MT[Veg+],Veg+,Comments

basisOfRecord,basisOfRecord

collectionCode,collectionCode

collectionID,collectionID

continent,continent

countryCode,countryCode

datasetName,datasetName

establishmentMeans,establishmentMeans

family,family

genus,genus

id,id

individualCount,individualCount

institutionCode,institutionCode

language,language

locality,locality

occurrenceRemarks,occurrenceRemarks

rights,rights

rightsHolder,rightsHolder

type,type

MT[Veg+],Veg+,Comments

"XAL[Veg+,darwin:]:/content/record/",Veg+,Comments

BasisOfRecord,BasisOfRecord

CatalogNumber,CatalogNumber

Class,Class

CollectionCode,CollectionCode

Collector,Collector

ContinentOcean,ContinentOcean

CoordinatePrecision,CoordinatePrecision

Country,Country

County,County

DateLastModified,DateLastModified

DayCollected,DayCollected

DayIdentified,DayIdentified

Family,Family

Genus,Genus

IdentifiedBy,IdentifiedBy

IndividualCount,IndividualCount

InstitutionCode,InstitutionCode

JulianDay,JulianDay

Kingdom,Kingdom

Latitude,Latitude

Locality,Locality

Longitude,Longitude

MaximumDepth,MaximumDepth

MaximumElevation,MaximumElevation

MinimumDepth,MinimumDepth

MinimumElevation,MinimumElevation

MonthCollected,MonthCollected

MonthIdentified,MonthIdentified

Notes,Notes

Order,Order

Phylum,Phylum

PreparationType,PreparationType

PreviousCatalogNumber,PreviousCatalogNumber

RelatedCatalogItem,RelatedCatalogItem

RelationshipType,RelationshipType

ScientificName,ScientificName

ScientificNameAuthor,ScientificNameAuthor

Sex,Sex

Species,Species

StateProvince,StateProvince

Subspecies,Subspecies

TimeOfDay,TimeOfDay

TypeStatus,TypeStatus

YearCollected,YearCollected

YearIdentified,YearIdentified

CollectorNumber,recordNumber/_alt/1,

FieldNumber,recordNumber/_alt/2,"This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). It is also unused: `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines."

"XAL[Veg+,darwin:]:/content/record/",Veg+,Comments

CollectorNumber,recordNumber/_alt/1,

FieldNumber,recordNumber/_alt/2,"This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). It is also unused: `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines."

NY[Veg+],Veg+,Comments

BasisOfRecord,BasisOfRecord

BoundingBox,BoundingBox

CatalogNumber,CatalogNumber

Class,Class

CollectionCode,CollectionCode

Collector,Collector

CollectorNumber,CollectorNumber

ContinentOcean,ContinentOcean

CoordinatePrecision,CoordinatePrecision

Country,Country

County,County

DateLastModified,DateLastModified

DayCollected,DayCollected

DayIdentified,DayIdentified

Family,Family

Genus,Genus

Habitat,Habitat

IdentifiedBy,IdentifiedBy

IndividualCount,IndividualCount

InstitutionCode,InstitutionCode

JulianDay,JulianDay

Kingdom,Kingdom

Latitude,Latitude

Locality,Locality/_merge/1,

Substrate,"Locality/_merge/2/_label[label=""substrate""]/value",

Vegetation,"Locality/_merge/3/_label[label=""vegetation""]/value",

Longitude,Longitude

MaximumDepth,MaximumDepth

MaximumElevation,MaximumElevation

MinimumDepth,MinimumDepth

MinimumElevation,MinimumElevation/_nullIf:[null=.]/value,

MonthCollected,MonthCollected

MonthIdentified,MonthIdentified

Notes,Notes/_merge/1,

PlantFungusDescription,"Notes/_merge/2/_label[label=""plant fungus""]/value",

Order,Order

Phylum,Phylum

PreparationType,PreparationType

PreviousCatalogNumber,PreviousCatalogNumber

RelatedCatalogItem,RelatedCatalogItem

RelationshipType,RelationshipType

ScientificName,ScientificName

ScientificNameAuthor,ScientificNameAuthor

Sex,Sex

Species,Species

StateProvince,StateProvince

Subspecies,Subspecies

TimeOfDay,TimeOfDay

TypeStatus,TypeStatus

YearCollected,YearCollected

YearIdentified,YearIdentified

UniqueNYInternalRecordNumber,occurrenceID,

FieldNumber,recordNumber,Usage inconsistent with DwC definition

key,,Not used because UniqueNYInternalRecordNumber is a better pkey

NY[Veg+],Veg+,Comments

key,,Not used because UniqueNYInternalRecordNumber is a better pkey

FieldNumber,recordNumber,Usage inconsistent with DwC definition

Locality,Locality/_merge/1,

MinimumElevation,MinimumElevation/_nullIf:[null=.]/value,

Notes,Notes/_merge/1,

PlantFungusDescription,"Notes/_merge/2/_label[label=""plant fungus""]/value",

Substrate,"Locality/_merge/2/_label[label=""substrate""]/value",

Vegetation,"Locality/_merge/3/_label[label=""vegetation""]/value",

UniqueNYInternalRecordNumber,occurrenceID,

Madidi,Veg+,Comments

Expedition,,

Inventory name,,

Number of inventory (general),,

Number of inventory (expedition),,

"Type Inventory (C, PP, TP)",,

Inventory code,,

Tag number,,

Tree number,,

Number of subplot,,

Index collector,,

Specimen,,

Similar specimen,,

Plot specimen,,

Expedition specimen,,

Project specimen,,

Field family,,

Field name,,

Family (revised),,

Specie+autor,,

Genera,,

Specific epithet,,

Species and morphotypes,,

Autor (revised),,

Determined by,,

Qualifier,,

Common name,,

Circumference,,

Diameter,,

Trunk,,

Total height,,

Bole height,,

Habit,,

Phenology,,

Crown position,,

Crown shape,,

Liana presence,,

Basal area,,

Subplot X,,

Subplot Y,,

Plot X,,

Plot Y,,

Observations,,

Madidi,Veg+,Comments

Autor (revised),,

Basal area,,

Bole height,,

Circumference,,

Common name,,

Crown position,,

Crown shape,,

Determined by,,

Diameter,,

Expedition,,

Expedition specimen,,

Family (revised),,

Field family,,

Field name,,

Genera,,

Habit,,

Index collector,,

Inventory code,,

Inventory name,,

Liana presence,,

Number of inventory (expedition),,

Number of inventory (general),,

Number of subplot,,

Observations,,

Phenology,,

Plot X,,

Plot Y,,

Plot specimen,,

Project specimen,,

Qualifier,,

Similar specimen,,

Specie+autor,,

Species and morphotypes,,

Specific epithet,,

Specimen,,

Subplot X,,

Subplot Y,,

Tag number,,

Total height,,

Tree number,,

Trunk,,

"Type Inventory (C, PP, TP)",,

Madidi,Veg+,Comments

Inventory number,,Not globally unique

Expedition number,projectID,Consistent (globally unique) between PPM and PT data

Expedition name,projectName,Consistent (globally unique) between PPM and PT data

Number of inventory (expedition),,The number of the event within the project

Inventory name,plotName,

Inventory code,locationID,

First evaluation,plotEventStartDate,

Installed and evaluated by,,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party"

Collaborators,,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party"

Related Epilocs,,"It appears to be a list of people, some with #s after them. It doesn't seem like the definition of Epiloc at <http://rithm.wikispaces.com/Tropicos.Epiloc>, which relates to individual specimens, not whole plots."

Area,plotArea,

Number of stems,,Do we want to store this data?

Number of trees,,Do we want to store this data?

Coordinates,,Concatenation of Latitude (DMS) and Longitude (DMS)

Latitude,decimalLatitude/_alt/1,

Longitude,decimalLongitude/_alt/1,

Latitude (DMS),decimalLatitude/_alt/2,

Longitude (DMS),decimalLongitude/_alt/2,

Altitude,verbatimElevation,

Minimum altitude,minimumElevationInMeters,

Locality,locality,

Locality description,communityName,Often begins with the text in Vegetation type

Direction,slopeAspect/_alt/1,Part files provide either this field or Direction

Vegetation type,communityID,

Topographical situation,landform,

Slope,slopeGradient,

Soil sample,,Always empty

pH acuoso (ISRIC 4–– 1 - 14),ph,

Conductividad electrica (ASPT 6–µS/cm– 1 - 10000),conductivity,

Nitrógeno total (ISRIC 6–%–0.0014),nitrogen,

"Carbón Orgánico (WSP S-9,10–%–0.06)",carbon,

"Materia Orgánica (WSP S-9,10–%–0.1)",organic,

Fósforo disponible (ISRIC 14-2–mg/Kg–1.5),phosphorus,

"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",sodium,

"Potasio intercambiable (WSP S-5,10–cmolc/Kg–0.0053)",potassium,

"Calcio intercambiable (WSP S-5,10–cmolc/Kg–0.016)",calcium,

"Magnesio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",magnesium,

Acidez intercambiable (ISRIC 11–cmolc/Kg–0.05),acidity,

CIC (ISRIC 11–cmolc/Kg–0.05),cationExchangeCapacity,

Arena (DIN 18 123–%–2.5),sand,

Limo (DIN 18 123–%–1),silt,

Arcilla (DIN 18 123–%–1),clay,

Textural class,texture,

Observaciones,plotNotes,

Orientación/exposicion,slopeAspect/_alt/2,Part files provide either this field or Orientación

Madidi,Veg+,Comments

Acidez intercambiable (ISRIC 11–cmolc/Kg–0.05),acidity,

"Calcio intercambiable (WSP S-5,10–cmolc/Kg–0.016)",calcium,

"Carbón Orgánico (WSP S-9,10–%–0.06)",carbon,

CIC (ISRIC 11–cmolc/Kg–0.05),cationExchangeCapacity,

Arcilla (DIN 18 123–%–1),clay,

Vegetation type,communityID,

Locality description,communityName,Often begins with the text in Vegetation type

Conductividad electrica (ASPT 6–µS/cm– 1 - 10000),conductivity,

Latitude,decimalLatitude/_alt/1,

Latitude (DMS),decimalLatitude/_alt/2,

Longitude,decimalLongitude/_alt/1,

Longitude (DMS),decimalLongitude/_alt/2,

Topographical situation,landform,

Locality,locality,

Inventory code,locationID,

"Magnesio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",magnesium,

Minimum altitude,minimumElevationInMeters,

Nitrógeno total (ISRIC 6–%–0.0014),nitrogen,

"Materia Orgánica (WSP S-9,10–%–0.1)",organic,

pH acuoso (ISRIC 4–– 1 - 14),ph,

Fósforo disponible (ISRIC 14-2–mg/Kg–1.5),phosphorus,

Area,plotArea,

First evaluation,plotEventStartDate,

Inventory name,plotName,

Observaciones,plotNotes,

"Potasio intercambiable (WSP S-5,10–cmolc/Kg–0.0053)",potassium,

Expedition number,projectID,Consistent (globally unique) between PPM and PT data

Expedition name,projectName,Consistent (globally unique) between PPM and PT data

Arena (DIN 18 123–%–2.5),sand,

Limo (DIN 18 123–%–1),silt,

Direction,slopeAspect/_alt/1,Part files provide either this field or Direction

Orientación/exposicion,slopeAspect/_alt/2,Part files provide either this field or Orientación

Slope,slopeGradient,

"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)",sodium,

Textural class,texture,

Altitude,verbatimElevation,

Collaborators,,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party"

Coordinates,,Concatenation of Latitude (DMS) and Longitude (DMS)

Installed and evaluated by,,"Need a way to store a verbatim list of people, or a function to parse it and insert it iteratively into party"

Inventory number,,Not globally unique

Number of inventory (expedition),,The number of the event within the project

Number of stems,,Do we want to store this data?

Number of trees,,Do we want to store this data?

Related Epilocs,,"It appears to be a list of people, some with #s after them. It doesn't seem like the definition of Epiloc at <http://rithm.wikispaces.com/Tropicos.Epiloc>, which relates to individual specimens, not whole plots."

Soil sample,,Always empty

UNCC[Veg+],Veg+,Comments

collector,Collector/_merge/1,

collector1,Collector/_merge/2,

collector2,Collector/_merge/3,

collector3,Collector/_merge/4,

sheetno,associatedMedia,?

collectno,collectorNumber,

country,country

county,county

collday,dayCollected,

cultivated,"establishmentMeans/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values

family,family

comment1,fieldNotes/_merge/1,

comment2,fieldNotes/_merge/2,

comment3,fieldNotes/_merge/3,

comment4,fieldNotes/_merge/4,

campus,"fieldNotes/_merge/5/_label[label=""campus""]/value",

loanto,"fieldNotes/_merge/6/_label[label=""loaned to""]/value",

inorout,"fieldNotes/_merge/7/_label[label=""in or out""]/value",

genus,genus

habitat,habitat

infraname,infraspecificEpithet,

herbarium,institutionCode,

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?"

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

SciName,scientificName,

authors,scientificNameAuthorship,

species,species

state,state

usdaRank,taxonRank/_alt/1,

infrarank,taxonRank/_alt/2,

collyear,yearCollected,

filler,,"Where used, same as family"

UNCC[Veg+],Veg+,Comments

accession,occurrenceID,

herbarium,institutionCode,

usdaRank,taxonRank/_alt/1,

infrarank,taxonRank/_alt/2,

infraname,infraspecificEpithet,

SciName,scientificName,

authors,scientificNameAuthorship,

collector,Collector/_merge/1,

collector1,Collector/_merge/2,

collector2,Collector/_merge/3,

collector3,Collector/_merge/4,

collectno,collectorNumber,

collmonth,monthCollected,

collday,dayCollected,

collyear,yearCollected,

campus,"fieldNotes/_merge/5/_label[label=""campus""]/value",

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

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?"

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

comment1,fieldNotes/_merge/1,

comment2,fieldNotes/_merge/2,

comment3,fieldNotes/_merge/3,

comment4,fieldNotes/_merge/4,

loanto,"fieldNotes/_merge/6/_label[label=""loaned to""]/value",

inorout,"fieldNotes/_merge/7/_label[label=""in or out""]/value",

sheetno,associatedMedia,?

cultivated,"establishmentMeans/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values

filler,,"Where used, same as family"

ACAD[Veg+],Veg+,Comments

basisOfRecord,basisOfRecord

bibliographicCitation,bibliographicCitation

catalogNumber,catalogNumber

class,class

collectionCode,collectionCode

collectionID,collectionID

continent,continent

country,country

county,county

dateIdentified,dateIdentified

decimalLatitude,decimalLatitude

decimalLongitude,decimalLongitude

dynamicProperties,dynamicProperties

eventDate,eventDate

family,family

genus,genus

geodeticDatum,geodeticDatum

georeferenceSources,georeferenceSources

georeferenceVerificationStatus,georeferenceVerificationStatus

habitat,habitat

id,id

identificationRemarks,identificationRemarks

identifiedBy,identifiedBy

infraspecificEpithet,infraspecificEpithet

institutionCode,institutionCode

kingdom,kingdom

language,language

locality,locality

locationRemarks,locationRemarks

modified,modified

municipality,municipality

occurrenceRemarks,occurrenceRemarks

order,order

ownerInstitutionCode,ownerInstitutionCode

phylum,phylum

recordNumber,recordNumber

recordedBy,recordedBy

reproductiveCondition,reproductiveCondition

rights,rights

rightsHolder,rightsHolder

scientificName,scientificName

scientificNameAuthorship,scientificNameAuthorship

specificEpithet,specificEpithet

stateProvince,stateProvince

taxonRank,taxonRank

type,type

verbatimDepth,verbatimDepth

verbatimElevation,verbatimElevation

ACAD[Veg+],Veg+,Comments

CVS,Veg+,Comments

authorObsCode,fieldNumber,

obsStartDate,plotEventStartDate,

realLatitude,decimalLatitude/_alt/1,

realLongitude,decimalLongitude/_alt/1,

locationAccuracy-m,coordinateUncertaintyInMeters,

publicLatitude,decimalLatitude/_alt/2,

publicLongitude,decimalLongitude/_alt/2,

confidentialityStatus,,

state,stateProvince,

county,county,

currentTaxonName sec Weakley 2006,scientificName,

%cover,coverPercent,

CVS,Veg+,Comments

locationAccuracy-m,coordinateUncertaintyInMeters,

county,county,

%cover,coverPercent,

realLatitude,decimalLatitude/_alt/1,

publicLatitude,decimalLatitude/_alt/2,

realLongitude,decimalLongitude/_alt/1,

publicLongitude,decimalLongitude/_alt/2,

authorObsCode,fieldNumber,

obsStartDate,plotEventStartDate,

currentTaxonName sec Weakley 2006,scientificName,

state,stateProvince,

confidentialityStatus,,

SALVIAS-CSV,Veg+,Comments

OBSERVATION_ID,individualID,"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."

PLOT_ID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."

plot_code,parentPlotName,"Brad: Same as plotCode, above"

census_no,censusNumber,"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."

census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:

-----

SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count

FROM ""SALVIAS-CSV"".organisms

WHERE subplot IS NOT NULL AND census_date IS NOT NULL

GROUP BY ""PLOT_ID"", subplot

HAVING count(DISTINCT census_date) > 1

-----"

subplot,plotName,

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."

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."

x_position,relativePlotX,"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,relativePlotY,Brad: See comment above for x_position

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: Incorrect. Map instead as for voucher_string

collector_code,,Brad: OMIT

coll_lastname,recordedBy.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."

coll_firstname,recordedBy.givenName,Brad: See comment above

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."

fam_status,,Brad: OMIT. This will be determined later by using TNRS.

gen_status,,Brad: OMIT. This will be determined later by using TNRS.

species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."

family,computer.family,

genus,computer.genus,

specific_epithet,computer.specificEpithet,

specific_authority,computer.scientificNameAuthorship,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.

infra_rank_1,computer.taxonRank,

infra_ep_1,computer.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

habit,"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: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

no_of_individuals,individualCount,"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,coverPercent,

intercept_cm,volumeCanopy,"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."

height_m,height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

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."

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

stem_dbh,diameterBreastHeight,

basal_diam,basalDiameter,

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

stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."

stem_canopy_form,canopyForm,Brad: Should also be userDefined for VegBank. 

stem_canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank. 

stem_liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank. 

notes,stemNotes,

orig_family,family,Brad: OMIT

orig_species,scientificName/_name/last,Brad: OMIT

SALVIAS-CSV,Veg+,Comments

basal_diam,basalDiameter,

stem_canopy_form,canopyForm,Brad: Should also be userDefined for VegBank. 

stem_canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank. 

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

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."

census_no,censusNumber,"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."

family,computer.family,

genus,computer.genus,

infra_ep_1,computer.infraspecificEpithet,

specific_authority,computer.scientificNameAuthorship,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.

specific_epithet,computer.specificEpithet,

infra_rank_1,computer.taxonRank,

cover_percent,coverPercent,

stem_dbh,diameterBreastHeight,

orig_family,family,Brad: OMIT

habit,"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: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

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

height_m,height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."

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."

no_of_individuals,individualCount,"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."

OBSERVATION_ID,individualID,"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."

stem_liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank. 

PLOT_ID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."

plot_code,parentPlotName,"Brad: Same as plotCode, above"

census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:

-----

SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count

FROM ""SALVIAS-CSV"".organisms

WHERE subplot IS NOT NULL AND census_date IS NOT NULL

GROUP BY ""PLOT_ID"", subplot

HAVING count(DISTINCT census_date) > 1

-----"

subplot,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: 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."

x_position,relativePlotX,"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,relativePlotY,Brad: See comment above for x_position

orig_species,scientificName/_name/last,Brad: OMIT

notes,stemNotes,

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."

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."

intercept_cm,volumeCanopy,"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."

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."

collector_code,,Brad: OMIT

comments,,Brad: OMIT

fam_status,,Brad: OMIT. This will be determined later by using TNRS.

gen_status,,Brad: OMIT. This will be determined later by using TNRS.

ind_id,,Brad: OMIT

species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."

SALVIAS-CSV,Veg+,Comments

project,projectName,

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

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

major_geo,continent,

country,country,

pol1,stateProvince,Brad: No; pol1=stateProvince

pol2,county,Brad: No pol2=countyParish

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"

lat_decimal,decimalLatitude,

long_decimal,decimalLongitude,

elev_m,verbatimElevation,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,

temp_c,temperature,

precip_mm,precipitation,

slope_aspect,slopeAspect,

slope_gradient,slopeGradient,

clay_percent,"clay/_units:[default=""%"",to=]/value",

silt_percent,"silt/_units:[default=""%"",to=]/value",

sand_percent,"sand/_units:[default=""%"",to=]/value",

organic_percent,"organic/_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_N,"nitrogen/_units:[default=""%"",to=]/value",

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

soil_C,"carbon/_units:[default=""%"",to=]/value",

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

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

soil_Ca,"calcium/_units:[default=""%"",to=]/value",

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

soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",

soil_base,"baseSaturation/_units:[default=""%"",to=]/value",

soil_cation_cap,cationExchangeCapacity,

soil_conductivity,conductivity,

soil_texture,texture,

holdridge_life_zone,communityID,

life_zone_code,communityName,

observation_type,,"Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type"

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"

date_start,plotEventStartDate,

date_finish,plotEventEndDate,

SALVIAS-CSV,Veg+,Comments

soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",

soil_base,"baseSaturation/_units:[default=""%"",to=]/value",

soil_Ca,"calcium/_units:[default=""%"",to=]/value",

soil_C,"carbon/_units:[default=""%"",to=]/value",

soil_cation_cap,cationExchangeCapacity,

clay_percent,"clay/_units:[default=""%"",to=]/value",

holdridge_life_zone,communityID,

life_zone_code,communityName,

soil_conductivity,conductivity,

major_geo,continent,

country,country,

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",

elev_max_m,maximumElevationInMeters,

elev_min_m,minimumElevationInMeters,

soil_N,"nitrogen/_units:[default=""%"",to=]/value",

organic_percent,"organic/_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"

date_finish,plotEventEndDate,

date_start,plotEventStartDate,

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,

project,projectName,

plot_methodology,samplingProtocol,

sand_percent,"sand/_units:[default=""%"",to=]/value",

silt_percent,"silt/_units:[default=""%"",to=]/value",

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,

elev_m,verbatimElevation,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.

observation_type,,"Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type"

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"

REMIB[Veg+],Veg+,Comments

acronym,collectionCode,

collector,collector

country,country

county,county

coll_day,dayCollected,

family,family

genus,genus

habitat,habitat

locality,locality

coll_month,monthCollected,

accession_number,occurrenceID,

preparation,preparation

specificEpithet,specificEpithet

state,state

lat_deg,verbatimLatitude,

long_deg,verbatimLongitude,

coll_year,yearCollected,

lat_min,,

lat_sec,,

long_min,,

long_sec,,

REMIB[Veg+],Veg+,Comments

acronym,collectionCode,

accession_number,occurrenceID,

long_deg,verbatimLongitude,

long_min,,

long_sec,,

lat_deg,verbatimLatitude,

lat_min,,

lat_sec,,

coll_day,dayCollected,

coll_month,monthCollected,

coll_year,yearCollected,

SALVIAS,Veg+,Comments

canopy_form,canopyForm,Brad: Should also be userDefined for VegBank. 

canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank. 

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

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."

census_no,censusNumber,"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."

Family,computer.family,

Genus,computer.genus,

infra_ep_1,computer.infraspecificEpithet,

auth,computer.scientificNameAuthorship,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,computer.specificEpithet,

infra_rank_1,computer.taxonRank,

cover_percent,coverPercent,

temp_dbh,diameterBreastHeight,

census_date,eventDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:

-----

SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count

FROM ""SALVIAS"".organisms

WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL

GROUP BY ""PlotID"", ""Line""

HAVING count(DISTINCT census_date) > 1

-----"

OrigFamily,family,Brad: OMIT

Notes,fieldNotes,

Habit,"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: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

height_m,height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

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."

NoInd,individualCount,"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."

PlotObsID,individualID,"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."

liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank. 

PlotID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."

PlotCode,parentPlotName,"Brad: Same as plotCode, above"

Line,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: 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."

x_position,relativePlotX,"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,relativePlotY,Brad: See comment above for x_position

OrigGenus,scientificName/_name/first,

OrigSpecies,scientificName/_name/last,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."

intercept_cm,volumeCanopy,"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."

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."

GenAuth,,

IsMorpho,,

OrigAuth,,

OrigRecordID,,

SpAuthStatus,,

coll_inits,,

collector_code,,Brad: OMIT

common_name,,

det_by,,

dist,,

fam_status,,Brad: OMIT. This will be determined later by using TNRS.

gen_status,,Brad: OMIT. This will be determined later by using TNRS.

height_class,,

height_m_commercial,,

ind_id,,Brad: OMIT

infra_auth_1,,

morphocf,,

morphoname,,

name_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."

other_annotations,,

perp_dist,,

phenology,,

species_code,,

temp_liandbh,,

tmp_del,,

SALVIAS,Veg+,Comments

soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",

soil_base,"baseSaturation/_units:[default=""%"",to=]/value",

soil_Ca,"calcium/_units:[default=""%"",to=]/value",

soil_C,"carbon/_units:[default=""%"",to=]/value",

soil_cation_cap,cationExchangeCapacity,

clay_percent,"clay/_units:[default=""%"",to=]/value",

life_zone_code,communityID,

life_zone,communityName,

soil_conductivity,conductivity,

MajorGeo,continent,

Country,country,

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",

elev_max_m,maximumElevationInMeters,

elev_min_m,minimumElevationInMeters,

soil_N,"nitrogen/_units:[default=""%"",to=]/value",

organic_percent,"organic/_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"

date_finish,plotEventEndDate,

date_start,plotEventStartDate,

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,

project_id,projectName,

PlotMethod,samplingProtocol,

sand_percent,"sand/_units:[default=""%"",to=]/value",

silt_percent,"silt/_units:[default=""%"",to=]/value",

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",

Elev,verbatimElevation,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.

AccessCode,,

ElevSource,,

Habitat,,

MethodCode,,

PrecipSource,,

PrimOwnerID,,

RevisionComments,,

SiteName,,

TempSource,,

bearing,,

lat_long_accuracy,,

lat_string,,

long_string,,

new_world,,

orig_filename,,

plot_administrator,,

plot_notes,,

pol1_type,,

pol2_type,,

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,,

topography_desc,,

vegetation_1,,

vegetation_2,,

SALVIAS,Veg+,Comments

basal_diam,basalDiameter,

stem_canopy_form,canopyForm,

stem_canopy_position,canopyPosition,

stem_dbh,diameterBreastHeight,

gentry_dbh,diameterBreastHeightGentry,

stem_height_m,height,

stem_height_first_branch_m,heightFirstBranch,

PlotObsID,individualID,

stem_liana_infestation,lianaInfestation,

stem_tag2,previousTag,

NoInd,stemCount,

stem_notes,stemNotes,

stem_tag1,tag,

origrecord_id_stems,,

stem_id,,

tmp_del,,

SALVIAS,Veg+,Comments

PlotObsID,individualID,"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."

PlotID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."

PlotCode,parentPlotName,"Brad: Same as plotCode, above"

census_no,censusNumber,"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."

census_date,eventDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:

-----

SELECT ""PlotID"", ""Line"", count(DISTINCT census_date) AS census_date_count

FROM ""SALVIAS"".organisms

WHERE ""Line"" IS NOT NULL AND census_date IS NOT NULL

GROUP BY ""PlotID"", ""Line""

HAVING count(DISTINCT census_date) > 1

-----"

OrigRecordID,,

Line,plotName,

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."

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."

x_position,relativePlotX,"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,relativePlotY,Brad: See comment above for x_position

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."

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

collector_code,,Brad: OMIT

coll_inits,,

coll_lastname,recordedBy.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."

coll_firstname,recordedBy.givenName,Brad: See comment above

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."

det_by,,

fam_status,,Brad: OMIT. This will be determined later by using TNRS.

gen_status,,Brad: OMIT. This will be determined later by using TNRS.

name_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."

SpAuthStatus,,

Family,computer.family,

Genus,computer.genus,

GenAuth,,

Species,computer.specificEpithet,

auth,computer.scientificNameAuthorship,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.

infra_rank_1,computer.taxonRank,

infra_ep_1,computer.infraspecificEpithet,

infra_auth_1,,

common_name,,

morphoname,,

species_code,,

Habit,"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: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."

height_class,,

height_m,height,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

height_m_commercial,,

ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob

NoInd,individualCount,"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,coverPercent,

intercept_cm,volumeCanopy,"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."

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."

other_annotations,,

morphocf,,

IsMorpho,,

OrigFamily,family,Brad: OMIT

OrigGenus,scientificName/_name/first,

OrigSpecies,scientificName/_name/last,Brad: OMIT

OrigAuth,,

phenology,,

canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank. 

canopy_form,canopyForm,Brad: Should also be userDefined for VegBank. 

liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank. 

Notes,fieldNotes,

temp_dbh,diameterBreastHeight,

temp_liandbh,,

tmp_del,,

SALVIAS,Veg+,Comments

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

orig_filename,,

AccessCode,,

project_id,projectName,

PrimOwnerID,,

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

SiteName,,

new_world,,

MajorGeo,continent,

Country,country,

PolDiv1,stateProvince,Brad: No; pol1=stateProvince

pol1_type,,

pol2,county,Brad: No pol2=countyParish

pol2_type,,

lat_string,,

long_string,,

LatDec,decimalLatitude,

LongDec,decimalLongitude,

lat_long_accuracy,,

Elev,verbatimElevation,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,,

Temp,temperature,

PrecipSource,,

TempSource,,

bearing,,

slope_aspect,slopeAspect,

slope_gradient,slopeGradient,

clay_percent,"clay/_units:[default=""%"",to=]/value",

silt_percent,"silt/_units:[default=""%"",to=]/value",

sand_percent,"sand/_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_N,"nitrogen/_units:[default=""%"",to=]/value",

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

soil_C,"carbon/_units:[default=""%"",to=]/value",

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

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

soil_Ca,"calcium/_units:[default=""%"",to=]/value",

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

soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",

soil_base,"baseSaturation/_units:[default=""%"",to=]/value",

soil_cation_cap,cationExchangeCapacity,

soil_conductivity,conductivity,

organic_percent,"organic/_units:[default=""%"",to=]/value",

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

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,,

vegetation_1,,

vegetation_2,,

Habitat,,

life_zone_code,communityID,

life_zone,communityName,

PlotMethod,samplingProtocol,

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"

date_start,plotEventStartDate,

date_finish,plotEventEndDate,

plot_administrator,,

plot_notes,,

tmp_del,,

SALVIAS,Veg+,Comments

stem_id,,

origrecord_id_stems,,

PlotObsID,individualID,

NoInd,stemCount,

basal_diam,basalDiameter,

stem_dbh,diameterBreastHeight,

gentry_dbh,diameterBreastHeightGentry,

stem_notes,stemNotes,

stem_tag1,tag,

stem_tag2,previousTag,

stem_height_m,height,

stem_height_first_branch_m,heightFirstBranch,

stem_canopy_form,canopyForm,

stem_canopy_position,canopyPosition,

stem_liana_infestation,lianaInfestation,

tmp_del,,

U[Veg+],Veg+,Comments

Barcode,CatalogNumber,

Collector,Collector/_merge/1,

Addcoll,Collector/_merge/2,

Country,Country

Colldd,DayCollected,

Lat,DecimalLatitude,

Long,DecimalLongitude,

Family,Family

Genus,Genus

ID,GlobalUniqueIdentifier,

Ecology,Habitat,

cf,IdentificationQualifier,

Detby,IdentifiedBy,

Collmm,MonthCollected,

Notes,Notes

Number,RecordNumber,

Phenology,ReproductiveCondition,

Gazetteer,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1",

Newgazett,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row

Locnotes,VerbatimLocality/_merge/2,

Collyy,YearCollected,

Detyy,YearIdentified,

Alt,,What is this?

Alt2,,What is this?

Coorsyst,,

DateInfo,,Not used

EW,,

Majorarea,,

NS,,

Prefix,,Not used

Suffix,,Not used

U[Veg+],Veg+,Comments

ID,GlobalUniqueIdentifier,

Barcode,CatalogNumber,

Collector,Collector/_merge/1,

Prefix,,Not used

Number,RecordNumber,

Suffix,,Not used

Addcoll,Collector/_merge/2,

Colldd,DayCollected,

Collmm,MonthCollected,

Collyy,YearCollected,

DateInfo,,Not used

cf,IdentificationQualifier,

Detby,IdentifiedBy,

Detyy,YearIdentified,

Gazetteer,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1",

Newgazett,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row

Majorarea,,

Locnotes,VerbatimLocality/_merge/2,

Coorsyst,,

Lat,DecimalLatitude,

NS,,

Long,DecimalLongitude,

EW,,

Alt,,What is this?

Alt2,,What is this?

Ecology,Habitat,

Phenology,ReproductiveCondition,

ARIZ[Veg+],Veg+,Comments

BasisOfRecord,BasisOfRecord

BoundingBox,BoundingBox

CatalogNumberNumeric,CatalogNumber,

Class,Class

CollectionCode,CollectionCode

Collector,Collector

CollectorNumber,CollectorNumber

ContinentOcean,ContinentOcean

CoordinateUncertaintyInMeters,CoordinateUncertaintyInMeters

Country,Country

County,County

DateLastModified,DateLastModified

DayCollected,DayCollected

DayIdentified,DayIdentified

DecimalLatitude,DecimalLatitude

DecimalLongitude,DecimalLongitude

Family,Family

FieldNotes,FieldNotes

Genus,Genus

GlobalUniqueIdentifier,GlobalUniqueIdentifier

HigherGeography,HigherGeography

IdentifiedBy,IdentifiedBy

IndividualCount,IndividualCount

InstitutionCode,InstitutionCode

Island,Island

IslandGroup,IslandGroup

JulianDay,JulianDay

Kingdom,Kingdom

Locality,Locality

MaximumDepthInMeters,MaximumDepthInMeters

MaximumElevationInMeters,MaximumElevationInMeters

MinimumDepthInMeters,MinimumDepthInMeters

MinimumElevationInMeters,MinimumElevationInMeters

MonthCollected,MonthCollected

MonthIdentified,MonthIdentified

Order,Order

Phylum,Phylum

Preparations,Preparations

OtherCatalogNumbers,RelatedCatalogItem,

RelatedCatalogedItems,RelatedCatalogItem,"Used only when OtherCatalogNumbers is NULL, so _alt not needed"

Remarks,Remarks

ScientificNameAuthor,ScientificName/_alt/1,Contains the binomial in addition to the authority

ScientificName,ScientificName/_alt/2,

Sex,Sex

Species,Species

StateProvince,StateProvince

Subspecies,Subspecies

TimeCollected,TimeOfDay,

TypeStatus,TypeStatus

VerbatimDepth,VerbatimDepth

VerbatimElevation,VerbatimElevation

VerbatimLatitude,VerbatimLatitude

VerbatimLongitude,VerbatimLongitude

YearCollected,YearCollected

YearIdentified,YearIdentified

GenBankNum,"associatedSequences/_label[label=""GenBank""]/value",

VerbatimCollectingDate,dateCollected/_alt/0,

GeorefMethod,georeferenceProtocol,

LatLongComments,georeferenceRemarks,

IdentificationModifier,identificationQualifier,

AgeClass,lifeStage,

FieldNumber,recordNumber,Usage inconsistent with DwC definition

OriginalCoordinateSystem,verbatimSRS,

CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric

HorizontalDatum,,Not used

Tissues,,Not used

ARIZ[Veg+],Veg+,Comments

CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric

CatalogNumberNumeric,CatalogNumber,

FieldNumber,recordNumber,Usage inconsistent with DwC definition

TimeCollected,TimeOfDay,

VerbatimCollectingDate,dateCollected/_alt/0,

HorizontalDatum,,Not used

OriginalCoordinateSystem,verbatimSRS,

GeorefMethod,georeferenceProtocol,

LatLongComments,georeferenceRemarks,

ScientificName,ScientificName/_alt/2,

ScientificNameAuthor,ScientificName/_alt/1,Contains the binomial in addition to the authority

IdentificationModifier,identificationQualifier,

Tissues,,Not used

AgeClass,lifeStage,

GenBankNum,"associatedSequences/_label[label=""GenBank""]/value",

OtherCatalogNumbers,RelatedCatalogItem,

RelatedCatalogedItems,RelatedCatalogItem,"Used only when OtherCatalogNumbers is NULL, so _alt not needed"