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Revision 4594

Added by Aaron Marcuse-Kubitza about 12 years ago

input.Makefile: Maps building: %/.map.csv.last_cleanup: Generate reports on new and unmapped terms in map.csv

View differences:

inputs/CTFS/SubplotObservation/unmapped_terms.csv
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Veg+
inputs/CTFS/Plot/new_terms.csv
1 
CTFS[Veg+]
2 
CountryID
3 
ReferenceX
4 
ReferenceY
5 
row_num
inputs/REMIB/Specimen/new_terms.csv
1 
REMIB[Veg+]
2 
acronym
3 
accession_number
4 
long_deg
5 
long_min
6 
long_sec
7 
lat_deg
8 
lat_min
9 
lat_sec
10 
coll_day
11 
coll_month
12 
coll_year
inputs/CTFS/StemObservation/unmapped_terms.csv
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Veg+
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
inputs/CTFS/Subplot/new_terms.csv
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CTFS[Veg+]
2 
DimX
3 
DimY
inputs/CTFS/PlotObservation/new_terms.csv
1 
CTFS[Veg+]
2 
Description
inputs/CTFS/TaxonOccurrence/new_terms.csv
1 
CTFS[Veg+]
2 
FamilyID
3 
GenusID
4 
SpeciesID
5 
SubSpeciesID
6 
SubSpeciesCurrentTaxonFlag
7 
SubSpeciesObsoleteTaxonFlag
8 
SubSpeciesMnemonic
9 
SubSpeciesAuthority
10 
InfraSpecificLevel
11 
SpeciesCurrentTaxonFlag
12 
SpeciesObsoleteTaxonFlag
13 
SpeciesReferenceID
14 
SpeciesMnemonic
15 
SpeciesAuthority
16 
IDLevel
17 
FieldFamily
18 
Description
19 
GenusReferenceID
20 
GenusAuthority
21 
ReferenceID
22 
row_num
inputs/CTFS/Plot/unmapped_terms.csv
1 
Veg+
2 
""
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""
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""
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""
inputs/FIA/Organism/unmapped_terms.csv
1 
Veg+
2 
""
inputs/SALVIAS/plotMetadata/new_terms.csv
1 
SALVIAS
2 
orig_filename
3 
AccessCode
4 
PrimOwnerID
5 
SiteCode
6 
SiteName
7 
new_world
8 
MajorGeo
9 
PolDiv1
10 
pol1_type
11 
pol2
12 
pol2_type
13 
lat_string
14 
long_string
15 
LatDec
16 
LongDec
17 
lat_long_accuracy
18 
Elev
19 
elev_max_m
20 
elev_min_m
21 
Precip
22 
ElevSource
23 
Temp
24 
PrecipSource
25 
TempSource
26 
bearing
27 
clay_percent
28 
silt_percent
29 
sand_percent
30 
soil_N
31 
soil_P
32 
soil_C
33 
soil_K
34 
soil_Mg
35 
soil_Ca
36 
soil_Na
37 
soil_acidity
38 
soil_base
39 
soil_cation_cap
40 
soil_conductivity
41 
organic_percent
42 
soil_texture
43 
RevisionComments
44 
Locality_Description
45 
topography_desc
46 
vegetation_1
47 
vegetation_2
48 
life_zone_code
49 
life_zone
50 
PlotMethod
51 
MethodCode
52 
plot_area_ha
53 
recensused
54 
date_start
55 
date_finish
56 
plot_administrator
57 
tmp_del
inputs/SALVIAS/stems/new_terms.csv
1 
SALVIAS
2 
origrecord_id_stems
3 
PlotObsID
4 
NoInd
5 
basal_diam
6 
stem_dbh
7 
gentry_dbh
8 
stem_tag1
9 
stem_tag2
10 
stem_height_m
11 
stem_height_first_branch_m
12 
stem_canopy_form
13 
stem_canopy_position
14 
stem_liana_infestation
15 
tmp_del
inputs/SALVIAS/projects/new_terms.csv
1 
SALVIAS[Veg+]
2 
project_pi
3 
allow_download_all
4 
ipr_specific
5 
ipr_specific_updated
6 
project_name_index
7 
on_project_list_index
8 
project_distinct_index
inputs/SALVIAS/plotObservations/unmapped_terms.csv
1 
Veg+
2 
""
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""
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""
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""
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catalogNumber/_alt/2
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catalogNumber/_alt/1
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
inputs/SALVIAS/plotMetadata/unmapped_terms.csv
1 
Veg+
2 
""
3 
""
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""
5 
""
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""
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""
8 
""
9 
""
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""
11 
""
12 
""
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""
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""
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""
16 
"clay/_units:[default=""%"",to=]/value"
17 
"silt/_units:[default=""%"",to=]/value"
18 
"sand/_units:[default=""%"",to=]/value"
19 
"nitrogen/_units:[default=""%"",to=]/value"
20 
"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value"
21 
"carbon/_units:[default=""%"",to=]/value"
22 
"potassium/_units:[default=""%"",to=]/value"
23 
"magnesium/_units:[default=""%"",to=]/value"
24 
"calcium/_units:[default=""%"",to=]/value"
25 
"sodium/_units:[default=""%"",to=]/value"
26 
"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value"
27 
"baseSaturation/_units:[default=""%"",to=]/value"
28 
"organic/_units:[default=""%"",to=]/value"
29 
"texture/_units:[default=""%"",to=]/value"
30 
""
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""
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""
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""
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""
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""
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""
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""
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""
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""
inputs/SALVIAS/stems/unmapped_terms.csv
1 
Veg+
2 
""
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""
inputs/U/Specimen/new_terms.csv
1 
U[Veg+]
2 
Barcode
3 
Prefix
4 
Number
5 
Suffix
6 
Addcoll
7 
Colldd
8 
Collmm
9 
Collyy
10 
DateInfo
11 
cf
12 
Detby
13 
Detyy
14 
Gazetteer
15 
Newgazett
16 
Majorarea
17 
Locnotes
18 
Coorsyst
19 
Lat
20 
NS
21 
Long
22 
EW
23 
Alt
24 
Alt2
25 
Ecology
26 
Phenology
inputs/GBIF/Specimen/new_terms.csv
1 
GBIF[Veg+]
2 
LatestDateCollected
3 
InstitutionCD
4 
CollectionCD
5 
CatalogNO
6 
LastDateModified
7 
ScientificNameOriginal
8 
AuthorOfScientificName
9 
GBIFFamilyOriginal
10 
GBIFGenusOriginal
11 
MinimumElevationInMeter
12 
MaximumElevationInMeter
inputs/SpeciesLink/Specimen/unmapped_terms.csv
1 
Veg+
2 
ScientificNameAuthor/_alt/3
3 
ScientificNameAuthor/_alt/2
4 
ScientificNameAuthor/_alt/1
5 
JulianDay/_alt/2
6 
JulianDay/_alt/1
7 
recordNumber/_alt/3
8 
recordNumber/_alt/2
9 
recordNumber/_alt/1
10 
recordNumber/_alt/2
11 
dcterms:modified
inputs/ARIZ/Specimen/unmapped_terms.csv
1 
Veg+
2 
CatalogNumber/_alt/2
3 
CatalogNumber/_alt/1
4 
OMIT
5 
eventTime
6 
dateCollected/_alt/0
7 
""
8 
verbatimSRS
9 
georeferenceProtocol
10 
georeferenceRemarks
11 
ScientificName/_alt/2
12 
ScientificName/_alt/1
13 
""
14 
lifeStage
15 
"associatedSequences/_label[label=""GenBank""]/value"
16 
RelatedCatalogItem/_alt/1
17 
RelatedCatalogItem/_alt/2
inputs/NCU-NCSC/Specimen/unmapped_terms.csv
1 
Veg+
2 
"Latitude/_replace:[""\?$""=]/value"
3 
"Longitude/_replace:[""\?$""=]/value"
4 
""
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""
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""
7 
preparations
8 
typeStatus
inputs/MT/Specimen/unmapped_terms.csv
1 
Veg+
inputs/MT/Specimen/new_terms.csv
1 
MT[Veg+]
inputs/XAL/Specimen/unmapped_terms.csv
1 
Veg+
2 
recordNumber/_alt/1
3 
recordNumber/_alt/2
inputs/XAL/Specimen/new_terms.csv
1 
"XAL[Veg+,darwin:]:/content/record/"
inputs/TEAM/VL/new_terms.csv
1 
TEAM[Veg+]
2 
SiteName
3 
1haPlotCode
4 
ObservationDate
5 
Collectors
6 
max_diam
7 
max_diam_pom
8 
ConditionCodes
9 
LocationCodes
10 
SamplingPeriod
11 
Comments
12 
SamplingUnitName
13 
Method
14 
X_1haPlot
15 
Y_1haPlot
16 
TreeNumber
17 
ProtocolVersion
18 
ResponsibleInstitution
19 
ProtocolLeadScientist
20 
ProtocolLeadScientistInstitution
inputs/TEAM/VL/unmapped_terms.csv
1 
Veg+
2 
""
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""
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""
5 
""
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""
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""
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""
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""
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""
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""
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""
inputs/TEAM/VT/new_terms.csv
1 
TEAM[Veg+]
2 
ObservationDate
3 
Collectors
4 
dbh_pom
5 
dbh_new
6 
dbh_new_pom
7 
ConditionCodes
8 
SamplingPeriod
9 
Comments
10 
SamplingUnitName
11 
Method
12 
X_1haPlot
13 
Y_1haPlot
14 
TreeNumber
15 
SiteName
16 
1haPlotCode
17 
ProtocolVersion
18 
ResponsibleInstitution
19 
ProtocolLeadScientist
20 
ProtocolLeadScientistInstitution
inputs/TEAM/VT/unmapped_terms.csv
1 
Veg+
2 
""
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""
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""
5 
""
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""
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""
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""
9 
""
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""
11 
""
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""
inputs/NY/Specimen/unmapped_terms.csv
1 
Veg+
2 
""
3 
OMIT
4 
Locality/_merge/1
5 
MinimumElevation/_nullIf:[null=.]/value
6 
Notes/_merge/1
7 
"Notes/_merge/2/_label[label=""plant fungus""]/value"
8 
"Locality/_merge/2/_label[label=""substrate""]/value"
9 
"Locality/_merge/3/_label[label=""vegetation""]/value"
inputs/NY/Specimen/new_terms.csv
1 
NY[Veg+]
2 
key
3 
PlantFungusDescription
4 
Substrate
5 
Vegetation
6 
UniqueNYInternalRecordNumber
inputs/Madidi/Organism/new_terms.csv
1 
Madidi[Veg+]
2 
Expedition
3 
Inventory name
4 
Number of inventory (general)
5 
Number of inventory (expedition)
6 
"Type Inventory (C, PP, TP)"
7 
Inventory code
8 
Tag number
9 
Tree number
10 
Number of subplot
11 
Index collector
12 
Specimen
13 
Similar specimen
14 
Plot specimen
15 
Expedition specimen
16 
Project specimen
17 
Field family
18 
Field name
19 
Family (revised)
20 
Specie+autor
21 
Genera
22 
Species and morphotypes
23 
Autor (revised)
24 
Determined by
25 
Qualifier
26 
Common name
27 
Circumference
28 
Diameter
29 
Trunk
30 
Total height
31 
Bole height
32 
Phenology
33 
Crown position
34 
Crown shape
35 
Liana presence
36 
Basal area
37 
Plot X
38 
Plot Y
39 
Observations
inputs/Madidi/Organism/unmapped_terms.csv
1 
Veg+
2 
""
3 
""
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""
5 
""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
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""
inputs/Madidi/Plot/unmapped_terms.csv
1 
Veg+
2 
""
3 
""
4 
""
5 
""
6 
""
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""
8 
""
9 
""
10 
slopeAspect/_alt/1
11 
""
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slopeAspect/_alt/2
inputs/Madidi/Plot/new_terms.csv
1 
Madidi[Veg+]
2 
Inventory number
3 
Expedition number
4 
Expedition name
5 
Number of inventory (expedition)
6 
Inventory name
7 
Inventory code
8 
First evaluation
9 
Installed and evaluated by
10 
Collaborators
11 
Related Epilocs
12 
Area
13 
Number of stems
14 
Number of trees
15 
Coordinates
16 
Latitude (DMS)
17 
Longitude (DMS)
18 
Altitude
19 
Minimum altitude
20 
Locality description
21 
Direction
22 
Vegetation type
23 
Topographical situation
24 
Slope
25 
Soil sample
26 
pH acuoso (ISRIC 4–– 1 - 14)
27 
Conductividad electrica (ASPT 6–µS/cm– 1 - 10000)
28 
Nitrógeno total (ISRIC 6–%–0.0014)
29 
"Carbón Orgánico (WSP S-9,10–%–0.06)"
30 
"Materia Orgánica (WSP S-9,10–%–0.1)"
31 
Fósforo disponible (ISRIC 14-2–mg/Kg–1.5)
32 
"Sodio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)"
33 
"Potasio intercambiable (WSP S-5,10–cmolc/Kg–0.0053)"
34 
"Calcio intercambiable (WSP S-5,10–cmolc/Kg–0.016)"
35 
"Magnesio intercambiable (WSP S-5,10–cmolc/Kg–0.00083)"
36 
Acidez intercambiable (ISRIC 11–cmolc/Kg–0.05)
37 
CIC (ISRIC 11–cmolc/Kg–0.05)
38 
Arena (DIN 18 123–%–2.5)
39 
Limo (DIN 18 123–%–1)
40 
Arcilla (DIN 18 123–%–1)
41 
Textural class
42 
Observaciones
43 
Orientación/exposicion
inputs/UNCC/Specimen/unmapped_terms.csv
1 
Veg+
2 
taxonRank/_alt/1
3 
taxonRank/_alt/2
4 
Collector/_merge/1
5 
Collector/_merge/2
6 
Collector/_merge/3
7 
Collector/_merge/4
8 
"fieldNotes/_merge/5/_label[label=""campus""]/value"
9 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
10 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
11 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
12 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
13 
fieldNotes/_merge/1
14 
fieldNotes/_merge/2
15 
fieldNotes/_merge/3
16 
fieldNotes/_merge/4
17 
"fieldNotes/_merge/6/_label[label=""loaned to""]/value"
18 
"fieldNotes/_merge/7/_label[label=""in or out""]/value"
19 
associatedMedia
20 
""
inputs/UNCC/Specimen/new_terms.csv
1 
UNCC[Veg+]
2 
accession
3 
herbarium
4 
usdaRank
5 
infrarank
6 
infraname
7 
SciName
8 
authors
9 
collector1
10 
collector2
11 
collector3
12 
collectno
13 
collmonth
14 
collday
15 
collyear
16 
campus
17 
leaves
18 
flower
19 
fruit
20 
root
21 
comment1
22 
comment2
23 
comment3
24 
comment4
25 
loanto
26 
inorout
27 
sheetno
28 
filler
inputs/ACAD/Specimen/unmapped_terms.csv
1 
Veg+
inputs/ACAD/Specimen/new_terms.csv
1 
ACAD[Veg+]
inputs/SALVIAS-CSV/Organism/new_terms.csv
1 
SALVIAS-CSV
2 
OBSERVATION_ID
3 
plot_code
4 
census_no
5 
census_date
6 
individual_code
7 
ind_id
8 
tag1
9 
tag2
10 
x_position
11 
y_position
12 
voucher_string
13 
coll_number
14 
collector_code
15 
coll_lastname
16 
coll_firstname
17 
det_type
18 
fam_status
19 
gen_status
20 
species_status
21 
specific_authority
22 
infra_rank_1
23 
infra_ep_1
24 
cf_aff
25 
comments
26 
no_of_individuals
27 
intercept_cm
28 
height_m
29 
ht_first_branch_m
30 
stem_tag1
31 
stem_tag2
32 
stem_dbh
33 
basal_diam
34 
stem_height_m
35 
stem_height_first_branch_m
36 
stem_canopy_form
37 
stem_canopy_position
38 
stem_liana_infestation
39 
orig_family
40 
orig_species
inputs/SALVIAS-CSV/Organism/unmapped_terms.csv
1 
Veg+
2 
""
3 
tag/_alt/1
4 
previousTag/_alt/1
5 
catalogNumber/_alt/2
6 
catalogNumber/_alt/1
7 
""
8 
""
9 
""
10 
""
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""
12 
height/_alt/2
13 
tag/_alt/2
14 
previousTag/_alt/2
15 
height/_alt/1
inputs/SALVIAS-CSV/Plot/unmapped_terms.csv
1 
Veg+
2 
"clay/_units:[default=""%"",to=]/value"
3 
"silt/_units:[default=""%"",to=]/value"
4 
"sand/_units:[default=""%"",to=]/value"
5 
"organic/_units:[default=""%"",to=]/value"
6 
"nitrogen/_units:[default=""%"",to=]/value"
7 
"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value"
8 
"carbon/_units:[default=""%"",to=]/value"
9 
"potassium/_units:[default=""%"",to=]/value"
10 
"magnesium/_units:[default=""%"",to=]/value"
11 
"calcium/_units:[default=""%"",to=]/value"
12 
"sodium/_units:[default=""%"",to=]/value"
13 
"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value"
14 
"baseSaturation/_units:[default=""%"",to=]/value"
15 
""
16 
""
inputs/SALVIAS-CSV/Plot/new_terms.csv
1 
SALVIAS-CSV
2 
project
3 
plot_code
4 
major_geo
5 
pol1
6 
pol2
7 
locality_description
8 
lat_decimal
9 
long_decimal
10 
elev_m
11 
elev_max_m
12 
elev_min_m
13 
temp_c
14 
precip_mm
15 
clay_percent
16 
silt_percent
17 
sand_percent
18 
organic_percent
19 
soil_N
20 
soil_P
21 
soil_C
22 
soil_K
23 
soil_Mg
24 
soil_Ca
25 
soil_Na
26 
soil_acidity
27 
soil_base
28 
soil_cation_cap
29 
soil_conductivity
30 
soil_texture
31 
holdridge_life_zone
32 
life_zone_code
33 
observation_type
34 
plot_methodology
35 
plot_area_ha
36 
recensused
37 
date_start
38 
date_finish
inputs/CVS/Organism/new_terms.csv
1 
CVS
2 
obsStartDate
3 
realLatitude
4 
realLongitude
5 
locationAccuracy-m
6 
publicLatitude
7 
publicLongitude
8 
confidentialityStatus
9 
currentTaxonName sec Weakley 2006
10 
%cover
inputs/CVS/Organism/unmapped_terms.csv
1 
Veg+
2 
OMIT
3 
OMIT
4 
""
inputs/REMIB/Specimen/unmapped_terms.csv
1 
Veg+
2 
""
3 
""
4 
""
5 
""
inputs/CTFS/StemObservation/new_terms.csv
1 
CTFS[Veg+]
2 
FamilyID
3 
GenusID
4 
SpeciesID
5 
SubSpeciesID
6 
TreeID
7 
MeasureID
8 
HOM
9 
PrimaryStem
10 
ExactDate
11 
StemDescription
12 
x
13 
y
14 
SubSpeciesCurrentTaxonFlag
15 
SubSpeciesObsoleteTaxonFlag
16 
SubSpeciesMnemonic
17 
SubSpeciesAuthority
18 
InfraSpecificLevel
19 
SpeciesCurrentTaxonFlag
20 
SpeciesObsoleteTaxonFlag
21 
SpeciesReferenceID
22 
SpeciesMnemonic
23 
SpeciesAuthority
24 
IDLevel
25 
FieldFamily
26 
Description
27 
GenusReferenceID
28 
GenusAuthority
29 
ReferenceID
30 
row_num
inputs/CTFS/Subplot/unmapped_terms.csv
1 
Veg+
2 
OMIT
3 
""
4 
""
inputs/CTFS/PlotObservation/unmapped_terms.csv
1 
Veg+
2 
""
inputs/CTFS/TaxonOccurrence/unmapped_terms.csv
1 
Veg+
2 
""
3 
""
4 
""
5 
""
6 
""
7 
""
8 
""
9 
""
10 
""
11 
""
12 
""
13 
""
14 
""
15 
""
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""
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""
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""
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""
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""
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""
22 
""
inputs/CTFS/SubplotObservation/new_terms.csv
1 
CTFS[Veg+]
inputs/FIA/Organism/new_terms.csv
1 
FIA[Veg+]
2 
TreeTag
3 
MeasYear
4 
MeasMon
5 
MeasDay
6 
PlotCD
7 
HOM
inputs/SALVIAS/projects/unmapped_terms.csv
1 
Veg+
2 
""
3 
""
4 
""
5 
""
6 
""
7 
""
8 
""
inputs/SALVIAS/plotObservations/new_terms.csv
1 
SALVIAS
2 
PlotObsID
3 
PlotCode
4 
census_no
5 
census_date
6 
OrigRecordID
7 
Line
8 
Ind
9 
ind_id
10 
tag1
11 
tag2
12 
x_position
13 
y_position
14 
dist
15 
perp_dist
16 
SourceVoucher
17 
coll_number
18 
collector_code
19 
coll_inits
20 
coll_lastname
21 
coll_firstname
22 
DetType
23 
det_by
24 
fam_status
25 
gen_status
26 
name_status
27 
SpAuthStatus
28 
GenAuth
29 
auth
30 
infra_rank_1
31 
infra_ep_1
32 
infra_auth_1
33 
common_name
34 
morphoname
35 
species_code
36 
height_class
37 
height_m
38 
height_m_commercial
39 
ht_first_branch_m
40 
NoInd
41 
intercept_cm
42 
cfaff
43 
other_annotations
44 
morphocf
45 
IsMorpho
46 
OrigFamily
47 
OrigGenus
48 
OrigSpecies
49 
OrigAuth
50 
phenology
51 
temp_dbh
52 
temp_liandbh
53 
tmp_del
inputs/ARIZ/Specimen/new_terms.csv
1 
ARIZ[Veg+]
2 
CatalogNumberNumeric
3 
TimeCollected
4 
VerbatimCollectingDate
5 
HorizontalDatum
6 
OriginalCoordinateSystem
7 
GeorefMethod
8 
LatLongComments
9 
IdentificationModifier
10 
Tissues
11 
AgeClass
12 
GenBankNum
13 
OtherCatalogNumbers
14 
RelatedCatalogedItems
inputs/NCU-NCSC/Specimen/new_terms.csv
1 
NCU-NCSC[Veg+]
2 
Accession Number
3 
SeriesName
4 
Barcode
5 
Full Taxon Name
6 
Collect Date
7 
Lat (-=S)
8 
Long (-=W)
9 
Accuracy
10 
FIPS
11 
Alt N/S
12 
Alt E/W
13 
Format
14 
Typology
inputs/U/Specimen/unmapped_terms.csv
1 
Veg+
2 
Collector/_merge/1
3 
""
4 
""
5 
Collector/_merge/2
6 
""
7 
"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1"
8 
"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2"
9 
""
10 
VerbatimLocality/_merge/2
11 
""
12 
""
13 
""
14 
""
15 
""
16 
ReproductiveCondition
inputs/GBIF/Specimen/unmapped_terms.csv
1 
Veg+
2 
dcterms:modified
inputs/MO/Specimen/unmapped_terms.csv
1 
Veg+
inputs/VegBank/observation_/new_terms.csv
1 
VegBank[Veg+]
2 
observation_id
3 
previousobs_id
4 
dateaccuracy
5 
covermethod_id
6 
coverdispersion
7 
autotaxoncover
8 
stratummethod_id
9 
methodnarrative
10 
taxonobservationarea
11 
stemsizelimit
12 
stemobservationarea
13 
stemsamplemethod
14 
originaldata
15 
effortlevel
16 
plotvalidationlevel
17 
floristicquality
18 
bryophytequality
19 
lichenquality
20 
observationnarrative
21 
landscapenarrative
22 
homogeneity
23 
phenologicaspect
24 
representativeness
25 
standmaturity
26 
successionalstatus
27 
basalarea
28 
hydrologicregime
29 
soilmoistureregime
30 
soildrainage
31 
watersalinity
32 
waterdepth
33 
shoredistance
34 
soildepth
35 
organicdepth
36 
soiltaxon_id
37 
soiltaxonsrc
38 
percentbedrock
39 
percentrockgravel
40 
percentwood
41 
percentlitter
42 
percentbaresoil
43 
percentwater
44 
percentother
45 
nameother
46 
treeht
47 
shrubht
48 
fieldht
49 
nonvascularht
50 
submergedht
51 
treecover
52 
shrubcover
53 
fieldcover
54 
nonvascularcover
55 
floatingcover
56 
submergedcover
57 
dominantstratum
58 
growthform1type
59 
growthform2type
60 
growthform3type
61 
growthform1cover
62 
growthform2cover
63 
growthform3cover
64 
totalcover
65 
notespublic
66 
notesmgt
67 
revisions
68 
obsstartdate
69 
obsenddate
70 
dateentered
71 
emb_observation
72 
interp_orig_ci_id
73 
interp_orig_cc_id
74 
interp_orig_sciname
75 
interp_orig_code
76 
interp_orig_party_id
77 
interp_orig_partyname
78 
interp_current_ci_id
79 
interp_current_cc_id
80 
interp_current_sciname
81 
interp_current_code
82 
interp_current_party_id
83 
interp_current_partyname
84 
interp_bestfit_ci_id
85 
interp_bestfit_cc_id
86 
interp_bestfit_sciname
87 
interp_bestfit_code
88 
interp_bestfit_party_id
89 
interp_bestfit_partyname
90 
toptaxon1name
91 
toptaxon2name
92 
toptaxon3name
93 
toptaxon4name
94 
toptaxon5name
95 
numberoftaxa
96 
accessioncode
97 
soilobs_id
98 
soilhorizon
99 
soildepthtop
100 
soildepthbottom
101 
soilcolor
102 
soilorganic
103 
soiltexture
104 
soilsand
105 
soilsilt
106 
soilclay
107 
soilcoarse
108 
soilph
109 
exchangecapacity
110 
soildescription
111 
emb_soilobs
112 
row_num
inputs/QMOR/Specimen/unmapped_terms.csv
1 
Veg+
inputs/MO/Specimen/new_terms.csv
1 
MO[Veg+]
2 
convertednotes
inputs/VegBank/taxonobservation_/new_terms.csv
1 
VegBank[Veg+]
2 
plantconcept_id
3 
taxonobservation_id
4 
observation_id
5 
authorplantname
6 
taxonobservation_reference_id
7 
taxoninferencearea
8 
emb_taxonobservation
9 
int_origplantconcept_id
10 
int_origplantscifull
11 
int_origplantscinamenoauth
12 
int_origplantcommon
13 
int_origplantcode
14 
int_currplantconcept_id
15 
int_currplantscifull
16 
int_currplantscinamenoauth
17 
int_currplantcommon
18 
int_currplantcode
19 
taxonobservation_accessioncode
20 
taxoninterpretation_id
21 
stemlocation_id
22 
taxoninterpretation_plantname_id
23 
party_id
24 
role_id
25 
interpretationtype
26 
reference_id
27 
originalinterpretation
28 
currentinterpretation
29 
taxonconfidence
30 
collector_id
31 
collectionnumber
32 
museum_id
33 
museumaccessionnumber
34 
grouptype
35 
notespublic
36 
notesmgt
37 
revisions
38 
interpretationdate
39 
collectiondate
40 
emb_taxoninterpretation
41 
taxoninterpretation_accessioncode
42 
plantname_id
43 
plantconcept__reference_id
44 
plantname
45 
plantcode
46 
plantdescription
47 
d_obscount
48 
d_currentaccepted
49 
plantconcept__accessioncode
50 
Subkingdom
51 
Superdivision
52 
Division
53 
Subdivision
54 
Subclass
55 
Variety
56 
Forma
57 
row_num
inputs/VegBank/plot_/unmapped_terms.csv
1 
Veg+
2 
""
3 
parentPlotID
4 
OMIT
5 
OMIT
6 
""
7 
""
8 
""
9 
""
10 
""
11 
""
12 
""
13 
""
14 
""
15 
""
16 
""
17 
""
18 
""
19 
""
20 
""
21 
""
22 
""
23 
""
24 
""
25 
""
26 
""
27 
""
28 
""
29 
""
30 
""
31 
""
32 
""
33 
""
34 
""
35 
""
36 
""
inputs/input.Makefile
282 282 

  		




  283
  283
  
    
# Via maps cleanup


  		




  284
  284
  
    
ifneq ($(filter %/.map.csv.last_cleanup,$(MAKECMDGOALS)),)


  		




  285
  
  
    
%/.map.csv.last_cleanup: %/map.csv $(coreMap) $(vocab) $(dict)


  		




  
  285
  
    
%/.map.csv.last_cleanup %/unmapped_terms.csv %/new_terms.csv: %/map.csv\


  		




  
  286
  
    
$(coreMap) $(vocab) $(dict)


  		




  286
  287
  
    
	$(bin)/in_place $< $(bin)/canon 1 $(word 3,$+)


  		




  287
  288
  
    
	$(bin)/in_place $< $(bin)/translate 1 $(word 4,$+)


  		




  288
  289
  
    
	$(bin)/in_place $< env ignore=1 $(bin)/subtract $(word 2,$+) 0 1 2


  		




  
  290
  
    
	$(bin)/filter_out_ci 1 $(word 3,$+) <$<|$(bin)/cols 1 >$*/unmapped_terms.csv


  		




  
  291
  
    
	$(bin)/filter_out_ci 0 $(word 3,$+) <$<|$(bin)/cols 0 >$*/new_terms.csv


  		




  289
  292
  
    
	touch $@


  		




  290
  293
  
    
# Include comment column so commented mappings are never removed


  		




  291
  294
  
    
else


  		












  

    
      inputs/VegBank/observation_/unmapped_terms.csv
    
  





  
  1
  
    
Veg+


  		




  
  2
  
    
""


  		




  
  3
  
    
""


  		




  
  4
  
    
""


  		




  
  5
  
    
""


  		




  
  6
  
    
""


  		




  
  7
  
    
""


  		




  
  8
  
    
""


  		




  
  9
  
    
""


  		




  
  10
  
    
""


  		




  
  11
  
    
""


  		




  
  12
  
    
""


  		




  
  13
  
    
""


  		




  
  14
  
    
""


  		




  
  15
  
    
""


  		




  
  16
  
    
""


  		




  
  17
  
    
""


  		




  
  18
  
    
""


  		




  
  19
  
    
""


  		




  
  20
  
    
""


  		




  
  21
  
    
""


  		




  
  22
  
    
""


  		




  
  23
  
    
""


  		




  
  24
  
    
""


  		




  
  25
  
    
""


  		




  
  26
  
    
""


  		




  
  27
  
    
""


  		




  
  28
  
    
""


  		




  
  29
  
    
""


  		




  
  30
  
    
""


  		




  
  31
  
    
""


  		




  
  32
  
    
""


  		




  
  33
  
    
""


  		




  
  34
  
    
""


  		




  
  35
  
    
""


  		




  
  36
  
    
""


  		




  
  37
  
    
""


  		




  
  38
  
    
""


  		




  
  39
  
    
""


  		




  
  40
  
    
""


  		




  
  41
  
    
""


  		




  
  42
  
    
""


  		




  
  43
  
    
""


  		




  
  44
  
    
""


  		




  
  45
  
    
""


  		




  
  46
  
    
""


  		




  
  47
  
    
""


  		




  
  48
  
    
""


  		




  
  49
  
    
""


  		




  
  50
  
    
""


  		




  
  51
  
    
""


  		




  
  52
  
    
""


  		




  
  53
  
    
""


  		




  
  54
  
    
""


  		




  
  55
  
    
""


  		




  
  56
  
    
""


  		




  
  57
  
    
""


  		




  
  58
  
    
""


  		




  
  59
  
    
""


  		




  
  60
  
    
""


  		




  
  61
  
    
""


  		




  
  62
  
    
""


  		




  
  63
  
    
""


  		




  
  64
  
    
""


  		




  
  65
  
    
""


  		




  
  66
  
    
""


  		




  
  67
  
    
""


  		




  
  68
  
    
""


  		




  
  69
  
    
""


  		




  
  70
  
    
""


  		




  
  71
  
    
""


  		




  
  72
  
    
""


  		




  
  73
  
    
""


  		




  
  74
  
    
""


  		




  
  75
  
    
""


  		




  
  76
  
    
""


  		




  
  77
  
    
""


  		




  
  78
  
    
""


  		




  
  79
  
    
""


  		




  
  80
  
    
""


  		




  
  81
  
    
""


  		




  
  82
  
    
""


  		




  
  83
  
    
""


  		




  
  84
  
    
""


  		




  
  85
  
    
""


  		




  
  86
  
    
""


  		




  
  87
  
    
""


  		




  
  88
  
    
""


  		




  
  89
  
    
""


  		




  
  90
  
    
""


  		




  
  91
  
    
""


  		




  
  92
  
    
""


  		




  
  93
  
    
""


  		




  
  94
  
    
""


  		




  
  95
  
    
""


  		




  
  96
  
    
""


  		




  
  97
  
    
""


  		




  
  98
  
    
""


  		




  
  99
  
    
""


  		




  
  100
  
    
""


  		




  
  101
  
    
""


  		








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