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Revision 6344

Added inputs/TRTE/Specimen/

View differences:

inputs/TRTE/Specimen/map.csv
1
TRTE,VegCore,Filter,Comments
2
id,occurrenceID,,
3
collectionCode,collectionCode,,
4
genus,genus,,
5
bibliographicCitation,dcterms:bibliographicCitation,,
6
verbatimLongitude,verbatimLongitude,,
7
eventDate,eventDate,,
8
decimalLongitude,decimalLongitude,,
9
catalogNumber,catalogNumber,,
10
language,dcterms:language,,
11
type,dcterms:type,,
12
institutionID,institutionID,,
13
kingdom,kingdom,,
14
scientificName,scientificName,,
15
verbatimLatitude,verbatimLatitude,,
16
family,family,,
17
locality,locality,,
18
recordNumber,recordNumber,,
19
basisOfRecord,basisOfRecord,,
20
country,country,,
21
associatedTaxa,associatedTaxa,,
22
scientificNameAuthorship,scientificNameAuthorship,,
23
locationRemarks,locationRemarks,,
24
verbatimCoordinates,verbatimCoordinates,,
25
taxonRank,taxonRank,,
26
verbatimEventDate,verbatimEventDate,,
27
municipality,municipality,,
28
geodeticDatum,geodeticDatum,,
29
institutionCode,institutionCode,,
30
nomenclaturalCode,nomenclaturalCode,,
31
modified,dcterms:modified,,
32
previousIdentifications,previousIdentifications,,
33
datasetName,datasetName,,
34
rights,dcterms:rights,,
35
ownerInstitutionCode,ownerInstitutionCode,,
36
county,county,,
37
infraspecificEpithet,infraspecificEpithet,,
38
rightsHolder,dcterms:rightsHolder,,
39
datasetID,datasetID,,
40
stateProvince,stateProvince,,
41
collectionID,collectionID,,
42
verbatimCoordinateSystem,verbatimCoordinateSystem,,
43
dateIdentified,dateIdentified,,
44
habitat,habitat,,
45
recordedBy,recordedBy,,
46
verbatimSRS,verbatimSRS,,
47
specificEpithet,specificEpithet,,
48
verbatimElevation,verbatimElevation,,
49
identifiedBy,identifiedBy,,
50
associatedReferences,associatedReferences,,
51
associatedMedia,associatedMedia,,
52
occurrenceRemarks,occurrenceRemarks,,
53
decimalLatitude,decimalLatitude,,
inputs/TRTE/Specimen/VegBIEN.csv
1
TRTE,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
3
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
4
institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1",
5
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",
6
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2",
7
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",
8
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value",
9
id,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
10
recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
11
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",
12
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",
13
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",
14
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,
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eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,
16
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
17
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
18
collectionCode,/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
19
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2,
20
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/name,
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id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
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recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
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scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",
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recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
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id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
26
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
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id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
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identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
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family,"/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",
30
scientificName,"/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",
31
genus,"/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/2/_join_words/2",
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specificEpithet,"/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/2/_join_words/3/_join_words/1",
33
infraspecificEpithet,"/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/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
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taxonRank,"/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/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
35
infraspecificEpithet,"/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/2/_join_words/5/_join_words/2",
36
scientificNameAuthorship,"/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/2",
37
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/creationdate/_alt/1/_dateRangeStart/value,
38
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
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taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank",
40
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
42
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
43
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",
44
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
45
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",
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infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
47
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
48
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
49
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family,
50
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/1,
51
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2,
52
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
53
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
54
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
55
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
56
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2,
57
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
58
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
59
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
60
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
61
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
62
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
63
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
64
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
65
locality,/location/locationnarrative/_merge/1,
66
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
67
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",
68
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",
69
verbatimLatitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude,
70
verbatimLongitude,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude,
71
country,/location/locationplace/*_id/place/country,
72
county,/location/locationplace/*_id/place/county,
73
decimalLatitude,"/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"
74
decimalLongitude,"/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"
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country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
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county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
77
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,
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stateProvince,/location/locationplace/*_id/place/stateprovince,
79
verbatimElevation,/location/verbatimelevation,
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associatedMedia,,** No join mapping for associatedMedia ** 
81
associatedReferences,,** No join mapping for associatedReferences ** 
82
associatedTaxa,,** No join mapping for associatedTaxa ** 
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basisOfRecord,,** No join mapping for basisOfRecord ** 
84
bibliographicCitation,,** No join mapping for dcterms:bibliographicCitation ** 
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datasetID,,** No join mapping for datasetID ** 
86
datasetName,,** No join mapping for datasetName ** 
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geodeticDatum,,** No join mapping for geodeticDatum ** 
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institutionID,,** No join mapping for institutionID ** 
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language,,** No join mapping for dcterms:language ** 
90
locationRemarks,,** No join mapping for locationRemarks ** 
91
modified,,** No join mapping for dcterms:modified ** 
92
municipality,,** No join mapping for municipality ** 
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nomenclaturalCode,,** No join mapping for nomenclaturalCode ** 
94
occurrenceRemarks,,** No join mapping for occurrenceRemarks ** 
95
ownerInstitutionCode,,** No join mapping for ownerInstitutionCode ** 
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previousIdentifications,,** No join mapping for previousIdentifications ** 
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rights,,** No join mapping for dcterms:rights ** 
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rightsHolder,,** No join mapping for dcterms:rightsHolder ** 
99
type,,** No join mapping for dcterms:type ** 
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verbatimCoordinateSystem,,** No join mapping for verbatimCoordinateSystem ** 
101
verbatimCoordinates,,** No join mapping for verbatimCoordinates ** 
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verbatimEventDate,,** No join mapping for verbatimEventDate ** 
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verbatimSRS,,** No join mapping for verbatimSRS ** 
inputs/TRTE/Specimen/test.xml.ref
1
Put template:
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<VegBIEN>
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    <_simplifyPath id="-1">
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        <next>parent_id</next>
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        <path>
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            <location>
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                <authorlocationcode>
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                    <_alt>
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                        <1>$id</1>
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                        <2>
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                            <_join>
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                                <1>$institutionCode</1>
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                                <2>
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                                    <_join>
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                                        <1>$collectionCode</1>
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                                        <2>$collectionID</2>
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                                    </_join>
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                                </2>
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                                <3>$catalogNumber</3>
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                            </_join>
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                        </2>
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                    </_alt>
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                </authorlocationcode>
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                <elevation_m>
25
                    <_units>
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                        <to>m</to>
27
                        <to></to>
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                        <value>$verbatimElevation</value>
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                    </_units>
30
                </elevation_m>
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                <locationevent>
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                    <obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate>
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                    <obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate>
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                    <taxonoccurrence>
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                        <aggregateoccurrence>
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                            <plantobservation>
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                                <collectionnumber>$recordNumber</collectionnumber>
38
                                <specimenreplicate>
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                                    <catalognumber_dwc>$catalogNumber</catalognumber_dwc>
40
                                    <collectioncode_dwc>
41
                                        <_join>
42
                                            <1>$collectionCode</1>
43
                                            <2>$collectionID</2>
44
                                        </_join>
45
                                    </collectioncode_dwc>
46
                                    <institution_id><sourcename><name>$institutionCode</name></sourcename></institution_id>
47
                                    <sourceaccessioncode>$id</sourceaccessioncode>
48
                                </specimenreplicate>
49
                            </plantobservation>
50
                        </aggregateoccurrence>
51
                        <collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
52
                        <sourceaccessioncode>$id</sourceaccessioncode>
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                        <taxondetermination>
54
                            <party_id><party><fullname>$identifiedBy</fullname></party></party_id>
55
                            <taxonverbatim_id>
56
                                <taxonverbatim>
57
                                    <taxonlabel_id>
58
                                        <taxonlabel>
59
                                            <matched_label_id>
60
                                                <taxonlabel>
61
                                                    <source_id><source><shortname>TNRS</shortname></source></source_id>
62
                                                    <taxonomicname>
63
                                                        <_join_words>
64
                                                            <1><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></1>
65
                                                            <2>
66
                                                                <_alt>
67
                                                                    <1>$scientificName</1>
68
                                                                    <2>
69
                                                                        <_join_words>
70
                                                                            <1>
71
                                                                                <_join_words>
72
                                                                                    <2>$genus</2>
73
                                                                                    <3>$specificEpithet</3>
74
                                                                                    <5>
75
                                                                                        <_join_words>
76
                                                                                            <1>
77
                                                                                                <_if name="if has infraspecificEpithet">
78
                                                                                                    <cond>$infraspecificEpithet</cond>
79
                                                                                                    <then>$taxonRank</then>
80
                                                                                                </_if>
81
                                                                                            </1>
82
                                                                                            <2>$infraspecificEpithet</2>
83
                                                                                        </_join_words>
84
                                                                                    </5>
85
                                                                                </_join_words>
86
                                                                            </1>
87
                                                                            <2>$scientificNameAuthorship</2>
88
                                                                        </_join_words>
89
                                                                    </2>
90
                                                                </_alt>
91
                                                            </2>
92
                                                        </_join_words>
93
                                                    </taxonomicname>
94
                                                </taxonlabel>
95
                                            </matched_label_id>
96
                                            <creationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></creationdate>
97
                                            <parent_id>
98
                                                <taxonlabel>
99
                                                    <rank>$taxonRank</rank>
100
                                                    <taxonverbatim><verbatimrank>$taxonRank</verbatimrank></taxonverbatim>
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                                                    <parent_id>
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                                                        <taxonlabel>
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                                                            <rank>cultivar</rank>
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                                                            <parent_id>
105
                                                                <taxonlabel>
106
                                                                    <rank>forma</rank>
107
                                                                    <parent_id>
108
                                                                        <taxonlabel>
109
                                                                            <rank>variety</rank>
110
                                                                            <parent_id>
111
                                                                                <taxonlabel>
112
                                                                                    <rank>subspecies</rank>
113
                                                                                    <parent_id>
114
                                                                                        <taxonlabel>
115
                                                                                            <rank>species</rank>
116
                                                                                            <taxonepithet>$specificEpithet</taxonepithet>
117
                                                                                            <parent_id>
118
                                                                                                <taxonlabel>
119
                                                                                                    <rank>genus</rank>
120
                                                                                                    <taxonepithet>$genus</taxonepithet>
121
                                                                                                    <parent_id>
122
                                                                                                        <taxonlabel>
123
                                                                                                            <rank>family</rank>
124
                                                                                                            <taxonepithet>$family</taxonepithet>
125
                                                                                                            <parent_id>
126
                                                                                                                <taxonlabel>
127
                                                                                                                    <rank>order</rank>
128
                                                                                                                    <parent_id>
129
                                                                                                                        <taxonlabel>
130
                                                                                                                            <rank>class</rank>
131
                                                                                                                            <parent_id>
132
                                                                                                                                <taxonlabel>
133
                                                                                                                                    <rank>phylum</rank>
134
                                                                                                                                    <parent_id>
135
                                                                                                                                        <taxonlabel>
136
                                                                                                                                            <rank>kingdom</rank>
137
                                                                                                                                            <taxonepithet>$kingdom</taxonepithet>
138
                                                                                                                                        </taxonlabel>
139
                                                                                                                                    </parent_id>
140
                                                                                                                                </taxonlabel>
141
                                                                                                                            </parent_id>
142
                                                                                                                        </taxonlabel>
143
                                                                                                                    </parent_id>
144
                                                                                                                </taxonlabel>
145
                                                                                                            </parent_id>
146
                                                                                                        </taxonlabel>
147
                                                                                                    </parent_id>
148
                                                                                                </taxonlabel>
149
                                                                                            </parent_id>
150
                                                                                        </taxonlabel>
151
                                                                                    </parent_id>
152
                                                                                </taxonlabel>
153
                                                                            </parent_id>
154
                                                                        </taxonlabel>
155
                                                                    </parent_id>
156
                                                                </taxonlabel>
157
                                                            </parent_id>
158
                                                        </taxonlabel>
159
                                                    </parent_id>
160
                                                    <taxonepithet>$infraspecificEpithet</taxonepithet>
161
                                                </taxonlabel>
162
                                            </parent_id>
163
                                            <rank>$taxonRank</rank>
164
                                            <taxonomicname>
165
                                                <_join_words>
166
                                                    <1><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></1>
167
                                                    <2>
168
                                                        <_alt>
169
                                                            <1>$scientificName</1>
170
                                                            <2>
171
                                                                <_join_words>
172
                                                                    <1>
173
                                                                        <_join_words>
174
                                                                            <2>$genus</2>
175
                                                                            <3>$specificEpithet</3>
176
                                                                            <5>
177
                                                                                <_join_words>
178
                                                                                    <1>
179
                                                                                        <_if name="if has infraspecificEpithet">
180
                                                                                            <cond>$infraspecificEpithet</cond>
181
                                                                                            <then>$taxonRank</then>
182
                                                                                        </_if>
183
                                                                                    </1>
184
                                                                                    <2>$infraspecificEpithet</2>
185
                                                                                </_join_words>
186
                                                                            </5>
187
                                                                        </_join_words>
188
                                                                    </1>
189
                                                                    <2>$scientificNameAuthorship</2>
190
                                                                </_join_words>
191
                                                            </2>
192
                                                        </_alt>
193
                                                    </2>
194
                                                </_join_words>
195
                                            </taxonomicname>
196
                                        </taxonlabel>
197
                                    </taxonlabel_id>
198
                                    <author>$scientificNameAuthorship</author>
199
                                    <family>$family</family>
200
                                    <genus>$genus</genus>
201
                                    <specific_epithet>$specificEpithet</specific_epithet>
202
                                    <taxonomicname>$scientificName</taxonomicname>
203
                                    <verbatimrank>$taxonRank</verbatimrank>
204
                                </taxonverbatim>
205
                            </taxonverbatim_id>
206
                            <determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
207
                        </taxondetermination>
208
                    </taxonoccurrence>
209
                </locationevent>
210
                <locationnarrative>
211
                    <_merge>
212
                        <1>$locality</1>
213
                        <3>
214
                            <_label>
215
                                <label>habitat</label>
216
                                <value>$habitat</value>
217
                            </_label>
218
                        </3>
219
                    </_merge>
220
                </locationnarrative>
221
                <locationplace>
222
                    <place_id>
223
                        <place>
224
                            <coordinates_id>
225
                                <coordinates>
226
                                    <latitude_deg>
227
                                        <_nullIf>
228
                                            <null>0</null>
229
                                            <type>float</type>
230
                                            <value>$decimalLatitude</value>
231
                                        </_nullIf>
232
                                    </latitude_deg>
233
                                    <longitude_deg>
234
                                        <_nullIf>
235
                                            <null>0</null>
236
                                            <type>float</type>
237
                                            <value>$decimalLongitude</value>
238
                                        </_nullIf>
239
                                    </longitude_deg>
240
                                    <verbatimlatitude>$verbatimLatitude</verbatimlatitude>
241
                                    <verbatimlongitude>$verbatimLongitude</verbatimlongitude>
242
                                </coordinates>
243
                            </coordinates_id>
244
                            <country>$country</country>
245
                            <county>$county</county>
246
                            <matched_place_id>
247
                                <place>
248
                                    <source_id><source><shortname>geoscrub</shortname></source></source_id>
249
                                    <coordinates_id>
250
                                        <coordinates>
251
                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
252
                                            <latitude_deg>
253
                                                <_nullIf>
254
                                                    <null>0</null>
255
                                                    <type>float</type>
256
                                                    <value>$decimalLatitude</value>
257
                                                </_nullIf>
258
                                            </latitude_deg>
259
                                            <longitude_deg>
260
                                                <_nullIf>
261
                                                    <null>0</null>
262
                                                    <type>float</type>
263
                                                    <value>$decimalLongitude</value>
264
                                                </_nullIf>
265
                                            </longitude_deg>
266
                                        </coordinates>
267
                                    </coordinates_id>
268
                                    <country>$country</country>
269
                                    <county>$county</county>
270
                                    <stateprovince>$stateProvince</stateprovince>
271
                                </place>
272
                            </matched_place_id>
273
                            <stateprovince>$stateProvince</stateprovince>
274
                        </place>
275
                    </place_id>
276
                </locationplace>
277
                <verbatimelevation>$verbatimElevation</verbatimelevation>
278
            </location>
279
        </path>
280
    </_simplifyPath>
281
</VegBIEN>
282
Inserted 34 new rows into database
inputs/TRTE/Specimen/unmapped_terms.csv
1
dcterms:bibliographicCitation
2
dcterms:language
3
dcterms:type
4
institutionID
5
basisOfRecord
6
associatedTaxa
7
locationRemarks
8
verbatimCoordinates
9
verbatimEventDate
10
municipality
11
geodeticDatum
12
nomenclaturalCode
13
dcterms:modified
14
previousIdentifications
15
datasetName
16
dcterms:rights
17
ownerInstitutionCode
18
dcterms:rightsHolder
19
datasetID
20
verbatimCoordinateSystem
21
verbatimSRS
22
associatedReferences
23
associatedMedia
24
occurrenceRemarks

Also available in: Unified diff