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Revision 4657

Added by Aaron Marcuse-Kubitza about 12 years ago

inputs/*/*/map.csv: Moved filter suffixes to separate filter column to enable automapping to work on those mappings' terms, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Map_refactoring#Move-filter-suffixes-to-separate-filter-column&gt;. Note that the only changes to VegBIEN.csvs are the (now automapped) names of terms in "No join mapping" comments.

View differences:

inputs/NCU-NCSC/Specimen/new_terms.csv
6 6 
Lat (-=S)
7 7 
Long (-=W)
8 8 
Accuracy
9 
FIPS
9 10 
Format
10 11 
Typology
inputs/SpeciesLink/Specimen/map.csv
15 15 
dwc_dwcore_Genus,genus,,
16 16 
dwc_dwcore_SpecificEpithet,specificEpithet,,
17 17 
dwc_dwcore_InfraspecificEpithet,infraspecificEpithet,,
18 
dwc_dwcore_AuthorYearOfScientificName,ScientificNameAuthor/_alt/3,,
18 
dwc_dwcore_AuthorYearOfScientificName,scientificNameAuthorship,/_alt/3,
19 19 
dwc_dwcore_Continent,continent,,
20 20 
dwc_dwcore_Country,country,,
21 21 
dwc_dwcore_StateProvince,stateProvince,,
......
25 25 
dwc_dwcore_MaximumElevationInMeters,maximumElevationInMeters,,
26 26 
dwc_dwcore_MinimumDepthInMeters,minimumDepthInMeters,,
27 27 
dwc_dwcore_MaximumDepthInMeters,maximumDepthInMeters,,
28 
dwc_dwcore_DayOfYear,JulianDay/_alt/2,,
28 
dwc_dwcore_DayOfYear,day,/_alt/2,
29 29 
dwc_dwcore_Collector,recordedBy,,
30 30 
dwc_dwcore_Sex,sex,,
31 31 
dwc_curatorial_IdentifiedBy,identifiedBy,,
32 
dwc_curatorial_CollectorNumber,recordNumber/_alt/3,,
33 
dwc_curatorial_FieldNumber,recordNumber/_alt/2,,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
32 
dwc_curatorial_CollectorNumber,recordNumber,/_alt/3,
33 
dwc_curatorial_FieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
34 34 
-----
35 35 
SELECT count(*) FROM ""SpeciesLink"".specimens
36 36 
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
......
51 51 
dwc_terms_typeStatus,typeStatus,,
52 52 
dwc_terms_catalogNumber,catalogNumber,,
53 53 
dwc_terms_occurrenceRemarks,occurrenceRemarks,,
54 
dwc_terms_recordNumber,recordNumber/_alt/1,,
54 
dwc_terms_recordNumber,recordNumber,/_alt/1,
55 55 
dwc_terms_recordedBy,recordedBy,,
56 56 
dwc_terms_individualCount,individualCount,,
57 57 
dwc_terms_sex,sex,,
......
63 63 
dwc_terms_year,year,,
64 64 
dwc_terms_month,month,,
65 65 
dwc_terms_day,day,,
66 
dwc_terms_fieldNumber,recordNumber/_alt/2,,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
66 
dwc_terms_fieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
67 67 
-----
68 68 
SELECT count(*) FROM ""SpeciesLink"".specimens
69 69 
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
......
91 91 
dwc_terms_genus,genus,,
92 92 
dwc_terms_specificEpithet,specificEpithet,,
93 93 
dwc_terms_infraspecificEpithet,infraspecificEpithet,,
94 
dwc_terms_scientificNameAuthorship,ScientificNameAuthor/_alt/1,,
94 
dwc_terms_scientificNameAuthorship,scientificNameAuthorship,/_alt/1,
95 95 
conceptual_darwin_2003_1_0_DateLastModified,dcterms:modified,,
96 96 
conceptual_darwin_2003_1_0_InstitutionCode,institutionCode,,
97 97 
conceptual_darwin_2003_1_0_CollectionCode,collectionCode,,
......
106 106 
conceptual_darwin_2003_1_0_Genus,genus,,
107 107 
conceptual_darwin_2003_1_0_Species,specificEpithet,,
108 108 
conceptual_darwin_2003_1_0_Subspecies,infraspecificEpithet,,
109 
conceptual_darwin_2003_1_0_ScientificNameAuthor,ScientificNameAuthor/_alt/2,,
109 
conceptual_darwin_2003_1_0_ScientificNameAuthor,scientificNameAuthorship,/_alt/2,
110 110 
conceptual_darwin_2003_1_0_IdentifiedBy,identifiedBy,,
111 111 
conceptual_darwin_2003_1_0_YearIdentified,yearIdentified,,
112 112 
conceptual_darwin_2003_1_0_MonthIdentified,monthIdentified,,
113 113 
conceptual_darwin_2003_1_0_DayIdentified,dayIdentified,,
114 114 
conceptual_darwin_2003_1_0_TypeStatus,TypeStatus,,
115 
conceptual_darwin_2003_1_0_CollectorNumber,recordNumber/_alt/3,,
116 
conceptual_darwin_2003_1_0_FieldNumber,recordNumber/_alt/2,,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
115 
conceptual_darwin_2003_1_0_CollectorNumber,recordNumber,/_alt/3,
116 
conceptual_darwin_2003_1_0_FieldNumber,recordNumber,/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
117 117 
-----
118 118 
SELECT count(*) FROM ""SpeciesLink"".specimens
119 119 
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
......
122 122 
conceptual_darwin_2003_1_0_YearCollected,yearCollected,,
123 123 
conceptual_darwin_2003_1_0_MonthCollected,monthCollected,,
124 124 
conceptual_darwin_2003_1_0_DayCollected,dayCollected,,
125 
conceptual_darwin_2003_1_0_JulianDay,JulianDay/_alt/1,,
125 
conceptual_darwin_2003_1_0_JulianDay,day,/_alt/1,
126 126 
conceptual_darwin_2003_1_0_TimeOfDay,eventTime,,
127 127 
conceptual_darwin_2003_1_0_ContinentOcean,continent,,
128 128 
conceptual_darwin_2003_1_0_Country,country,,
inputs/SpeciesLink/Specimen/unmapped_terms.csv
1 1 
BasisOfRecord
2 
ScientificNameAuthor/_alt/3
3 
JulianDay/_alt/2
4 
recordNumber/_alt/3
5 
recordNumber/_alt/2
2 
day
6 3 
TypeStatus
7 4 
dcterms:modified
8 5 
basisOfRecord
9 6 
typeStatus
10 7 
occurrenceRemarks
11 
recordNumber/_alt/1
12 8 
preparations
13 9 
otherCatalogNumbers
14 10 
eventTime
......
17 13 
year
18 14 
month
19 15 
day
20 
recordNumber/_alt/2
21 
ScientificNameAuthor/_alt/1
22 16 
dcterms:modified
23 17 
BasisOfRecord
24 
ScientificNameAuthor/_alt/2
25 18 
TypeStatus
26 
recordNumber/_alt/3
27 
recordNumber/_alt/2
28 
JulianDay/_alt/1
19 
day
29 20 
eventTime
30 21 
preparations
31 22 
otherCatalogNumbers
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,/_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."
24 24 
darwin:Collector,recordedBy,,
25 25 
darwin:YearCollected,yearCollected,,
26 26 
darwin:MonthCollected,monthCollected,,
inputs/XAL/Specimen/unmapped_terms.csv
1 1 
BasisOfRecord
2 2 
TypeStatus
3 
recordNumber/_alt/1
4 
recordNumber/_alt/2
5 3 
day
6 4 
eventTime
7 5 
preparations
inputs/NY/Specimen/map.csv
34 34 
Country,country,,
35 35 
StateProvince,stateProvince,,
36 36 
County,county,,
37 
Locality,Locality/_merge/1,,
37 
Locality,locality,/_merge/1,
38 38 
Longitude,verbatimLongitude,,
39 39 
Latitude,verbatimLatitude,,
40 40 
CoordinatePrecision,coordinatePrecision,,
41 41 
BoundingBox,footprintWKT,,
42 
MinimumElevation,MinimumElevation/_nullIf:[null=.]/value,,
42 
MinimumElevation,minimumElevationInMeters,/_nullIf:[null=.]/value,
43 43 
MaximumElevation,maximumElevationInMeters,,
44 44 
MinimumDepth,minimumDepthInMeters,,
45 45 
MaximumDepth,maximumDepthInMeters,,
......
49 49 
PreviousCatalogNumber,otherCatalogNumbers,,
50 50 
RelationshipType,relationshipOfResource,,
51 51 
RelatedCatalogItem,relatedResourceID,,
52 
Notes,Notes/_merge/1,,
52 
Notes,fieldNotes,/_merge/1,
53 53 
Habitat,habitat,,
54 
PlantFungusDescription,"Notes/_merge/2/_label[label=""plant fungus""]/value",,
55 
Substrate,"Locality/_merge/2/_label[label=""substrate""]/value",,
56 
Vegetation,"Locality/_merge/3/_label[label=""vegetation""]/value",,
54 
PlantFungusDescription,fieldNotes,"/_merge/2/_label[label=""plant fungus""]/value",
55 
Substrate,locality,"/_merge/2/_label[label=""substrate""]/value",
56 
Vegetation,locality,"/_merge/3/_label[label=""vegetation""]/value",
57 57 
UniqueNYInternalRecordNumber,occurrenceID,,
inputs/NY/Specimen/unmapped_terms.csv
4 4 
OMIT
5 5 
day
6 6 
eventTime
7 
Locality/_merge/1
8 
MinimumElevation/_nullIf:[null=.]/value
9 7 
preparations
10 8 
otherCatalogNumbers
11 9 
relationshipOfResource
12 10 
relatedResourceID
13 
Notes/_merge/1
14 
"Notes/_merge/2/_label[label=""plant fungus""]/value"
15 
"Locality/_merge/2/_label[label=""substrate""]/value"
16 
"Locality/_merge/3/_label[label=""vegetation""]/value"
inputs/Madidi/Plot/map.csv
21 21 
Minimum altitude,minimumElevationInMeters,,
22 22 
Locality,locality,,
23 23 
Locality description,communityName,,Often begins with the text in Vegetation type
24 
Direction,slopeAspect/_alt/1,,Part files provide either this field or Direction
24 
Direction,slopeAspect,/_alt/1,Part files provide either this field or Direction
25 25 
Vegetation type,communityID,,
26 26 
Topographical situation,landform,,
27 27 
Slope,slopeGradient,,
......
43 43 
Arcilla (DIN 18 123–%–1),clay,,
44 44 
Textural class,texture,,
45 45 
Observaciones,plotNotes,,
46 
Orientación/exposicion,slopeAspect/_alt/2,,Part files provide either this field or Orientación
46 
Orientación/exposicion,slopeAspect,/_alt/2,Part files provide either this field or Orientación
inputs/Madidi/Plot/unmapped_terms.csv
5 5 
Number of stems
6 6 
Number of trees
7 7 
Coordinates
8 
slopeAspect/_alt/1
9 8 
Soil sample
10 
slopeAspect/_alt/2
inputs/UNCC/Specimen/map.csv
4 4 
family,family,,
5 5 
genus,genus,,
6 6 
species,specificEpithet,,
7 
usdaRank,taxonRank/_alt/1,,
8 
infrarank,taxonRank/_alt/2,,
7 
usdaRank,taxonRank,/_alt/1,
8 
infrarank,taxonRank,/_alt/2,
9 9 
infraname,infraspecificEpithet,,
10 10 
SciName,scientificName,,
11 11 
authors,scientificNameAuthorship,,
12 
collector,Collector/_merge/1,,
13 
collector1,Collector/_merge/2,,
14 
collector2,Collector/_merge/3,,
15 
collector3,Collector/_merge/4,,
12 
collector,recordedBy,/_merge/1,
13 
collector1,recordedBy,/_merge/2,
14 
collector2,recordedBy,/_merge/3,
15 
collector3,recordedBy,/_merge/4,
16 16 
collectno,recordNumber,,
17 17 
collmonth,monthCollected,,
18 18 
collday,dayCollected,,
......
20 20 
country,country,,
21 21 
state,stateProvince,,
22 22 
county,county,,
23 
campus,"fieldNotes/_merge/5/_label[label=""campus""]/value",,
24 
leaves,"reproductiveCondition/_map:[A=*,I=*,M=*]/value",,"Main values are A, I, and M. What do they mean?"
25 
flower,"reproductiveCondition/_map:[A=*,I=*,M=*]/value",,"Main values are A, I, and M. What do they mean?"
26 
fruit,"reproductiveCondition/_map:[A=*,I=*,M=*]/value",,"Main values are A, I, and M. What do they mean?"
27 
root,"reproductiveCondition/_map:[A=*,I=*,M=*]/value",,"Main values are A, I, and M. What do they mean?"
23 
campus,fieldNotes,"/_merge/5/_label[label=""campus""]/value",
24 
leaves,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
25 
flower,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
26 
fruit,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
27 
root,reproductiveCondition,"/_map:[A=*,I=*,M=*]/value","Main values are A, I, and M. What do they mean?"
28 28 
locality,locality,,
29 29 
habitat,habitat,,
30 
comment1,fieldNotes/_merge/1,,
31 
comment2,fieldNotes/_merge/2,,
32 
comment3,fieldNotes/_merge/3,,
33 
comment4,fieldNotes/_merge/4,,
34 
loanto,"fieldNotes/_merge/6/_label[label=""loaned to""]/value",,
35 
inorout,"fieldNotes/_merge/7/_label[label=""in or out""]/value",,
30 
comment1,fieldNotes,/_merge/1,
31 
comment2,fieldNotes,/_merge/2,
32 
comment3,fieldNotes,/_merge/3,
33 
comment4,fieldNotes,/_merge/4,
34 
loanto,fieldNotes,"/_merge/6/_label[label=""loaned to""]/value",
35 
inorout,fieldNotes,"/_merge/7/_label[label=""in or out""]/value",
36 36 
sheetno,associatedMedia,,?
37 37 
cultivated,cultivated,,Ignore other values
38 38 
filler,filler,,"Where used, same as family"
inputs/UNCC/Specimen/unmapped_terms.csv
1 
taxonRank/_alt/2
2 
Collector/_merge/1
3 
Collector/_merge/2
4 
Collector/_merge/3
5 
Collector/_merge/4
6 
"fieldNotes/_merge/5/_label[label=""campus""]/value"
7 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
8 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
9 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
10 
"reproductiveCondition/_map:[A=*,I=*,M=*]/value"
11 
fieldNotes/_merge/1
12 
fieldNotes/_merge/2
13 
fieldNotes/_merge/3
14 
fieldNotes/_merge/4
15 
"fieldNotes/_merge/6/_label[label=""loaned to""]/value"
16 
"fieldNotes/_merge/7/_label[label=""in or out""]/value"
1 
reproductiveCondition
2 
reproductiveCondition
3 
reproductiveCondition
17 4 
associatedMedia
18 5 
filler
inputs/SALVIAS-CSV/Organism/map.csv
14 14 
subplot,subplot,,
15 15 
individual_code,recordNumber,,"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."
16 16 
ind_id,ind_id,,Brad: OMIT
17 
tag1,tag/_alt/1,,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
18 
tag2,previousTag/_alt/1,,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
17 
tag1,tag,/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
18 
tag2,previousTag,/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
19 19 
x_position,organismX,,"Brad: These are important, fundamental values of many tree plots"
20 20 
y_position,organismY,,Brad: See comment above for x_position
21 
voucher_string,catalogNumber/_alt/2,,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
22 
coll_number,catalogNumber/_alt/1,,Brad: Map instead as for voucher_string
21 
voucher_string,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
22 
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
23 23 
collector_code,collector_code,,Brad: OMIT
24 24 
coll_lastname,recordedBy.surName,,"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."
25 25 
coll_firstname,recordedBy.givenName,,Brad: See comment above
......
39 39 
no_of_individuals,individualCount,,"Brad: This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
40 40 
cover_percent,coverPercent,,
41 41 
intercept_cm,volumeCanopy,,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
42 
height_m,height/_alt/2,,
42 
height_m,height,/_alt/2,
43 43 
ht_first_branch_m,heightFirstBranch,,
44 
stem_tag1,tag/_alt/2,,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
45 
stem_tag2,previousTag/_alt/2,,Brad: see above
44 
stem_tag1,tag,/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
45 
stem_tag2,previousTag,/_alt/2,Brad: see above
46 46 
stem_dbh,diameterBreastHeight,,
47 47 
basal_diam,basalDiameter,,
48 
stem_height_m,height/_alt/1,,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
48 
stem_height_m,height,/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
49 49 
stem_height_first_branch_m,heightFirstBranch,,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
50 50 
stem_canopy_form,canopyForm,,
51 51 
stem_canopy_position,canopyPosition,,
inputs/SALVIAS-CSV/Organism/unmapped_terms.csv
1 
tag/_alt/1
2 
previousTag/_alt/1
3 
catalogNumber/_alt/2
4 
catalogNumber/_alt/1
5 1 
collector_code
6 2 
fam_status
7 3 
gen_status
8 4 
species_status
9 5 
comments
10 
height/_alt/2
11 
tag/_alt/2
12 
previousTag/_alt/2
13 
height/_alt/1
inputs/SALVIAS-CSV/Plot/map.csv
16 16 
precip_mm,precipitation,,
17 17 
slope_aspect,slopeAspect,,
18 18 
slope_gradient,slopeGradient,,
19 
clay_percent,"clay/_units:[default=""%"",to=]/value",,
20 
silt_percent,"silt/_units:[default=""%"",to=]/value",,
21 
sand_percent,"sand/_units:[default=""%"",to=]/value",,
22 
organic_percent,"organic/_units:[default=""%"",to=]/value",,
19 
clay_percent,clay,"/_units:[default=""%"",to=]/value",
20 
silt_percent,silt,"/_units:[default=""%"",to=]/value",
21 
sand_percent,sand,"/_units:[default=""%"",to=]/value",
22 
organic_percent,organic,"/_units:[default=""%"",to=]/value",
23 23 
pH,ph,,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."
24 
soil_N,"nitrogen/_units:[default=""%"",to=]/value",,
25 
soil_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",,
26 
soil_C,"carbon/_units:[default=""%"",to=]/value",,
27 
soil_K,"potassium/_units:[default=""%"",to=]/value",,
28 
soil_Mg,"magnesium/_units:[default=""%"",to=]/value",,
29 
soil_Ca,"calcium/_units:[default=""%"",to=]/value",,
30 
soil_Na,"sodium/_units:[default=""%"",to=]/value",,
31 
soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",,
32 
soil_base,"baseSaturation/_units:[default=""%"",to=]/value",,
24 
soil_N,nitrogen,"/_units:[default=""%"",to=]/value",
25 
soil_P,phosphorus,"/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
26 
soil_C,carbon,"/_units:[default=""%"",to=]/value",
27 
soil_K,potassium,"/_units:[default=""%"",to=]/value",
28 
soil_Mg,magnesium,"/_units:[default=""%"",to=]/value",
29 
soil_Ca,calcium,"/_units:[default=""%"",to=]/value",
30 
soil_Na,sodium,"/_units:[default=""%"",to=]/value",
31 
soil_acidity,acidity,"/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
32 
soil_base,baseSaturation,"/_units:[default=""%"",to=]/value",
33 33 
soil_cation_cap,cationExchangeCapacity,,
34 34 
soil_conductivity,conductivity,,
35 35 
soil_texture,texture,,
inputs/SALVIAS-CSV/Plot/new_terms.csv
29 29 
soil_texture
30 30 
holdridge_life_zone
31 31 
life_zone_code
32 
observation_type
32 33 
plot_methodology
33 34 
plot_area_ha
34 35 
date_start
inputs/SALVIAS-CSV/Plot/unmapped_terms.csv
1 
"silt/_units:[default=""%"",to=]/value"
2 
"sand/_units:[default=""%"",to=]/value"
3 
"organic/_units:[default=""%"",to=]/value"
4 
"nitrogen/_units:[default=""%"",to=]/value"
5 
"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value"
6 
"carbon/_units:[default=""%"",to=]/value"
7 
"potassium/_units:[default=""%"",to=]/value"
8 
"magnesium/_units:[default=""%"",to=]/value"
9 
"calcium/_units:[default=""%"",to=]/value"
10 
"sodium/_units:[default=""%"",to=]/value"
11 
"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value"
12 
"baseSaturation/_units:[default=""%"",to=]/value"
13 
observation_type
14 1 
recensused
inputs/SALVIAS/plotMetadata/map.csv
29 29 
bearing,bearing,,
30 30 
slope_aspect,slopeAspect,,
31 31 
slope_gradient,slopeGradient,,
32 
clay_percent,"clay/_units:[default=""%"",to=]/value",,
33 
silt_percent,"silt/_units:[default=""%"",to=]/value",,
34 
sand_percent,"sand/_units:[default=""%"",to=]/value",,
32 
clay_percent,clay,"/_units:[default=""%"",to=]/value",
33 
silt_percent,silt,"/_units:[default=""%"",to=]/value",
34 
sand_percent,sand,"/_units:[default=""%"",to=]/value",
35 35 
pH,ph,,"Brad: For all these soil variables, how do we store information on method, units. Seems like an ontological structure would be more appropriate (measurementName, measurementValue, measurementUnits, measurementMethod). Same as BIEN traits table. Something to discuss."
36 
soil_N,"nitrogen/_units:[default=""%"",to=]/value",,
37 
soil_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",,
38 
soil_C,"carbon/_units:[default=""%"",to=]/value",,
39 
soil_K,"potassium/_units:[default=""%"",to=]/value",,
40 
soil_Mg,"magnesium/_units:[default=""%"",to=]/value",,
41 
soil_Ca,"calcium/_units:[default=""%"",to=]/value",,
42 
soil_Na,"sodium/_units:[default=""%"",to=]/value",,
43 
soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",,
44 
soil_base,"baseSaturation/_units:[default=""%"",to=]/value",,
36 
soil_N,nitrogen,"/_units:[default=""%"",to=]/value",
37 
soil_P,phosphorus,"/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
38 
soil_C,carbon,"/_units:[default=""%"",to=]/value",
39 
soil_K,potassium,"/_units:[default=""%"",to=]/value",
40 
soil_Mg,magnesium,"/_units:[default=""%"",to=]/value",
41 
soil_Ca,calcium,"/_units:[default=""%"",to=]/value",
42 
soil_Na,sodium,"/_units:[default=""%"",to=]/value",
43 
soil_acidity,acidity,"/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
44 
soil_base,baseSaturation,"/_units:[default=""%"",to=]/value",
45 45 
soil_cation_cap,cationExchangeCapacity,,
46 46 
soil_conductivity,conductivity,,
47 
organic_percent,"organic/_units:[default=""%"",to=]/value",,
48 
soil_texture,"texture/_units:[default=""%"",to=]/value",,
47 
organic_percent,organic,"/_units:[default=""%"",to=]/value",
48 
soil_texture,texture,"/_units:[default=""%"",to=]/value",
49 49 
RevisionComments,RevisionComments,,
50 50 
Locality_Description,locality,,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
51 51 
topography_desc,topography_desc,,
inputs/SALVIAS/plotMetadata/unmapped_terms.csv
11 11 
PrecipSource
12 12 
TempSource
13 13 
bearing
14 
"clay/_units:[default=""%"",to=]/value"
15 
"silt/_units:[default=""%"",to=]/value"
16 
"sand/_units:[default=""%"",to=]/value"
17 
"nitrogen/_units:[default=""%"",to=]/value"
18 
"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value"
19 
"carbon/_units:[default=""%"",to=]/value"
20 
"potassium/_units:[default=""%"",to=]/value"
21 
"magnesium/_units:[default=""%"",to=]/value"
22 
"calcium/_units:[default=""%"",to=]/value"
23 
"sodium/_units:[default=""%"",to=]/value"
24 
"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value"
25 
"baseSaturation/_units:[default=""%"",to=]/value"
26 
"organic/_units:[default=""%"",to=]/value"
27 
"texture/_units:[default=""%"",to=]/value"
28 14 
RevisionComments
29 15 
topography_desc
30 16 
vegetation_1
inputs/SALVIAS/plotObservations/map.csv
21 21 
y_position,organismY,,Brad: See comment above for x_position
22 22 
dist,dist,,
23 23 
perp_dist,perp_dist,,
24 
SourceVoucher,catalogNumber/_alt/2,,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
25 
coll_number,catalogNumber/_alt/1,,Brad: Map instead as for voucher_string
24 
SourceVoucher,catalogNumber,/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
25 
coll_number,catalogNumber,/_alt/1,Brad: Map instead as for voucher_string
26 26 
collector_code,collector_code,,Brad: OMIT
27 27 
coll_inits,coll_inits,,
28 28 
coll_lastname,recordedBy.surName,,"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."
inputs/SALVIAS/plotObservations/unmapped_terms.csv
1 1 
ind_id
2 2 
dist
3 3 
perp_dist
4 
catalogNumber/_alt/2
5 
catalogNumber/_alt/1
6 4 
collector_code
7 5 
coll_inits
8 6 
det_by
inputs/U/Specimen/map.csv
1 1 
U,Veg+,Filter,Comments
2 2 
ID,occurrenceID,,
3 3 
Barcode,catalogNumber,,
4 
Collector,Collector/_merge/1,,
4 
Collector,recordedBy,/_merge/1,
5 5 
Prefix,Prefix,,Not used
6 6 
Number,recordNumber,,
7 7 
Suffix,Suffix,,Not used
8 
Addcoll,Collector/_merge/2,,
8 
Addcoll,recordedBy,/_merge/2,
9 9 
Colldd,dayCollected,,
10 10 
Collmm,monthCollected,,
11 11 
Collyy,yearCollected,,
......
15 15 
cf,identificationQualifier,,
16 16 
Detby,identifiedBy,,
17 17 
Detyy,yearIdentified,,
18 
Gazetteer,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1",,
19 
Newgazett,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2",,Only used in 1 row
18 
Gazetteer,verbatimLocality,"/_merge/1/_label[label=""gazetteer""]/value/_merge/1",
19 
Newgazett,verbatimLocality,"/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row
20 20 
Majorarea,Majorarea,,
21 21 
Country,country,,
22 
Locnotes,VerbatimLocality/_merge/2,,
22 
Locnotes,verbatimLocality,/_merge/2,
23 23 
Coorsyst,Coorsyst,,
24 24 
Lat,decimalLatitude,,
25 25 
NS,NS,,
inputs/U/Specimen/new_terms.csv
1 1 
Barcode
2 
Prefix
2 3 
Number
3 4 
Addcoll
4 5 
Colldd
inputs/U/Specimen/unmapped_terms.csv
1 
Prefix
2 1 
Suffix
3 
Collector/_merge/2
4 2 
DateInfo
5 
"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1"
6 
"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2"
7 3 
Majorarea
8 
VerbatimLocality/_merge/2
9 4 
Coorsyst
10 5 
NS
11 6 
EW
inputs/ARIZ/Specimen/map.csv
4 4 
BasisOfRecord,BasisOfRecord,,
5 5 
InstitutionCode,institutionCode,,
6 6 
CollectionCode,collectionCode,,
7 
CatalogNumber,CatalogNumber/_alt/2,,Don't overwrite CatalogNumberNumeric
8 
CatalogNumberNumeric,CatalogNumber/_alt/1,,
7 
CatalogNumber,catalogNumber,/_alt/2,Don't overwrite CatalogNumberNumeric
8 
CatalogNumberNumeric,catalogNumber,/_alt/1,
9 9 
Collector,recordedBy,,
10 10 
CollectorNumber,recordNumber,,
11 11 
FieldNumber,OMIT,,"Usage inconsistent with DwC definition: meaning is recordNumber. Identical to CollectorNumber [1], so does not need to be mapped.
......
15 15 
MonthCollected,monthCollected,,
16 16 
DayCollected,dayCollected,,
17 17 
TimeCollected,eventTime,,
18 
VerbatimCollectingDate,dateCollected/_alt/0,,
18 
VerbatimCollectingDate,dateCollected,/_alt/0,
19 19 
FieldNotes,fieldNotes,,
20 20 
JulianDay,day,,
21 21 
HigherGeography,HigherGeography,,
......
42 42 
MinimumDepthInMeters,minimumDepthInMeters,,
43 43 
MaximumDepthInMeters,maximumDepthInMeters,,
44 44 
VerbatimDepth,VerbatimDepth,,
45 
ScientificName,ScientificName/_alt/2,,
45 
ScientificName,scientificName,/_alt/2,
46 46 
Kingdom,kingdom,,
47 47 
Phylum,phylum,,
48 48 
Class,class,,
......
51 51 
Genus,genus,,
52 52 
Species,specificEpithet,,
53 53 
Subspecies,infraspecificEpithet,,
54 
ScientificNameAuthor,ScientificName/_alt/1,,Contains the binomial in addition to the authority
54 
ScientificNameAuthor,scientificName,/_alt/1,Contains the binomial in addition to the authority
55 55 
IdentifiedBy,identifiedBy,,
56 56 
IdentificationModifier,identificationQualifier,,
57 57 
YearIdentified,yearIdentified,,
......
63 63 
Tissues,Tissues,,Not used
64 64 
IndividualCount,individualCount,,
65 65 
AgeClass,lifeStage,,
66 
GenBankNum,"associatedSequences/_label[label=""GenBank""]/value",,
67 
OtherCatalogNumbers,RelatedCatalogItem/_alt/1,,
68 
RelatedCatalogedItems,RelatedCatalogItem/_alt/2,,Used only when OtherCatalogNumbers is NULL
66 
GenBankNum,associatedSequences,"/_label[label=""GenBank""]/value",
67 
OtherCatalogNumbers,relatedResourceID,/_alt/1,
68 
RelatedCatalogedItems,relatedResourceID,/_alt/2,Used only when OtherCatalogNumbers is NULL
69 69 
Remarks,taxonRemarks,,
inputs/ARIZ/Specimen/VegBIEN.csv
75 75 
JulianDay,,** No join mapping for day **
76 76 
LatLongComments,,** No join mapping for georeferenceRemarks **
77 77 
OriginalCoordinateSystem,,** No join mapping for verbatimSRS **
78 
OtherCatalogNumbers,,** No join mapping for RelatedCatalogItem/_alt/1 **
78 
OtherCatalogNumbers,,** No join mapping for relatedResourceID/_alt/1 **
79 79 
Preparations,,** No join mapping for Preparations **
80 
RelatedCatalogedItems,,** No join mapping for RelatedCatalogItem/_alt/2 ** Used only when OtherCatalogNumbers is NULL
80 
RelatedCatalogedItems,,** No join mapping for relatedResourceID/_alt/2 ** Used only when OtherCatalogNumbers is NULL
81 81 
TimeCollected,,** No join mapping for eventTime **
82 82 
Tissues,,** No join mapping for Tissues ** Not used
83 83 
TypeStatus,,** No join mapping for TypeStatus **
inputs/ARIZ/Specimen/unmapped_terms.csv
1 1 
BasisOfRecord
2 
CatalogNumber/_alt/2
3 
CatalogNumber/_alt/1
4 2 
OMIT
5 3 
eventTime
6 
dateCollected/_alt/0
7 4 
day
8 5 
HigherGeography
9 6 
IslandGroup
......
13 10 
georeferenceProtocol
14 11 
georeferenceRemarks
15 12 
VerbatimDepth
16 
ScientificName/_alt/2
17 
ScientificName/_alt/1
18 13 
TypeStatus
19 14 
Preparations
20 15 
Tissues
21 16 
lifeStage
22 
"associatedSequences/_label[label=""GenBank""]/value"
23 
RelatedCatalogItem/_alt/1
24 
RelatedCatalogItem/_alt/2
17 
associatedSequences
18 
relatedResourceID
19 
relatedResourceID
inputs/NCU-NCSC/Specimen/map.csv
9 9 
County,county,,
10 10 
Cultivated?,cultivated,,
11 11 
Elevation,verbatimElevation,,
12 
Lat (-=S),"Latitude/_replace:[""\?$""=]/value",,
13 
Long (-=W),"Longitude/_replace:[""\?$""=]/value",,
12 
Lat (-=S),verbatimLatitude,"/_replace:[""\?$""=]/value",
13 
Long (-=W),verbatimLongitude,"/_replace:[""\?$""=]/value",
14 14 
Accuracy,coordinateUncertaintyInMeters,,
15 15 
FIPS,FIPS,,FIPS county code
16 16 
Alt N/S,Alt N/S,,
17 17 
Alt E/W,Alt E/W,,
18 18 
Format,preparations,,
19 19 
Typology,typeStatus,,
20 
,,,
inputs/NCU-NCSC/Specimen/VegBIEN.csv
22 22 
FIPS,,** No join mapping for FIPS ** FIPS county code
23 23 
Format,,** No join mapping for preparations **
24 24 
Typology,,** No join mapping for typeStatus **
25 
,,** No input mapping for  **
inputs/NCU-NCSC/Specimen/unmapped_terms.csv
1 
"Longitude/_replace:[""\?$""=]/value"
2 
FIPS
3 1 
Alt N/S
4 2 
Alt E/W
5 3 
preparations
6 4 
typeStatus
7 
""
inputs/SpeciesLink/Specimen/VegBIEN.csv
171 171 
dwc_terms_locality,/location/locationnarrative/_merge/1,
172 172 
conceptual_darwin_2003_1_0_BasisOfRecord,,** No join mapping for BasisOfRecord **
173 173 
conceptual_darwin_2003_1_0_DateLastModified,,** No join mapping for dcterms:modified **
174 
conceptual_darwin_2003_1_0_JulianDay,,** No join mapping for JulianDay/_alt/1 **
174 
conceptual_darwin_2003_1_0_JulianDay,,** No join mapping for day/_alt/1 **
175 175 
conceptual_darwin_2003_1_0_PreparationType,,** No join mapping for preparations **
176 176 
conceptual_darwin_2003_1_0_PreviousCatalogNumber,,** No join mapping for otherCatalogNumbers **
177 177 
conceptual_darwin_2003_1_0_RelatedCatalogItem,,** No join mapping for relatedResourceID **
......
181 181 
dwc_curatorial_TypeStatus,,** No join mapping for TypeStatus **
182 182 
dwc_dwcore_BasisOfRecord,,** No join mapping for BasisOfRecord **
183 183 
dwc_dwcore_DateLastModified,,** No join mapping for dcterms:modified **
184 
dwc_dwcore_DayOfYear,,** No join mapping for JulianDay/_alt/2 **
184 
dwc_dwcore_DayOfYear,,** No join mapping for day/_alt/2 **
185 185 
dwc_terms_basisOfRecord,,** No join mapping for basisOfRecord **
186 186 
dwc_terms_day,,** No join mapping for day **
187 187 
dwc_terms_endDayOfYear,,** No join mapping for endDayOfYear **

Also available in: Unified diff