Revision 4832
Added by Aaron Marcuse-Kubitza about 12 years ago
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 103 | 103 |
tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| 104 | 104 |
organismX,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
| 105 | 105 |
organismY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 106 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
|
| 106 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 107 |
locationID,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 108 |
plotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 109 |
tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 107 | 110 |
verbatimScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
| 108 | 111 |
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
| 109 | 112 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/3, |
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| 18 | 18 |
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
| 19 | 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 20 |
1haPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 21 |
TreeNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 20 | 22 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 21 | 23 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 22 | 24 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| inputs/TEAM/VL/test.xml.ref | ||
|---|---|---|
| 39 | 39 |
</stemobservation> |
| 40 | 40 |
</plantobservation> |
| 41 | 41 |
</aggregateoccurrence> |
| 42 |
<authortaxoncode>$TreeNumber</authortaxoncode> |
|
| 42 | 43 |
<taxondetermination> |
| 43 | 44 |
<taxonpath_id> |
| 44 | 45 |
<taxonpath> |
| ... | ... | |
| 55 | 56 |
</path> |
| 56 | 57 |
</_simplifyPath> |
| 57 | 58 |
</VegBIEN> |
| 58 |
Inserted 16 new rows into database |
|
| 59 |
Inserted 20 new rows into database |
|
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| 18 | 18 |
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
| 19 | 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 20 |
1haPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 21 |
TreeNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 20 | 22 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 21 | 23 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 22 | 24 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| inputs/TEAM/VT/test.xml.ref | ||
|---|---|---|
| 39 | 39 |
</stemobservation> |
| 40 | 40 |
</plantobservation> |
| 41 | 41 |
</aggregateoccurrence> |
| 42 |
<authortaxoncode>$TreeNumber</authortaxoncode> |
|
| 42 | 43 |
<taxondetermination> |
| 43 | 44 |
<taxonpath_id> |
| 44 | 45 |
<taxonpath> |
| ... | ... | |
| 55 | 56 |
</path> |
| 56 | 57 |
</_simplifyPath> |
| 57 | 58 |
</VegBIEN> |
| 58 |
Inserted 16 new rows into database |
|
| 59 |
Inserted 20 new rows into database |
|
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
Tag number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| 22 | 22 |
Subplot X,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m, |
| 23 | 23 |
Subplot Y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 24 |
Tree number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
|
| 24 |
Tree number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 25 |
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 26 |
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 27 |
Tag number,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 25 | 28 |
Specie+autor,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
| 26 | 29 |
Species and morphotypes,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/3,"Contains less than ""Specie+autor""" |
| 27 | 30 |
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>"
|
| inputs/Madidi/Organism/test.xml.ref | ||
|---|---|---|
| 40 | 40 |
</aggregateoccurrence> |
| 41 | 41 |
<authortaxoncode> |
| 42 | 42 |
<_alt> |
| 43 |
<1>$Tree number</1> |
|
| 43 |
<1> |
|
| 44 |
<_alt> |
|
| 45 |
<1>$Tree number</1> |
|
| 46 |
<2>$Tag number</2> |
|
| 47 |
</_alt> |
|
| 48 |
</1> |
|
| 44 | 49 |
<2> |
| 45 | 50 |
<_alt> |
| 46 | 51 |
<2>$Specie+autor</2> |
| inputs/Madidi/Plot/VegBIEN.csv | ||
|---|---|---|
| 85 | 85 |
Limo (DIN 18 123–%–1),/location/locationevent/soilobs/silt_fraction, |
| 86 | 86 |
"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",/location/locationevent/soilobs/sodium_fraction, |
| 87 | 87 |
Textural class,/location/locationevent/soilobs/texture, |
| 88 |
Inventory code,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 89 |
Inventory name,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 88 | 90 |
Locality,/location/locationnarrative/_merge/1, |
| 89 | 91 |
Observaciones,/location/notespublic, |
| 90 | 92 |
Direction,/location/slopeaspect_deg/_alt/1/_compass/value/_alt/1,Part files provide either this field or Orientación |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 53 | 53 |
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." |
| 54 | 54 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots" |
| 55 | 55 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position |
| 56 |
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/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 |
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 57 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 58 |
plot_code,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 59 |
stem_tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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 |
|
| 60 |
stem_tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 61 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 62 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 57 | 63 |
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>"
|
| 58 | 64 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,"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." |
| 59 | 65 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| inputs/SALVIAS-CSV/Organism/test.xml.ref | ||
|---|---|---|
| 121 | 121 |
</stemobservation> |
| 122 | 122 |
</plantobservation> |
| 123 | 123 |
</aggregateoccurrence> |
| 124 |
<authortaxoncode>$individual_code</authortaxoncode> |
|
| 124 |
<authortaxoncode> |
|
| 125 |
<_alt> |
|
| 126 |
<1>$individual_code</1> |
|
| 127 |
<2> |
|
| 128 |
<_alt> |
|
| 129 |
<1> |
|
| 130 |
<_alt> |
|
| 131 |
<1>$stem_tag2</1> |
|
| 132 |
<2>$stem_tag1</2> |
|
| 133 |
</_alt> |
|
| 134 |
</1> |
|
| 135 |
<2> |
|
| 136 |
<_alt> |
|
| 137 |
<1>$tag2</1> |
|
| 138 |
<2>$tag1</2> |
|
| 139 |
</_alt> |
|
| 140 |
</2> |
|
| 141 |
</_alt> |
|
| 142 |
</2> |
|
| 143 |
</_alt> |
|
| 144 |
</authortaxoncode> |
|
| 125 | 145 |
<growthform> |
| 126 | 146 |
<_map> |
| 127 | 147 |
<T>tree</T> |
| inputs/SALVIAS-CSV/Plot/VegBIEN.csv | ||
|---|---|---|
| 36 | 36 |
silt_percent,"/location/locationevent/soilobs/silt_fraction/_units:[default=""%"",to=]/value", |
| 37 | 37 |
soil_Na,"/location/locationevent/soilobs/sodium_fraction/_units:[default=""%"",to=]/value", |
| 38 | 38 |
soil_texture,/location/locationevent/soilobs/texture, |
| 39 |
PLOT_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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/_alt/1/_alt/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 | 41 |
temp_c,/location/locationevent/temperature_c, |
| 40 | 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" |
| 41 | 43 |
major_geo,/location/locationplace/*_id/placepath/continent, |
| 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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 20 |
StemTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 21 |
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 19 | 22 |
MeasureID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2, |
| 20 | 23 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 21 | 24 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| inputs/CTFS/StemObservation/test.xml.ref | ||
|---|---|---|
| 31 | 31 |
</stemobservation> |
| 32 | 32 |
</plantobservation> |
| 33 | 33 |
</aggregateoccurrence> |
| 34 |
<authortaxoncode> |
|
| 35 |
<_alt> |
|
| 36 |
<0>$StemTag</0> |
|
| 37 |
<1>$Tag</1> |
|
| 38 |
</_alt> |
|
| 39 |
</authortaxoncode> |
|
| 34 | 40 |
<sourceaccessioncode>$MeasureID</sourceaccessioncode> |
| 35 | 41 |
<taxondetermination> |
| 36 | 42 |
<taxonpath_id> |
| 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/_first/2",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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 9 | 10 |
StartX,/location/sublocationxposition_m, |
| 10 | 11 |
StartY,/location/sublocationyposition_m, |
| 11 | 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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 15 | 16 |
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/_first/1", |
| 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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 9 | 10 |
SpeciesInvID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
| 10 | 11 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 11 | 12 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| inputs/CTFS/SubplotObservation/VegBIEN.csv | ||
|---|---|---|
| 9 | 9 |
CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if event""]/cond/_exists/_first/1", |
| 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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| inputs/CTFS/Plot/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
Longitude,"/location/locationcoords/longitude_deg/_alt/2/_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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 23 |
PlotName,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 22 | 24 |
DescriptionOfSite,/location/locationnarrative/_merge/1, |
| 23 | 25 |
LocationName,/location/locationnarrative/_merge/1, |
| 24 | 26 |
CountryName,/location/locationplace/*_id/placepath/country, |
| inputs/FIA/Organism/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m, |
| 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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 16 |
TreeTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/then", |
|
| 15 | 17 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 16 | 18 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 17 | 19 |
County,/location/locationplace/*_id/placepath/county, |
| inputs/FIA/Organism/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</stemobservation> |
| 59 | 59 |
</plantobservation> |
| 60 | 60 |
</aggregateoccurrence> |
| 61 |
<authortaxoncode>$TreeTag</authortaxoncode> |
|
| 61 | 62 |
<taxondetermination> |
| 62 | 63 |
<taxonpath_id> |
| 63 | 64 |
<taxonpath> |
| ... | ... | |
| 80 | 81 |
</path> |
| 81 | 82 |
</_simplifyPath> |
| 82 | 83 |
</VegBIEN> |
| 83 |
Inserted 12 new rows into database |
|
| 84 |
Inserted 17 new rows into database |
|
| inputs/SALVIAS/plotMetadata/VegBIEN.csv | ||
|---|---|---|
| 36 | 36 |
silt_percent,"/location/locationevent/soilobs/silt_fraction/_units:[default=""%"",to=]/value", |
| 37 | 37 |
soil_Na,"/location/locationevent/soilobs/sodium_fraction/_units:[default=""%"",to=]/value", |
| 38 | 38 |
soil_texture,"/location/locationevent/soilobs/texture/_units:[default=""%"",to=]/value", |
| 39 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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/_alt/1/_alt/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 | 41 |
Temp,/location/locationevent/temperature_c, |
| 40 | 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" |
| 41 | 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/_alt/1/_alt/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/_alt/1/_alt/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 | 18 |
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2, |
| 17 | 19 |
origrecord_id_stems,,** No join mapping for origrecord_id_stems ** |
| 18 | 20 |
plotobs_id_index,,** No join mapping for plotobs_id_index ** |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 48 | 48 |
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." |
| 49 | 49 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots" |
| 50 | 50 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position |
| 51 |
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/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." |
|
| 51 |
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 52 |
PlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 53 |
PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 54 |
tag2,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 55 |
tag1,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/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." |
|
| 52 | 56 |
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>"
|
| 53 | 57 |
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,"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." |
| 54 | 58 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| inputs/SALVIAS/plotObservations/test.xml.ref | ||
|---|---|---|
| 92 | 92 |
</stemobservation> |
| 93 | 93 |
</plantobservation> |
| 94 | 94 |
</aggregateoccurrence> |
| 95 |
<authortaxoncode>$Ind</authortaxoncode> |
|
| 95 |
<authortaxoncode> |
|
| 96 |
<_alt> |
|
| 97 |
<1>$Ind</1> |
|
| 98 |
<2> |
|
| 99 |
<_alt> |
|
| 100 |
<1>$tag2</1> |
|
| 101 |
<2>$tag1</2> |
|
| 102 |
</_alt> |
|
| 103 |
</2> |
|
| 104 |
</_alt> |
|
| 105 |
</authortaxoncode> |
|
| 96 | 106 |
<growthform> |
| 97 | 107 |
<_map> |
| 98 | 108 |
<T>tree</T> |
| inputs/VegBank/observation_/VegBIEN.csv | ||
|---|---|---|
| 22 | 22 |
soilsand,/location/locationevent/soilobs/sand_fraction, |
| 23 | 23 |
soilsilt,/location/locationevent/soilobs/silt_fraction, |
| 24 | 24 |
soiltexture,/location/locationevent/soilobs/texture, |
| 25 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 25 | 26 |
accessioncode,,** No join mapping for accessioncode ** |
| 26 | 27 |
autotaxoncover,,** No join mapping for autotaxoncover ** |
| 27 | 28 |
basalarea,,** No join mapping for basalarea ** |
| inputs/VegBank/plot_/VegBIEN.csv | ||
|---|---|---|
| 13 | 13 |
longitude,"/location/locationcoords/longitude_deg/_alt/2/_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/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 17 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2/_if[@name=""if is organism""]/cond/_exists", |
|
| 16 | 18 |
locationnarrative,/location/locationnarrative/_merge/1, |
| 17 | 19 |
continent,/location/locationplace/*_id/placepath/continent, |
| 18 | 20 |
area|country|territory,/location/locationplace/*_id/placepath/country, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 104 | 104 |
organismX,//stemobservation/xposition_m, |
| 105 | 105 |
organismY,//stemobservation/yposition_m, |
| 106 | 106 |
recordNumber,//taxonoccurrence/authortaxoncode, |
| 107 |
locationID,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/cond/_exists", |
|
| 108 |
plotName,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/cond/_exists", |
|
| 109 |
tag,"//taxonoccurrence/authortaxoncode/_if[@name=""if is organism""]/then", |
|
| 107 | 110 |
verbatimScientificName,//taxonoccurrence/authortaxoncode, |
| 108 | 111 |
scientificNameWithAuthorship,//taxonoccurrence/authortaxoncode, |
| 109 | 112 |
scientificName,//taxonoccurrence/authortaxoncode, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Mapped tag to taxonoccurrence.authortaxoncode when the record is an organism, in case there is no other ID for the taxonoccurrence. This fixes a bug in FIA and TEAM data where all organisms in a plot used the same taxonoccurrence because taxonoccurrence was not properly constrained, causing the loss of individual taxondeterminations on each organism.