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Revision 6314

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

View differences:

inputs/XAL/Specimen/VegBIEN.csv
5 5
darwin: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",
6 6
darwin:MaximumElevation,/location/elevation_m/_alt/2/_avg/max,
7 7
darwin:MinimumElevation,/location/elevation_m/_alt/2/_avg/min,
8
darwin:CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
8 9
darwin:DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
9 10
darwin:MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
10 11
darwin:YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
......
18 19
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",
19 20
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
20 21
darwin:Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
22
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
21 23
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
22 24
darwin: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",
23 25
darwin: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/2/_join_words/1/_alt/1",
inputs/SALVIAS/plotObservations/VegBIEN.csv
11 11
PlotCode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
12 12
PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
13 13
Line,/location/authorlocationcode,
14
Ind,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
14 15
PlotObsID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
15 16
Line,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
16 17
census_date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists","This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
......
85 86
coll_firstname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/1,Brad: See comment above
86 87
coll_lastname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/2,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
87 88
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
89
Ind,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
88 90
PlotObsID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
89 91
PlotObsID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else","Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
90 92
det_by,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
inputs/U/Specimen/VegBIEN.csv
3 3
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
4 4
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",
5 5
ID,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
6
Number,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
6 7
Colldd,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
7 8
Collmm,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
8 9
Collyy,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
......
14 15
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/1,
15 16
Addcoll,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/2,
16 17
ID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
18
Number,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
17 19
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
18 20
Detby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
19 21
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",
inputs/SpeciesLink/Specimen/VegBIEN.csv
20 20
dwc_dwcore_MinimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min,
21 21
dwc_terms_minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min,
22 22
dwc_dwcore_GlobalUniqueIdentifier,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
23
dwc_terms_recordNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",
24
conceptual_darwin_2003_1_0_FieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
25
-----
26
SELECT count(*) FROM ""SpeciesLink"".specimens
27
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
28
-----"
29
dwc_curatorial_FieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
30
-----
31
SELECT count(*) FROM ""SpeciesLink"".specimens
32
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
33
-----"
34
dwc_terms_fieldNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
35
-----
36
SELECT count(*) FROM ""SpeciesLink"".specimens
37
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
38
-----"
39
conceptual_darwin_2003_1_0_CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3",
40
dwc_curatorial_CollectorNumber,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3",
23 41
conceptual_darwin_2003_1_0_DayCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
24 42
conceptual_darwin_2003_1_0_MonthCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
25 43
conceptual_darwin_2003_1_0_YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
......
84 102
dwc_dwcore_Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
85 103
dwc_terms_recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
86 104
dwc_dwcore_GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
105
dwc_terms_recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/1",
106
conceptual_darwin_2003_1_0_FieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
107
-----
108
SELECT count(*) FROM ""SpeciesLink"".specimens
109
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
110
-----"
111
dwc_curatorial_FieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
112
-----
113
SELECT count(*) FROM ""SpeciesLink"".specimens
114
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
115
-----"
116
dwc_terms_fieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
117
-----
118
SELECT count(*) FROM ""SpeciesLink"".specimens
119
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
120
-----"
121
conceptual_darwin_2003_1_0_CollectorNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3",
122
dwc_curatorial_CollectorNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_alt/3",
87 123
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
88 124
conceptual_darwin_2003_1_0_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
89 125
dwc_curatorial_IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
inputs/UNCC/Specimen/VegBIEN.csv
18 18
GROUP BY herbarium, accession
19 19
HAVING count(*) > 1
20 20
-----"
21
collectno,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/cond/_exists",
21 22
cultivated,"/location/iscultivated/_if[@name=""if TaxonOccurrence""]/else",Ignore other values
22 23
collday,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
23 24
collmonth,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
......
55 56
GROUP BY herbarium, accession
56 57
HAVING count(*) > 1
57 58
-----"
59
collectno,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
58 60
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then",Ignore other values
59 61
accession,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,"Globally unique, although occasionally duplicated. [1]
60 62

  

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