plotMetadata_

SELECT *

FROM "plotMetadata"

LEFT JOIN "lookup_MethodCode" USING ("MethodCode")

MethodCode,PlotID,orig_filename,AccessCode,project_id,PrimOwnerID,SiteCode,SiteName,new_world,MajorGeo,Country,PolDiv1,pol1_type,pol2,pol2_type,lat_string,long_string,LatDec,LongDec,lat_long_accuracy,Elev,elev_max_m,elev_min_m,Precip,ElevSource,Temp,PrecipSource,TempSource,bearing,slope_aspect,slope_gradient,clay_percent,silt_percent,sand_percent,pH,soil_N,soil_P,soil_C,soil_K,soil_Mg,soil_Ca,soil_Na,soil_acidity,soil_base,soil_cation_cap,soil_conductivity,organic_percent,soil_texture,RevisionComments,Locality_Description,topography_desc,vegetation_1,vegetation_2,Habitat,life_zone_code,life_zone,PlotMethod,plot_area_ha,recensused,date_start,date_finish,plot_administrator,plot_notes,tmp_del,Country_index,PrimOwnerID_index,plot_administrator_index,project_id_index,Description

SALVIAS,VegCore,Filter,Comments

MethodCode,*MethodCode,,

PlotID,locationID,,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

orig_filename,*orig_filename,,

AccessCode,*AccessCode,,

project_id,projectID,,

PrimOwnerID,*PrimOwnerID,,

SiteCode,plotName,,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

SiteName,*SiteName,,

new_world,*new_world,,

MajorGeo,continent,,

Country,country,,

PolDiv1,stateProvince,,Brad: No; pol1=stateProvince

pol1_type,*pol1_type,,

pol2,county,,Brad: No pol2=countyParish

pol2_type,*pol2_type,,

lat_string,*lat_string,,

long_string,*long_string,,

LatDec,decimalLatitude,,

LongDec,decimalLongitude,,

lat_long_accuracy,*lat_long_accuracy,,

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.

elev_max_m,maximumElevationInMeters,,

elev_min_m,minimumElevationInMeters,,

Precip,precipitation,,

ElevSource,*ElevSource,,

Temp,temperature,,

PrecipSource,*PrecipSource,,

TempSource,*TempSource,,

bearing,*bearing,,

slope_aspect,slopeAspect,,

slope_gradient,slopeGradient,,

clay_percent,clay_percent,,

silt_percent,silt_percent,,

sand_percent,sand_percent,,

pH,ph,,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."

soil_N,nitrogen_percent,,Assuming units are % based on the range of values

soil_P,phosphorus_percent,"/_map:[""<1,5""=0,*=*]/value",Assuming units are % based on the range of values

soil_C,carbon_percent,,Assuming units are % based on the range of values

soil_K,potassium_percent,,Assuming units are % based on the range of values

soil_Mg,magnesium_percent,,Assuming units are % based on the range of values

soil_Ca,calcium_percent,,Assuming units are % based on the range of values

soil_Na,sodium_percent,,Assuming units are % based on the range of values

soil_acidity,acidity_percent,"/_map:[""<0.05""=0,*=*]/value",Assuming units are % based on the range of values

soil_base,baseSaturation_percent,,Assuming units are % based on the range of values

soil_cation_cap,cationExchangeCapacity_cmol_kg,,

soil_conductivity,conductivity,,

organic_percent,organic_percent,,

soil_texture,texture,,

RevisionComments,*RevisionComments,,

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"

topography_desc,*topography_desc,,

vegetation_1,*vegetation_1,,

vegetation_2,*vegetation_2,,

Habitat,habitat,,

life_zone_code,communityID,,

life_zone,communityName,,

PlotMethod,samplingProtocol,,

plot_area_ha,plotArea_ha,,"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"

recensused,*recensused,,"Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a  plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values"

date_start,startDate,,

date_finish,endDate,,

plot_administrator,*plot_administrator,,

plot_notes,plotNotes,,

tmp_del,*tmp_del,,

Country_index,*Country_index,,

PrimOwnerID_index,*PrimOwnerID_index,,

plot_administrator_index,*plot_administrator_index,,

project_id_index,*project_id_index,,

Description,*Description,,

SALVIAS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments

SiteCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode/_if[@name=""if geovalidation""]/else","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

SiteCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

plot_area_ha,/location/area_m2/_ha_to_m2/value,"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"

Elev,/location/elevation_m/_alt/1,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.

elev_max_m,/location/elevation_m/_alt/2/_avg/max,

elev_min_m,/location/elevation_m/_alt/2/_avg/min,

PlotMethod,/location/locationevent/*_id/method/name,

project_id,/location/locationevent/*_id/project/sourceaccessioncode,

date_finish,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",

date_start,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",

SiteCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

PlotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_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."

date_finish,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_*/date/_alt/1",

date_start,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_*/date/_alt/1",

life_zone_code,/location/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,

life_zone,/location/locationevent/commclass/commdetermination/*_id/commconcept/commdescription,

date_finish,/location/locationevent/obsenddate/_*/date/_alt/1,

date_start,/location/locationevent/obsstartdate/_*/date/_alt/1,

Precip,/location/locationevent/precipitation_m,

soil_acidity,"/location/locationevent/soilobs/acidity_fraction/_percent_to_fraction/value/_map:[""<0.05""=0,*=*]/value",Assuming units are % based on the range of values

soil_base,/location/locationevent/soilobs/basesaturation_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

soil_Ca,/location/locationevent/soilobs/calcium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

soil_C,/location/locationevent/soilobs/carbon_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

soil_cation_cap,/location/locationevent/soilobs/cationexchangecapacity_cmol_kg,

clay_percent,/location/locationevent/soilobs/clay_fraction/_percent_to_fraction/value,

soil_conductivity,/location/locationevent/soilobs/conductivity,

soil_Mg,/location/locationevent/soilobs/magnesium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

soil_N,/location/locationevent/soilobs/nitrogen_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

organic_percent,/location/locationevent/soilobs/organic_fraction/_percent_to_fraction/value,

pH,/location/locationevent/soilobs/ph,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."

soil_P,"/location/locationevent/soilobs/phosphorus_fraction/_percent_to_fraction/value/_map:[""<1,5""=0,*=*]/value",Assuming units are % based on the range of values

soil_K,/location/locationevent/soilobs/potassium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

sand_percent,/location/locationevent/soilobs/sand_fraction/_percent_to_fraction/value,

silt_percent,/location/locationevent/soilobs/silt_fraction/_percent_to_fraction/value,

soil_Na,/location/locationevent/soilobs/sodium_fraction/_percent_to_fraction/value,Assuming units are % based on the range of values

soil_texture,/location/locationevent/soilobs/texture,

PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

SiteCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

Temp,/location/locationevent/temperature_c,

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"

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?"

LatDec,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",

LongDec,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",

MajorGeo,/location/locationplace/*_id/place/continent,

Country,/location/locationplace/*_id/place/country,

pol2,/location/locationplace/*_id/place/county,Brad: No pol2=countyParish

LatDec,"/location/locationplace/*_id/place/matched_place_id/place:[reference_id/reference/shortname=geoscrub]/*_id/coordinates/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",

LongDec,"/location/locationplace/*_id/place/matched_place_id/place:[reference_id/reference/shortname=geoscrub]/*_id/coordinates/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",

Country,/location/locationplace/*_id/place/matched_place_id/place:[reference_id/reference/shortname=geoscrub]/country/_first/2,

PolDiv1,/location/locationplace/*_id/place/matched_place_id/place:[reference_id/reference/shortname=geoscrub]/stateprovince/_first/2,Brad: No; pol1=stateProvince

PlotID,"/location/locationplace/*_id/place/placecode/_if[@name=""if geovalidation""]/then","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

PolDiv1,/location/locationplace/*_id/place/stateprovince,Brad: No; pol1=stateProvince

plot_notes,/location/notespublic,

slope_aspect,/location/slopeaspect_deg/_alt/1/_compass/value,

slope_gradient,/location/slopegradient_fraction/_alt/1,

PlotID,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/1","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."

SiteCode,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

AccessCode,,** No join mapping for *AccessCode ** 

Country_index,,** No join mapping for *Country_index ** 

Description,,** No join mapping for *Description ** 

ElevSource,,** No join mapping for *ElevSource ** 

MethodCode,,** No join mapping for *MethodCode ** 

PrecipSource,,** No join mapping for *PrecipSource ** 

PrimOwnerID,,** No join mapping for *PrimOwnerID ** 

PrimOwnerID_index,,** No join mapping for *PrimOwnerID_index ** 

RevisionComments,,** No join mapping for *RevisionComments ** 

SiteName,,** No join mapping for *SiteName ** 

TempSource,,** No join mapping for *TempSource ** 

bearing,,** No join mapping for *bearing ** 

lat_long_accuracy,,** No join mapping for *lat_long_accuracy ** 

lat_string,,** No join mapping for *lat_string ** 

long_string,,** No join mapping for *long_string ** 

new_world,,** No join mapping for *new_world ** 

orig_filename,,** No join mapping for *orig_filename ** 

plot_administrator,,** No join mapping for *plot_administrator ** 

plot_administrator_index,,** No join mapping for *plot_administrator_index ** 

pol1_type,,** No join mapping for *pol1_type ** 

pol2_type,,** No join mapping for *pol2_type ** 

project_id_index,,** No join mapping for *project_id_index ** 

recensused,,"** No join mapping for *recensused ** Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a  plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values"

tmp_del,,** No join mapping for *tmp_del ** 

topography_desc,,** No join mapping for *topography_desc ** 

vegetation_1,,** No join mapping for *vegetation_1 ** 

vegetation_2,,** No join mapping for *vegetation_2 ** 

*MethodCode

*orig_filename

*AccessCode

*PrimOwnerID

*SiteName

*new_world

*pol1_type

*pol2_type

*lat_string

*long_string

*lat_long_accuracy

*ElevSource

*PrecipSource

*TempSource

*bearing

*RevisionComments

*topography_desc

*vegetation_1

*vegetation_2

*recensused

*plot_administrator

*tmp_del

*Country_index

*PrimOwnerID_index

*plot_administrator_index

*project_id_index

*Description

Put template:

<VegBIEN>

    <_simplifyPath id="-1">

        <next>parent_id</next>

        <path>

            <location>

                <authorlocationcode>$SiteCode</authorlocationcode>

                <sourceaccessioncode>$PlotID</sourceaccessioncode>

                <area_m2><_ha_to_m2><value>$plot_area_ha</value></_ha_to_m2></area_m2>

                <elevation_m>

                    <_alt>

                        <1>$Elev</1>

                        <2>

                            <_avg>

                                <max>$elev_max_m</max>

                                <min>$elev_min_m</min>

                            </_avg>

                        </2>

                    </_alt>

                </elevation_m>

                <locationevent>

                    <method_id><method><name>$PlotMethod</name></method></method_id>

                    <project_id><project><sourceaccessioncode>$project_id</sourceaccessioncode></project></project_id>

                    <commclass>

                        <commdetermination>

                            <commconcept_id>

                                <commconcept>

                                    <commname_id><commname><commname>$life_zone_code</commname></commname></commname_id>

                                    <commdescription>$life_zone</commdescription>

                                </commconcept>

                            </commconcept_id>

                        </commdetermination>

                    </commclass>

                    <obsenddate><_date><date>$date_finish</date></_date></obsenddate>

                    <obsstartdate><_date><date>$date_start</date></_date></obsstartdate>

                    <precipitation_m>$Precip</precipitation_m>

                    <soilobs>

                        <acidity_fraction>

                            <_percent_to_fraction>

                                <value>

                                    <_map>

                                        <<0.05>0</<0.05>

                                        <*>*</*>

                                        <value>$soil_acidity</value>

                                    </_map>

                                </value>

                            </_percent_to_fraction>

                        </acidity_fraction>

                        <basesaturation_fraction><_percent_to_fraction><value>$soil_base</value></_percent_to_fraction></basesaturation_fraction>

                        <calcium_fraction><_percent_to_fraction><value>$soil_Ca</value></_percent_to_fraction></calcium_fraction>

                        <carbon_fraction><_percent_to_fraction><value>$soil_C</value></_percent_to_fraction></carbon_fraction>

                        <cationexchangecapacity_cmol_kg>$soil_cation_cap</cationexchangecapacity_cmol_kg>

                        <clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction>

                        <conductivity>$soil_conductivity</conductivity>

                        <magnesium_fraction><_percent_to_fraction><value>$soil_Mg</value></_percent_to_fraction></magnesium_fraction>

                        <nitrogen_fraction><_percent_to_fraction><value>$soil_N</value></_percent_to_fraction></nitrogen_fraction>

                        <organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction>

                        <ph>$pH</ph>

                        <phosphorus_fraction>

                            <_percent_to_fraction>

                                <value>

                                    <_map>

                                        <<1,5>0</<1,5>

                                        <*>*</*>

                                        <value>$soil_P</value>

                                    </_map>

                                </value>

                            </_percent_to_fraction>

                        </phosphorus_fraction>

                        <potassium_fraction><_percent_to_fraction><value>$soil_K</value></_percent_to_fraction></potassium_fraction>

                        <sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction>

                        <silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction>

                        <sodium_fraction><_percent_to_fraction><value>$soil_Na</value></_percent_to_fraction></sodium_fraction>

                        <texture>$soil_texture</texture>

                    </soilobs>

                    <temperature_c>$Temp</temperature_c>

                </locationevent>

                <locationnarrative>

                    <_merge>

                        <1>$Locality_Description</1>

                        <3>

                            <_label>

                                <label>habitat</label>

                                <value>$Habitat</value>

                            </_label>

                        </3>

                    </_merge>

                </locationnarrative>

                <locationplace>

                    <place_id>

                        <place>

                            <coordinates_id>

                                <coordinates>

                                    <latitude_deg>

                                        <_nullIf>

                                            <null>0</null>

                                            <type>float</type>

                                            <value>$LatDec</value>

                                        </_nullIf>

                                    </latitude_deg>

                                    <longitude_deg>

                                        <_nullIf>

                                            <null>0</null>

                                            <type>float</type>

                                            <value>$LongDec</value>

                                        </_nullIf>

                                    </longitude_deg>

                                </coordinates>

                            </coordinates_id>

                            <continent>$MajorGeo</continent>

                            <country>$Country</country>

                            <county>$pol2</county>

                            <matched_place_id>

                                <place>

                                    <reference_id><reference><shortname>geoscrub</shortname></reference></reference_id>

                                    <coordinates_id>

                                        <coordinates>

                                            <latitude_deg>

                                                <_nullIf>

                                                    <null>0</null>

                                                    <type>float</type>

                                                    <value>$LatDec</value>

                                                </_nullIf>

                                            </latitude_deg>

                                            <longitude_deg>

                                                <_nullIf>

                                                    <null>0</null>

                                                    <type>float</type>

                                                    <value>$LongDec</value>

                                                </_nullIf>

                                            </longitude_deg>

                                        </coordinates>

                                    </coordinates_id>

                                    <country>$Country</country>

                                    <stateprovince>$PolDiv1</stateprovince>

                                </place>

                            </matched_place_id>

                            <stateprovince>$PolDiv1</stateprovince>

                        </place>

                    </place_id>

                </locationplace>

                <notespublic>$plot_notes</notespublic>

                <slopeaspect_deg><_compass><value>$slope_aspect</value></_compass></slopeaspect_deg>

                <slopegradient_fraction>$slope_gradient</slopegradient_fraction>

            </location>

        </path>

    </_simplifyPath>

</VegBIEN>

Inserted 26 new rows into database

SiteCode,plotName,,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)

MajorGeo,continent,,

PolDiv1,stateProvince,,Brad: No; pol1=stateProvince

pol2,county,,Brad: No pol2=countyParish

LatDec,decimalLatitude,,

LongDec,decimalLongitude,,

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.

elev_max_m,maximumElevationInMeters,,

elev_min_m,minimumElevationInMeters,,

Precip,precipitation,,

Temp,temperature,,

soil_N,nitrogen_percent,,Assuming units are % based on the range of values

soil_P,phosphorus_percent,"/_map:[""<1,5""=0,*=*]/value",Assuming units are % based on the range of values

soil_C,carbon_percent,,Assuming units are % based on the range of values

soil_K,potassium_percent,,Assuming units are % based on the range of values

soil_Mg,magnesium_percent,,Assuming units are % based on the range of values

soil_Ca,calcium_percent,,Assuming units are % based on the range of values

soil_Na,sodium_percent,,Assuming units are % based on the range of values

soil_acidity,acidity_percent,"/_map:[""<0.05""=0,*=*]/value",Assuming units are % based on the range of values

soil_base,baseSaturation_percent,,Assuming units are % based on the range of values

soil_cation_cap,cationExchangeCapacity_cmol_kg,,

soil_conductivity,conductivity,,

soil_texture,texture,,

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"

life_zone_code,communityID,,

life_zone,communityName,,

PlotMethod,samplingProtocol,,

date_start,startDate,,

date_finish,endDate,,