Revision 5176
Added by Aaron Marcuse-Kubitza about 12 years ago
inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
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71 | 71 |
dwc_dwcore_InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
72 | 72 |
dwc_terms_institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
73 | 73 |
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
74 |
dwc_terms_recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/1,
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75 |
conceptual_darwin_2003_1_0_FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
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74 |
dwc_terms_recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/1",
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75 |
conceptual_darwin_2003_1_0_FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
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76 | 76 |
----- |
77 | 77 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
78 | 78 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber"" |
79 | 79 |
-----" |
80 |
dwc_curatorial_FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
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80 |
dwc_curatorial_FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
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81 | 81 |
----- |
82 | 82 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
83 | 83 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber"" |
84 | 84 |
-----" |
85 |
dwc_terms_fieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
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85 |
dwc_terms_fieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
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86 | 86 |
----- |
87 | 87 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
88 | 88 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber"" |
89 | 89 |
-----" |
90 |
conceptual_darwin_2003_1_0_CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/3,
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91 |
dwc_curatorial_CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1/_alt/3,
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92 |
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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93 |
dwc_dwcore_ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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94 |
dwc_terms_scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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90 |
conceptual_darwin_2003_1_0_CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/3",
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91 |
dwc_curatorial_CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/3",
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92 |
conceptual_darwin_2003_1_0_ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
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93 |
dwc_dwcore_ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
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94 |
dwc_terms_scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
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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/test.xml.ref | ||
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77 | 77 |
</specimenreplicate> |
78 | 78 |
</plantobservation> |
79 | 79 |
</aggregateoccurrence> |
80 |
<authortaxoncode>$CollectorNumber</authortaxoncode> |
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81 | 80 |
<taxondetermination> |
82 | 81 |
<party_id> |
83 | 82 |
<party> |
inputs/VegBank/plot_/VegBIEN.csv | ||
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13 | 13 |
longitude,"/location/locationcoords/longitude_deg/_nullIf:[null=0,type=float]/value", |
14 | 14 |
authorplotcode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode", |
15 | 15 |
plot_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode", |
16 |
authorplotcode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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17 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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16 |
authorplotcode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
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17 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
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18 | 18 |
locationnarrative,/location/locationnarrative/_merge/1, |
19 | 19 |
continent,/location/locationplace/*_id/placepath/continent, |
20 | 20 |
area|country|territory,/location/locationplace/*_id/placepath/country, |
mappings/VegCore-VegBIEN.csv | ||
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109 | 109 |
organismX,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
110 | 110 |
organismY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
111 | 111 |
aggregateOccurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
112 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
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113 |
locationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
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114 |
plotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
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115 |
tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
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116 |
scientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/cond/_exists", |
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117 |
originalScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/1", |
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118 |
scientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2", |
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119 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3", |
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112 |
eventID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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113 |
fieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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114 |
locationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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115 |
plotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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116 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
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117 |
tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2", |
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118 |
originalScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
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119 |
scientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
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120 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
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120 | 121 |
growthForm,/location/locationevent/taxonoccurrence/growthform, |
121 | 122 |
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>" |
122 | 123 |
cultivated,/location/locationevent/taxonoccurrence/iscultivated/_alt/1, |
inputs/.TNRS/tnrs/VegBIEN.csv | ||
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1 | 1 |
TNRS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments |
2 |
Name_submitted,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/cond/_exists", |
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3 |
Name_submitted,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2", |
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4 |
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3", |
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2 |
Name_submitted,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
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3 |
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
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5 | 4 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/cond/_exists", |
6 | 5 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/1", |
7 | 6 |
Name_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1", |
inputs/U/Specimen/test.xml.ref | ||
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63 | 63 |
</specimenreplicate> |
64 | 64 |
</plantobservation> |
65 | 65 |
</aggregateoccurrence> |
66 |
<authortaxoncode>$Number</authortaxoncode> |
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67 | 66 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
68 | 67 |
<taxondetermination> |
69 | 68 |
<party_id> |
inputs/ARIZ/Specimen/test.xml.ref | ||
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104 | 104 |
</specimenreplicate> |
105 | 105 |
</plantobservation> |
106 | 106 |
</aggregateoccurrence> |
107 |
<authortaxoncode>$CollectorNumber</authortaxoncode> |
|
108 | 107 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
109 | 108 |
<taxondetermination> |
110 | 109 |
<party_id> |
inputs/GBIF/Specimen/test.xml.ref | ||
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45 | 45 |
</specimenreplicate> |
46 | 46 |
</plantobservation> |
47 | 47 |
</aggregateoccurrence> |
48 |
<authortaxoncode>$ScientificNameOriginal</authortaxoncode> |
|
49 | 48 |
<taxondetermination> |
50 | 49 |
<party_id> |
51 | 50 |
<party> |
inputs/NCU-NCSC/Specimen/test.xml.ref | ||
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61 | 61 |
</specimenreplicate> |
62 | 62 |
</plantobservation> |
63 | 63 |
</aggregateoccurrence> |
64 |
<authortaxoncode>$Full Taxon Name</authortaxoncode> |
|
65 | 64 |
<iscultivated>$Cultivated?</iscultivated> |
66 | 65 |
<sourceaccessioncode>$Accession Number</sourceaccessioncode> |
67 | 66 |
<taxondetermination> |
inputs/MO/Specimen/VegBIEN.csv | ||
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17 | 17 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
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 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
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21 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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20 |
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
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21 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
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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/observation_/VegBIEN.csv | ||
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22 | 22 |
soilsand,/location/locationevent/soilobs/sand_fraction/_percent_to_fraction/value,"""Percent sand in the soil horizon"" (soilSand definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
23 | 23 |
soilsilt,/location/locationevent/soilobs/silt_fraction/_percent_to_fraction/value,"""Percent silt in the soil horizon"" (soilSilt definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
24 | 24 |
soiltexture,/location/locationevent/soilobs/texture, |
25 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
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25 |
authorobscode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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26 |
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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27 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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26 | 28 |
accessioncode,,** No join mapping for *accessioncode ** |
27 | 29 |
autotaxoncover,,** No join mapping for *autotaxoncover ** |
28 | 30 |
basalarea,,** No join mapping for *basalarea ** |
inputs/QMOR/Specimen/test.xml.ref | ||
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88 | 88 |
</specimenreplicate> |
89 | 89 |
</plantobservation> |
90 | 90 |
</aggregateoccurrence> |
91 |
<authortaxoncode>$scientificName</authortaxoncode> |
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92 | 91 |
<sourceaccessioncode>$id</sourceaccessioncode> |
93 | 92 |
<taxondetermination> |
94 | 93 |
<party_id> |
inputs/XAL/Specimen/VegBIEN.csv | ||
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18 | 18 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
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 |
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
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22 |
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
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21 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
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22 |
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
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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/TEAM/VL/VegBIEN.csv | ||
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17 | 17 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
18 | 18 |
1ha Plot X Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
19 | 19 |
1ha Plot Y Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
20 |
1ha Plot Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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21 |
Tree Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
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20 |
1ha Plot Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
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21 |
Tree Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2",
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22 | 22 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
23 | 23 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
24 | 24 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
inputs/TEAM/VT/VegBIEN.csv | ||
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17 | 17 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
18 | 18 |
1ha Plot X Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
19 | 19 |
1ha Plot Y Coordinate,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
20 |
1ha Plot Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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21 |
Tree Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
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20 |
1ha Plot Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
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21 |
Tree Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2",
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22 | 22 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
23 | 23 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
24 | 24 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
inputs/TEAM/TEAM_Sites/VegBIEN.csv | ||
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7 | 7 |
Name,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode", |
8 | 8 |
CollectionDate,/location/locationevent/obsenddate/_*/date/_alt/2/_dateRangeEnd/value, |
9 | 9 |
CollectionDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value, |
10 |
Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
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10 |
Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
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11 | 11 |
1ha Plot Coordinate,,** No join mapping for *1ha Plot Coordinate ** |
inputs/NY/Specimen/VegBIEN.csv | ||
---|---|---|
22 | 22 |
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 |
23 | 23 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
24 | 24 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
25 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,Usage inconsistent with DwC definition
|
|
26 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
|
|
25 |
FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",Usage inconsistent with DwC definition
|
|
26 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_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/NY/Specimen/test.xml.ref | ||
---|---|---|
104 | 104 |
</specimenreplicate> |
105 | 105 |
</plantobservation> |
106 | 106 |
</aggregateoccurrence> |
107 |
<authortaxoncode>$FieldNumber</authortaxoncode> |
|
108 | 107 |
<sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode> |
109 | 108 |
<taxondetermination> |
110 | 109 |
<party_id> |
inputs/Madidi/Organism/VegBIEN.csv | ||
---|---|---|
22 | 22 |
Tag number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
23 | 23 |
Subplot X,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
24 | 24 |
Subplot Y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
25 |
Tree number,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
|
26 |
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
|
27 |
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
|
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/_if[@name=""if is taxonpath only""]/cond/_exists", |
|
30 |
Specie+autor,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2", |
|
31 |
Species and morphotypes,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3","Contains less than ""Specie+autor""" |
|
25 |
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
26 |
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
27 |
Tree number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
|
28 |
Tag number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2", |
|
29 |
Specie+autor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
|
30 |
Species and morphotypes,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3","Contains less than ""Specie+autor""" |
|
32 | 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>" |
33 | 32 |
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
34 | 33 |
Determined by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
inputs/Madidi/Plot/VegBIEN.csv | ||
---|---|---|
85 | 85 |
Limo (DIN 18 123–%–1),/location/locationevent/soilobs/silt_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
86 | 86 |
"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",/location/locationevent/soilobs/sodium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
87 | 87 |
Textural class,/location/locationevent/soilobs/texture, |
88 |
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
89 |
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
88 |
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
89 |
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
90 | 90 |
Locality,/location/locationnarrative/_merge/1, |
91 | 91 |
Observaciones,/location/notespublic, |
92 | 92 |
Direction,/location/slopeaspect_deg/_alt/1/_compass/value/_alt/1,Part files provide either this field or Orientación |
inputs/UNCC/Specimen/VegBIEN.csv | ||
---|---|---|
30 | 30 |
GROUP BY herbarium, accession |
31 | 31 |
HAVING count(*) > 1 |
32 | 32 |
-----" |
33 |
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
|
|
34 |
SciName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
|
|
33 |
collectno,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
|
|
34 |
SciName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
|
|
35 | 35 |
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/UNCC/Specimen/test.xml.ref | ||
---|---|---|
67 | 67 |
</specimenreplicate> |
68 | 68 |
</plantobservation> |
69 | 69 |
</aggregateoccurrence> |
70 |
<authortaxoncode>$collectno</authortaxoncode> |
|
71 | 70 |
<iscultivated>$cultivated</iscultivated> |
72 | 71 |
<sourceaccessioncode>$accession</sourceaccessioncode> |
73 | 72 |
<taxondetermination> |
inputs/ACAD/Specimen/VegBIEN.csv | ||
---|---|---|
16 | 16 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
17 | 17 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
18 | 18 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
19 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
|
20 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/cond/_exists", |
|
21 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2", |
|
19 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
|
20 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
|
22 | 21 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
23 | 22 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
24 | 23 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
inputs/ACAD/Specimen/test.xml.ref | ||
---|---|---|
64 | 64 |
</specimenreplicate> |
65 | 65 |
</plantobservation> |
66 | 66 |
</aggregateoccurrence> |
67 |
<authortaxoncode>$recordNumber</authortaxoncode> |
|
68 | 67 |
<sourceaccessioncode>$id</sourceaccessioncode> |
69 | 68 |
<taxondetermination> |
70 | 69 |
<party_id> |
inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
---|---|---|
55 | 55 |
tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_alt/2/_alt/2,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
56 | 56 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots" |
57 | 57 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position |
58 |
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
|
|
59 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
60 |
plot_code,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
61 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/1/_alt/1",The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above
|
|
62 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/1/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
|
|
63 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/2/_alt/1","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
64 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/2/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
58 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
59 |
plot_code,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
60 |
individual_code,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
|
|
61 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/1/_alt/1",The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above
|
|
62 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/1/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
|
|
63 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/2/_alt/1","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
64 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/2/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
65 | 65 |
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","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>" |
66 | 66 |
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
67 | 67 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
inputs/SALVIAS-CSV/Plot/VegBIEN.csv | ||
---|---|---|
36 | 36 |
silt_percent,/location/locationevent/soilobs/silt_fraction/_percent_to_fraction/value, |
37 | 37 |
soil_Na,/location/locationevent/soilobs/sodium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
38 | 38 |
soil_texture,/location/locationevent/soilobs/texture, |
39 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
40 |
plot_code,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
39 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
40 |
plot_code,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
41 | 41 |
temp_c,/location/locationevent/temperature_c, |
42 | 42 |
locality_description,/location/locationnarrative/_merge/1,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX" |
43 | 43 |
major_geo,/location/locationplace/*_id/placepath/continent, |
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, |
11 |
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3", |
|
11 |
authorObsCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
12 |
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
12 | 13 |
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1", |
13 | 14 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
14 | 15 |
county,/location/locationplace/*_id/placepath/county, |
inputs/CTFS/StemObservation/VegBIEN.csv | ||
---|---|---|
16 | 16 |
Tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
17 | 17 |
x,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
18 | 18 |
y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
19 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
|
20 |
StemTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
|
21 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
|
19 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
20 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
21 |
StemTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2", |
|
22 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2", |
|
22 | 23 |
MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
23 | 24 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
24 | 25 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
inputs/CTFS/Subplot/VegBIEN.csv | ||
---|---|---|
6 | 6 |
QuadratID,/location/authorlocationcode,Not globally unique; unique only within Site |
7 | 7 |
QuadratID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",Not globally unique; unique only within Site |
8 | 8 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode", |
9 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
9 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
10 | 10 |
StartX,/location/sublocationxposition_m, |
11 | 11 |
StartY,/location/sublocationyposition_m, |
12 | 12 |
DimX,,** No join mapping for *DimX ** |
inputs/CTFS/PlotObservation/VegBIEN.csv | ||
---|---|---|
12 | 12 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/sourceaccessioncode", |
13 | 13 |
EndDate,/location/locationevent/obsenddate/_*/date/_alt/1, |
14 | 14 |
StartDate,/location/locationevent/obsstartdate/_*/date/_alt/1, |
15 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
|
15 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
16 |
PlotCensusNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
17 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
16 | 18 |
Description,,** No join mapping for *Description ** |
inputs/CTFS/TaxonOccurrence/VegBIEN.csv | ||
---|---|---|
6 | 6 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/cond/_exists", |
7 | 7 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode", |
8 | 8 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/sourceaccessioncode", |
9 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
|
9 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
10 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
10 | 11 |
SpeciesInvID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
11 | 12 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
12 | 13 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
inputs/CTFS/SubplotObservation/VegBIEN.csv | ||
---|---|---|
9 | 9 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/cond/_exists", |
10 | 10 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode", |
11 | 11 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/sourceaccessioncode", |
12 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
|
12 |
CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
13 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
inputs/CTFS/Plot/VegBIEN.csv | ||
---|---|---|
19 | 19 |
Longitude,"/location/locationcoords/longitude_deg/_nullIf:[null=0,type=float]/value", |
20 | 20 |
PlotName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/authorlocationcode", |
21 | 21 |
PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode", |
22 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
23 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
22 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
23 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
24 | 24 |
DescriptionOfSite,/location/locationnarrative/_merge/1, |
25 | 25 |
LocationName,/location/locationnarrative/_merge/1, |
26 | 26 |
CountryName,/location/locationplace/*_id/placepath/country, |
inputs/FIA/Organism/VegBIEN.csv | ||
---|---|---|
12 | 12 |
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_in_to_m/value,Assuming units based on the range and precision of values and location inside the U.S. |
13 | 13 |
Height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m, |
14 | 14 |
TreeTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
15 |
PlotCD,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
16 |
TreeTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then",
|
|
15 |
PlotCD,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
16 |
TreeTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2",
|
|
17 | 17 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
18 | 18 |
SpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/3", |
19 | 19 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
inputs/SALVIAS/plotMetadata/VegBIEN.csv | ||
---|---|---|
36 | 36 |
silt_percent,/location/locationevent/soilobs/silt_fraction/_percent_to_fraction/value, |
37 | 37 |
soil_Na,/location/locationevent/soilobs/sodium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values |
38 | 38 |
soil_texture,/location/locationevent/soilobs/texture, |
39 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
40 |
SiteCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
39 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
40 |
SiteCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
41 | 41 |
Temp,/location/locationevent/temperature_c, |
42 | 42 |
Locality_Description,/location/locationnarrative/_merge/1,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX" |
43 | 43 |
Habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
inputs/SALVIAS/stems/VegBIEN.csv | ||
---|---|---|
13 | 13 |
stem_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode, |
14 | 14 |
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_alt/1,"The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
15 | 15 |
stem_tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_alt/2,"The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
16 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
17 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
16 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
17 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
18 | 18 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else", |
19 | 19 |
origrecord_id_stems,,** No join mapping for *origrecord_id_stems ** |
20 | 20 |
plotobs_id_index,,** No join mapping for *plotobs_id_index ** |
inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
---|---|---|
50 | 50 |
tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_alt/2,"The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once." |
51 | 51 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots" |
52 | 52 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position |
53 |
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
|
|
54 |
PlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
55 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists",
|
|
56 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
57 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
53 |
PlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
54 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
|
|
55 |
Ind,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
|
|
56 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
|
|
57 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/2/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
|
|
58 | 58 |
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","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>" |
59 | 59 |
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
60 | 60 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
inputs/U/Specimen/VegBIEN.csv | ||
---|---|---|
11 | 11 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
12 | 12 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
13 | 13 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
14 |
Number,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,
|
|
14 |
Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
|
|
15 | 15 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
16 | 16 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
17 | 17 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
inputs/ARIZ/Specimen/VegBIEN.csv | ||
---|---|---|
25 | 25 |
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 |
26 | 26 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
27 | 27 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
28 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
|
29 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/cond/_exists",Contains the binomial in addition to the authority |
|
30 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/2",Contains the binomial in addition to the authority |
|
31 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3", |
|
28 |
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
|
29 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",Contains the binomial in addition to the authority |
|
30 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
32 | 31 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
33 | 32 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
34 | 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, |
14 |
ScientificNameOriginal,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/1",
|
|
15 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
|
|
14 |
ScientificNameOriginal,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1",
|
|
15 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
|
|
16 | 16 |
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, |
14 |
Full Taxon Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_if[@name=""if is taxonpath only""]/else/_first/3",
|
|
14 |
Full Taxon Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
|
|
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/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1", |
inputs/SpeciesLink/Specimen/test.xml.ref | ||
---|---|---|
213 | 213 |
</specimenreplicate> |
214 | 214 |
</plantobservation> |
215 | 215 |
</aggregateoccurrence> |
216 |
<authortaxoncode> |
|
217 |
<_alt> |
|
218 |
<1>$dwc_terms_recordNumber</1> |
|
219 |
<2> |
|
220 |
<_alt> |
|
221 |
<0>$conceptual_darwin_2003_1_0_FieldNumber</0> |
|
222 |
<1>$dwc_curatorial_FieldNumber</1> |
|
223 |
<2>$dwc_terms_fieldNumber</2> |
|
224 |
</_alt> |
|
225 |
</2> |
|
226 |
<3> |
|
227 |
<_alt> |
|
228 |
<0>$conceptual_darwin_2003_1_0_CollectorNumber</0> |
|
229 |
<1>$dwc_curatorial_CollectorNumber</1> |
|
230 |
</_alt> |
|
231 |
</3> |
|
232 |
</_alt> |
|
233 |
</authortaxoncode> |
|
234 | 216 |
<sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode> |
235 | 217 |
<taxondetermination> |
236 | 218 |
<party_id> |
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/_if[@name=""if is taxonpath only""]/else/_first/1", |
|
10 |
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
11 |
authorplantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
|
11 | 12 |
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
12 | 13 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/1", |
13 | 14 |
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/_if[@name=""if has accepted name""]/{then/.,else/canon_taxonpath_id/taxonpath:[datasource_id/party/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/2", |
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/_if[@name=""if is taxonpath only""]/else/_first/3",
|
|
27 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_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/for_review/VegCore-VegBIEN.csv | ||
---|---|---|
109 | 109 |
organismX,//stemobservation/xposition_m, |
110 | 110 |
organismY,//stemobservation/yposition_m, |
111 | 111 |
aggregateOccurrenceID,//aggregateoccurrence/sourceaccessioncode, |
112 |
recordNumber,//taxonoccurrence/authortaxoncode, |
|
113 |
locationID,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/cond/_exists", |
|
114 |
plotName,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/cond/_exists", |
|
115 |
tag,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/then", |
|
116 |
scientificNameWithAuthorship,"//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", |
|
112 |
eventID,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
113 |
fieldNumber,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
114 |
locationID,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
115 |
plotName,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
116 |
recordNumber,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then", |
|
117 |
tag,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then", |
|
118 |
originalScientificName,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then", |
|
119 |
scientificNameWithAuthorship,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then", |
|
120 |
scientificName,"//taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then", |
|
120 | 121 |
growthForm,//taxonoccurrence/growthform, |
121 | 122 |
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>" |
122 | 123 |
cultivated,//taxonoccurrence/iscultivated, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: taxonoccurrence.authortaxoncode: Only populate if needed to distinguish the taxonoccurrence within a plot