
76
                                    </taxonomicnamewithauthor>
70 77
                                </taxonpath>
71 78
                            </taxonpath_id>
72 79
                        </taxondetermination>
inputs/CTFS/StemObservation/VegBIEN.csv
25 25
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
26 26
SpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
27 27
SubSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
28
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
29
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
30
SpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
31
SubSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
32
SpeciesAuthority,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
28 33
Description,,** No join mapping for *Description ** 
29 34
ExactDate,,** No join mapping for *ExactDate ** 
30 35
FamilyID,,** No join mapping for *FamilyID ** 
inputs/CTFS/StemObservation/test.xml.ref
46 46
                                    <genus>$Genus</genus>
47 47
                                    <species>$SpeciesName</species>
48 48
                                    <subspecies>$SubSpeciesName</subspecies>
49
                                    <taxonomicnamewithauthor>
50
                                        <_join_words>
51
                                            <1>
52
                                                <_join_words>
53
                                                    <1>$Family</1>
54
                                                    <2>$Genus</2>
55
                                                    <3>$SpeciesName</3>
56
                                                    <4>$SubSpeciesName</4>
57
                                                </_join_words>
58
                                            </1>
59
                                            <2>$SpeciesAuthority</2>
60
                                        </_join_words>
61
                                    </taxonomicnamewithauthor>
49 62
                                </taxonpath>
50 63
                            </taxonpath_id>
51 64
                        </taxondetermination>
inputs/CTFS/TaxonOccurrence/VegBIEN.csv
12 12
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
13 13
SpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
14 14
SubSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
15
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
16
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
17
SpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
18
SubSpeciesName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
15 19
Description,,** No join mapping for *Description ** 
16 20
FamilyID,,** No join mapping for *FamilyID ** 
17 21
FieldFamily,,** No join mapping for *FieldFamily ** 
inputs/CTFS/TaxonOccurrence/test.xml.ref
16 16
                                    <genus>$Genus</genus>
17 17
                                    <species>$SpeciesName</species>
18 18
                                    <subspecies>$SubSpeciesName</subspecies>
19
                                    <taxonomicnamewithauthor>
20
                                        <_join_words>
21
                                            <1>$Family</1>
22
                                            <2>$Genus</2>
23
                                            <3>$SpeciesName</3>
24
                                            <4>$SubSpeciesName</4>
25
                                        </_join_words>
26
                                    </taxonomicnamewithauthor>
19 27
                                </taxonpath>
20 28
                            </taxonpath_id>
21 29
                        </taxondetermination>
inputs/FIA/Organism/VegBIEN.csv
16 16
TreeTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
17 17
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
18 18
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
19
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
20
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
19 21
County,/location/locationplace/*_id/placepath/county,
20 22
StateProvince,/location/locationplace/*_id/placepath/stateprovince,
21 23
HOM,,** No join mapping for *HOM ** 
inputs/SALVIAS/plotObservations/VegBIEN.csv
63 63
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
64 64
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
65 65
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
66
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
67
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
68
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
69
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
70
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
71
auth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,Brad: This is the author of the scientificName.
66 72
cfaff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
67 73
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,Brad: OMIT
68 74
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus,
inputs/U/Specimen/VegBIEN.csv
18 18
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last,
19 19
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
20 20
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
21
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
22
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
21 23
Detyy,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
22 24
cf,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
23 25
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1,
inputs/ARIZ/Specimen/VegBIEN.csv
41 41
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
42 42
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1,
43 43
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
44
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor,Contains the binomial in addition to the authority
44
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/1,Contains the binomial in addition to the authority
45
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
46
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
47
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
48
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
49
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
45 50
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
46 51
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
47 52
YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
inputs/GBIF/Specimen/test.xml.ref
62 62
                                    <species>$SpecificEpithet</species>
63 63
                                    <subspecies>$InfraspecificEpithet</subspecies>
64 64
                                    <taxonomicname>$ScientificName</taxonomicname>
65
                                    <taxonomicnamewithauthor>
66
                                        <_join_words>
67
                                            <1>$ScientificName</1>
68
                                            <2>$AuthorOfScientificName</2>
69
                                        </_join_words>
70
                                    </taxonomicnamewithauthor>
65 71
                                </taxonpath>
66 72
                            </taxonpath_id>
67 73
                        </taxondetermination>
inputs/SpeciesLink/Specimen/VegBIEN.csv
132 132
conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
133 133
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
134 134
dwc_terms_scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
135
conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
136
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
137
dwc_terms_scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
138
conceptual_darwin_2003_1_0_Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
139
dwc_dwcore_Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
140
dwc_terms_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
141
conceptual_darwin_2003_1_0_Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
142
dwc_dwcore_Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
143
dwc_terms_genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
144
conceptual_darwin_2003_1_0_Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
145
dwc_dwcore_SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
146
dwc_terms_specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
147
conceptual_darwin_2003_1_0_Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/4,
148
dwc_dwcore_InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
149
dwc_terms_infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
150
dwc_terms_scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2/_alt/1,
151
conceptual_darwin_2003_1_0_ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2/_alt/2,
152
dwc_dwcore_AuthorYearOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2/_alt/3,
135 153
dwc_terms_dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
136 154
conceptual_darwin_2003_1_0_DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
137 155
conceptual_darwin_2003_1_0_MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
inputs/MO/Specimen/test.xml.ref
95 95
                                    <species>$species</species>
96 96
                                    <subspecies>$Subspecies</subspecies>
97 97
                                    <taxonomicname>$ScientificName</taxonomicname>
98
                                    <taxonomicnamewithauthor>
99
                                        <_join_words>
100
                                            <1>$ScientificName</1>
101
                                            <2>$ScientificNameAuthor</2>
102
                                        </_join_words>
103
                                    </taxonomicnamewithauthor>
98 104
                                </taxonpath>
99 105
                            </taxonpath_id>
100 106
                        </taxondetermination>
inputs/QMOR/Specimen/VegBIEN.csv
40 40
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
41 41
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
42 42
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname,
43
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1,
44
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1,
45
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2,
46
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3,
47
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/1,
48
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/5/_join_words/2,
49
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/2,
43 50
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value,
44 51
identificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
45 52
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname,

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