link ../../mappings/SALVIAS_db-VegX.organisms.csv

SALVIAS:plotMetadata,VegBIEN:/plotevent,Comments

plot_area_ha,/*_ID/plot/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"

Elev,/*_ID/plot/elevation,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.

Country,"/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""area|country|territory""])/placeName",

PolDiv1,"/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""region|state|province""])/placeName",Brad: No; pol1=stateProvince

MajorGeo,/*_ID/plot/place(/*_ID/namedPlace[placeSystem=continent])/placeName,

pol2,/*_ID/plot/place(/*_ID/namedPlace[placeSystem=county])/placeName,Brad: No pol2=countyParish

Locality_Description,/*_ID/plot/place/*_ID/namedPlace/placeDescription,"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"

LatDec,/*_ID/plot/realLatitude,

LongDec,/*_ID/plot/realLongitude,

slope_aspect,/*_ID/plot/slopeAspect,

slope_gradient,/*_ID/plot/slopeGradient,

elev_max_m,"/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}",

elev_min_m,"/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}",

project_id,/*_ID/project/projectName,

life_zone_code,/commClass/commInterpretation/*_ID/commConcept/*_ID/*/commName,

life_zone,/commClass/commInterpretation/*_ID/commConcept/commDescription,

Precip,"/definedValue[*_ID/userDefined[tableName=plotevent,userDefinedName=precipitationMm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

Temp,"/definedValue[*_ID/userDefined[tableName=plotevent,userDefinedName=temperatureC]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

PlotMethod,/methodNarrative,

date_finish,/obsEndDate/_date/date,

date_start,/obsStartDate/_date/date,

soil_acidity,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilAcidity]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_base,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilBase]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_Ca,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCalcium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_C,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCarbon]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_cation_cap,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCationCap]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_conductivity,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilConductivity]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_Mg,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilMagnesium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_N,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilNitrogen]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_P,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilPhosphorus]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_K,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilPotassium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

soil_Na,"/soilObs:[soilHorizon=unknown]/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilSodium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",

clay_percent,/soilObs:[soilHorizon=unknown]/soilClay,

organic_percent,/soilObs:[soilHorizon=unknown]/soilOrganic,

pH,/soilObs:[soilHorizon=unknown]/soilPH,"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."

sand_percent,/soilObs:[soilHorizon=unknown]/soilSand,

silt_percent,/soilObs:[soilHorizon=unknown]/soilSilt,

soil_texture,/soilObs:[soilHorizon=unknown]/soilTexture,

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)

SALVIAS:plotObservations,VegBIEN:/taxonoccurrence,Comments

PlotCode,"/*_ID/plotevent/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/2,authorObsCode}","Brad: Same as plotCode, above"

NoInd,/collectiveobs/*/stemCount/_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."

cover_percent,/collectiveobs/cover,

intercept_cm,"/collectiveobs/definedValue[*_ID/userDefined[tableName=collectiveobs,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."

ht_first_branch_m,"/collectiveobs/stemCount/individual/definedValue[*_ID/userDefined[tableName=individual,userDefinedName=heightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue",Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

tag2,/collectiveobs/stemCount/individual/stemCode/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

tag1,/collectiveobs/stemCount/individual/stemCode/_alt/2,"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."

x_position,/collectiveobs/stemCount/individual/stemXPosition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."

y_position,/collectiveobs/stemCount/individual/stemYPosition,Brad: See comment above for x_position

temp_dbh,/collectiveobs/stemCount/stemDiameter,

height_m,/collectiveobs/stemCount/stemHeight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

census_date,/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/collectionDate/_date/date,

coll_number,/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber,Brad: Incorrect. Map instead as for voucher_string

coll_firstname,"/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/{givenName/_namePart/first,middleName/_namePart/last}",Brad: See comment above

coll_lastname,/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/{surName},"Brad: Correct for VegBank. 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."

census_no,"/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxondetermination,userDefinedName=censusNo]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","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."

cfaff,"/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxondetermination,userDefinedName=cfAff]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","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."

DetType,"/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxondetermination,userDefinedName=determinationType]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","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."

Habit,"/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxondetermination,userDefinedName=habit]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

Ind,"/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxondetermination,userDefinedName=individualCode]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","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."

Notes,/taxondetermination[ROLE_ID/aux_Role/roleCode=collector]/notes,

Family,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",

Genus,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",

auth,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/plantName/reference_ID/reference/shortName",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.

Species,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",

infra_rank_1,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/first",

infra_ep_1,"/taxondetermination[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/last",

OrigFamily,"/taxondetermination[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName",Brad: OMIT

OrigSpecies,"/{taxondetermination[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=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

PlotObsID,":[collectiveobs/*/stemCount/_alt/2=1]/{taxondetermination[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=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."

link ../../mappings/SALVIAS_db-VegX.plots.csv

table = $(shell s="$(*F)"; echo "$${s\#\#*.}")# remove sort order prefix

	$(root)/bin/join_sort <$< $(root)/mappings/VegX-VegBIEN.$(table).csv >$@