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Revision 6737

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/NCU/: Refreshed data with new export from Bob

View differences:

inputs/NCU/Specimen/+header.csv
1 
!'Accession Number','SeriesName','Barcode','Full Taxon Name','Collect Date','Country','State','County','Cultivated?','Elevation','Lat (-=S)','Long (-=W)','Accuracy','FIPS','Alt N/S','Alt E/W','Format','Typology'
inputs/NCU/Specimen/map.csv
1 1 
NCU,VegCore,Filter,Comments
2 
Accession Number,occurrenceID,,
3 
SeriesName,collectionCode,,
4 
Barcode,catalogNumber,,
5 
Full Taxon Name,taxonName,,
6 
Collect Date,dateCollected,,
2 
SpecimenPK,occurrenceID,,
3 
DerivedFromID,*DerivedFromID,,
4 
CollectionObjectTypeID,*CollectionObjectTypeID,,
5 
CollectionObjectID,*CollectionObjectID,,
6 
database,*database,,
7 
OwnerInstitution,institutionCode,/_alt/2,
8 
CollectionGUID,collectionID,,
9 
OriginalTaxonLabel,originalScientificName,,
10 
CurrentScientificName,taxonName,,
11 
CurrentScientificNameWithAuthor,scientificName,,
12 
TypeStatus,typeStatus,,
13 
CollectionDate,dateCollected,,
14 
BarCode,OMIT,,"Omitted because this isn't specified on all rows, but SpecimenPK is"
15 
CatalogNumber,catalogNumber,,
16 
CatalogSeriesPrefix,institutionCode,/_alt/1,
17 
Description,fieldNotes,,
18 
LandOwner,*LandOwner,,
19 
BlockLocationReason,*BlockLocationReason,,
20 
BlockSpecificLocation,*BlockSpecificLocation,,
21 
VerbatimLocality,verbatimLocality,/_alt/1,
22 
EventRemarks,eventRemarks,,
7 23 
Country,country,,
8 24 
State,stateProvince,,
9 
County,county,,
10 
Cultivated?,cultivated,,
11 
Elevation,verbatimElevation,,
12 
Lat (-=S),decimalLatitude,"/_replace:[""\?$""=]/value",
13 
Long (-=W),decimalLongitude,"/_replace:[""\?$""=]/value",
14 
Accuracy,coordinateUncertaintyInMeters,,
15 
FIPS,*FIPS,,FIPS county code
16 
Alt N/S,*Alt N/S,,
17 
Alt E/W,*Alt E/W,,
18 
Format,preparations,,
19 
Typology,typeStatus,,
25 
county,county,,
26 
FIPSStateCounty,*FIPSStateCounty,,
27 
CityLocality,verbatimLocality,/_alt/2,
28 
Cultivated,cultivated,"/_nullIf:[null=""-1""]/value",
29 
Latitude1,decimalLatitude,,
30 
Longitude1,decimalLongitude,,
31 
Loc_AltN,verbatimLatitude,,
32 
Loc_AltE,verbatimLongitude,,
33 
firstCollectorName,recordedBy,,
34 
firstCollectorRemarks,recordNumber,,"Actually the collector's number, not remarks"
35 
LastAnnotationLabelTaxon,*LastAnnotationLabelTaxon,,
36 
LastAnnotationDateVerbatim,*LastAnnotationDateVerbatim,,
37 
LastAnnotationRemarks,*LastAnnotationRemarks,,
38 
lastAnnotationAgent,*lastAnnotationAgent,,
inputs/NCU/Specimen/VegBIEN.csv
1 1 
NCU,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 
Accession Number,"/_if[@name=""if specimen""]/cond/_exists",
3 
Barcode,"/_if[@name=""if specimen""]/cond/_exists",
4 
Accession Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
5 
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
6 
Accession Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
7 
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
8 
SeriesName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",
9 
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",
10 
Elevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value",
11 
Accession Number,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
12 
Cultivated?,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2",
13 
Collect Date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1,
14 
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
15 
SeriesName,/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
16 
Accession Number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
17 
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
18 
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
19 
Full Taxon Name,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
20 
Accession Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
21 
Cultivated?,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2",
22 
Accession Number,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
23 
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1",
24 
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1",
25 
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1,
26 
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1,
27 
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
28 
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
29 
Accuracy,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value,
30 
Lat (-=S),"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",
31 
Long (-=W),"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",
2 
CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists",
3 
SpecimenPK,"/_if[@name=""if specimen""]/cond/_exists",
4 
CatalogSeriesPrefix,"/_if[@name=""if specimen""]/else/source/shortname/_first/1/_alt/1",
5 
OwnerInstitution,"/_if[@name=""if specimen""]/else/source/shortname/_first/1/_alt/2",
6 
SpecimenPK,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
7 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
8 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
9 
SpecimenPK,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
10 
CatalogSeriesPrefix,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_alt/1",
11 
OwnerInstitution,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_alt/2",
12 
CollectionGUID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2",
13 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",
14 
SpecimenPK,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
15 
firstCollectorRemarks,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Actually the collector's number, not remarks"
16 
Cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2/_nullIf:[null=""-1""]/value",
17 
VerbatimLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_alt/1,
18 
CityLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_alt/2,
19 
CollectionDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1,
20 
Description,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
21 
firstCollectorRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"Actually the collector's number, not remarks"
22 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
23 
CollectionGUID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
24 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
25 
SpecimenPK,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
26 
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname/_alt/1",
27 
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname/_alt/2",
28 
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name/_alt/1",
29 
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name/_alt/2",
30 
SpecimenPK,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
31 
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1","Actually the collector's number, not remarks"
32 
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",
33 
CurrentScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
34 
firstCollectorName,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
35 
SpecimenPK,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
36 
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Actually the collector's number, not remarks"
37 
Cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2/_nullIf:[null=""-1""]/value",
38 
SpecimenPK,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
39 
CurrentScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1",
40 
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/2",
41 
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/1",
42 
CurrentScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1",
43 
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1,
44 
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/2,
45 
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/1,
46 
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1,
47 
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
48 
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
49 
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/2,
50 
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/1,
51 
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/2,
52 
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/1,
53 
OriginalTaxonLabel,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname,
54 
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
55 
VerbatimLocality,/location/locationnarrative/_merge/2/_alt/1,
56 
CityLocality,/location/locationnarrative/_merge/2/_alt/2,
57 
Latitude1,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",
58 
Longitude1,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",
59 
Loc_AltN,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude,
60 
Loc_AltE,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude,
32 61 
Country,/location/locationplace/*_id/place/country,
33 
County,/location/locationplace/*_id/place/county,
34 
Lat (-=S),"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",""".,"" sorts it with other coordinates mappings"
35 
Long (-=W),"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",""".,"" sorts it with other coordinates mappings"
62 
county,/location/locationplace/*_id/place/county,
63 
Latitude1,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
64 
Longitude1,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
36 65 
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
37 
County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
66 
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
38 67 
State,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,
39 68 
State,/location/locationplace/*_id/place/stateprovince,
40 
Elevation,/location/verbatimelevation,
41 
Alt E/W,,** No join mapping for *Alt E/W **
42 
Alt N/S,,** No join mapping for *Alt N/S **
43 
FIPS,,** No join mapping for *FIPS ** FIPS county code
44 
Format,,** No join mapping for preparations **
45 
Typology,,** No join mapping for typeStatus **
69 
BarCode,,"** No non-empty join mapping for OMIT ** Omitted because this isn't specified on all rows, but SpecimenPK is"
70 
BlockLocationReason,,** No join mapping for *BlockLocationReason **
71 
BlockSpecificLocation,,** No join mapping for *BlockSpecificLocation **
72 
CollectionObjectID,,** No join mapping for *CollectionObjectID **
73 
CollectionObjectTypeID,,** No join mapping for *CollectionObjectTypeID **
74 
DerivedFromID,,** No join mapping for *DerivedFromID **
75 
EventRemarks,,** No join mapping for eventRemarks **
76 
FIPSStateCounty,,** No join mapping for *FIPSStateCounty **
77 
LandOwner,,** No join mapping for *LandOwner **
78 
LastAnnotationDateVerbatim,,** No join mapping for *LastAnnotationDateVerbatim **
79 
LastAnnotationLabelTaxon,,** No join mapping for *LastAnnotationLabelTaxon **
80 
LastAnnotationRemarks,,** No join mapping for *LastAnnotationRemarks **
81 
TypeStatus,,** No join mapping for typeStatus **
82 
database,,** No join mapping for *database **
83 
lastAnnotationAgent,,** No join mapping for *lastAnnotationAgent **
inputs/NCU/Specimen/test.xml.ref
9 9 
                    <location>
10 10 
                        <authorlocationcode>
11 11 
                            <_alt>
12 
                                <1>$Accession Number</1>
12 
                                <1>$SpecimenPK</1>
13 13 
                                <2>
14 14 
                                    <_join>
15 
                                        <2>$SeriesName</2>
16 
                                        <3>$Barcode</3>
15 
                                        <1>
16 
                                            <_alt>
17 
                                                <1>$CatalogSeriesPrefix</1>
18 
                                                <2>$OwnerInstitution</2>
19 
                                            </_alt>
20 
                                        </1>
21 
                                        <2>$CollectionGUID</2>
22 
                                        <3>$CatalogNumber</3>
17 23 
                                    </_join>
18 24 
                                </2>
19 25 
                            </_alt>
20 26 
                        </authorlocationcode>
21 
                        <elevation_m>
22 
                            <_units>
23 
                                <to>m</to>
24 
                                <to></to>
25 
                                <value>$Elevation</value>
26 
                            </_units>
27 
                        </elevation_m>
27 
                        <iscultivated>
28 
                            <_locationnarrative_is_cultivated>
29 
                                <locationnarrative>
30 
                                    <_alt>
31 
                                        <1>$VerbatimLocality</1>
32 
                                        <2>$CityLocality</2>
33 
                                    </_alt>
34 
                                </locationnarrative>
35 
                            </_locationnarrative_is_cultivated>
36 
                        </iscultivated>
28 37 
                        <locationevent>
29 38 
                            <taxonoccurrence>
30 39 
                                <aggregateoccurrence>
31 
                                    <collectiondate>$Collect Date</collectiondate>
40 
                                    <collectiondate>$CollectionDate</collectiondate>
41 
                                    <notes>$Description</notes>
32 42 
                                    <plantobservation>
43 
                                        <collectionnumber>$firstCollectorRemarks</collectionnumber>
33 44 
                                        <specimenreplicate>
34 
                                            <catalognumber_dwc>$Barcode</catalognumber_dwc>
35 
                                            <collectioncode_dwc>$SeriesName</collectioncode_dwc>
36 
                                            <sourceaccessioncode>$Accession Number</sourceaccessioncode>
45 
                                            <catalognumber_dwc>$CatalogNumber</catalognumber_dwc>
46 
                                            <collectioncode_dwc>$CollectionGUID</collectioncode_dwc>
47 
                                            <institution_id>
48 
                                                <sourcename>
49 
                                                    <matched_source_id>
50 
                                                        <source>
51 
                                                            <shortname>
52 
                                                                <_alt>
53 
                                                                    <1>$CatalogSeriesPrefix</1>
54 
                                                                    <2>$OwnerInstitution</2>
55 
                                                                </_alt>
56 
                                                            </shortname>
57 
                                                        </source>
58 
                                                    </matched_source_id>
59 
                                                    <name>
60 
                                                        <_alt>
61 
                                                            <1>$CatalogSeriesPrefix</1>
62 
                                                            <2>$OwnerInstitution</2>
63 
                                                        </_alt>
64 
                                                    </name>
65 
                                                </sourcename>
66 
                                            </institution_id>
67 
                                            <sourceaccessioncode>$SpecimenPK</sourceaccessioncode>
37 68 
                                        </specimenreplicate>
38 69 
                                    </plantobservation>
39 70 
                                </aggregateoccurrence>
40 
                                <iscultivated>$Cultivated?</iscultivated>
41 
                                <sourceaccessioncode>$Accession Number</sourceaccessioncode>
71 
                                <collector_id><party><fullname>$firstCollectorName</fullname></party></collector_id>
72 
                                <iscultivated>
73 
                                    <_nullIf>
74 
                                        <null>-1</null>
75 
                                        <value>$Cultivated</value>
76 
                                    </_nullIf>
77 
                                </iscultivated>
78 
                                <sourceaccessioncode>$SpecimenPK</sourceaccessioncode>
42 79 
                                <taxondetermination>
43 80 
                                    <taxonverbatim_id>
44 81 
                                        <taxonverbatim>
......
47 84 
                                                    <matched_label_id>
48 85 
                                                        <taxonlabel>
49 86 
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
50 
                                                            <taxonomicname>$Full Taxon Name</taxonomicname>
87 
                                                            <taxonomicname>
88 
                                                                <_alt>
89 
                                                                    <1>$CurrentScientificNameWithAuthor</1>
90 
                                                                    <2>$CurrentScientificName</2>
91 
                                                                </_alt>
92 
                                                            </taxonomicname>
51 93 
                                                        </taxonlabel>
52 94 
                                                    </matched_label_id>
53 
                                                    <taxonomicname>$Full Taxon Name</taxonomicname>
95 
                                                    <taxonomicname>
96 
                                                        <_alt>
97 
                                                            <1>$CurrentScientificNameWithAuthor</1>
98 
                                                            <2>$CurrentScientificName</2>
99 
                                                        </_alt>
100 
                                                    </taxonomicname>
54 101 
                                                </taxonlabel>
55 102 
                                            </taxonlabel_id>
56 
                                            <taxonname>$Full Taxon Name</taxonname>
103 
                                            <taxonname>$CurrentScientificName</taxonname>
104 
                                            <taxonomicname>$CurrentScientificNameWithAuthor</taxonomicname>
57 105 
                                        </taxonverbatim>
58 106 
                                    </taxonverbatim_id>
59 107 
                                </taxondetermination>
108 
                                <taxondetermination>
109 
                                    <isoriginal>true</isoriginal>
110 
                                    <taxonverbatim_id>
111 
                                        <taxonverbatim>
112 
                                            <taxonlabel_id>
113 
                                                <taxonlabel>
114 
                                                    <matched_label_id>
115 
                                                        <taxonlabel>
116 
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
117 
                                                            <taxonomicname>$OriginalTaxonLabel</taxonomicname>
118 
                                                        </taxonlabel>
119 
                                                    </matched_label_id>
120 
                                                    <taxonomicname>$OriginalTaxonLabel</taxonomicname>
121 
                                                </taxonlabel>
122 
                                            </taxonlabel_id>
123 
                                            <taxonomicname>$OriginalTaxonLabel</taxonomicname>
124 
                                        </taxonverbatim>
125 
                                    </taxonverbatim_id>
126 
                                </taxondetermination>
60 127 
                            </taxonoccurrence>
61 128 
                        </locationevent>
129 
                        <locationnarrative>
130 
                            <_alt>
131 
                                <1>$VerbatimLocality</1>
132 
                                <2>$CityLocality</2>
133 
                            </_alt>
134 
                        </locationnarrative>
62 135 
                        <locationplace>
63 136 
                            <place_id>
64 137 
                                <place>
65 138 
                                    <coordinates_id>
66 139 
                                        <coordinates>
67 
                                            <coordsaccuracy_m><_noCV><value>$Accuracy</value></_noCV></coordsaccuracy_m>
68 140 
                                            <latitude_deg>
69 141 
                                                <_nullIf>
70 142 
                                                    <null>0</null>
71 143 
                                                    <type>float</type>
72 
                                                    <value>
73 
                                                        <_replace>
74 
                                                            <\?$></\?$>
75 
                                                            <value>$Lat (-=S)</value>
76 
                                                        </_replace>
77 
                                                    </value>
144 
                                                    <value>$Latitude1</value>
78 145 
                                                </_nullIf>
79 146 
                                            </latitude_deg>
80 147 
                                            <longitude_deg>
81 148 
                                                <_nullIf>
82 149 
                                                    <null>0</null>
83 150 
                                                    <type>float</type>
84 
                                                    <value>
85 
                                                        <_replace>
86 
                                                            <\?$></\?$>
87 
                                                            <value>$Long (-=W)</value>
88 
                                                        </_replace>
89 
                                                    </value>
151 
                                                    <value>$Longitude1</value>
90 152 
                                                </_nullIf>
91 153 
                                            </longitude_deg>
154 
                                            <verbatimlatitude>$Loc_AltN</verbatimlatitude>
155 
                                            <verbatimlongitude>$Loc_AltE</verbatimlongitude>
92 156 
                                        </coordinates>
93 157 
                                    </coordinates_id>
94 158 
                                    <country>$Country</country>
95 
                                    <county>$County</county>
159 
                                    <county>$county</county>
96 160 
                                    <matched_place_id>
97 161 
                                        <place>
98 162 
                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
......
103 167 
                                                        <_nullIf>
104 168 
                                                            <null>0</null>
105 169 
                                                            <type>float</type>
106 
                                                            <value>
107 
                                                                <_replace>
108 
                                                                    <\?$></\?$>
109 
                                                                    <value>$Lat (-=S)</value>
110 
                                                                </_replace>
111 
                                                            </value>
170 
                                                            <value>$Latitude1</value>
112 171 
                                                        </_nullIf>
113 172 
                                                    </latitude_deg>
114 173 
                                                    <longitude_deg>
115 174 
                                                        <_nullIf>
116 175 
                                                            <null>0</null>
117 176 
                                                            <type>float</type>
118 
                                                            <value>
119 
                                                                <_replace>
120 
                                                                    <\?$></\?$>
121 
                                                                    <value>$Long (-=W)</value>
122 
                                                                </_replace>
123 
                                                            </value>
177 
                                                            <value>$Longitude1</value>
124 178 
                                                        </_nullIf>
125 179 
                                                    </longitude_deg>
126 180 
                                                </coordinates>
127 181 
                                            </coordinates_id>
128 182 
                                            <country>$Country</country>
129 
                                            <county>$County</county>
183 
                                            <county>$county</county>
130 184 
                                            <stateprovince>$State</stateprovince>
131 185 
                                        </place>
132 186 
                                    </matched_place_id>
......
134 188 
                                </place>
135 189 
                            </place_id>
136 190 
                        </locationplace>
137 
                        <verbatimelevation>$Elevation</verbatimelevation>
138 191 
                    </location>
139 192 
                </path>
140 193 
            </_simplifyPath>
141 194 
        </path>
142 195 
    </_setDefault>
143 196 
</VegBIEN>
144 
Inserted 29 new rows into database
197 
Inserted 40 new rows into database
inputs/NCU/Specimen/new_terms.csv
1 
Accession Number,occurrenceID,,
2 
SeriesName,collectionCode,,
3 
Barcode,catalogNumber,,
4 
Full Taxon Name,taxonName,,
5 
Collect Date,dateCollected,,
6 
Lat (-=S),decimalLatitude,"/_replace:[""\?$""=]/value",
7 
Long (-=W),decimalLongitude,"/_replace:[""\?$""=]/value",
8 
Accuracy,coordinateUncertaintyInMeters,,
9 
Format,preparations,,
10 
Typology,typeStatus,,
1 
SpecimenPK,occurrenceID,,
2 
OwnerInstitution,institutionCode,/_alt/2,
3 
CollectionGUID,collectionID,,
4 
OriginalTaxonLabel,originalScientificName,,
5 
CurrentScientificName,taxonName,,
6 
CurrentScientificNameWithAuthor,scientificName,,
7 
CollectionDate,dateCollected,,
8 
BarCode,OMIT,,"Omitted because this isn't specified on all rows, but SpecimenPK is"
9 
CatalogSeriesPrefix,institutionCode,/_alt/1,
10 
Description,fieldNotes,,
11 
CityLocality,verbatimLocality,/_alt/2,
12 
Latitude1,decimalLatitude,,
13 
Longitude1,decimalLongitude,,
14 
Loc_AltN,verbatimLatitude,,
15 
Loc_AltE,verbatimLongitude,,
16 
firstCollectorName,recordedBy,,
17 
firstCollectorRemarks,recordNumber,,"Actually the collector's number, not remarks"
inputs/NCU/Specimen/unmapped_terms.csv
1 
*FIPS
2 
*Alt N/S
3 
*Alt E/W
4 
preparations
1 
*DerivedFromID
2 
*CollectionObjectTypeID
3 
*CollectionObjectID
4 
*database
5 5 
typeStatus
6 
*LandOwner
7 
*BlockLocationReason
8 
*BlockSpecificLocation
9 
eventRemarks
10 
*FIPSStateCounty
11 
*LastAnnotationLabelTaxon
12 
*LastAnnotationDateVerbatim
13 
*LastAnnotationRemarks
14 
*lastAnnotationAgent

Also available in: Unified diff