-----

-----"

Addcoll,recordedBy,/_join/2,

AgeClass,lifeStage,,

Altitude,elevationInMeters,,"Assuming units are m based on the range of values [1] and the region the data is from (Madidi National Park) [2].

Area,plotArea_ha,,"""0.1 ha transects"" (""Madidi Transects"" description in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/BIEN2.datasources.xlsx>)"

AuthorOfScientificName,scientificNameAuthorship,,

Autor (revised),scientificNameAuthorship,,

Barcode,catalogNumber,,

CatalogNO,catalogNumber,,

CatalogNumberNumeric,catalogNumber,/_alt/1,

Colldd,dayCollected,,

CollectionCD,collectionCode,,

CollectionDate,eventDate,,

Collmm,monthCollected,,

Collyy,yearCollected,,

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

DateInfo,UNUSED,,

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."

Detby,identifiedBy,,

Determined by,identifiedBy,,

Diameter at 1.3m,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 7 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>)"

Diameter,diameterBreastHeight_cm,,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 7 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>)"

Diameter,diameterBreastHeight_cm,,Assuming units based on the range and precision of values

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

Ecology,habitat,,

Elev,elevationInMeters,,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.

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

Expedition,projectName,,

FROM ""Madidi"".""Plot""

FROM ""SALVIAS"".organisms

FROM ""SALVIAS-CSV"".organisms

Family (revised),family,,

First evaluation,eventDate,,

GROUP BY ""Altitude""::real , ""Locality""

GROUP BY ""Minimum altitude"" , ""Locality""

GROUP BY ""PLOT_ID"", subplot

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

Gazetteer,verbatimLocality,"/_join/1/_label[label=""gazetteer""]/value/_join/1",

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

Genera,genus,,

GeorefMethod,georeferenceProtocol,,

HAVING count(DISTINCT census_date) > 1

HorizontalDatum,UNUSED,,

IdentificationModifier,identificationQualifier,,

Index collector,recordedBy,,

InfraSpecificLevel,UNUSED,,

InstitutionCD,institutionCode,,

Inventory code,locationID,,

Lat,decimalLatitude,,

LatDec,decimalLatitude,,

LatLongComments,georeferenceRemarks,,

LatestDateCollected,dateCollected,,

Liana presence,lianaInfestation,,

Line,subplot,,

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

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"

Locnotes,verbatimLocality,/_join/2,

Long,decimalLongitude,,

LongDec,decimalLongitude,,

MajorGeo,continent,,

MaximumElevationInMeter,maximumElevationInMeters,,

MeasDay,dayCollected,,

MeasMon,monthCollected,,

MeasYear,yearCollected,,

MeasureID,individualID,,

Minimum altitude,verbatimElevation_m,,"This is a range [1], not a minimum. Assuming units are m based on the range of values [1] and the region the data is from (Madidi National Park) [2].

MinimumElevationInMeter,minimumElevationInMeters,,

Names of Collectors,recordedBy,,

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

NoInd,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."

NoInd,stemCount,,

Number of subplot,subplot,,

Number,recordNumber,,

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."

ORDER BY ""Altitude""::real DESC

Observaciones,plotNotes,,

Observation Date,eventDate,,

Observations,fieldNotes,,

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

OriginalCoordinateSystem,verbatimSRS,,

Phenology,reproductiveCondition,,

PlantFungusDescription,fieldNotes,"/_join/2/_label[label=""plant fungus""]/value",

PlotCD,locationID,,

PlotMethod,samplingProtocol,,

PlotObsID,individualID,,

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."

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

Precip,precipitation,,

Prefix,UNUSED,,

Qualifier,identificationQualifier,,

RelatedCatalogedItems,relatedResourceID,/_alt/2,Used only when OtherCatalogNumbers is NULL

SELECT ""Altitude""::real, ""Locality""

SELECT ""Minimum altitude"", ""Locality""

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

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

SELECT count(*) FROM ""SpeciesLink"".specimens

Site Name,projectName,,

SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)"

Slope,slopeGradient,,

SpeciesAuthority,scientificNameAuthorship,,

Specimen,catalogNumber,,

Subplot Number,subplot,,

Substrate,locality,"/_join/2/_label[label=""substrate""]/value",

Suffix,UNUSED,,

Tag number,tag,,

Temp,temperature,,

Textural class,texture,,

TimeCollected,eventTime,,

Tissues,UNUSED,,

Topographical situation,landform,,

Tree Number,tag,,

TreeTag,tag,,

Trunk,authorStemCode,,

Vegetation type,communityID,,

Vegetation,locality,"/_join/3/_label[label=""vegetation""]/value",

VerbatimCollectingDate,dateCollected,/_alt/0,

WHERE ""Altitude"" IS NOT NULL AND ""Altitude"" != ' 1430'

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

WHERE ""Minimum altitude"" IS NOT NULL

WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""

WHERE subplot IS NOT NULL AND census_date IS NOT NULL

[1] Using the following query:

[2] This map shows both flat and mountainous regions: <https://maps.google.com/maps/ms?ie=UTF8&hl=en&t=h&msa=0&msid=103363035880599665829.00047e9cf84b87448387d&ll=-13.96448,-68.380065&spn=3.730927,4.669189&z=7>"

area,plotArea_m2,,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)"

area|country|territory,country,,

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

authors,scientificNameAuthorship,,

basal_diam,basalDiameter,,

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

cf,identificationQualifier,,

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."

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."

coll_day,dayCollected,,

coll_month,monthCollected,,

coll_year,yearCollected,,

collday,dayCollected,,

collectiondate,dateCollected,,

collectno,recordNumber,,

collector1,recordedBy,/_join/2,

conceptual_darwin_2003_1_0_CoordinatePrecision,coordinatePrecision,,

conceptual_darwin_2003_1_0_Country,country,,

conceptual_darwin_2003_1_0_County,county,,

conceptual_darwin_2003_1_0_DayCollected,dayCollected,,

conceptual_darwin_2003_1_0_DayIdentified,dayIdentified,,

conceptual_darwin_2003_1_0_Family,family,,

conceptual_darwin_2003_1_0_InstitutionCode,institutionCode,,

conceptual_darwin_2003_1_0_JulianDay,day,/_alt/1,

conceptual_darwin_2003_1_0_Kingdom,kingdom,,

conceptual_darwin_2003_1_0_Locality,locality,,

conceptual_darwin_2003_1_0_MaximumDepth,maximumDepthInMeters,,

conceptual_darwin_2003_1_0_MaximumElevation,maximumElevationInMeters,,

conceptual_darwin_2003_1_0_MinimumDepth,minimumDepthInMeters,,

conceptual_darwin_2003_1_0_PreviousCatalogNumber,otherCatalogNumbers,,

conceptual_darwin_2003_1_0_RelatedCatalogItem,relatedResourceID,,

conceptual_darwin_2003_1_0_RelationshipType,relationshipOfResource,,

conceptual_darwin_2003_1_0_ScientificNameAuthor,scientificNameAuthorship,/_alt/2,

conceptual_darwin_2003_1_0_Sex,sex,,

conceptual_darwin_2003_1_0_Species,specificEpithet,,

conceptual_darwin_2003_1_0_TypeStatus,typeStatus,,

conceptual_darwin_2003_1_0_YearCollected,yearCollected,,

conceptual_darwin_2003_1_0_YearIdentified,yearIdentified,,

convertednotes,fieldNotes,,

darwin:BasisOfRecord,basisOfRecord,,

darwin:CatalogNumber,catalogNumber,,

darwin:Class,class,,

darwin:Collector,recordedBy,,

darwin:CollectorNumber,recordNumber,,

darwin:ContinentOcean,continent,,

darwin:Country,country,,

darwin:County,county,,

darwin:DayCollected,dayCollected,,

darwin:DayIdentified,dayIdentified,,

darwin:Family,family,,

darwin:Genus,genus,,

darwin:IdentifiedBy,identifiedBy,,

darwin:IndividualCount,individualCount,,

darwin:InstitutionCode,institutionCode,,

darwin:JulianDay,day,,

darwin:Kingdom,kingdom,,

darwin:Locality,locality,,

darwin:MaximumDepth,maximumDepthInMeters,,

darwin:MaximumElevation,maximumElevationInMeters,,

darwin:MinimumDepth,minimumDepthInMeters,,

darwin:PreviousCatalogNumber,otherCatalogNumbers,,

darwin:RelatedCatalogItem,relatedResourceID,,

darwin:RelationshipType,relationshipOfResource,,

darwin:ScientificNameAuthor,scientificNameAuthorship,,

darwin:Sex,sex,,

darwin:Species,specificEpithet,,

darwin:YearIdentified,yearIdentified,,

date_finish,endDate,,

date_start,startDate,,

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."

dwc_curatorial_CollectorNumber,recordNumber,/_alt/3,

dwc_curatorial_FieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)

dwc_dwcore_Continent,continent,,

dwc_dwcore_Country,country,,

dwc_dwcore_County,county,,

dwc_dwcore_DayOfYear,day,/_alt/2,

dwc_dwcore_Family,family,,

dwc_dwcore_Genus,genus,,

dwc_dwcore_Order,order,,

dwc_dwcore_Phylum,phylum,,

dwc_dwcore_Remarks,taxonRemarks,,

dwc_dwcore_Sex,sex,,

dwc_dwcore_SpecificEpithet,specificEpithet,,

dwc_dwcore_StateProvince,stateProvince,,

dwc_geospatial_DecimalLatitude,decimalLatitude,,

dwc_geospatial_DecimalLongitude,decimalLongitude,,

dwc_terms_basisOfRecord,basisOfRecord,,

dwc_terms_catalogNumber,catalogNumber,,

dwc_terms_class,class,,

dwc_terms_preparations,preparations,,

dwc_terms_recordNumber,recordNumber,/_alt/1,

dwc_terms_recordedBy,recordedBy,,

dwc_terms_scientificNameAuthorship,scientificNameAuthorship,/_alt/1,

dwc_terms_sex,sex,,

dwc_terms_specificEpithet,specificEpithet,,

elev_m,elevationInMeters,,Brad: Mean elevation in meters. This is a constrained decimal value; is there no place for this in VegX other than verbatimElevation? Check with Nick.

elev_max_m,maximumElevationInMeters,,

elev_min_m,minimumElevationInMeters,,

elevationrange,UNUSED,,

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?"

gentry_dbh,diameterBreastHeightGentry,,

herbarium,institutionCode,,

holdridge_life_zone,communityID,,

ht_first_branch_m,heightFirstBranch,,

infra_ep_1,infraspecificEpithet,,

infra_rank_1,taxonRank,,

infraname,infraspecificEpithet,,

infrarank,taxonRank,/_alt/2,

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

interpretationdate,dateIdentified,,

key,OMIT,,UniqueNYInternalRecordNumber is a better pkey

lat_decimal,decimalLatitude,,

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

life_zone_code,communityName,,

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

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"

long_decimal,decimalLongitude,,

major_geo,continent,,

methodnarrative,samplingProtocol,,

museumaccessionnumber,catalogNumber,,

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."

obsStartDate,startDate,,

obsenddate,endDate,,

observation_id,eventID,,

obsstartdate,startDate,,

pH acuoso (ISRIC 4–– 1 - 14),ph,,

parent_id,parentLocationID,,

plot_methodology,samplingProtocol,,

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

pol2,county,,Brad: No pol2=countyParish

precip_mm,precipitation,,

project,projectName,,

region|state|province,stateProvince,,

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

shape,footprintWKT,,

sheetno,associatedMedia,,?

soil_conductivity,conductivity,,

soil_texture,texture,,

soilph,ph,,

soiltexture,texture,,

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

stem_canopy_form,canopyForm,,

stem_canopy_position,canopyPosition,,

stem_dbh,diameterBreastHeight_cm,,"Assuming units based on the units for intercept_cm, which measures the same dimension"

stem_dbh,diameterBreastHeight_cm,,"Assuming units based on the units for plotObservations.intercept_cm, which measures the same dimension"

stem_height_first_branch_m,heightFirstBranch,,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."

stem_liana_infestation,lianaInfestation,,

stem_tag1,tag,/_alt/1/_alt/2,"The second tag supercedes the first. The stem tag supercedes the tree tag. 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_tag1,tag,/_alt/2,"The second tag supercedes the first. 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_tag2,tag,/_alt/1,"The second tag supercedes the first. 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,tag,/_alt/1/_alt/1,The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above

tag1,tag,/_alt/2,"The second tag supercedes the first. 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."

tag1,tag,/_alt/2/_alt/2,"The second tag supercedes the first. The stem tag supercedes the tree 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,tag,/_alt/1,"The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

tag2,tag,/_alt/2/_alt/1,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."

temp_c,temperature,,

temp_dbh,diameterBreastHeight_cm,,"Assuming units based on the units for intercept_cm, which measures the same dimension"

usdaRank,taxonRank,/_alt/1,