stem_id,stemID,,

PlotObsID,individualID,,

NoInd,stemCount,,

basal_diam,basalDiameter,,

stem_dbh,diameterBreastHeight_m,,

gentry_dbh,diameterBreastHeightGentry,,

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_height_m,height,,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."

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

stem_canopy_form,canopyForm,,

stem_canopy_position,canopyPosition,,

stem_liana_infestation,lianaInfestation,,

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."

PlotCode,plotName,,

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

-----"

Line,subplot,,

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."

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."

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."

x_position,organismX,,"Brad: These are important, fundamental values of many tree plots"

y_position,organismY,,Brad: See comment above for x_position

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: Map instead as for voucher_string

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."

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."

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

infra_rank_1,taxonRank,,

infra_ep_1,infraspecificEpithet,,

height_m,height,,

ht_first_branch_m,heightFirstBranch,,

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."

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."

OrigFamily,verbatimFamily,,Brad: OMIT

OrigGenus,verbatimGenus,,

OrigSpecies,verbatimSpecificEpithet,,Brad: OMIT

temp_dbh,diameterBreastHeight_m,,

Accession Number,occurrenceID,,

SeriesName,collectionCode,,

Barcode,catalogNumber,,

Full Taxon Name,scientificName,,

Collect Date,dateCollected,,

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

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

Accuracy,coordinateUncertaintyInMeters,,

Format,preparations,,

Typology,typeStatus,,

-----

-----"

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

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

conceptual_darwin_2003_1_0_BasisOfRecord,basisOfRecord,,

conceptual_darwin_2003_1_0_BoundingBox,footprintWKT,,

conceptual_darwin_2003_1_0_CatalogNumber,catalogNumber,,

conceptual_darwin_2003_1_0_Class,class,,

conceptual_darwin_2003_1_0_CollectionCode,collectionCode,,

conceptual_darwin_2003_1_0_Collector,recordedBy,,

conceptual_darwin_2003_1_0_CollectorNumber,recordNumber,/_alt/3,

conceptual_darwin_2003_1_0_ContinentOcean,continent,,

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_DateLastModified,dcterms:modified,,

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_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)

conceptual_darwin_2003_1_0_Genus,genus,,

conceptual_darwin_2003_1_0_IdentifiedBy,identifiedBy,,

conceptual_darwin_2003_1_0_IndividualCount,individualCount,,

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_Latitude,verbatimLatitude,,

conceptual_darwin_2003_1_0_Locality,locality,,

conceptual_darwin_2003_1_0_Longitude,verbatimLongitude,,

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_MinimumElevation,minimumElevationInMeters,,

conceptual_darwin_2003_1_0_MonthCollected,monthCollected,,

conceptual_darwin_2003_1_0_MonthIdentified,monthIdentified,,

conceptual_darwin_2003_1_0_Notes,fieldNotes,,

conceptual_darwin_2003_1_0_Order,order,,

conceptual_darwin_2003_1_0_Phylum,phylum,,

conceptual_darwin_2003_1_0_PreparationType,preparations,,

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_ScientificName,scientificName,,

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_StateProvince,stateProvince,,

conceptual_darwin_2003_1_0_Subspecies,subspecies,,

conceptual_darwin_2003_1_0_TimeOfDay,eventTime,,

conceptual_darwin_2003_1_0_TypeStatus,typeStatus,,

conceptual_darwin_2003_1_0_YearCollected,yearCollected,,

conceptual_darwin_2003_1_0_YearIdentified,yearIdentified,,

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_curatorial_IdentifiedBy,identifiedBy,,

dwc_curatorial_IndividualCount,individualCount,,

dwc_curatorial_TypeStatus,typeStatus,,

dwc_dwcore_AuthorYearOfScientificName,scientificNameAuthorship,/_alt/3,

dwc_dwcore_BasisOfRecord,basisOfRecord,,

dwc_dwcore_CatalogNumber,catalogNumber,,

dwc_dwcore_Class,class,,

dwc_dwcore_CollectionCode,collectionCode,,

dwc_dwcore_Collector,recordedBy,,

dwc_dwcore_Continent,continent,,

dwc_dwcore_Country,country,,

dwc_dwcore_County,county,,

dwc_dwcore_DateLastModified,dcterms:modified,,

dwc_dwcore_DayOfYear,day,/_alt/2,

dwc_dwcore_Family,family,,

dwc_dwcore_Genus,genus,,

dwc_dwcore_GlobalUniqueIdentifier,occurrenceID,,

dwc_dwcore_InfraspecificEpithet,infraspecificEpithet,,

dwc_dwcore_InstitutionCode,institutionCode,,

dwc_dwcore_Kingdom,kingdom,,

dwc_dwcore_Locality,locality,,

dwc_dwcore_MaximumDepthInMeters,maximumDepthInMeters,,

dwc_dwcore_MaximumElevationInMeters,maximumElevationInMeters,,

dwc_dwcore_MinimumDepthInMeters,minimumDepthInMeters,,

dwc_dwcore_MinimumElevationInMeters,minimumElevationInMeters,,

dwc_dwcore_Order,order,,

dwc_dwcore_Phylum,phylum,,

dwc_dwcore_Remarks,taxonRemarks,,

dwc_dwcore_ScientificName,scientificName,,

dwc_dwcore_Sex,sex,,

dwc_dwcore_SpecificEpithet,specificEpithet,,

dwc_dwcore_StateProvince,stateProvince,,

dwc_geospatial_DecimalLatitude,decimalLatitude,,

dwc_geospatial_DecimalLongitude,decimalLongitude,,

dwc_geospatial_VerbatimLatitude,verbatimLatitude,,

dwc_geospatial_VerbatimLongitude,verbatimLongitude,,

dwc_terms_basisOfRecord,basisOfRecord,,

dwc_terms_catalogNumber,catalogNumber,,

dwc_terms_class,class,,

dwc_terms_collectionCode,collectionCode,,

dwc_terms_collectionID,collectionID,,

dwc_terms_continent,continent,,

dwc_terms_coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,

dwc_terms_country,country,,

dwc_terms_county,county,,

dwc_terms_dateIdentified,dateIdentified,,

dwc_terms_day,day,,

dwc_terms_decimalLatitude,decimalLatitude,,

dwc_terms_decimalLongitude,decimalLongitude,,

dwc_terms_endDayOfYear,endDayOfYear,,

dwc_terms_eventTime,eventTime,,

dwc_terms_family,family,,

dwc_terms_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_terms_genus,genus,,

dwc_terms_identifiedBy,identifiedBy,,

dwc_terms_individualCount,individualCount,,

dwc_terms_infraspecificEpithet,infraspecificEpithet,,

dwc_terms_institutionCode,institutionCode,,

dwc_terms_kingdom,kingdom,,

dwc_terms_locality,locality,,

dwc_terms_maximumDepthInMeters,maximumDepthInMeters,,

dwc_terms_maximumElevationInMeters,maximumElevationInMeters,,

dwc_terms_minimumDepthInMeters,minimumDepthInMeters,,

dwc_terms_minimumElevationInMeters,minimumElevationInMeters,,

dwc_terms_month,month,,

dwc_terms_occurrenceRemarks,occurrenceRemarks,,

dwc_terms_order,order,,

dwc_terms_otherCatalogNumbers,otherCatalogNumbers,,

dwc_terms_phylum,phylum,,

dwc_terms_preparations,preparations,,

dwc_terms_recordNumber,recordNumber,/_alt/1,

dwc_terms_recordedBy,recordedBy,,

dwc_terms_scientificName,scientificName,,

dwc_terms_scientificNameAuthorship,scientificNameAuthorship,/_alt/1,

dwc_terms_sex,sex,,

dwc_terms_specificEpithet,specificEpithet,,

dwc_terms_startDayOfYear,startDayOfYear,,

dwc_terms_stateProvince,stateProvince,,

dwc_terms_typeStatus,typeStatus,,

dwc_terms_verbatimLatitude,verbatimLatitude,,

dwc_terms_verbatimLongitude,verbatimLongitude,,

dwc_terms_year,year,,

http__purl_org_dc_terms_modified,dcterms:modified,,

define unmappedTerms

	$(call unmappedTerms,1,|$(bin)/filter_out_ci 0 $(coreMap))

	$(newTerms)

	$(bin)/autoremove $@

newTerms = tail -n +2 $<|$(bin)/filter_out_ci 0 $(vocab)|$(bin)/filter_out_ci 0\

$(dict) $(if $(wildcard $(word 4,$+)),|$(bin)/filter_out_ci 0 $(word 4,$+)) >$@

Addcoll,recordedBy,/_join/2,

Barcode,catalogNumber,,

Colldd,dayCollected,,

Collmm,monthCollected,,

Collyy,yearCollected,,

DateInfo,UNUSED,,

Detby,identifiedBy,,

Detyy,yearIdentified,,

Ecology,habitat,,

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

Lat,decimalLatitude,,

Locnotes,verbatimLocality,/_join/2,

Long,decimalLongitude,,

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

Number,recordNumber,,

Phenology,reproductiveCondition,,

Prefix,UNUSED,,

Suffix,UNUSED,,

cf,identificationQualifier,,

AgeClass,lifeStage,,

CatalogNumberNumeric,catalogNumber,/_alt/1,

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

GeorefMethod,georeferenceProtocol,,

HorizontalDatum,UNUSED,,

IdentificationModifier,identificationQualifier,,

LatLongComments,georeferenceRemarks,,

OriginalCoordinateSystem,verbatimSRS,,

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

TimeCollected,eventTime,,

Tissues,UNUSED,,

VerbatimCollectingDate,dateCollected,/_alt/0,

AuthorOfScientificName,scientificNameAuthorship,,

CatalogNO,catalogNumber,,

CollectionCD,collectionCode,,

GBIFFamilyOriginal,verbatimFamily,,

GBIFGenusOriginal,verbatimGenus,,

InstitutionCD,institutionCode,,

LastDateModified,dcterms:modified,,

LatestDateCollected,dateCollected,,

MaximumElevationInMeter,maximumElevationInMeters,,

MinimumElevationInMeter,minimumElevationInMeters,,

ScientificNameOriginal,verbatimScientificName,,

dwc_dwcore_GlobalUniqueIdentifier,occurrenceID,,

dwc_dwcore_DateLastModified,dcterms:modified,,

dwc_dwcore_BasisOfRecord,basisOfRecord,,

dwc_dwcore_InstitutionCode,institutionCode,,

dwc_dwcore_CollectionCode,collectionCode,,

dwc_dwcore_CatalogNumber,catalogNumber,,

dwc_dwcore_Remarks,taxonRemarks,,

dwc_dwcore_ScientificName,scientificName,,

dwc_dwcore_Kingdom,kingdom,,

dwc_dwcore_Phylum,phylum,,

dwc_dwcore_Class,class,,

dwc_dwcore_Order,order,,

dwc_dwcore_Family,family,,

dwc_dwcore_Genus,genus,,

dwc_dwcore_SpecificEpithet,specificEpithet,,

dwc_dwcore_InfraspecificEpithet,infraspecificEpithet,,

dwc_dwcore_AuthorYearOfScientificName,scientificNameAuthorship,/_alt/3,

dwc_dwcore_Continent,continent,,

dwc_dwcore_Country,country,,

dwc_dwcore_StateProvince,stateProvince,,

dwc_dwcore_County,county,,

dwc_dwcore_Locality,locality,,

dwc_dwcore_MinimumElevationInMeters,minimumElevationInMeters,,

dwc_dwcore_MaximumElevationInMeters,maximumElevationInMeters,,

dwc_dwcore_MinimumDepthInMeters,minimumDepthInMeters,,

dwc_dwcore_MaximumDepthInMeters,maximumDepthInMeters,,

dwc_dwcore_DayOfYear,day,/_alt/2,

dwc_dwcore_Collector,recordedBy,,

dwc_dwcore_Sex,sex,,

dwc_curatorial_IdentifiedBy,identifiedBy,,

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)

-----

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

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

-----"

dwc_curatorial_TypeStatus,typeStatus,,

dwc_curatorial_IndividualCount,individualCount,,

dwc_geospatial_DecimalLatitude,decimalLatitude,,

dwc_geospatial_DecimalLongitude,decimalLongitude,,

dwc_geospatial_VerbatimLatitude,verbatimLatitude,,

dwc_geospatial_VerbatimLongitude,verbatimLongitude,,

http__purl_org_dc_terms_modified,dcterms:modified,,

dwc_terms_collectionID,collectionID,,

dwc_terms_institutionCode,institutionCode,,

dwc_terms_collectionCode,collectionCode,,

dwc_terms_basisOfRecord,basisOfRecord,,

dwc_terms_identifiedBy,identifiedBy,,

dwc_terms_dateIdentified,dateIdentified,,

dwc_terms_typeStatus,typeStatus,,

dwc_terms_catalogNumber,catalogNumber,,

dwc_terms_occurrenceRemarks,occurrenceRemarks,,

dwc_terms_recordNumber,recordNumber,/_alt/1,

dwc_terms_recordedBy,recordedBy,,

dwc_terms_individualCount,individualCount,,

dwc_terms_sex,sex,,

dwc_terms_preparations,preparations,,

dwc_terms_otherCatalogNumbers,otherCatalogNumbers,,

dwc_terms_eventTime,eventTime,,

dwc_terms_startDayOfYear,startDayOfYear,,

dwc_terms_endDayOfYear,endDayOfYear,,

dwc_terms_year,year,,

dwc_terms_month,month,,

dwc_terms_day,day,,

dwc_terms_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)

-----

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

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

-----"

dwc_terms_continent,continent,,

dwc_terms_country,country,,

dwc_terms_stateProvince,stateProvince,,

dwc_terms_county,county,,

dwc_terms_locality,locality,,

dwc_terms_minimumElevationInMeters,minimumElevationInMeters,,

dwc_terms_maximumElevationInMeters,maximumElevationInMeters,,

dwc_terms_minimumDepthInMeters,minimumDepthInMeters,,

dwc_terms_maximumDepthInMeters,maximumDepthInMeters,,

dwc_terms_verbatimLatitude,verbatimLatitude,,

dwc_terms_verbatimLongitude,verbatimLongitude,,

dwc_terms_decimalLatitude,decimalLatitude,,

dwc_terms_decimalLongitude,decimalLongitude,,

dwc_terms_coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,

dwc_terms_scientificName,scientificName,,

dwc_terms_kingdom,kingdom,,

dwc_terms_phylum,phylum,,

dwc_terms_class,class,,

dwc_terms_order,order,,

dwc_terms_family,family,,

dwc_terms_genus,genus,,

dwc_terms_specificEpithet,specificEpithet,,

dwc_terms_infraspecificEpithet,infraspecificEpithet,,

dwc_terms_scientificNameAuthorship,scientificNameAuthorship,/_alt/1,

conceptual_darwin_2003_1_0_DateLastModified,dcterms:modified,,

conceptual_darwin_2003_1_0_InstitutionCode,institutionCode,,

conceptual_darwin_2003_1_0_CollectionCode,collectionCode,,

conceptual_darwin_2003_1_0_CatalogNumber,catalogNumber,,

conceptual_darwin_2003_1_0_ScientificName,scientificName,,

conceptual_darwin_2003_1_0_BasisOfRecord,basisOfRecord,,

conceptual_darwin_2003_1_0_Kingdom,kingdom,,

conceptual_darwin_2003_1_0_Phylum,phylum,,

conceptual_darwin_2003_1_0_Class,class,,

conceptual_darwin_2003_1_0_Order,order,,

conceptual_darwin_2003_1_0_Family,family,,

conceptual_darwin_2003_1_0_Genus,genus,,

conceptual_darwin_2003_1_0_Species,specificEpithet,,

conceptual_darwin_2003_1_0_Subspecies,subspecies,,

conceptual_darwin_2003_1_0_ScientificNameAuthor,scientificNameAuthorship,/_alt/2,

conceptual_darwin_2003_1_0_IdentifiedBy,identifiedBy,,

conceptual_darwin_2003_1_0_YearIdentified,yearIdentified,,

conceptual_darwin_2003_1_0_MonthIdentified,monthIdentified,,

conceptual_darwin_2003_1_0_DayIdentified,dayIdentified,,

conceptual_darwin_2003_1_0_TypeStatus,typeStatus,,

conceptual_darwin_2003_1_0_CollectorNumber,recordNumber,/_alt/3,

conceptual_darwin_2003_1_0_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)

-----

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

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

-----"

conceptual_darwin_2003_1_0_Collector,recordedBy,,

conceptual_darwin_2003_1_0_YearCollected,yearCollected,,

conceptual_darwin_2003_1_0_MonthCollected,monthCollected,,

conceptual_darwin_2003_1_0_DayCollected,dayCollected,,

conceptual_darwin_2003_1_0_JulianDay,day,/_alt/1,

conceptual_darwin_2003_1_0_TimeOfDay,eventTime,,

conceptual_darwin_2003_1_0_ContinentOcean,continent,,

conceptual_darwin_2003_1_0_Country,country,,

conceptual_darwin_2003_1_0_StateProvince,stateProvince,,

conceptual_darwin_2003_1_0_County,county,,

conceptual_darwin_2003_1_0_Locality,locality,,

conceptual_darwin_2003_1_0_Longitude,verbatimLongitude,,

conceptual_darwin_2003_1_0_Latitude,verbatimLatitude,,

conceptual_darwin_2003_1_0_CoordinatePrecision,coordinatePrecision,,

conceptual_darwin_2003_1_0_BoundingBox,footprintWKT,,

conceptual_darwin_2003_1_0_MinimumElevation,minimumElevationInMeters,,

conceptual_darwin_2003_1_0_MaximumElevation,maximumElevationInMeters,,

conceptual_darwin_2003_1_0_MinimumDepth,minimumDepthInMeters,,

conceptual_darwin_2003_1_0_MaximumDepth,maximumDepthInMeters,,

conceptual_darwin_2003_1_0_Sex,sex,,

conceptual_darwin_2003_1_0_PreparationType,preparations,,

conceptual_darwin_2003_1_0_IndividualCount,individualCount,,

conceptual_darwin_2003_1_0_PreviousCatalogNumber,otherCatalogNumbers,,

conceptual_darwin_2003_1_0_RelationshipType,relationshipOfResource,,

conceptual_darwin_2003_1_0_RelatedCatalogItem,relatedResourceID,,

conceptual_darwin_2003_1_0_Notes,fieldNotes,,

convertednotes,fieldNotes,,

darwin:DateLastModified,dcterms:modified,,

darwin:InstitutionCode,institutionCode,,

darwin:CollectionCode,collectionCode,,

darwin:CatalogNumber,catalogNumber,,

darwin:ScientificName,scientificName,,

darwin:BasisOfRecord,basisOfRecord,,

darwin:Kingdom,kingdom,,

darwin:Phylum,phylum,,

darwin:Class,class,,

darwin:Order,order,,

darwin:Family,family,,

darwin:Genus,genus,,

darwin:Species,specificEpithet,,

darwin:Subspecies,subspecies,,

darwin:ScientificNameAuthor,scientificNameAuthorship,,

darwin:IdentifiedBy,identifiedBy,,

darwin:YearIdentified,yearIdentified,,

darwin:MonthIdentified,monthIdentified,,

darwin:DayIdentified,dayIdentified,,

darwin:TypeStatus,typeStatus,,

darwin:CollectorNumber,recordNumber,,

darwin:FieldNumber,UNUSED,,"`grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines. 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)."

darwin:Collector,recordedBy,,

darwin:YearCollected,yearCollected,,

darwin:MonthCollected,monthCollected,,

darwin:DayCollected,dayCollected,,

darwin:JulianDay,day,,

darwin:TimeOfDay,eventTime,,

darwin:ContinentOcean,continent,,

darwin:Country,country,,

darwin:StateProvince,stateProvince,,

darwin:County,county,,

darwin:Locality,locality,,

darwin:Longitude,verbatimLongitude,,

darwin:Latitude,verbatimLatitude,,

darwin:CoordinatePrecision,coordinatePrecision,,

darwin:MinimumElevation,minimumElevationInMeters,,

darwin:MaximumElevation,maximumElevationInMeters,,

darwin:MinimumDepth,minimumDepthInMeters,,

darwin:MaximumDepth,maximumDepthInMeters,,

darwin:Sex,sex,,

darwin:PreparationType,preparations,,

darwin:IndividualCount,individualCount,,

darwin:PreviousCatalogNumber,otherCatalogNumbers,,

darwin:RelationshipType,relationshipOfResource,,

darwin:RelatedCatalogItem,relatedResourceID,,

darwin:Notes,fieldNotes,,

SiteName,projectName,,

1haPlotCode,plotName,,

ObservationDate,eventDate,,

Collectors,recordedBy,,

Method,samplingProtocol,,

X_1haPlot,organismX,,

Y_1haPlot,organismY,,

TreeNumber,tag,,

ObservationDate,eventDate,,

Collectors,recordedBy,,

Method,samplingProtocol,,

X_1haPlot,organismX,,

Y_1haPlot,organismY,,

TreeNumber,tag,,

SiteName,projectName,,

1haPlotCode,plotName,,

1haPlotCode,plotName,,

Collectors,recordedBy,,

Method,samplingProtocol,,

ObservationDate,eventDate,,

SiteName,projectName,,

TreeNumber,tag,,

X_1haPlot,organismX,,

Y_1haPlot,organismY,,

key,OMIT,,UniqueNYInternalRecordNumber is a better pkey

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

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

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

UniqueNYInternalRecordNumber,occurrenceID,,

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

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

UniqueNYInternalRecordNumber,occurrenceID,,

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

key,OMIT,,UniqueNYInternalRecordNumber is a better pkey

Expedition,projectName,,

Inventory name,plotName,,

Inventory code,locationID,,

Tag number,tag,,

Tree number,recordNumber,,

Number of subplot,subplot,,

Index collector,recordedBy,,

Specimen,catalogNumber,,

Field family,verbatimFamily,,

Field name,verbatimGenus,,Often = Genera

Family (revised),family,,

Specie+autor,scientificNameWithAuthorship,,

Genera,genus,,

Species and morphotypes,scientificName,,"Contains less than ""Specie+autor"""

Autor (revised),scientificNameAuthorship,,

Determined by,identifiedBy,,

Qualifier,identificationQualifier,,

Diameter,diameterBreastHeight_m,,

Trunk,authorStemCode,,

Total height,height,,

Liana presence,lianaInfestation,,

Observations,fieldNotes,,

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

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

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

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

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

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

-----

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

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

Arcilla (DIN 18 123–%–1),clay,,

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>)"

Arena (DIN 18 123–%–2.5),sand,,

Autor (revised),scientificNameAuthorship,,

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

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

Determined by,identifiedBy,,

Diameter,diameterBreastHeight_m,,

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

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

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

Expedition,projectName,,

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

Family (revised),family,,

Field family,verbatimFamily,,

Field name,verbatimGenus,,Often = Genera

First evaluation,eventDate,,

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

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

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

Genera,genus,,

Index collector,recordedBy,,

Inventory code,locationID,,

Inventory name,plotName,,

Latitude (DMS),verbatimLatitude,,

Liana presence,lianaInfestation,,

Limo (DIN 18 123–%–1),silt,,

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

Longitude (DMS),verbatimLongitude,,

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].

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

Number of subplot,subplot,,

ORDER BY ""Altitude""::real DESC

Observaciones,plotNotes,,

Observations,fieldNotes,,

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

Qualifier,identificationQualifier,,

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

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

Slope,slopeGradient,,

Specie+autor,scientificNameWithAuthorship,,

Species and morphotypes,scientificName,,"Contains less than ""Specie+autor"""

Specimen,catalogNumber,,

Tag number,tag,,

Textural class,texture,,

Topographical situation,landform,,

Total height,height,,

Tree number,recordNumber,,

Trunk,authorStemCode,,

Vegetation type,communityID,,

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

WHERE ""Minimum altitude"" 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>"

pH acuoso (ISRIC 4–– 1 - 14),ph,,

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

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

Inventory name,plotName,,

Inventory code,locationID,,

First evaluation,eventDate,,

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>)"

Latitude (DMS),verbatimLatitude,,

Longitude (DMS),verbatimLongitude,,

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

[1] Using the following query:

-----

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

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

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

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

ORDER BY ""Altitude""::real DESC

-----

[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>"

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].

[1] Using the following query:

-----

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

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

WHERE ""Minimum altitude"" IS NOT NULL

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

-----

[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>"

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

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

Vegetation type,communityID,,

Topographical situation,landform,,

Slope,slopeGradient,,

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 Direction

accession,occurrenceID,,

herbarium,institutionCode,,

usdaRank,taxonRank,/_alt/1,

infrarank,taxonRank,/_alt/2,

infraname,infraspecificEpithet,,

SciName,scientificName,,

authors,scientificNameAuthorship,,

collector1,recordedBy,/_join/2,

collector2,recordedBy,/_join/3,

collector3,recordedBy,/_join/4,

collectno,recordNumber,,

collmonth,monthCollected,,

collday,dayCollected,,

collyear,yearCollected,,

campus,fieldNotes,"/_join/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,/_join/1,

comment2,fieldNotes,/_join/2,

comment3,fieldNotes,/_join/3,

comment4,fieldNotes,/_join/4,

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

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

sheetno,associatedMedia,,?

SciName,scientificName,,

accession,occurrenceID,,

authors,scientificNameAuthorship,,

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

collday,dayCollected,,

collectno,recordNumber,,

collector1,recordedBy,/_join/2,

collector2,recordedBy,/_join/3,

collector3,recordedBy,/_join/4,

collmonth,monthCollected,,

collyear,yearCollected,,

comment1,fieldNotes,/_join/1,

comment2,fieldNotes,/_join/2,

comment3,fieldNotes,/_join/3,

comment4,fieldNotes,/_join/4,

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?"

herbarium,institutionCode,,

infraname,infraspecificEpithet,,

infrarank,taxonRank,/_alt/2,

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

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

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

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

sheetno,associatedMedia,,?

usdaRank,taxonRank,/_alt/1,

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_code,plotName,,

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 ""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

-----"

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."

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/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."

x_position,organismX,,"Brad: These are important, fundamental values of many tree plots"

y_position,organismY,,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: Map instead as for voucher_string

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."

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."

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

infra_rank_1,taxonRank,,

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."

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."

height_m,height,/_alt/2,

ht_first_branch_m,heightFirstBranch,,

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

stem_dbh,diameterBreastHeight_m,,

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

stem_canopy_form,canopyForm,,

stem_canopy_position,canopyPosition,,

stem_liana_infestation,lianaInfestation,,

orig_family,verbatimFamily,,Brad: OMIT

orig_species,verbatimSpecificEpithet,,Brad: OMIT