Revision 6314
Added by Aaron Marcuse-Kubitza over 12 years ago
inputs/XAL/Specimen/VegBIEN.csv | ||
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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 | ||
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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 | ||
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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 | ||
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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 | ||
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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 |
|
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot