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Revision 4857

input.Makefile: Maps validation: %/new_terms.csv: Include the entire map spreadsheet row, so that each new term is listed together with its mapping. This facilitates adding new mappings to mappings/Veg+-VegCore.csv directly from any new_terms.csv. Note that the use of `sort -u` (in lib/mappings.Makefile) causes multiline comments to be separated, leading to spurious lines for each multiline comment line.

View differences:

new_terms.csv
1
"Calcio intercambiable (WSP S-5,10–cmolc/Kg–0.016)"
2
"Carbón Orgánico (WSP S-9,10–%–0.06)"
3
"Magnesio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)"
4
"Materia Orgánica (WSP S-9,10–%–0.1)"
5
"Potasio intercambiable (WSP S-5,10–cmolc/Kg–0.0053)"
6
"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)"
7
%cover
8
1haPlotCode
9
Accession Number
10
Accuracy
11
Acidez intercambiable (ISRIC 11–cmolc/Kg–0.05)
12
Addcoll
13
AgeClass
14
Altitude
15
Arcilla (DIN 18 123–%–1)
16
Area
17
Arena (DIN 18 123–%–2.5)
18
AuthorOfScientificName
19
Autor (revised)
20
Barcode
21
CIC (ISRIC 11–cmolc/Kg–0.05)
22
CatalogNO
23
CatalogNumberNumeric
24
Colldd
25
Collect Date
26
CollectionCD
27
Collectors
28
Collmm
29
Collyy
30
Conductividad electrica (ASPT 6–µS/cm– 1 - 10000)
31
DateInfo
32
DetType
33
Detby
34
Determined by
35
Detyy
36
Diameter
37
Direction
38
Ecology
39
Elev
40
Expedition
41
Expedition name
42
Expedition number
43
Family (revised)
44
Field family
45
Field name
46
First evaluation
47
Format
48
Full Taxon Name
49
Fósforo disponible (ISRIC 14-2–mg/Kg–1.5)
50
GBIFFamilyOriginal
51
GBIFGenusOriginal
52
Gazetteer
53
GenBankNum
54
Genera
55
GeorefMethod
56
HorizontalDatum
57
IdentificationModifier
58
Ind
59
Index collector
60
InfraSpecificLevel
61
InstitutionCD
62
Inventory code
63
Inventory name
64
LastDateModified
65
Lat
66
Lat (-=S)
67
LatDec
68
LatLongComments
69
LatestDateCollected
70
Latitude (DMS)
71
Liana presence
72
Limo (DIN 18 123–%–1)
73
Line
74
Locality description
75
Locality_Description
76
Locnotes
77
Long
78
Long (-=W)
79
LongDec
80
Longitude (DMS)
81
MajorGeo
82
MaximumElevationInMeter
83
MeasDay
84
MeasMon
85
MeasYear
86
MeasureID
87
Method
88
Minimum altitude
89
MinimumElevationInMeter
90
Newgazett
91
Nitrógeno total (ISRIC 6–%–0.0014)
92
NoInd
93
Number
94
Number of subplot
95
OBSERVATION_ID
96
Observaciones
97
ObservationDate
98
Observations
99
Orientación/exposicion
100
OrigFamily
101
OrigGenus
102
OrigSpecies
103
OriginalCoordinateSystem
104
Phenology
105
PlantFungusDescription
106
PlotCD
107
PlotCode
108
PlotMethod
109
PlotObsID
110
PolDiv1
111
Precip
112
Prefix
113
Qualifier
114
RelatedCatalogedItems
115
SciName
116
ScientificNameOriginal
117
SeriesName
118
SiteCode
119
SiteName
120
SizeOfSite
121
Slope
122
SourceVoucher
123
Specie+autor
124
Species and morphotypes
125
SpeciesAuthority
126
Specimen
127
StemID
128
Substrate
129
Suffix
130
Tag number
131
Temp
132
Textural class
133
TimeCollected
134
Tissues
135
Topographical situation
136
Total height
137
Tree number
138
TreeNumber
139
TreeTag
140
Trunk
141
Typology
142
UniqueNYInternalRecordNumber
143
Vegetation
144
Vegetation type
145
VerbatimCollectingDate
146
X_1haPlot
147
Y_1haPlot
148
accession
149
accession_number
150
acronym
151
area
152
area|country|territory
153
auth
154
authorplantname
155
authorplotcode
156
authors
157
basal_diam
158
campus
159
census_date
160
census_no
161
cf
162
cf_aff
163
cfaff
164
clay_percent
165
coll_day
166
coll_firstname
167
coll_lastname
168
coll_month
169
coll_number
170
coll_year
171
collday
172
collectiondate
173
collectno
174
collector1
175
collector2
176
collector3
177
collmonth
178
collyear
179
comment1
180
comment2
181
comment3
182
comment4
183
conceptual_darwin_2003_1_0_BasisOfRecord
184
conceptual_darwin_2003_1_0_BoundingBox
185
conceptual_darwin_2003_1_0_CatalogNumber
186
conceptual_darwin_2003_1_0_Class
187
conceptual_darwin_2003_1_0_CollectionCode
188
conceptual_darwin_2003_1_0_Collector
189
conceptual_darwin_2003_1_0_CollectorNumber
190
conceptual_darwin_2003_1_0_ContinentOcean
191
conceptual_darwin_2003_1_0_CoordinatePrecision
192
conceptual_darwin_2003_1_0_Country
193
conceptual_darwin_2003_1_0_County
194
conceptual_darwin_2003_1_0_DateLastModified
195
conceptual_darwin_2003_1_0_DayCollected
196
conceptual_darwin_2003_1_0_DayIdentified
197
conceptual_darwin_2003_1_0_Family
198
conceptual_darwin_2003_1_0_FieldNumber
199
conceptual_darwin_2003_1_0_Genus
200
conceptual_darwin_2003_1_0_IdentifiedBy
201
conceptual_darwin_2003_1_0_IndividualCount
202
conceptual_darwin_2003_1_0_InstitutionCode
203
conceptual_darwin_2003_1_0_JulianDay
204
conceptual_darwin_2003_1_0_Kingdom
205
conceptual_darwin_2003_1_0_Latitude
206
conceptual_darwin_2003_1_0_Locality
207
conceptual_darwin_2003_1_0_Longitude
208
conceptual_darwin_2003_1_0_MaximumDepth
209
conceptual_darwin_2003_1_0_MaximumElevation
210
conceptual_darwin_2003_1_0_MinimumDepth
211
conceptual_darwin_2003_1_0_MinimumElevation
212
conceptual_darwin_2003_1_0_MonthCollected
213
conceptual_darwin_2003_1_0_MonthIdentified
214
conceptual_darwin_2003_1_0_Notes
215
conceptual_darwin_2003_1_0_Order
216
conceptual_darwin_2003_1_0_Phylum
217
conceptual_darwin_2003_1_0_PreparationType
218
conceptual_darwin_2003_1_0_PreviousCatalogNumber
219
conceptual_darwin_2003_1_0_RelatedCatalogItem
220
conceptual_darwin_2003_1_0_RelationshipType
221
conceptual_darwin_2003_1_0_ScientificName
222
conceptual_darwin_2003_1_0_ScientificNameAuthor
223
conceptual_darwin_2003_1_0_Sex
224
conceptual_darwin_2003_1_0_Species
225
conceptual_darwin_2003_1_0_StateProvince
226
conceptual_darwin_2003_1_0_Subspecies
227
conceptual_darwin_2003_1_0_TimeOfDay
228
conceptual_darwin_2003_1_0_TypeStatus
229
conceptual_darwin_2003_1_0_YearCollected
230
conceptual_darwin_2003_1_0_YearIdentified
231
convertednotes
232
currentTaxonName sec Weakley 2006
233
date_finish
234
date_start
235
det_type
236
dwc_curatorial_CollectorNumber
237
dwc_curatorial_FieldNumber
238
dwc_curatorial_IdentifiedBy
239
dwc_curatorial_IndividualCount
240
dwc_curatorial_TypeStatus
241
dwc_dwcore_AuthorYearOfScientificName
242
dwc_dwcore_BasisOfRecord
243
dwc_dwcore_CatalogNumber
244
dwc_dwcore_Class
245
dwc_dwcore_CollectionCode
246
dwc_dwcore_Collector
247
dwc_dwcore_Continent
248
dwc_dwcore_Country
249
dwc_dwcore_County
250
dwc_dwcore_DateLastModified
251
dwc_dwcore_DayOfYear
252
dwc_dwcore_Family
253
dwc_dwcore_Genus
254
dwc_dwcore_GlobalUniqueIdentifier
255
dwc_dwcore_InfraspecificEpithet
256
dwc_dwcore_InstitutionCode
257
dwc_dwcore_Kingdom
258
dwc_dwcore_Locality
259
dwc_dwcore_MaximumDepthInMeters
260
dwc_dwcore_MaximumElevationInMeters
261
dwc_dwcore_MinimumDepthInMeters
262
dwc_dwcore_MinimumElevationInMeters
263
dwc_dwcore_Order
264
dwc_dwcore_Phylum
265
dwc_dwcore_Remarks
266
dwc_dwcore_ScientificName
267
dwc_dwcore_Sex
268
dwc_dwcore_SpecificEpithet
269
dwc_dwcore_StateProvince
270
dwc_geospatial_DecimalLatitude
271
dwc_geospatial_DecimalLongitude
272
dwc_geospatial_VerbatimLatitude
273
dwc_geospatial_VerbatimLongitude
274
dwc_terms_basisOfRecord
275
dwc_terms_catalogNumber
276
dwc_terms_class
277
dwc_terms_collectionCode
278
dwc_terms_collectionID
279
dwc_terms_continent
280
dwc_terms_coordinateUncertaintyInMeters
281
dwc_terms_country
282
dwc_terms_county
283
dwc_terms_dateIdentified
284
dwc_terms_day
285
dwc_terms_decimalLatitude
286
dwc_terms_decimalLongitude
287
dwc_terms_endDayOfYear
288
dwc_terms_eventTime
289
dwc_terms_family
290
dwc_terms_fieldNumber
291
dwc_terms_genus
292
dwc_terms_identifiedBy
293
dwc_terms_individualCount
294
dwc_terms_infraspecificEpithet
295
dwc_terms_institutionCode
296
dwc_terms_kingdom
297
dwc_terms_locality
298
dwc_terms_maximumDepthInMeters
299
dwc_terms_maximumElevationInMeters
300
dwc_terms_minimumDepthInMeters
301
dwc_terms_minimumElevationInMeters
302
dwc_terms_month
303
dwc_terms_occurrenceRemarks
304
dwc_terms_order
305
dwc_terms_otherCatalogNumbers
306
dwc_terms_phylum
307
dwc_terms_preparations
308
dwc_terms_recordNumber
309
dwc_terms_recordedBy
310
dwc_terms_scientificName
311
dwc_terms_scientificNameAuthorship
312
dwc_terms_sex
313
dwc_terms_specificEpithet
314
dwc_terms_startDayOfYear
315
dwc_terms_stateProvince
316
dwc_terms_typeStatus
317
dwc_terms_verbatimLatitude
318
dwc_terms_verbatimLongitude
319
dwc_terms_year
320
elev_m
321
elev_max_m
322
elev_min_m
323
elevationrange
324
exchangecapacity
325
flower
326
fruit
327
gentry_dbh
328
height_m
329
herbarium
330
holdridge_life_zone
331
ht_first_branch_m
332
http__purl_org_dc_terms_modified
333
individual_code
334
infra_ep_1
335
infra_rank_1
336
infraname
337
infrarank
338
inorout
339
interpretationdate
340
key
341
lat_decimal
342
lat_deg
343
leaves
344
life_zone
345
life_zone_code
346
loanto
347
locality_description
348
locationAccuracy-m
349
locationaccuracy
350
long_decimal
351
long_deg
352
major_geo
353
methodnarrative
354
museumaccessionnumber
355
no_of_individuals
356
obsStartDate
357
obsenddate
358
observation_id
359
obsstartdate
360
organic_percent
361
orig_family
362
orig_species
363
pH acuoso (ISRIC 4–– 1 - 14)
364
parent_id
365
plot_code
366
plot_methodology
367
pol1
368
pol2
369
precip_mm
370
project
371
publicLatitude
372
publicLongitude
373
region|state|province
374
root
375
sand_percent
376
shape
377
sheetno
378
silt_percent
379
soil_C
380
soil_Ca
381
soil_K
382
soil_Mg
383
soil_N
384
soil_Na
385
soil_P
386
soil_acidity
387
soil_base
388
soil_cation_cap
389
soil_conductivity
390
soil_texture
391
soilclay
392
soilorganic
393
soilph
394
soilsand
395
soilsilt
396
soiltexture
397
specific_authority
398
stem_canopy_form
399
stem_canopy_position
400
stem_dbh
401
stem_height_first_branch_m
402
stem_height_m
403
stem_id
404
stem_liana_infestation
405
stem_tag1
406
stem_tag2
407
tag1
408
tag2
409
taxonobservation_id
410
temp_c
411
temp_dbh
412
usdaRank
413
voucher_string
414
x
415
x_position
416
y
417
y_position
1

  
2
"Calcio intercambiable (WSP S-5,10–cmolc/Kg–0.016)",calcium,,
3
"Carbón Orgánico (WSP S-9,10–%–0.06)",carbon,,
4
"Magnesio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",magnesium,,
5
"Materia Orgánica (WSP S-9,10–%–0.1)",organic,,
6
"Potasio intercambiable (WSP S-5,10–cmolc/Kg–0.0053)",potassium,,
7
"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",sodium,,
8
%cover,coverPercent,,
9
-----
10
-----"
11
1haPlotCode,plotName,,
12
Accession Number,occurrenceID,,
13
Accuracy,coordinateUncertaintyInMeters,,
14
Acidez intercambiable (ISRIC 11–cmolc/Kg–0.05),acidity,,
15
Addcoll,recordedBy,/_join/2,
16
AgeClass,lifeStage,,
17
Altitude,elevationInMeters,,"Assuming units are m based on the range of values [1] and the region the data is from (Madidi National Park) [2].
18
Arcilla (DIN 18 123–%–1),clay,,
19
Area,plotArea_ha,,"""0.1 ha transects"" (""Madidi Transects"" description in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/BIEN2.datasources.xlsx>)"
20
Arena (DIN 18 123–%–2.5),sand,,
21
AuthorOfScientificName,scientificNameAuthorship,,
22
Autor (revised),scientificNameAuthorship,,
23
Barcode,catalogNumber,,
24
CIC (ISRIC 11–cmolc/Kg–0.05),cationExchangeCapacity,,
25
CatalogNO,catalogNumber,,
26
CatalogNumberNumeric,catalogNumber,/_alt/1,
27
Colldd,dayCollected,,
28
Collect Date,dateCollected,,
29
CollectionCD,collectionCode,,
30
Collectors,recordedBy,,
31
Collmm,monthCollected,,
32
Collyy,yearCollected,,
33
Conductividad electrica (ASPT 6–µS/cm– 1 - 10000),conductivity,,
34
DateInfo,UNUSED,,
35
DetType,voucherType,,"Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
36
Detby,identifiedBy,,
37
Determined by,identifiedBy,,
38
Detyy,yearIdentified,,
39
Diameter,diameterBreastHeight_m,,
40
Direction,slopeAspect,/_alt/1,Part files provide either this field or Orientación
41
Ecology,habitat,,
42
Elev,elevationInMeters,,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.
43
Expedition name,projectName,,Consistent (globally unique) between PPM and PT data
44
Expedition number,projectID,,Consistent (globally unique) between PPM and PT data
45
Expedition,projectName,,
46
FROM ""Madidi"".""Plot""
47
FROM ""SALVIAS"".organisms
48
FROM ""SALVIAS-CSV"".organisms
49
Family (revised),family,,
50
Field family,verbatimFamily,,
51
Field name,verbatimGenus,,Often = Genera
52
First evaluation,eventDate,,
53
Format,preparations,,
54
Full Taxon Name,scientificName,,
55
Fósforo disponible (ISRIC 14-2–mg/Kg–1.5),phosphorus,,
56
GBIFFamilyOriginal,verbatimFamily,,
57
GBIFGenusOriginal,verbatimGenus,,
58
GROUP BY ""Altitude""::real , ""Locality""
59
GROUP BY ""Minimum altitude"" , ""Locality""
60
GROUP BY ""PLOT_ID"", subplot
61
GROUP BY ""PlotID"", ""Line""
62
Gazetteer,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/1",
63
GenBankNum,associatedSequences,"/_label[label=""GenBank""]/value",
64
Genera,genus,,
65
GeorefMethod,georeferenceProtocol,,
66
HAVING count(DISTINCT census_date) > 1
67
HorizontalDatum,UNUSED,,
68
IdentificationModifier,identificationQualifier,,
69
Ind,recordNumber,,"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."
70
Index collector,recordedBy,,
71
InfraSpecificLevel,UNUSED,,
72
InstitutionCD,institutionCode,,
73
Inventory code,locationID,,
74
Inventory name,plotName,,
75
LastDateModified,dcterms:modified,,
76
Lat (-=S),verbatimLatitude,"/_replace:[""\?$""=]/value",
77
Lat,decimalLatitude,,
78
LatDec,decimalLatitude,,
79
LatLongComments,georeferenceRemarks,,
80
LatestDateCollected,dateCollected,,
81
Latitude (DMS),verbatimLatitude,,
82
Liana presence,lianaInfestation,,
83
Limo (DIN 18 123–%–1),silt,,
84
Line,subplot,,
85
Locality description,communityName,,Often begins with the text in Vegetation type
86
Locality_Description,locality,,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
87
Locnotes,verbatimLocality,/_join/2,
88
Long (-=W),verbatimLongitude,"/_replace:[""\?$""=]/value",
89
Long,decimalLongitude,,
90
LongDec,decimalLongitude,,
91
Longitude (DMS),verbatimLongitude,,
92
MajorGeo,continent,,
93
MaximumElevationInMeter,maximumElevationInMeters,,
94
MeasDay,dayCollected,,
95
MeasMon,monthCollected,,
96
MeasYear,yearCollected,,
97
MeasureID,individualID,,
98
Method,samplingProtocol,,
99
Minimum altitude,verbatimElevation_m,,"This is a range [1], not a minimum. Assuming units are m based on the range of values [1] and the region the data is from (Madidi National Park) [2].
100
MinimumElevationInMeter,minimumElevationInMeters,,
101
Newgazett,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/2",Only used in 1 row
102
Nitrógeno total (ISRIC 6–%–0.0014),nitrogen,,
103
NoInd,individualCount,,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
104
NoInd,stemCount,,
105
Number of subplot,subplot,,
106
Number,recordNumber,,
107
OBSERVATION_ID,individualID,,"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."
108
ORDER BY ""Altitude""::real DESC
109
Observaciones,plotNotes,,
110
ObservationDate,eventDate,,
111
Observations,fieldNotes,,
112
Orientación/exposicion,slopeAspect,/_alt/2,Part files provide either this field or Direction
113
OrigFamily,verbatimFamily,,Brad: OMIT
114
OrigGenus,verbatimGenus,,
115
OrigSpecies,verbatimSpecificEpithet,,Brad: OMIT
116
OriginalCoordinateSystem,verbatimSRS,,
117
Phenology,reproductiveCondition,,
118
PlantFungusDescription,fieldNotes,"/_join/2/_label[label=""plant fungus""]/value",
119
PlotCD,locationID,,
120
PlotCode,plotName,,
121
PlotMethod,samplingProtocol,,
122
PlotObsID,individualID,,
123
PlotObsID,individualID,,"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."
124
PolDiv1,stateProvince,,Brad: No; pol1=stateProvince
125
Precip,precipitation,,
126
Prefix,UNUSED,,
127
Qualifier,identificationQualifier,,
128
RelatedCatalogedItems,relatedResourceID,/_alt/2,Used only when OtherCatalogNumbers is NULL
129
SELECT ""Altitude""::real, ""Locality""
130
SELECT ""Minimum altitude"", ""Locality""
131
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
132
SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count
133
SELECT count(*) FROM ""SpeciesLink"".specimens
134
SciName,scientificName,,
135
ScientificNameOriginal,verbatimScientificName,,
136
SeriesName,collectionCode,,
137
SiteCode,plotName,,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
138
SiteName,projectName,,
139
SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)"
140
Slope,slopeGradient,,
141
SourceVoucher,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
142
Specie+autor,scientificNameWithAuthorship,,
143
Species and morphotypes,scientificName,,"Contains less than ""Specie+autor"""
144
SpeciesAuthority,scientificNameAuthorship,,
145
Specimen,catalogNumber,,
146
StemID,authorStemCode,,
147
Substrate,locality,"/_join/2/_label[label=""substrate""]/value",
148
Suffix,UNUSED,,
149
Tag number,tag,,
150
Temp,temperature,,
151
Textural class,texture,,
152
TimeCollected,eventTime,,
153
Tissues,UNUSED,,
154
Topographical situation,landform,,
155
Total height,height,,
156
Tree number,recordNumber,,
157
TreeNumber,tag,,
158
TreeTag,tag,,
159
Trunk,authorStemCode,,
160
Typology,typeStatus,,
161
UniqueNYInternalRecordNumber,occurrenceID,,
162
Vegetation type,communityID,,
163
Vegetation,locality,"/_join/3/_label[label=""vegetation""]/value",
164
VerbatimCollectingDate,dateCollected,/_alt/0,
165
WHERE ""Altitude"" IS NOT NULL AND ""Altitude"" != ' 1430'
166
WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL
167
WHERE ""Minimum altitude"" IS NOT NULL
168
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
169
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
170
X_1haPlot,organismX,,
171
Y_1haPlot,organismY,,
172
[1] Using the following query:
173
[2] This map shows both flat and mountainous regions: <https://maps.google.com/maps/ms?ie=UTF8&hl=en&t=h&msa=0&msid=103363035880599665829.00047e9cf84b87448387d&ll=-13.96448,-68.380065&spn=3.730927,4.669189&z=7>"
174
accession,occurrenceID,,
175
accession_number,occurrenceID,,
176
acronym,collectionCode,,
177
area,plotArea_m2,,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)"
178
area|country|territory,country,,
179
auth,scientificNameAuthorship,,Brad: This is the author of the scientificName.
180
authorplantname,verbatimScientificName,,
181
authorplotcode,plotName,,
182
authors,scientificNameAuthorship,,
183
basal_diam,basalDiameter,,
184
campus,fieldNotes,"/_join/5/_label[label=""campus""]/value",
185
census_date,eventDate,,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
186
census_no,censusNumber,,"Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
187
cf,identificationQualifier,,
188
cf_aff,identificationQualifier,,"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."
189
cfaff,identificationQualifier,,"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."
190
clay_percent,clay,"/_units:[default=""%"",to=]/value",
191
coll_day,dayCollected,,
192
coll_firstname,recordedBy.givenName,,Brad: See comment above
193
coll_lastname,recordedBy.surName,,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
194
coll_month,monthCollected,,
195
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
196
coll_year,yearCollected,,
197
collday,dayCollected,,
198
collectiondate,dateCollected,,
199
collectno,recordNumber,,
200
collector1,recordedBy,/_join/2,
201
collector2,recordedBy,/_join/3,
202
collector3,recordedBy,/_join/4,
203
collmonth,monthCollected,,
204
collyear,yearCollected,,
205
comment1,fieldNotes,/_join/1,
206
comment2,fieldNotes,/_join/2,
207
comment3,fieldNotes,/_join/3,
208
comment4,fieldNotes,/_join/4,
209
conceptual_darwin_2003_1_0_BasisOfRecord,basisOfRecord,,
210
conceptual_darwin_2003_1_0_BoundingBox,footprintWKT,,
211
conceptual_darwin_2003_1_0_CatalogNumber,catalogNumber,,
212
conceptual_darwin_2003_1_0_Class,class,,
213
conceptual_darwin_2003_1_0_CollectionCode,collectionCode,,
214
conceptual_darwin_2003_1_0_Collector,recordedBy,,
215
conceptual_darwin_2003_1_0_CollectorNumber,recordNumber,/_alt/3,
216
conceptual_darwin_2003_1_0_ContinentOcean,continent,,
217
conceptual_darwin_2003_1_0_CoordinatePrecision,coordinatePrecision,,
218
conceptual_darwin_2003_1_0_Country,country,,
219
conceptual_darwin_2003_1_0_County,county,,
220
conceptual_darwin_2003_1_0_DateLastModified,dcterms:modified,,
221
conceptual_darwin_2003_1_0_DayCollected,dayCollected,,
222
conceptual_darwin_2003_1_0_DayIdentified,dayIdentified,,
223
conceptual_darwin_2003_1_0_Family,family,,
224
conceptual_darwin_2003_1_0_FieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
225
conceptual_darwin_2003_1_0_Genus,genus,,
226
conceptual_darwin_2003_1_0_IdentifiedBy,identifiedBy,,
227
conceptual_darwin_2003_1_0_IndividualCount,individualCount,,
228
conceptual_darwin_2003_1_0_InstitutionCode,institutionCode,,
229
conceptual_darwin_2003_1_0_JulianDay,day,/_alt/1,
230
conceptual_darwin_2003_1_0_Kingdom,kingdom,,
231
conceptual_darwin_2003_1_0_Latitude,verbatimLatitude,,
232
conceptual_darwin_2003_1_0_Locality,locality,,
233
conceptual_darwin_2003_1_0_Longitude,verbatimLongitude,,
234
conceptual_darwin_2003_1_0_MaximumDepth,maximumDepthInMeters,,
235
conceptual_darwin_2003_1_0_MaximumElevation,maximumElevationInMeters,,
236
conceptual_darwin_2003_1_0_MinimumDepth,minimumDepthInMeters,,
237
conceptual_darwin_2003_1_0_MinimumElevation,minimumElevationInMeters,,
238
conceptual_darwin_2003_1_0_MonthCollected,monthCollected,,
239
conceptual_darwin_2003_1_0_MonthIdentified,monthIdentified,,
240
conceptual_darwin_2003_1_0_Notes,fieldNotes,,
241
conceptual_darwin_2003_1_0_Order,order,,
242
conceptual_darwin_2003_1_0_Phylum,phylum,,
243
conceptual_darwin_2003_1_0_PreparationType,preparations,,
244
conceptual_darwin_2003_1_0_PreviousCatalogNumber,otherCatalogNumbers,,
245
conceptual_darwin_2003_1_0_RelatedCatalogItem,relatedResourceID,,
246
conceptual_darwin_2003_1_0_RelationshipType,relationshipOfResource,,
247
conceptual_darwin_2003_1_0_ScientificName,scientificName,,
248
conceptual_darwin_2003_1_0_ScientificNameAuthor,scientificNameAuthorship,/_alt/2,
249
conceptual_darwin_2003_1_0_Sex,sex,,
250
conceptual_darwin_2003_1_0_Species,specificEpithet,,
251
conceptual_darwin_2003_1_0_StateProvince,stateProvince,,
252
conceptual_darwin_2003_1_0_Subspecies,subspecies,,
253
conceptual_darwin_2003_1_0_TimeOfDay,eventTime,,
254
conceptual_darwin_2003_1_0_TypeStatus,typeStatus,,
255
conceptual_darwin_2003_1_0_YearCollected,yearCollected,,
256
conceptual_darwin_2003_1_0_YearIdentified,yearIdentified,,
257
convertednotes,fieldNotes,,
258
currentTaxonName sec Weakley 2006,scientificName,,
259
darwin:BasisOfRecord,basisOfRecord,,
260
darwin:CatalogNumber,catalogNumber,,
261
darwin:Class,class,,
262
darwin:CollectionCode,collectionCode,,
263
darwin:Collector,recordedBy,,
264
darwin:CollectorNumber,recordNumber,,
265
darwin:ContinentOcean,continent,,
266
darwin:CoordinatePrecision,coordinatePrecision,,
267
darwin:Country,country,,
268
darwin:County,county,,
269
darwin:DateLastModified,dcterms:modified,,
270
darwin:DayCollected,dayCollected,,
271
darwin:DayIdentified,dayIdentified,,
272
darwin:Family,family,,
273
darwin:FieldNumber,UNUSED,,"`grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines. This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber)."
274
darwin:Genus,genus,,
275
darwin:IdentifiedBy,identifiedBy,,
276
darwin:IndividualCount,individualCount,,
277
darwin:InstitutionCode,institutionCode,,
278
darwin:JulianDay,day,,
279
darwin:Kingdom,kingdom,,
280
darwin:Latitude,verbatimLatitude,,
281
darwin:Locality,locality,,
282
darwin:Longitude,verbatimLongitude,,
283
darwin:MaximumDepth,maximumDepthInMeters,,
284
darwin:MaximumElevation,maximumElevationInMeters,,
285
darwin:MinimumDepth,minimumDepthInMeters,,
286
darwin:MinimumElevation,minimumElevationInMeters,,
287
darwin:MonthCollected,monthCollected,,
288
darwin:MonthIdentified,monthIdentified,,
289
darwin:Notes,fieldNotes,,
290
darwin:Order,order,,
291
darwin:Phylum,phylum,,
292
darwin:PreparationType,preparations,,
293
darwin:PreviousCatalogNumber,otherCatalogNumbers,,
294
darwin:RelatedCatalogItem,relatedResourceID,,
295
darwin:RelationshipType,relationshipOfResource,,
296
darwin:ScientificName,scientificName,,
297
darwin:ScientificNameAuthor,scientificNameAuthorship,,
298
darwin:Sex,sex,,
299
darwin:Species,specificEpithet,,
300
darwin:StateProvince,stateProvince,,
301
darwin:Subspecies,subspecies,,
302
darwin:TimeOfDay,eventTime,,
303
darwin:TypeStatus,typeStatus,,
304
darwin:YearCollected,yearCollected,,
305
darwin:YearIdentified,yearIdentified,,
306
date_finish,endDate,,
307
date_start,startDate,,
308
det_type,voucherType,,"Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
309
dwc_curatorial_CollectorNumber,recordNumber,/_alt/3,
310
dwc_curatorial_FieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
311
dwc_curatorial_IdentifiedBy,identifiedBy,,
312
dwc_curatorial_IndividualCount,individualCount,,
313
dwc_curatorial_TypeStatus,typeStatus,,
314
dwc_dwcore_AuthorYearOfScientificName,scientificNameAuthorship,/_alt/3,
315
dwc_dwcore_BasisOfRecord,basisOfRecord,,
316
dwc_dwcore_CatalogNumber,catalogNumber,,
317
dwc_dwcore_Class,class,,
318
dwc_dwcore_CollectionCode,collectionCode,,
319
dwc_dwcore_Collector,recordedBy,,
320
dwc_dwcore_Continent,continent,,
321
dwc_dwcore_Country,country,,
322
dwc_dwcore_County,county,,
323
dwc_dwcore_DateLastModified,dcterms:modified,,
324
dwc_dwcore_DayOfYear,day,/_alt/2,
325
dwc_dwcore_Family,family,,
326
dwc_dwcore_Genus,genus,,
327
dwc_dwcore_GlobalUniqueIdentifier,occurrenceID,,
328
dwc_dwcore_InfraspecificEpithet,infraspecificEpithet,,
329
dwc_dwcore_InstitutionCode,institutionCode,,
330
dwc_dwcore_Kingdom,kingdom,,
331
dwc_dwcore_Locality,locality,,
332
dwc_dwcore_MaximumDepthInMeters,maximumDepthInMeters,,
333
dwc_dwcore_MaximumElevationInMeters,maximumElevationInMeters,,
334
dwc_dwcore_MinimumDepthInMeters,minimumDepthInMeters,,
335
dwc_dwcore_MinimumElevationInMeters,minimumElevationInMeters,,
336
dwc_dwcore_Order,order,,
337
dwc_dwcore_Phylum,phylum,,
338
dwc_dwcore_Remarks,taxonRemarks,,
339
dwc_dwcore_ScientificName,scientificName,,
340
dwc_dwcore_Sex,sex,,
341
dwc_dwcore_SpecificEpithet,specificEpithet,,
342
dwc_dwcore_StateProvince,stateProvince,,
343
dwc_geospatial_DecimalLatitude,decimalLatitude,,
344
dwc_geospatial_DecimalLongitude,decimalLongitude,,
345
dwc_geospatial_VerbatimLatitude,verbatimLatitude,,
346
dwc_geospatial_VerbatimLongitude,verbatimLongitude,,
347
dwc_terms_basisOfRecord,basisOfRecord,,
348
dwc_terms_catalogNumber,catalogNumber,,
349
dwc_terms_class,class,,
350
dwc_terms_collectionCode,collectionCode,,
351
dwc_terms_collectionID,collectionID,,
352
dwc_terms_continent,continent,,
353
dwc_terms_coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,
354
dwc_terms_country,country,,
355
dwc_terms_county,county,,
356
dwc_terms_dateIdentified,dateIdentified,,
357
dwc_terms_day,day,,
358
dwc_terms_decimalLatitude,decimalLatitude,,
359
dwc_terms_decimalLongitude,decimalLongitude,,
360
dwc_terms_endDayOfYear,endDayOfYear,,
361
dwc_terms_eventTime,eventTime,,
362
dwc_terms_family,family,,
363
dwc_terms_fieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
364
dwc_terms_genus,genus,,
365
dwc_terms_identifiedBy,identifiedBy,,
366
dwc_terms_individualCount,individualCount,,
367
dwc_terms_infraspecificEpithet,infraspecificEpithet,,
368
dwc_terms_institutionCode,institutionCode,,
369
dwc_terms_kingdom,kingdom,,
370
dwc_terms_locality,locality,,
371
dwc_terms_maximumDepthInMeters,maximumDepthInMeters,,
372
dwc_terms_maximumElevationInMeters,maximumElevationInMeters,,
373
dwc_terms_minimumDepthInMeters,minimumDepthInMeters,,
374
dwc_terms_minimumElevationInMeters,minimumElevationInMeters,,
375
dwc_terms_month,month,,
376
dwc_terms_occurrenceRemarks,occurrenceRemarks,,
377
dwc_terms_order,order,,
378
dwc_terms_otherCatalogNumbers,otherCatalogNumbers,,
379
dwc_terms_phylum,phylum,,
380
dwc_terms_preparations,preparations,,
381
dwc_terms_recordNumber,recordNumber,/_alt/1,
382
dwc_terms_recordedBy,recordedBy,,
383
dwc_terms_scientificName,scientificName,,
384
dwc_terms_scientificNameAuthorship,scientificNameAuthorship,/_alt/1,
385
dwc_terms_sex,sex,,
386
dwc_terms_specificEpithet,specificEpithet,,
387
dwc_terms_startDayOfYear,startDayOfYear,,
388
dwc_terms_stateProvince,stateProvince,,
389
dwc_terms_typeStatus,typeStatus,,
390
dwc_terms_verbatimLatitude,verbatimLatitude,,
391
dwc_terms_verbatimLongitude,verbatimLongitude,,
392
dwc_terms_year,year,,
393
elev_m,elevationInMeters,,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.
394
elev_max_m,maximumElevationInMeters,,
395
elev_min_m,minimumElevationInMeters,,
396
elevationrange,UNUSED,,
397
exchangecapacity,cationExchangeCapacity,,
398
flower,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
399
fruit,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
400
gentry_dbh,diameterBreastHeightGentry,,
401
height_m,height,,
402
height_m,height,/_alt/2,
403
herbarium,institutionCode,,
404
holdridge_life_zone,communityID,,
405
ht_first_branch_m,heightFirstBranch,,
406
http__purl_org_dc_terms_modified,dcterms:modified,,
407
individual_code,recordNumber,,"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."
408
infra_ep_1,infraspecificEpithet,,
409
infra_rank_1,taxonRank,,
410
infraname,infraspecificEpithet,,
411
infrarank,taxonRank,/_alt/2,
412
inorout,fieldNotes,"/_join/7/_label[label=""in or out""]/value",
413
interpretationdate,dateIdentified,,
414
key,OMIT,,UniqueNYInternalRecordNumber is a better pkey
415
lat_decimal,decimalLatitude,,
416
lat_deg,verbatimLatitude,,
417
leaves,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
418
life_zone,communityName,,
419
life_zone_code,communityID,,
420
life_zone_code,communityName,,
421
loanto,fieldNotes,"/_join/6/_label[label=""loaned to""]/value",
422
locality_description,locality,,"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"
423
locationAccuracy-m,coordinateUncertaintyInMeters,,
424
locationaccuracy,coordinateUncertaintyInMeters,,
425
long_decimal,decimalLongitude,,
426
long_deg,verbatimLongitude,,
427
major_geo,continent,,
428
methodnarrative,samplingProtocol,,
429
museumaccessionnumber,catalogNumber,,
430
no_of_individuals,individualCount,,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
431
obsStartDate,startDate,,
432
obsenddate,endDate,,
433
observation_id,eventID,,
434
obsstartdate,startDate,,
435
organic_percent,organic,"/_units:[default=""%"",to=]/value",
436
orig_family,verbatimFamily,,Brad: OMIT
437
orig_species,verbatimSpecificEpithet,,Brad: OMIT
438
pH acuoso (ISRIC 4–– 1 - 14),ph,,
439
parent_id,parentLocationID,,
440
plot_code,plotName,,
441
plot_code,plotName,,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
442
plot_methodology,samplingProtocol,,
443
pol1,stateProvince,,Brad: No; pol1=stateProvince
444
pol2,county,,Brad: No pol2=countyParish
445
precip_mm,precipitation,,
446
project,projectName,,
447
publicLatitude,decimalLatitude,,
448
publicLongitude,decimalLongitude,,
449
region|state|province,stateProvince,,
450
root,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
451
sand_percent,sand,"/_units:[default=""%"",to=]/value",
452
shape,footprintWKT,,
453
sheetno,associatedMedia,,?
454
silt_percent,silt,"/_units:[default=""%"",to=]/value",
455
soil_C,carbon,"/_units:[default=""%"",to=]/value",
456
soil_Ca,calcium,"/_units:[default=""%"",to=]/value",
457
soil_K,potassium,"/_units:[default=""%"",to=]/value",
458
soil_Mg,magnesium,"/_units:[default=""%"",to=]/value",
459
soil_N,nitrogen,"/_units:[default=""%"",to=]/value",
460
soil_Na,sodium,"/_units:[default=""%"",to=]/value",
461
soil_P,phosphorus,"/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
462
soil_acidity,acidity,"/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
463
soil_base,baseSaturation,"/_units:[default=""%"",to=]/value",
464
soil_cation_cap,cationExchangeCapacity,,
465
soil_conductivity,conductivity,,
466
soil_texture,texture,"/_units:[default=""%"",to=]/value",
467
soil_texture,texture,,
468
soilclay,clay,,
469
soilorganic,organic,,
470
soilph,ph,,
471
soilsand,sand,,
472
soilsilt,silt,,
473
soiltexture,texture,,
474
specific_authority,scientificNameAuthorship,,Brad: This is the author of the scientificName.
475
stem_canopy_form,canopyForm,,
476
stem_canopy_position,canopyPosition,,
477
stem_dbh,diameterBreastHeight_m,,
478
stem_height_first_branch_m,heightFirstBranch,,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
479
stem_height_m,height,,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
480
stem_height_m,height,/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
481
stem_id,stemID,,
482
stem_liana_infestation,lianaInfestation,,
483
stem_tag1,tag,/_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."
484
stem_tag1,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."
485
stem_tag2,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."
486
stem_tag2,tag,/_alt/1/_alt/1,The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above
487
tag1,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."
488
tag1,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."
489
tag2,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."
490
tag2,tag,/_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."
491
taxonobservation_id,taxonOccurrenceID,,
492
temp_c,temperature,,
493
temp_dbh,diameterBreastHeight_m,,
494
usdaRank,taxonRank,/_alt/1,
495
voucher_string,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
496
x,organismX,,
497
x_position,organismX,,"Brad: These are important, fundamental values of many tree plots"
498
y,organismY,,
499
y_position,organismY,,Brad: See comment above for x_position

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