collector,/location/locationevent/taxonoccurrence/verbatimcollectorname,

CatalogNO,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",

locality,/location/locationnarrative/_merge/1,

Lat (-=S),"Latitude/_replace:[""\?$""=]/value",

Long (-=W),"Longitude/_replace:[""\?$""=]/value",

Barcode,catalogNumber,

SeriesName,collectionCode,

Accuracy,coordinateUncertaintyInMeters,

country,country

county,county

Cultivated?,cultivated,

Accession Number,occurrenceID,

Full Taxon Name,scientificName,

state,state

Typology,typeStatus,

MO[Veg+],Veg+,Comments

coreMap := $(mappings)/$(via)-VegBIEN.csv

coreSelfMap := $(mappings)/$(via).self.csv

vocab := $(mappings)/$(via).vocab.csv

viaMaps := $(wildcard $(tables:%=%/map.csv))

viaMaps += $(filter-out $(viaMaps),$(srcMaps:%/src.csv=%/map.csv))

# Via maps cleanup

ifneq ($(filter %/.map.csv.last_cleanup,$(MAKECMDGOALS)),)

	$(bin)/in_place $< $(bin)/canon 1 $(word 3,$+)

	$(bin)/in_place $< env ignore=1 $(bin)/subtract $(word 2,$+) 0 1 2

	touch $@

# Include comment column so commented mappings are never removed

VegBank[Veg+],Veg+,Comments

museumaccessionnumber,catalogNumber,

class,class

observation_id,eventID,

family,family

genus,genus

kingdom,kingdom

notes,notes

order,order

VegBank[Veg+],Veg+,Comments

authorplotcode,plotName,

reference_id,,

parent_id,parentPlotID,

TEAM[Veg+],Veg+,Comments

ObservationDate,eventDate,

Collectors,recordedBy,

dbh_pom,,

dbh_new,,

dbh_new_pom,,

TEAM[Veg+],Veg+,Comments

ObservationDate,eventDate,

family,family

genus,genus

latitude,latitude

longitude,longitude

X_1haPlot,organismX,

Y_1haPlot,organismY,

1haPlotCode,plotName,

collector1,Collector/_merge/2,

collector2,Collector/_merge/3,

collector3,Collector/_merge/4,

collmonth,monthCollected,

collday,dayCollected,

collyear,yearCollected,

collector2,Collector/_merge/3,

collector3,Collector/_merge/4,

sheetno,associatedMedia,?

country,country

county,county

cultivated,cultivated,Ignore other values

locality,locality

collmonth,monthCollected,

accession,occurrenceID,

flower,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"

fruit,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"

leaves,"reproductiveCondition/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"

ind_id,,Brad: OMIT

tag1,tag/_alt/1,"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."

tag2,previousTag/_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."

voucher_string,catalogNumber/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."

coll_number,catalogNumber/_alt/1,Brad: Map instead as for voucher_string

collector_code,,Brad: OMIT

infra_ep_1,infraspecificEpithet,

cf_aff,identificationQualifier,"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."

comments,,Brad: OMIT

no_of_individuals,individualCount,"Brad: 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,coverPercent,

intercept_cm,volumeCanopy,"Brad: 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."

-----"

family,family,

genus,genus,

stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."

height_m,height/_alt/2,

ht_first_branch_m,heightFirstBranch,

infra_ep_1,infraspecificEpithet,

stem_liana_infestation,lianaInfestation,

PLOT_ID,locationID,

plot_code,plotName,

tag2,previousTag/_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."

stem_tag2,previousTag/_alt/2,Brad: see above

individual_code,recordNumber,"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."

coll_firstname,recordedBy.givenName,Brad: See comment above

coll_lastname,recordedBy.surName,"Brad: 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."

specific_authority,scientificNameAuthorship,Brad: This is the author of the scientificName.

specific_epithet,specificEpithet,

notes,stemNotes,

stem_tag1,tag/_alt/2,"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."

infra_rank_1,taxonRank,

orig_family,verbatimFamily,Brad: OMIT

orig_species,verbatimSpecificEpithet,Brad: OMIT

intercept_cm,volumeCanopy,"Brad: 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."

det_type,voucherType,"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."

plot_methodology,samplingProtocol,

plot_area_ha,plotArea,"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,,"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"

pol2,county,Brad: No pol2=countyParish

lat_decimal,decimalLatitude,

long_decimal,decimalLongitude,

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"

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

soil_Mg,"magnesium/_units:[default=""%"",to=]/value",

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_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",

plot_area_ha,plotArea,"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"

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

soil_K,"potassium/_units:[default=""%"",to=]/value",

precip_mm,precipitation,

slope_aspect,slopeAspect,

slope_gradient,slopeGradient,

soil_Na,"sodium/_units:[default=""%"",to=]/value",

pol1,stateProvince,Brad: No; pol1=stateProvince

temp_c,temperature,

soil_texture,texture,

CVS,Veg+,Comments

authorObsCode,fieldNumber,

realLatitude,OMIT,

realLongitude,OMIT,

locationAccuracy-m,coordinateUncertaintyInMeters,

publicLatitude,decimalLatitude,

publicLongitude,decimalLongitude,

authorObsCode,fieldNumber,

currentTaxonName sec Weakley 2006,scientificName,

state,stateProvince,

MeasYear,yearCollected,

MeasMon,monthCollected,

MeasDay,dayCollected,

HOM,,

decimalLongitude,decimalLongitude

genus,genus

height,height

MeasMon,monthCollected,

specificEpithet,specificEpithet

stateProvince,stateProvince

TreeTag,tag,

MethodCode,,

plot_area_ha,plotArea,"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,,"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"

plot_administrator,,

plot_notes,,

tmp_del,,

pol2,county,Brad: No pol2=countyParish

LatDec,decimalLatitude,

LongDec,decimalLongitude,

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"

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

soil_Mg,"magnesium/_units:[default=""%"",to=]/value",

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_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",

plot_area_ha,plotArea,"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"

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

soil_K,"potassium/_units:[default=""%"",to=]/value",

Precip,precipitation,

slope_aspect,slopeAspect,

slope_gradient,slopeGradient,

soil_Na,"sodium/_units:[default=""%"",to=]/value",

PolDiv1,stateProvince,Brad: No; pol1=stateProvince

Temp,temperature,

soil_texture,"texture/_units:[default=""%"",to=]/value",

SALVIAS,Veg+,Comments

origrecord_id_stems,,

PlotObsID,individualID,

NoInd,stemCount,

stem_liana_infestation,lianaInfestation,

stem_tag2,previousTag,

NoInd,stemCount,

stem_notes,stemNotes,

stem_tag1,tag,

ind_id,,Brad: OMIT

tag1,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."

tag2,previousTag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

dist,,

perp_dist,,

SourceVoucher,catalogNumber/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."

common_name,,

morphoname,,

species_code,,

height_class,,

height_m,height,

height_m_commercial,,

Family,family,

Notes,fieldNotes,

Genus,genus,

height_m,height,

ht_first_branch_m,heightFirstBranch,

cfaff,identificationQualifier,"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."

infra_ep_1,infraspecificEpithet,

liana_infestation,lianaInfestation,

PlotID,locationID,

PlotCode,plotName,

tag2,previousTag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

Ind,recordNumber,"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."

coll_firstname,recordedBy.givenName,Brad: See comment above

coll_lastname,recordedBy.surName,"Brad: 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."

auth,scientificNameAuthorship,Brad: This is the author of the scientificName.

Species,specificEpithet,

Line,subplot,

infra_rank_1,taxonRank,

OrigFamily,verbatimFamily,Brad: OMIT

OrigGenus,verbatimGenus,

OrigSpecies,verbatimSpecificEpithet,Brad: OMIT

intercept_cm,volumeCanopy,"Brad: 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."

DetType,voucherType,"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."

U[Veg+],Veg+,Comments

Barcode,catalogNumber,

Collector,Collector/_merge/1,

Prefix,,Not used

Long,decimalLongitude,

family,family

genus,genus

Ecology,habitat,

cf,identificationQualifier,

Detby,identifiedBy,

Collmm,monthCollected,

notes,notes

Number,recordNumber,

Collyy,yearCollected,

Detyy,yearIdentified,

FieldNumber,OMIT,"Usage inconsistent with DwC definition: meaning is recordNumber. Identical to CollectorNumber [1], so does not need to be mapped.

[1] The following query returns no rows: SELECT * FROM ""ARIZ"".""Specimen"" WHERE ""CollectorNumber"" IS DISTINCT FROM ""FieldNumber"""

VerbatimCollectingDate,dateCollected/_alt/0,

HorizontalDatum,,Not used

OriginalCoordinateSystem,verbatimSRS,

dayIdentified,dayIdentified

decimalLatitude,decimalLatitude

decimalLongitude,decimalLongitude

family,family

fieldNotes,fieldNotes

genus,genus

species,species

stateProvince,stateProvince

subspecies,subspecies

verbatimElevation,verbatimElevation

verbatimLatitude,verbatimLatitude

verbatimLongitude,verbatimLongitude

OriginalCoordinateSystem,,** No join mapping for verbatimSRS ** 

OtherCatalogNumbers,,** No join mapping for RelatedCatalogItem/_alt/1 ** 

RelatedCatalogedItems,,** No join mapping for RelatedCatalogItem/_alt/2 ** Used only when OtherCatalogNumbers is NULL

InstitutionCD,institutionCode,

CollectionCD,collectionCode,

CatalogNO,catalogNumber,

ScientificNameOriginal,verbatimScientificName,

GBIFFamilyOriginal,verbatimFamily,

GBIFGenusOriginal,verbatimGenus,

MinimumElevationInMeter,minimumElevationInMeters,

country,country

county,county

LatestDateCollected,dateCollected,

decimalLatitude,decimalLatitude

decimalLongitude,decimalLongitude

family,family

MaximumElevationInMeter,maximumElevationInMeters,

MinimumElevationInMeter,minimumElevationInMeters,

scientificName,scientificName

specificEpithet,specificEpithet

stateProvince,stateProvince

GBIFFamilyOriginal,verbatimFamily,

SeriesName,collectionCode,

Barcode,catalogNumber,

Full Taxon Name,scientificName,

Cultivated?,cultivated,

Elevation,verbatimElevation,

Lat (-=S),"Latitude/_replace:[""\?$""=]/value",

FIPS,,FIPS county code

Alt N/S,,

Alt E/W,,

Typology,typeStatus,

Cultivated?,/location/locationevent/taxonoccurrence/iscultivated/_alt/1,

Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",

Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",

Typology,,** No join mapping for typeStatus ** 

county,county

dayCollected,dayCollected

family,family

genus,genus

identifiedBy,identifiedBy

individualCount,individualCount

maximumElevation,maximumElevation

minimumElevation,minimumElevation

monthCollected,monthCollected

notes,notes

scientificName,scientificName

scientificNameAuthor,scientificNameAuthor

notespublic,,

notesmgt,,

revisions,,

emb_taxoninterpretation,,

taxoninterpretation_accessioncode,,

plantname_id,,

shape,footprintWKT,

landform,landform

latitude,latitude

locationNarrative,locationNarrative

longitude,longitude

maxSlopeAspect,maxSlopeAspect

minSlopeGradient,minSlopeGradient

parent_id,parentPlotID,

area,plotArea,

authorplotcode,plotName,

slopeAspect,slopeAspect

slopeGradient,slopeGradient