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Revision 4814

inputs/*/*/map.csv: Remapped all unused terms to special value UNUSED. Remapped all private terms to special value PRIVATE. Remapped all deliberately unmapped terms to special value OMIT.

View differences:

inputs/XAL/Specimen/map.csv
19 19
darwin:MonthIdentified,monthIdentified,,
20 20
darwin:DayIdentified,dayIdentified,,
21 21
darwin:TypeStatus,TypeStatus,,
22
darwin:CollectorNumber,recordNumber,/_alt/1,
23
darwin:FieldNumber,recordNumber,/_alt/2,"This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). It is also unused: `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines."
22
darwin:CollectorNumber,recordNumber,,
23
darwin:FieldNumber,UNUSED,,"`grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines. This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber)."
24 24
darwin:Collector,recordedBy,,
25 25
darwin:YearCollected,yearCollected,,
26 26
darwin:MonthCollected,monthCollected,,
inputs/XAL/Specimen/VegBIEN.csv
15 15
darwin:YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
16 16
darwin:IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
17 17
darwin:Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
18
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/1,
19
darwin:FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/2,"This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). It is also unused: `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines."
18
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
20 19
darwin:Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
21 20
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
22 21
darwin: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
23 22
darwin:InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
24
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
25
darwin:FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). It is also unused: `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines."
23
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,
26 24
darwin:ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/3,
27 25
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/givenname/_namePart/first,
28 26
darwin:IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/middlename/_namePart/middle,
......
51 49
darwin:StateProvince,/location/locationplace/*_id/placepath/stateprovince,
52 50
darwin:BasisOfRecord,,** No join mapping for BasisOfRecord ** 
53 51
darwin:DateLastModified,,** No join mapping for dcterms:modified ** 
52
darwin:FieldNumber,,"** No join mapping for UNUSED ** `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines. This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber)."
54 53
darwin:JulianDay,,** No join mapping for day ** 
55 54
darwin:PreparationType,,** No join mapping for preparations ** 
56 55
darwin:PreviousCatalogNumber,,** No join mapping for otherCatalogNumbers ** 
inputs/XAL/Specimen/unmapped_terms.csv
1 1
dcterms:modified
2 2
BasisOfRecord
3 3
TypeStatus
4
UNUSED
4 5
day
5 6
eventTime
6 7
preparations
inputs/NY/Specimen/map.csv
1 1
NY,VegCore,Filter,Comments
2
key,key,,Not used because UniqueNYInternalRecordNumber is a better pkey
2
key,OMIT,,UniqueNYInternalRecordNumber is a better pkey
3 3
DateLastModified,dcterms:modified,,
4 4
InstitutionCode,institutionCode,,
5 5
CollectionCode,collectionCode,,
......
20 20
MonthIdentified,monthIdentified,,
21 21
DayIdentified,dayIdentified,,
22 22
TypeStatus,TypeStatus,,
23
CollectorNumber,OMIT,,"Not used [1], so does not need to be mapped.
24

  
25
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL"
23
CollectorNumber,UNUSED,,
26 24
FieldNumber,recordNumber,,Usage inconsistent with DwC definition
27 25
Collector,recordedBy,,
28 26
YearCollected,yearCollected,,
inputs/NY/Specimen/VegBIEN.csv
55 55
County,/location/locationplace/*_id/placepath/county,
56 56
StateProvince,/location/locationplace/*_id/placepath/stateprovince,
57 57
BasisOfRecord,,** No join mapping for BasisOfRecord ** 
58
CollectorNumber,,"** No join mapping for OMIT ** Not used [1], so does not need to be mapped.
59

  
60
[1] The following query returns no rows: SELECT * FROM ""NY"".""Specimen"" WHERE ""CollectorNumber"" IS NOT NULL"
58
CollectorNumber,,** No join mapping for UNUSED ** 
61 59
DateLastModified,,** No join mapping for dcterms:modified ** 
62 60
JulianDay,,** No join mapping for day ** 
63 61
PreparationType,,** No join mapping for preparations ** 
......
66 64
RelationshipType,,** No join mapping for relationshipOfResource ** 
67 65
TimeOfDay,,** No join mapping for eventTime ** 
68 66
TypeStatus,,** No join mapping for TypeStatus ** 
69
key,,** No join mapping for key ** Not used because UniqueNYInternalRecordNumber is a better pkey
67
key,,** No join mapping for OMIT ** UniqueNYInternalRecordNumber is a better pkey
inputs/NY/Specimen/new_terms.csv
1
key
1 2
PlantFungusDescription
2 3
Substrate
3 4
Vegetation
inputs/NY/Specimen/unmapped_terms.csv
1
key
1
OMIT
2 2
dcterms:modified
3 3
BasisOfRecord
4 4
TypeStatus
5
OMIT
5
UNUSED
6 6
day
7 7
eventTime
8 8
preparations
inputs/CVS/Organism/map.csv
1 1
CVS,VegCore,Filter,Comments
2 2
authorObsCode,fieldNumber,,
3 3
obsStartDate,startDate,,
4
realLatitude,OMIT,,
5
realLongitude,OMIT,,
4
realLatitude,PRIVATE,,
5
realLongitude,PRIVATE,,
6 6
locationAccuracy-m,coordinateUncertaintyInMeters,,
7 7
publicLatitude,decimalLatitude,,
8 8
publicLongitude,decimalLongitude,,
inputs/CVS/Organism/VegBIEN.csv
13 13
county,/location/locationplace/*_id/placepath/county,
14 14
state,/location/locationplace/*_id/placepath/stateprovince,
15 15
confidentialityStatus,,** No join mapping for confidentialityStatus ** 
16
realLatitude,,** No join mapping for OMIT ** 
17
realLongitude,,** No join mapping for OMIT ** 
16
realLatitude,,** No join mapping for PRIVATE ** 
17
realLongitude,,** No join mapping for PRIVATE ** 
inputs/CVS/Organism/unmapped_terms.csv
1
OMIT
2
OMIT
1
PRIVATE
2
PRIVATE
3 3
confidentialityStatus
inputs/CTFS/TaxonOccurrence/map.csv
11 11
SubSpeciesName,subspecies,,
12 12
SubSpeciesMnemonic,SubSpeciesMnemonic,,
13 13
SubSpeciesAuthority,SubSpeciesAuthority,,
14
InfraSpecificLevel,InfraSpecificLevel,,"Not used, as the following query returns zero:
15
-----
16
SELECT COUNT(*) FROM ""CTFS"".""InfraspecificEpithet.src""
17
WHERE ""InfraSpecificLevel"" IS NOT NULL
18
-----"
14
InfraSpecificLevel,UNUSED,,
19 15
SpeciesCurrentTaxonFlag,SpeciesCurrentTaxonFlag,,
20 16
SpeciesObsoleteTaxonFlag,SpeciesObsoleteTaxonFlag,,
21 17
SpeciesReferenceID,SpeciesReferenceID,,
inputs/CTFS/TaxonOccurrence/VegBIEN.csv
18 18
GenusID,,** No join mapping for GenusID ** 
19 19
GenusReferenceID,,** No join mapping for GenusReferenceID ** 
20 20
IDLevel,,** No join mapping for IDLevel ** 
21
InfraSpecificLevel,,"** No join mapping for InfraSpecificLevel ** Not used, as the following query returns zero:
22
-----
23
SELECT COUNT(*) FROM ""CTFS"".""InfraspecificEpithet.src""
24
WHERE ""InfraSpecificLevel"" IS NOT NULL
25
-----"
21
InfraSpecificLevel,,** No join mapping for UNUSED ** 
26 22
ReferenceID,,** No join mapping for ReferenceID ** 
27 23
SpeciesAuthority,,** No join mapping for SpeciesAuthority ** 
28 24
SpeciesCurrentTaxonFlag,,** No join mapping for SpeciesCurrentTaxonFlag ** 
inputs/CTFS/TaxonOccurrence/unmapped_terms.csv
6 6
SubSpeciesObsoleteTaxonFlag
7 7
SubSpeciesMnemonic
8 8
SubSpeciesAuthority
9
InfraSpecificLevel
9
UNUSED
10 10
SpeciesCurrentTaxonFlag
11 11
SpeciesObsoleteTaxonFlag
12 12
SpeciesReferenceID
inputs/U/Specimen/map.csv
2 2
ID,occurrenceID,,
3 3
Barcode,catalogNumber,,
4 4
Collector,recordedBy,/_join/1,
5
Prefix,Prefix,,Not used
5
Prefix,UNUSED,,
6 6
Number,recordNumber,,
7
Suffix,Suffix,,Not used
7
Suffix,UNUSED,,
8 8
Addcoll,recordedBy,/_join/2,
9 9
Colldd,dayCollected,,
10 10
Collmm,monthCollected,,
11 11
Collyy,yearCollected,,
12
DateInfo,DateInfo,,Not used
12
DateInfo,UNUSED,,
13 13
Family,family,,
14 14
Genus,genus,,
15 15
cf,identificationQualifier,,
inputs/U/Specimen/VegBIEN.csv
29 29
Alt,,** No join mapping for Alt ** What is this?
30 30
Alt2,,** No join mapping for Alt2 ** What is this?
31 31
Coorsyst,,** No join mapping for Coorsyst ** 
32
DateInfo,,** No join mapping for DateInfo ** Not used
32
DateInfo,,** No join mapping for UNUSED ** 
33 33
EW,,** No join mapping for EW ** 
34 34
Majorarea,,** No join mapping for Majorarea ** 
35 35
NS,,** No join mapping for NS ** 
36 36
Phenology,,** No join mapping for ReproductiveCondition ** 
37
Prefix,,** No join mapping for Prefix ** Not used
38
Suffix,,** No join mapping for Suffix ** Not used
37
Prefix,,** No join mapping for UNUSED ** 
38
Suffix,,** No join mapping for UNUSED ** 
inputs/U/Specimen/new_terms.csv
1 1
Barcode
2
Prefix
2 3
Number
4
Suffix
3 5
Addcoll
4 6
Colldd
5 7
Collmm
6 8
Collyy
9
DateInfo
7 10
cf
8 11
Detby
9 12
Detyy
inputs/U/Specimen/unmapped_terms.csv
1
Prefix
2
Suffix
3
DateInfo
1
UNUSED
2
UNUSED
3
UNUSED
4 4
Majorarea
5 5
Coorsyst
6 6
NS
inputs/ARIZ/Specimen/map.csv
28 28
Locality,locality,,
29 29
DecimalLatitude,decimalLatitude,,
30 30
DecimalLongitude,decimalLongitude,,
31
HorizontalDatum,HorizontalDatum,,Not used
31
HorizontalDatum,UNUSED,,
32 32
OriginalCoordinateSystem,verbatimSRS,,
33 33
VerbatimLatitude,verbatimLatitude,,
34 34
VerbatimLongitude,verbatimLongitude,,
......
60 60
TypeStatus,TypeStatus,,
61 61
Sex,sex,,
62 62
Preparations,Preparations,,
63
Tissues,Tissues,,Not used
63
Tissues,UNUSED,,
64 64
IndividualCount,individualCount,,
65 65
AgeClass,lifeStage,,
66 66
GenBankNum,associatedSequences,"/_label[label=""GenBank""]/value",
inputs/ARIZ/Specimen/VegBIEN.csv
69 69
GenBankNum,,"** No join mapping for associatedSequences/_label[label=""GenBank""]/value ** "
70 70
GeorefMethod,,** No join mapping for georeferenceProtocol ** 
71 71
HigherGeography,,** No join mapping for HigherGeography ** 
72
HorizontalDatum,,** No join mapping for HorizontalDatum ** Not used
72
HorizontalDatum,,** No join mapping for UNUSED ** 
73 73
Island,,** No join mapping for Island ** 
74 74
IslandGroup,,** No join mapping for IslandGroup ** 
75 75
JulianDay,,** No join mapping for day ** 
......
79 79
Preparations,,** No join mapping for Preparations ** 
80 80
RelatedCatalogedItems,,** No join mapping for relatedResourceID/_alt/2 ** Used only when OtherCatalogNumbers is NULL
81 81
TimeCollected,,** No join mapping for eventTime ** 
82
Tissues,,** No join mapping for Tissues ** Not used
82
Tissues,,** No join mapping for UNUSED ** 
83 83
TypeStatus,,** No join mapping for TypeStatus ** 
84 84
VerbatimDepth,,** No join mapping for VerbatimDepth ** 
inputs/ARIZ/Specimen/new_terms.csv
1 1
CatalogNumberNumeric
2 2
TimeCollected
3 3
VerbatimCollectingDate
4
HorizontalDatum
4 5
OriginalCoordinateSystem
5 6
GeorefMethod
6 7
LatLongComments
7 8
IdentificationModifier
9
Tissues
8 10
AgeClass
9 11
GenBankNum
10 12
OtherCatalogNumbers
inputs/ARIZ/Specimen/unmapped_terms.csv
6 6
HigherGeography
7 7
IslandGroup
8 8
Island
9
HorizontalDatum
9
UNUSED
10 10
verbatimSRS
11 11
georeferenceProtocol
12 12
georeferenceRemarks
13 13
VerbatimDepth
14 14
TypeStatus
15 15
Preparations
16
Tissues
16
UNUSED
17 17
lifeStage
18 18
associatedSequences
19 19
relatedResourceID
inputs/VegBank/plot_/map.csv
3 3
authorplotcode,plotName,,
4 4
reference_id,reference_id,,
5 5
parent_id,parentPlotID,,
6
reallatitude,OMIT,,
7
reallongitude,OMIT,,
6
reallatitude,PRIVATE,,
7
reallongitude,PRIVATE,,
8 8
locationaccuracy,coordinateUncertaintyInMeters,,
9 9
confidentialitystatus,confidentialitystatus,,
10 10
confidentialityreason,confidentialityreason,,
......
26 26
layoutnarrative,layoutnarrative,,
27 27
elevation,elevationInMeters,,"""The elevation of the plot origin in meters above sea level"" (elevation definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)"
28 28
elevationaccuracy,elevationaccuracy,,
29
elevationrange,elevationrange,,"Unused [1]
30

  
31
[1] The following query returns no rows: SELECT count(*) FROM ""VegBank"".plot WHERE elevationrange IS NOT NULL"
29
elevationrange,UNUSED,,
32 30
slopeaspect,slopeAspect,,
33 31
minslopeaspect,minSlopeAspect,,
34 32
maxslopeaspect,maxSlopeAspect,,
inputs/VegBank/plot_/VegBIEN.csv
39 39
dateentered,,** No join mapping for dateentered ** 
40 40
dsgpoly,,** No join mapping for dsgpoly ** 
41 41
elevationaccuracy,,** No join mapping for elevationaccuracy ** 
42
elevationrange,,"** No join mapping for elevationrange ** Unused [1]
43

  
44
[1] The following query returns no rows: SELECT count(*) FROM ""VegBank"".plot WHERE elevationrange IS NOT NULL"
42
elevationrange,,** No join mapping for UNUSED ** 
45 43
emb_plot,,** No join mapping for emb_plot ** 
46 44
layoutnarrative,,** No join mapping for layoutnarrative ** 
47 45
notesmgt,,** No join mapping for notesmgt ** 
......
51 49
placementmethod,,** No join mapping for placementmethod ** 
52 50
plotrationalenarrative,,** No join mapping for plotrationalenarrative ** 
53 51
quadrangle,,** No join mapping for quadrangle ** 
54
reallatitude,,** No join mapping for OMIT ** 
55
reallongitude,,** No join mapping for OMIT ** 
52
reallatitude,,** No join mapping for PRIVATE ** 
53
reallongitude,,** No join mapping for PRIVATE ** 
56 54
reference_id,,** No join mapping for reference_id ** 
57 55
revisions,,** No join mapping for revisions ** 
58 56
rocktype,,** No join mapping for rocktype ** 
inputs/VegBank/plot_/new_terms.csv
3 3
locationaccuracy
4 4
shape
5 5
area
6
elevationrange
6 7
area|country|territory
7 8
region|state|province
inputs/VegBank/plot_/unmapped_terms.csv
1 1
reference_id
2 2
parentPlotID
3
OMIT
4
OMIT
3
PRIVATE
4
PRIVATE
5 5
confidentialitystatus
6 6
confidentialityreason
7 7
authore
......
16 16
permanence
17 17
layoutnarrative
18 18
elevationaccuracy
19
elevationrange
19
UNUSED
20 20
topoposition
21 21
surficialdeposits
22 22
rocktype

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