Revision 4834
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 10 | 10 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 11 | 11 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
| 12 | 12 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 13 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 13 | 14 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 14 | 15 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 15 | 16 |
locality,/location/locationnarrative/_merge/1, |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 53 | 53 |
<value>$establishmentMeans</value> |
| 54 | 54 |
</_map> |
| 55 | 55 |
</isnative> |
| 56 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 56 | 57 |
<taxondetermination> |
| 57 | 58 |
<taxonpath_id> |
| 58 | 59 |
<taxonpath> |
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 20 | 20 |
1haPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
| 21 | 21 |
TreeNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
| 22 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 22 | 23 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 23 | 24 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 24 | 25 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| inputs/TEAM/VL/test.xml.ref | ||
|---|---|---|
| 40 | 40 |
</plantobservation> |
| 41 | 41 |
</aggregateoccurrence> |
| 42 | 42 |
<authortaxoncode>$TreeNumber</authortaxoncode> |
| 43 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 43 | 44 |
<taxondetermination> |
| 44 | 45 |
<taxonpath_id> |
| 45 | 46 |
<taxonpath> |
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m, |
| 20 | 20 |
1haPlotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/cond/_exists", |
| 21 | 21 |
TreeNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/2/_if[@name=""if is organism""]/then", |
| 22 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 22 | 23 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 23 | 24 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 24 | 25 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| inputs/TEAM/VT/test.xml.ref | ||
|---|---|---|
| 40 | 40 |
</plantobservation> |
| 41 | 41 |
</aggregateoccurrence> |
| 42 | 42 |
<authortaxoncode>$TreeNumber</authortaxoncode> |
| 43 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 43 | 44 |
<taxondetermination> |
| 44 | 45 |
<taxonpath_id> |
| 45 | 46 |
<taxonpath> |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 23 | 23 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 24 | 24 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1,Usage inconsistent with DwC definition |
| 25 | 25 |
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 26 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 26 | 27 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 27 | 28 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 28 | 29 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 105 | 105 |
</plantobservation> |
| 106 | 106 |
</aggregateoccurrence> |
| 107 | 107 |
<authortaxoncode>$FieldNumber</authortaxoncode> |
| 108 |
<sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode> |
|
| 108 | 109 |
<taxondetermination> |
| 109 | 110 |
<party_id> |
| 110 | 111 |
<party> |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
| 18 | 18 |
SciName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 19 | 19 |
cultivated,/location/locationevent/taxonoccurrence/iscultivated/_alt/1,Ignore other values |
| 20 |
accession,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 20 | 21 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 21 | 22 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 22 | 23 |
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/scientificname, |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 74 | 74 |
</aggregateoccurrence> |
| 75 | 75 |
<authortaxoncode>$collectno</authortaxoncode> |
| 76 | 76 |
<iscultivated>$cultivated</iscultivated> |
| 77 |
<sourceaccessioncode>$accession</sourceaccessioncode> |
|
| 77 | 78 |
<taxondetermination> |
| 78 | 79 |
<taxonpath_id> |
| 79 | 80 |
<taxonpath> |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 18 | 18 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
| 19 | 19 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 20 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 20 | 21 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 21 | 22 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 22 | 23 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 65 | 65 |
</plantobservation> |
| 66 | 66 |
</aggregateoccurrence> |
| 67 | 67 |
<authortaxoncode>$recordNumber</authortaxoncode> |
| 68 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 68 | 69 |
<taxondetermination> |
| 69 | 70 |
<party_id> |
| 70 | 71 |
<party> |
| inputs/REMIB/Specimen/VegBIEN.csv | ||
|---|---|---|
| 8 | 8 |
coll_year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 9 | 9 |
acronym,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 10 | 10 |
accession_number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 11 |
accession_number,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 11 | 12 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 12 | 13 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 13 | 14 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| inputs/REMIB/Specimen/test.xml.ref | ||
|---|---|---|
| 61 | 61 |
</specimenreplicate> |
| 62 | 62 |
</plantobservation> |
| 63 | 63 |
</aggregateoccurrence> |
| 64 |
<sourceaccessioncode>$accession_number</sourceaccessioncode> |
|
| 64 | 65 |
<taxondetermination> |
| 65 | 66 |
<taxonpath_id> |
| 66 | 67 |
<taxonpath> |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 11 | 11 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 12 | 12 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 13 | 13 |
Number,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
| 14 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 14 | 15 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 15 | 16 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 16 | 17 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
| inputs/U/Specimen/test.xml.ref | ||
|---|---|---|
| 64 | 64 |
</plantobservation> |
| 65 | 65 |
</aggregateoccurrence> |
| 66 | 66 |
<authortaxoncode>$Number</authortaxoncode> |
| 67 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 67 | 68 |
<taxondetermination> |
| 68 | 69 |
<party_id> |
| 69 | 70 |
<party> |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 28 | 28 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_first/1/_first/1, |
| 29 | 29 |
ScientificNameAuthor,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3/_alt/1,Contains the binomial in addition to the authority |
| 30 | 30 |
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3/_alt/2, |
| 31 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 31 | 32 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 32 | 33 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 33 | 34 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 127 | 127 |
</plantobservation> |
| 128 | 128 |
</aggregateoccurrence> |
| 129 | 129 |
<authortaxoncode>$CollectorNumber</authortaxoncode> |
| 130 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
|
| 130 | 131 |
<taxondetermination> |
| 131 | 132 |
<party_id> |
| 132 | 133 |
<party> |
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 13 | 13 |
Full Taxon Name,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 14 | 14 |
Cultivated?,/location/locationevent/taxonoccurrence/iscultivated/_alt/1, |
| 15 |
Accession Number,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 15 | 16 |
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/scientificname, |
| 16 | 17 |
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 17 | 18 |
Country,/location/locationplace/*_id/placepath/country, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 117 | 117 |
establishmentMeans,//taxonoccurrence/isnative, |
| 118 | 118 |
taxonOccurrenceID,//taxonoccurrence/sourceaccessioncode, |
| 119 | 119 |
individualID,//taxonoccurrence/sourceaccessioncode, |
| 120 |
occurrenceID,//taxonoccurrence/sourceaccessioncode, |
|
| 120 | 121 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/givenname, |
| 121 | 122 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/middlename, |
| 122 | 123 |
identifiedBy,//taxonoccurrence/taxondetermination[]/*_id/party/surname, |
| inputs/NCU-NCSC/Specimen/test.xml.ref | ||
|---|---|---|
| 63 | 63 |
</aggregateoccurrence> |
| 64 | 64 |
<authortaxoncode>$Full Taxon Name</authortaxoncode> |
| 65 | 65 |
<iscultivated>$Cultivated?</iscultivated> |
| 66 |
<sourceaccessioncode>$Accession Number</sourceaccessioncode> |
|
| 66 | 67 |
<taxondetermination><taxonpath_id><taxonpath><scientificname>$Full Taxon Name</scientificname></taxonpath></taxonpath_id></taxondetermination> |
| 67 | 68 |
</taxonoccurrence> |
| 68 | 69 |
</locationevent> |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 89 | 89 |
conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 90 | 90 |
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 91 | 91 |
dwc_terms_scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 92 |
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 92 | 93 |
conceptual_darwin_2003_1_0_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 93 | 94 |
dwc_curatorial_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 94 | 95 |
dwc_terms_identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 251 | 251 |
</3> |
| 252 | 252 |
</_alt> |
| 253 | 253 |
</authortaxoncode> |
| 254 |
<sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode> |
|
| 254 | 255 |
<taxondetermination> |
| 255 | 256 |
<party_id> |
| 256 | 257 |
<party> |
| inputs/QMOR/Specimen/VegBIEN.csv | ||
|---|---|---|
| 24 | 24 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 25 | 25 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 26 | 26 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_first/2/_first/3, |
| 27 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 27 | 28 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 28 | 29 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 29 | 30 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
| inputs/QMOR/Specimen/test.xml.ref | ||
|---|---|---|
| 109 | 109 |
</plantobservation> |
| 110 | 110 |
</aggregateoccurrence> |
| 111 | 111 |
<authortaxoncode>$scientificName</authortaxoncode> |
| 112 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 112 | 113 |
<taxondetermination> |
| 113 | 114 |
<party_id> |
| 114 | 115 |
<party> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 117 | 117 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 118 | 118 |
taxonOccurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
| 119 | 119 |
individualID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2, |
| 120 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 120 | 121 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first, |
| 121 | 122 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle, |
| 122 | 123 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/surname/_namePart/last, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Forward occurrenceID to taxonoccurrence.sourceaccessioncode when there is no other taxonoccurrence.sourceaccessioncode, to ensure that taxonoccurrence is uniquely identified so that there is one taxonoccurrence per organism