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Revision 4231

mappings/VegCore-VegBIEN.csv: locationID, plotName: Redirect to /location/parent_id/location/* if subplot field is specified

View differences:

inputs/Madidi/0.plots/VegBIEN.csv
1 1
Madidi,VegBIEN:,Comments
2 2
Area,/location/area,
3
Inventory name,/location/authorlocationcode/_alt/1,
3
Inventory name,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
4 4
Altitude,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
5 5
Minimum altitude,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
6 6
Minimum altitude,"/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
33 33
Textural class,/location/locationevent/soilobs/texture,
34 34
Locality,/location/locationnarrative/_merge/1,
35 35
Observaciones,/location/notespublic,
36
Inventory name,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
37
Inventory code,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
36 38
Direction,/location/slopeaspect/_compass/value/_alt/1,Part files provide either this field or Direction
37 39
OrientaciĆ³n/exposicion,/location/slopeaspect/_compass/value/_alt/2,Part files provide either this field or OrientaciĆ³n
38 40
Slope,/location/slopegradient,
39
Inventory code,/location/sourceaccessioncode,
41
Inventory code,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
inputs/SALVIAS-CSV/0.plots/VegBIEN.csv
1 1
SALVIAS-CSV,VegBIEN:,Comments
2 2
plot_area_ha,/location/area,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
3
plot_code,/location/authorlocationcode/_alt/1,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
3
plot_code,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
4 4
elev_m,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",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.
5 5
elev_max_m,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
6 6
elev_min_m,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
39 39
soil_texture,/location/locationevent/soilobs/texture,
40 40
temp_c,/location/locationevent/temperature,
41 41
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"
42
plot_code,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
43
PLOT_ID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
42 44
slope_aspect,/location/slopeaspect/_compass/value,
43 45
slope_gradient,/location/slopegradient,
44
PLOT_ID,/location/sourceaccessioncode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
46
PLOT_ID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
inputs/SALVIAS-CSV/1.organisms/VegBIEN.csv
1 1
SALVIAS-CSV,VegBIEN:,Comments
2
subplot,/location/authorlocationcode/_alt/1,
2
subplot,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
3 3
det_type,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","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."
4 4
coll_number,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
5 5
voucher_string,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
......
54 54
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
55 55
voucher_string,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
56 56
plot_code,/location/parent_id/location/authorlocationcode,
57
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
57 58
PLOT_ID,/location/parent_id/location/sourceaccessioncode,
inputs/SALVIAS/0.plots/VegBIEN.csv
1 1
SALVIAS,VegBIEN:,Comments
2 2
plot_area_ha,/location/area,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
3
SiteCode,/location/authorlocationcode/_alt/1,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
3
SiteCode,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
4 4
Elev,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",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.
5 5
elev_max_m,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
6 6
elev_min_m,"/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace:[""\bca\.?""=]/value",
......
39 39
soil_texture,"/location/locationevent/soilobs/texture/_units:[default=""%"",to=]/value",
40 40
Temp,/location/locationevent/temperature,
41 41
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"
42
SiteCode,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
43
PlotID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
42 44
slope_aspect,/location/slopeaspect/_compass/value,
43 45
slope_gradient,/location/slopegradient,
44
PlotID,/location/sourceaccessioncode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
46
PlotID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
inputs/SALVIAS/1.organisms/VegBIEN.csv
1 1
SALVIAS,VegBIEN:,Comments
2
Line,/location/authorlocationcode/_alt/1,
2
Line,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
3 3
DetType,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","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."
4 4
coll_number,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string
5 5
SourceVoucher,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
......
58 58
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string
59 59
SourceVoucher,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
60 60
PlotCode,/location/parent_id/location/authorlocationcode,
61
Line,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
61 62
PlotID,/location/parent_id/location/sourceaccessioncode,
mappings/VegCore-VegBIEN.csv
1 1
VegCore[Veg+],VegBIEN:,Comments
2 2
plotArea,/location/area,
3
plotName,/location/authorlocationcode/_alt/1,
3
subplot,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/cond",
4
plotName,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
4 5
fieldNumber,/location/authorlocationcode/_alt/2,
5 6
occurrenceID,/location/authorlocationcode/_alt/3,
6 7
institutionCode,/location/authorlocationcode/_alt/4/_merge/1,
......
133 134
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?"
134 135
plotNotes,/location/notespublic,
135 136
parentPlotName,/location/parent_id/location/authorlocationcode,
137
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
138
plotName,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
136 139
parentLocationID,/location/parent_id/location/sourceaccessioncode,
140
subplot,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
141
locationID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
137 142
slopeAspect,/location/slopeaspect/_compass/value,
138 143
slopeGradient,/location/slopegradient,
139
locationID,/location/sourceaccessioncode,
144
subplot,"/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
145
locationID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
140 146
acceptedNameUsage,,
141 147
acceptedNameUsageID,,
142 148
associatedMedia,,
mappings/Veg+-VegBIEN.csv
1 1
Veg+,VegBIEN:,Comments
2 2
PlotArea,/location/area,
3 3
plotArea,/location/area,
4
PlotName,/location/authorlocationcode/_alt/1,
5
plotName,/location/authorlocationcode/_alt/1,
4
Subplot,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/cond",
5
subplot,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/cond",
6
PlotName,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
7
plotName,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
6 8
AuthorObsCode,/location/authorlocationcode/_alt/2,
7 9
FieldNumber,/location/authorlocationcode/_alt/2,
8 10
authorObsCode,/location/authorlocationcode/_alt/2,
......
381 383
plotNotes,/location/notespublic,
382 384
ParentPlotName,/location/parent_id/location/authorlocationcode,
383 385
parentPlotName,/location/parent_id/location/authorlocationcode,
386
Subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
387
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
388
PlotName,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
389
plotName,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
384 390
ParentLocationID,/location/parent_id/location/sourceaccessioncode,
385 391
ParentPlotID,/location/parent_id/location/sourceaccessioncode,
386 392
parentLocationID,/location/parent_id/location/sourceaccessioncode,
387 393
parentPlotID,/location/parent_id/location/sourceaccessioncode,
394
Subplot,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
395
subplot,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
396
LocationID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
397
PlotID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
398
locationID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
399
plotID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
388 400
SlopeAspect,/location/slopeaspect/_compass/value,
389 401
slopeAspect,/location/slopeaspect/_compass/value,
390 402
SlopeGradient,/location/slopegradient,
391 403
slopeGradient,/location/slopegradient,
392
LocationID,/location/sourceaccessioncode,
393
PlotID,/location/sourceaccessioncode,
394
locationID,/location/sourceaccessioncode,
395
plotID,/location/sourceaccessioncode,
404
Subplot,"/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
405
subplot,"/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
406
LocationID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
407
PlotID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
408
locationID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
409
plotID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
mappings/Veg+.cs-VegBIEN.csv
1 1
Veg+,VegBIEN:,Comments
2 2
plotArea,/location/area,
3
plotName,/location/authorlocationcode/_alt/1,
3
subplot,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/cond",
4
plotName,"/location/authorlocationcode/_alt/1/_if[@name=""if subplot""]/else",
4 5
authorObsCode,/location/authorlocationcode/_alt/2,
5 6
fieldNumber,/location/authorlocationcode/_alt/2,
6 7
globalUniqueIdentifier,/location/authorlocationcode/_alt/3,
......
190 191
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?"
191 192
plotNotes,/location/notespublic,
192 193
parentPlotName,/location/parent_id/location/authorlocationcode,
194
subplot,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/cond",
195
plotName,"/location/parent_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
193 196
parentLocationID,/location/parent_id/location/sourceaccessioncode,
194 197
parentPlotID,/location/parent_id/location/sourceaccessioncode,
198
subplot,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
199
locationID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
200
plotID,"/location/parent_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then",
195 201
slopeAspect,/location/slopeaspect/_compass/value,
196 202
slopeGradient,/location/slopegradient,
197
locationID,/location/sourceaccessioncode,
198
plotID,/location/sourceaccessioncode,
203
subplot,"/location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
204
locationID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
205
plotID,"/location/sourceaccessioncode/_if[@name=""if subplot""]/else",
mappings/for_review/VegCore-VegBIEN.csv
1 1
VegCore[Veg+],VegBIEN:,Comments
2 2
plotArea,//location/area,
3
plotName,//location/authorlocationcode,
3
subplot,"//location/authorlocationcode/_if[@name=""if subplot""]/cond",
4
plotName,"//location/authorlocationcode/_if[@name=""if subplot""]/else",
4 5
fieldNumber,//location/authorlocationcode,
5 6
occurrenceID,//location/authorlocationcode,
6 7
institutionCode,//location/authorlocationcode,
......
133 134
habitat,"//location/locationnarrative/_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?"
134 135
plotNotes,//location/notespublic,
135 136
parentPlotName,//location/authorlocationcode,
137
subplot,"//location/authorlocationcode/_if[@name=""if subplot""]/cond",
138
plotName,"//location/authorlocationcode/_if[@name=""if subplot""]/then",
136 139
parentLocationID,//location/sourceaccessioncode,
140
subplot,"//location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
141
locationID,"//location/sourceaccessioncode/_if[@name=""if subplot""]/then",
137 142
slopeAspect,//location/slopeaspect,
138 143
slopeGradient,//location/slopegradient,
139
locationID,//location/sourceaccessioncode,
144
subplot,"//location/sourceaccessioncode/_if[@name=""if subplot""]/cond",
145
locationID,"//location/sourceaccessioncode/_if[@name=""if subplot""]/else",
140 146
acceptedNameUsage,,
141 147
acceptedNameUsageID,,
142 148
associatedMedia,,

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