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Revision 1279

inputs/UArizona/maps/DwC.specimens.csv: Finished mappings

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inputs/UArizona/maps/DwC.specimens.csv
1 1
"UArizona[DwC]:ariz_raw","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/","Comments"
2 2
"GlobalUniqueIdentifier","occurrenceID",
3 3
"CatalogNumber",,"Map to nothing so it doesn't overwrite CatalogNumberNumeric"
4
"CatalogNumberNumeric","catalogNumber",
4
"CatalogNumberNumeric","CatalogNumber",
5 5
"CollectedDate","eventDate/_alt/2",
6 6
"VerbatimCollectingDate","eventDate/_alt/0",
7
"HorizontalDatum",,
8
"OriginalCoordinateSystem",,
9
"GeoRefMethod",,
10
"LatLongComments",,
11
"IdentificationModifier",,
7
"HorizontalDatum",,"Not used"
8
"OriginalCoordinateSystem","verbatimSRS",
9
"GeoRefMethod","georeferenceProtocol",
10
"LatLongComments","georeferenceRemarks",
11
"IdentificationModifier","identificationQualifier",
12 12
"IdentifiedDate","dateIdentified/_alt/0",
13
"Tissues",,
14
"AgeClass",,
15
"GenGankNum",,
16
"OtherCatalogNumber",,
17
"RelatedCatalogItems",,
18
"Remarks",,
13
"Tissues",,"Not used"
14
"AgeClass","lifeStage",
15
"GenGankNum","associatedSequences/_label[label=""GenBank""]/value","This is a typo of GenBankNum from the original CSV"
16
"OtherCatalogNumber","RelatedCatalogItem",
17
"RelatedCatalogItems","RelatedCatalogItem",
18
"Remarks","Notes",
inputs/UArizona/maps/DwC.specimens.full.csv
10 10
Bed,Bed
11 11
Behavior,Behavior
12 12
BoundingBox,BoundingBox
13
CatalogNumberNumeric,CatalogNumber,
13 14
Class,Class
14 15
CollectionCode,CollectionCode
15 16
CollectionID,CollectionID
......
137 138
NomenclaturalCode,NomenclaturalCode
138 139
NomenclaturalStatus,NomenclaturalStatus
139 140
Notes,Notes
141
Remarks,Notes,
140 142
OccurrenceID,OccurrenceID
141 143
OccurrenceRemarks,OccurrenceRemarks
142 144
OccurrenceStatus,OccurrenceStatus
......
155 157
PreviousIdentifications,PreviousIdentifications
156 158
RecordNumber,RecordNumber
157 159
RecordedBy,RecordedBy
160
OtherCatalogNumber,RelatedCatalogItem,
158 161
RelatedCatalogItem,RelatedCatalogItem
162
RelatedCatalogItems,RelatedCatalogItem,
159 163
RelatedResourceID,RelatedResourceID
160 164
RelationshipAccordingTo,RelationshipAccordingTo
161 165
RelationshipEstablishedDate,RelationshipEstablishedDate
......
206 210
associatedOccurrences,associatedOccurrences
207 211
associatedReferences,associatedReferences
208 212
associatedSequences,associatedSequences
213
GenGankNum,"associatedSequences/_label[label=""GenBank""]/value",This is a typo of GenBankNum from the original CSV
209 214
associatedTaxa,associatedTaxa
210 215
basisOfRecord,basisOfRecord
211 216
bed,bed
212 217
behavior,behavior
213
CatalogNumberNumeric,catalogNumber,
214 218
catalogNumber,catalogNumber
215 219
class,class
216 220
collectionCode,collectionCode
......
262 266
genus,genus
263 267
geodeticDatum,geodeticDatum
264 268
geologicalContextID,geologicalContextID
269
GeoRefMethod,georeferenceProtocol,
265 270
georeferenceProtocol,georeferenceProtocol
271
LatLongComments,georeferenceRemarks,
266 272
georeferenceRemarks,georeferenceRemarks
267 273
georeferenceSources,georeferenceSources
268 274
georeferenceVerificationStatus,georeferenceVerificationStatus
......
275 281
higherGeographyID,higherGeographyID
276 282
highestBiostratigraphicZone,highestBiostratigraphicZone
277 283
identificationID,identificationID
284
IdentificationModifier,identificationQualifier,
278 285
identificationQualifier,identificationQualifier
279 286
identificationReferences,identificationReferences
280 287
identificationRemarks,identificationRemarks
......
294 301
latestEpochOrHighestSeries,latestEpochOrHighestSeries
295 302
latestEraOrHighestErathem,latestEraOrHighestErathem
296 303
latestPeriodOrHighestSystem,latestPeriodOrHighestSystem
304
AgeClass,lifeStage,
297 305
lifeStage,lifeStage
298 306
lithostratigraphicTerms,lithostratigraphicTerms
299 307
locality,locality
......
375 383
verbatimLatitude,verbatimLatitude
376 384
verbatimLocality,verbatimLocality
377 385
verbatimLongitude,verbatimLongitude
386
OriginalCoordinateSystem,verbatimSRS,
378 387
verbatimSRS,verbatimSRS
379 388
verbatimTaxonRank,verbatimTaxonRank
380 389
vernacularName,vernacularName
381 390
waterBody,waterBody
382 391
year,year
383
AgeClass,,
384 392
CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric
385
GenGankNum,,
386
GeoRefMethod,,
387
HorizontalDatum,,
388
IdentificationModifier,,
389
LatLongComments,,
390
OriginalCoordinateSystem,,
391
OtherCatalogNumber,,
392
RelatedCatalogItems,,
393
Remarks,,
394
Tissues,,
393
HorizontalDatum,,Not used
394
Tissues,,Not used
inputs/UArizona/maps/VegBIEN.specimens.csv
76 76
InfraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
77 77
Subspecies,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
78 78
infraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
79
GenGankNum,"/_label[label=""GenBank""]/value",This is a typo of GenBankNum from the original CSV,39
79 80
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
80 81
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
81 82
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
82 83
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
83 84
FieldNotes,/description,,
84 85
Notes,/description,,
86
Remarks,/description,,
85 87
fieldNotes,/description,,
86 88
Collector,/verbatimcollectorname,,23
87 89
RecordedBy,/verbatimcollectorname,,23
......
102 104
occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
103 105
AcceptedNameUsage,,,135
104 106
AcceptedNameUsageID,,,128
105
AgeClass,,
107
AgeClass,,,27
106 108
AssociatedMedia,,,36
107 109
AssociatedOccurrences,,,38
108 110
AssociatedReferences,,,37
......
144 146
FootprintSRS,,,92
145 147
FootprintSpatialFit,,,93
146 148
Formation,,,115
147
GenGankNum,,
148
GeoRefMethod,,
149
GeoRefMethod,,,96
149 150
GeodeticDatum,,,87
150 151
GeologicalContextID,,,100
151 152
GeoreferenceProtocol,,,96
......
159 160
HigherGeography,,,58
160 161
HigherGeographyID,,,57
161 162
HighestBiostratigraphicZone,,,112
162
HorizontalDatum,,
163
HorizontalDatum,,Not used
163 164
IdentificationID,,,118
164
IdentificationModifier,,
165
IdentificationModifier,,,124
165 166
IdentificationQualifier,,,124
166 167
IdentificationReferences,,,121
167 168
IdentificationRemarks,,,123
......
173 174
Island,,,62
174 175
IslandGroup,,,61
175 176
JulianDay,,Brad: OMIT,50
176
LatLongComments,,
177
LatLongComments,,,99
177 178
LatestAgeOrHighestStage,,,110
178 179
LatestEonOrHighestEonothem,,,102
179 180
LatestEpochOrHighestSeries,,,108
......
208 209
NomenclaturalStatus,,,157
209 210
OccurrenceRemarks,,,21
210 211
OccurrenceStatus,,,31
211
OriginalCoordinateSystem,,
212
OriginalCoordinateSystem,,,84
212 213
OriginalNameUsage,,,137
213 214
OriginalNameUsageID,,,130
214
OtherCatalogNumber,,
215
OtherCatalogNumber,,Brad: OMIT,161
215 216
OtherCatalogNumbers,,,34
216 217
OwnerInstitutionCode,,,14
217 218
ParentNameUsage,,,136
......
222 223
PreviousCatalogNumber,,?; Brad: OMIT,35
223 224
PreviousIdentifications,,Brad: OMIT,35
224 225
RelatedCatalogItem,,Brad: OMIT,161
225
RelatedCatalogItems,,
226
RelatedCatalogItems,,Brad: OMIT,161
226 227
RelatedResourceID,,Brad: OMIT,161
227 228
RelationshipAccordingTo,,,163
228 229
RelationshipEstablishedDate,,,164
229 230
RelationshipOfResource,,Brad: OMIT,162
230 231
RelationshipRemarks,,,165
231 232
RelationshipType,,Brad: OMIT,162
232
Remarks,,
233 233
ReproductiveCondition,,,28
234 234
ResourceID,,,160
235 235
ResourceRelationshipID,,,159
......
244 244
TaxonRemarks,,,158
245 245
TaxonomicStatus,,,156
246 246
TimeOfDay,,Brad: OMIT,45
247
Tissues,,
247
Tissues,,Not used
248 248
TypeStatus,,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN,125
249 249
VerbatimCoordinateSystem,,,83
250 250
VerbatimCoordinates,,,80

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