Revision 159
Added by Aaron Marcuse-Kubitza almost 13 years ago
| NYBG-VegBank.organisms.csv | ||
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| 1 | 1 |
NYBG,VegBank:/taxonObservation,Comments |
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:1,/taxonImportance/*/stemCount, |
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InstitutionCode,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/first, |
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CollectionCode,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/last,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
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ScientificName,"/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName/_alt/1}","Brad: Bob, Nick, please is this mapping OK?"
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Kingdom,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Kingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Phylum,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subkingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Class,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Class]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Order,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Order]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Family,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Genus,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Species,"/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept/*_ID/*/plantName/_alt/2}",
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Subspecies,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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ScientificNameAuthor,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/reference/referenceContributor/*_ID/referenceParty/{givenName,surname}","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"
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IdentifiedBy,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=false,currentInterpretation=true]/*_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}",Brad: Bob: does this look correct for VegBank?
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YearIdentified,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/year", |
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MonthIdentified,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/month", |
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DayIdentified,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/day", |
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FieldNumber,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?" |
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Collector,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}",Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?
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YearCollected,/*_ID/observation/obsStartDate/_date/year, |
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MonthCollected,/*_ID/observation/obsStartDate/_date/month, |
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DayCollected,/*_ID/observation/obsStartDate/_date/day, |
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BoundingBox,/*_ID/observation/*_ID/plot/dsgpoly, |
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CoordinatePrecision,/*_ID/observation/*_ID/plot/locationAccuracy, |
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Country,"/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""area|country|territory""])/placeName",Brad: Required; reject record if this field NULL |
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StateProvince,"/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""region|state|province""])/placeName", |
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County,/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=county])/placeName, |
| 27 | 7 |
Locality,/*_ID/observation/*_ID/plot/place/*_ID/namedPlace/placeDescription,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one." |
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Latitude,/*_ID/observation/*_ID/plot/realLatitude, |
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Longitude,/*_ID/observation/*_ID/plot/realLongitude, |
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Latitude,/*_ID/observation/*_ID/plot/realLatitude, |
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CoordinatePrecision,/*_ID/observation/*_ID/plot/locationAccuracy, |
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BoundingBox,/*_ID/observation/*_ID/plot/dsgpoly, |
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MaximumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}",
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MinimumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}",
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MaximumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}",
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DayCollected,/*_ID/observation/obsStartDate/_date/day, |
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MonthCollected,/*_ID/observation/obsStartDate/_date/month, |
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YearCollected,/*_ID/observation/obsStartDate/_date/year, |
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MaximumDepth,/*_ID/observation/waterDepth/max, |
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MinimumDepth,/*_ID/observation/waterDepth/min, |
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MaximumDepth,/*_ID/observation/waterDepth/max, |
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Sex,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=sex]:[userDefinedType=varchar]]:[@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" |
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Notes,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes,"Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes" |
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:1,/taxonImportance/*/stemCount, |
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| 38 | 18 |
Habitat,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=habitat]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
| 39 | 19 |
PlantFungusDescription,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=plantFungusDescription]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Incorrect mapping to VB, also possibly to VX; this is the specimenDescription field, as used by this institution (NOT a standard DwC element). Very important! Bob, Nick, where would this go in VB and VX?" |
| 40 | 20 |
Substrate,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=substrate]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Incorrect mapping to VB and VX; refers to geological substrate or soils where specimen collected. Often concatenated with habitat, or included with specimen description. Bob, Nick, is there an element for this in VB/VX, or shall we just use userDefined?" |
| 41 | 21 |
Vegetation,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=vegetation]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Habitat'. Bob, Nick: keep as user defined or create special element?" |
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FieldNumber,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?" |
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Collector,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}",Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?
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Sex,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=sex]:[userDefinedType=varchar]]:[@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" |
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InstitutionCode,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/first, |
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CollectionCode,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/last,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
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Notes,/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes,"Brad: mapping OK; NY appears to be using this field for almost anything, but mostly internal collections notes" |
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DayIdentified,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/day", |
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MonthIdentified,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/month", |
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YearIdentified,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/year", |
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IdentifiedBy,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=false,currentInterpretation=true]/*_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}",Brad: Bob: does this look correct for VegBank?
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Class,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Class]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Family,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Genus,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Kingdom,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Kingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Order,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Order]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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ScientificNameAuthor,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/reference/referenceContributor/*_ID/referenceParty/{givenName,surname}","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"
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Phylum,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subkingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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Subspecies,"/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName", |
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| 42 | 40 |
UniqueNYInternalRecordNumber,"/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=epoch,*_ID/plantConcept:[*_ID/reference],*_ID/party]/museumAccessionNumber,*_ID/observation/*_ID/plot:[confidentialityStatus=0]/authorPlotCode/_alt/3}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key"
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ScientificName,"/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName/_alt/1}","Brad: Bob, Nick, please is this mapping OK?"
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Species,"/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept/*_ID/*/plantName/_alt/2}",
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Also available in: Unified diff
mappings to VegBank: Sorted by output column to help VegX-VegBank conversion put elements in the same order as source-VegBank