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Revision 1716

inputs/XAL: Added maps

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inputs/XAL/maps/src.specimens.csv
1
"XAL[DwC,darwin:]:/content/record/","Original name"
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"DateLastModified","darwin:DateLastModified"
3
"InstitutionCode","darwin:InstitutionCode"
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"CollectionCode","darwin:CollectionCode"
5
"CatalogNumber","darwin:CatalogNumber"
6
"ScientificName","darwin:ScientificName"
7
"BasisOfRecord","darwin:BasisOfRecord"
8
"Kingdom","darwin:Kingdom"
9
"Phylum","darwin:Phylum"
10
"Class","darwin:Class"
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"Order","darwin:Order"
12
"Family","darwin:Family"
13
"Genus","darwin:Genus"
14
"Species","darwin:Species"
15
"Subspecies","darwin:Subspecies"
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"ScientificNameAuthor","darwin:ScientificNameAuthor"
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"IdentifiedBy","darwin:IdentifiedBy"
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"YearIdentified","darwin:YearIdentified"
19
"MonthIdentified","darwin:MonthIdentified"
20
"DayIdentified","darwin:DayIdentified"
21
"TypeStatus","darwin:TypeStatus"
22
"CollectorNumber","darwin:CollectorNumber"
23
"FieldNumber","darwin:FieldNumber"
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"Collector","darwin:Collector"
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"YearCollected","darwin:YearCollected"
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"MonthCollected","darwin:MonthCollected"
27
"DayCollected","darwin:DayCollected"
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"JulianDay","darwin:JulianDay"
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"TimeOfDay","darwin:TimeOfDay"
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"ContinentOcean","darwin:ContinentOcean"
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"Country","darwin:Country"
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"StateProvince","darwin:StateProvince"
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"County","darwin:County"
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"Locality","darwin:Locality"
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"Longitude","darwin:Longitude"
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"Latitude","darwin:Latitude"
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"CoordinatePrecision","darwin:CoordinatePrecision"
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"MinimumElevation","darwin:MinimumElevation"
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"MaximumElevation","darwin:MaximumElevation"
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"MinimumDepth","darwin:MinimumDepth"
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"MaximumDepth","darwin:MaximumDepth"
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"Sex","darwin:Sex"
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"PreparationType","darwin:PreparationType"
44
"IndividualCount","darwin:IndividualCount"
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"PreviousCatalogNumber","darwin:PreviousCatalogNumber"
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"RelationshipType","darwin:RelationshipType"
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"RelatedCatalogItem","darwin:RelatedCatalogItem"
48
"Notes","darwin:Notes"
inputs/XAL/maps/DwC.specimens.csv
1
"XAL[DwC,darwin:]:/content/record/","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/",Comments
inputs/XAL/maps/DwC.specimens.full.csv
1
"XAL[DwC,darwin:]:/content/record/","DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/",Comments
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BasisOfRecord,BasisOfRecord
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CatalogNumber,CatalogNumber
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Class,Class
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CollectionCode,CollectionCode
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Collector,Collector
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CollectorNumber,CollectorNumber
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ContinentOcean,ContinentOcean
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CoordinatePrecision,CoordinatePrecision
10
Country,Country
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County,County
12
DateLastModified,DateLastModified
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DayCollected,DayCollected
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DayIdentified,DayIdentified
15
Family,Family
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FieldNumber,FieldNumber
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Genus,Genus
18
IdentifiedBy,IdentifiedBy
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IndividualCount,IndividualCount
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InstitutionCode,InstitutionCode
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JulianDay,JulianDay
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Kingdom,Kingdom
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Latitude,Latitude
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Locality,Locality
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Longitude,Longitude
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MaximumDepth,MaximumDepth
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MaximumElevation,MaximumElevation
28
MinimumDepth,MinimumDepth
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MinimumElevation,MinimumElevation
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MonthCollected,MonthCollected
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MonthIdentified,MonthIdentified
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Notes,Notes
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Order,Order
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Phylum,Phylum
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PreparationType,PreparationType
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PreviousCatalogNumber,PreviousCatalogNumber
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RelatedCatalogItem,RelatedCatalogItem
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RelationshipType,RelationshipType
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ScientificName,ScientificName
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ScientificNameAuthor,ScientificNameAuthor
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Sex,Sex
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Species,Species
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StateProvince,StateProvince
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Subspecies,Subspecies
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TimeOfDay,TimeOfDay
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TypeStatus,TypeStatus
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YearCollected,YearCollected
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YearIdentified,YearIdentified
inputs/XAL/maps/VegBIEN.specimens.csv
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"XAL[DwC,darwin:]:/content/record/",VegBIEN:/specimenreplicate,Comments,Order
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CoordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89
3
County,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
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StateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",,65
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Country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
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ContinentOcean,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,country,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=continent]/placename",Brad: OMIT,59
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Locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_merge/1,,68
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MinimumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{./{elevation/_alt/2/_avg/min,elevationrange/_range/from}/_units:[default=m,to=m,to=]/value/_rangeStart/value,elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/2/_rangeEnd/value}/_replace[""\bca\.?""=]/value",,71
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MaximumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value,elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/1}",,72
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Latitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/latitude,centerlatitude}/_alt/2/_nullIf:[null=0,type=float]/value",,81
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Longitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/2/_nullIf:[null=0,type=float]/value",,82
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MaximumDepth,"/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value",,75
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MinimumDepth,"/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value",,74
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DayCollected,"/*_id/taxonoccurrence/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
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MonthCollected,"/*_id/taxonoccurrence/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
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YearCollected,"/*_id/taxonoccurrence/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
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DayIdentified,"/*_id/taxonoccurrence/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,120
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MonthIdentified,"/*_id/taxonoccurrence/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,120
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YearIdentified,"/*_id/taxonoccurrence/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,120
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IdentifiedBy,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
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ScientificName,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname","Brad: Bob, Nick, please is this mapping OK?",134
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ScientificNameAuthor,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153
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Subspecies,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname",,150
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Species,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",,149
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Genus,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",,147
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Family,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",,146
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Order,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=order]/plantname",,145
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Class,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",,144
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Phylum,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
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Kingdom,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
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Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
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CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
33
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
34
Notes,/description/_merge/1,,
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CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
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CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
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FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
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BasisOfRecord,,** No join mapping for BasisOfRecord ** 
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DateLastModified,,** No join mapping for DateLastModified ** 
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IndividualCount,,** No join mapping for IndividualCount ** 
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InstitutionCode,,** No join mapping for InstitutionCode ** 
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JulianDay,,** No join mapping for JulianDay ** 
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PreparationType,,** No join mapping for PreparationType ** 
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PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber ** 
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RelatedCatalogItem,,** No join mapping for RelatedCatalogItem ** 
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RelationshipType,,** No join mapping for RelationshipType ** 
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TimeOfDay,,** No join mapping for TimeOfDay ** 
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TypeStatus,,** No join mapping for TypeStatus ** 

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