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Revision 406

Added by Aaron Marcuse-Kubitza about 13 years ago

SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode

View differences:

inputs/SALVIAS/map.VegBIEN.0.plots.csv
13 13 
elev_max_m,"/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}",
14 14 
elev_min_m,"/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}",
15 15 
project_id,/*_ID/project/projectName,
16 
PlotID,/authorObsCode/_alt/1,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
16 17 
life_zone_code,/commClass/commdetermination/*_ID/commConcept/*_ID/*/commName,
17 18 
life_zone,/commClass/commdetermination/*_ID/commConcept/commDescription,
18 19 
Precip,"/definedValue[*_ID/userDefined[tableName=plotevent,userDefinedName=precipitationMm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",
......
37 38 
sand_percent,/soilObs:[soilHorizon=unknown]/soilSand,
38 39 
silt_percent,/soilObs:[soilHorizon=unknown]/soilSilt,
39 40 
soil_texture,/soilObs:[soilHorizon=unknown]/soilTexture,
40 
SiteCode,"/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode}",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
41 
SiteCode,"/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode/_alt/2}",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
inputs/SALVIAS/map.VegBIEN.1.organisms.csv
1 1 
SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments
2 
PlotCode,"/*_ID/plotevent/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode}","Brad: Same as plotCode, above"
2 
PlotID,/*_ID/plotevent/authorObsCode/_alt/1,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
3 
PlotCode,"/*_ID/plotevent/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode/_alt/2}","Brad: Same as plotCode, above"
3 4 
NoInd,/collectiveobservation/count/_alt/1,"Brad: Incorrect for VegX. 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."
4 5 
cover_percent,/collectiveobservation/cover,
5 6 
intercept_cm,"/collectiveobservation/definedValue[*_ID/userDefined[tableName=collectiveobservation,userDefinedName=interceptCm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
......
28 29 
infra_ep_1,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]:[determinationType=""Computer (automated)"",originaldetermination=false,currentdetermination=true,determinationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/last",
29 30 
OrigFamily,"/taxondetermination[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[determinationType=Author,originaldetermination=true,currentdetermination=true,determinationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",Brad: OMIT
30 31 
OrigSpecies,"/{taxondetermination[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[determinationType=Author,originaldetermination=true,currentdetermination=true,determinationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName,taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept/*_ID/*/plantName/_alt/2}",Brad: OMIT
31 
PlotObsID,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[ROLE_ID/aux_Role/roleCode=collector]:[determinationType=Author,originaldetermination=true,currentdetermination=false,determinationDate=epoch,*_ID/plantConcept:[*_ID/reference],*_ID/party]/museumAccessionNumber,*_ID/plotevent/*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/3}","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."
32 
PlotObsID,":[collectiveobservation/count/_alt/2=1]/{taxondetermination[ROLE_ID/aux_Role/roleCode=collector]:[determinationType=Author,originaldetermination=true,currentdetermination=false,determinationDate=epoch,*_ID/plantConcept:[*_ID/reference],*_ID/party]/museumAccessionNumber,*_ID/plotevent/authorObsCode/_alt/2,*_ID/plotevent/*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/3}","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."

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