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Revision 104

Moved VegBank mapping joins to main mappings dir so they would have similar paths for the upcoming all-sources tester

View differences:

mappings/joins/NYBG-VegBank.organisms.csv
1
NYBG,VegBank:/taxonObservation
2
:1,/taxonImportance/*/stemCount
3
InstitutionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/first
4
CollectionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/last
5
ScientificName,"/taxonImportance/stemCount/stemLocation/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName}"
6
Kingdom,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Kingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
7
Phylum,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subkingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
8
Class,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Class]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
9
Order,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Order]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
10
Family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
11
Genus,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
12
Species,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
13
Subspecies,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
14
ScientificNameAuthor,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/reference/referenceContributor/*_ID/referenceParty/{givenName,surname}"
15
IdentifiedBy,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=false,currentInterpretation=true]/*_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}"
16
YearIdentified,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/year"
17
MonthIdentified,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/month"
18
DayIdentified,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/day"
19
FieldNumber,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber
20
Collector,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}"
21
YearCollected,/*_ID/observation/obsStartDate/_date/year
22
MonthCollected,/*_ID/observation/obsStartDate/_date/month
23
DayCollected,/*_ID/observation/obsStartDate/_date/day
24
Country,"/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""area|country|territory""])/placeName"
25
StateProvince,"/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""region|state|province""])/placeName"
26
County,/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=county])/placeName
27
Locality,/*_ID/observation/*_ID/plot/place/*_ID/namedPlace/placeDescription
28
Longitude,/*_ID/observation/*_ID/plot/realLongitude
29
Latitude,/*_ID/observation/*_ID/plot/realLatitude
30
CoordinatePrecision,/*_ID/observation/*_ID/plot/locationAccuracy
31
BoundingBox,/*_ID/observation/*_ID/plot/dsgpoly
32
MinimumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"
33
MaximumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"
34
MinimumDepth,/*_ID/observation/waterDepth/min
35
MaximumDepth,/*_ID/observation/waterDepth/max
36
Sex,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=sex]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
37
Notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes
38
Habitat,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=habitat]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
39
PlantFungusDescription,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=plantFungusDescription]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
40
Substrate,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=substrate]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
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Vegetation,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=vegetation]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
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UniqueNYInternalRecordNumber,"/{taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=epoch,*_ID/plantConcept,*_ID/party]/museumAccessionNumber,*_ID/observation/*_ID/plot:[confidentialityStatus=0]/authorPlotCode}"
mappings/joins/SALVIAS-VegBank.plots.csv
1
SALVIAS,VegBank:/observation
2
project,/*_ID/project/projectName
3
plot_code,"/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode,authorObsCode}"
4
major_geo,/*_ID/plot/place(/*_ID/namedPlace[placeSystem=continent])/placeName
5
country,"/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""area|country|territory""])/placeName"
6
pol1,"/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""region|state|province""])/placeName"
7
pol2,/*_ID/plot/place(/*_ID/namedPlace[placeSystem=county])/placeName
8
locality_description,/*_ID/plot/place/*_ID/namedPlace/placeDescription
9
lat_decimal,/*_ID/plot/realLatitude
10
long_decimal,/*_ID/plot/realLongitude
11
elev_m,/*_ID/plot/elevation
12
elev_max_m,"/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"
13
elev_min_m,"/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"
14
temp_c,"/definedValue[*_ID/userDefined[tableName=observation,userDefinedName=temperatureC]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
15
precip_mm,"/definedValue[*_ID/userDefined[tableName=observation,userDefinedName=precipitationMm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
16
slope_aspect,/*_ID/plot/slopeAspect
17
slope_gradient,/*_ID/plot/slopeGradient
18
clay_percent,/soilObs/soilClay
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silt_percent,/soilObs/soilSilt
20
sand_percent,/soilObs/soilSand
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organic_percent,/soilObs/soilOrganic
22
pH,/soilObs/soilPH
23
soil_N,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilNitrogen]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
24
soil_P,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilPhosphorus]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
25
soil_C,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCarbon]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
26
soil_K,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilPotassium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
27
soil_Mg,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilMagnesium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
28
soil_Ca,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCalcium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
29
soil_Na,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilSodium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
30
soil_acidity,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilAcidity]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
31
soil_base,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilBase]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
32
soil_cation_cap,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCationCap]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
33
soil_conductivity,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilConductivity]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
34
soil_texture,/soilObs/soilTexture
35
holdridge_life_zone,/commClass/commInterpretation/*_ID/commConcept/commDescription
36
life_zone_code,/commClass/commInterpretation/commconcept_ID/*_ID/observation/commClass/commInterpretation/*_ID/commConcept/*_ID/*/commName
37
plot_methodology,/methodNarrative
38
plot_area_ha,/*_ID/plot/area
39
date_start,/obsStartDate
40
date_finish,/obsEndDate
mappings/joins/SALVIAS-VegBank.organisms.csv
1
SALVIAS,VegBank:/taxonObservation
2
OBSERVATION_ID,"/{taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=epoch,*_ID/plantConcept,*_ID/party]/museumAccessionNumber,*_ID/observation/*_ID/plot:[confidentialityStatus=0]/authorPlotCode}"
3
plot_code,/*_ID/observation/*_ID/plot/PARENT_ID/plot:[confidentialityStatus=0]/authorPlotCode
4
census_no,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=censusNo]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
5
census_date,/*_ID/observation/obsStartDate
6
subplot,"/*_ID/observation/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode,authorObsCode}"
7
individual_code,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=individualCode]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
8
tag1,/taxonImportance/stemCount/stemLocation/stemCode
9
tag2,/taxonImportance/stemCount/stemLocation/stemCode
10
x_position,/taxonImportance/stemCount/stemLocation/stemXPosition
11
y_position,/taxonImportance/stemCount/stemLocation/stemYPosition
12
coll_number,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber
13
coll_lastname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/surName
14
coll_firstname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/givenName
15
det_type,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=determinationType]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
16
family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
17
genus,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
18
specific_epithet,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
19
specific_authority,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/plantName/reference_ID/reference/shortName"
20
infra_rank_1,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/first"
21
infra_ep_1,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/last"
22
cf_aff,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=cfAff]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
23
habit,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=habit]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
24
no_of_individuals,/taxonImportance/*/stemCount
25
cover_percent,/taxonImportance/cover
26
intercept_cm,"/taxonImportance/definedValue[*_ID/userDefined[tableName=taxonImportance,userDefinedName=interceptCm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
27
height_m,/taxonImportance/stemCount/stemHeight
28
ht_first_branch_m,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=heightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
29
stem_tag1,/taxonImportance/stemCount/stemLocation/stemCode
30
stem_tag2,/taxonImportance/stemCount/stemLocation/stemCode
31
stem_dbh,/taxonImportance/stemCount/stemDiameter
32
basal_diam,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemBasalDiameter]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
33
stem_height_m,/taxonImportance/stemCount/stemHeight
34
stem_height_first_branch_m,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemHeightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
35
stem_canopy_form,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemCanopyForm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
36
stem_canopy_position,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemCanopyPosition]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
37
stem_liana_infestation,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemLianaInfestation]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
38
notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes
39
orig_family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
40
orig_species,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
mappings/join_all_vegbank
8 8
    type="${map%.csv}" # remove extension
9 9
    type="${type#*.}" # remove up to last "."
10 10
    ../scripts/util/join_maps "VegX-VegBank.$type.csv" <"$map" \
11
    >"joins/${map/VegX/VegBank}"
11
    >"${map/VegX/VegBank}"
12 12
done
mappings/NYBG-VegBank.organisms.csv
1
NYBG,VegBank:/taxonObservation
2
:1,/taxonImportance/*/stemCount
3
InstitutionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/first
4
CollectionCode,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/museum_ID/party/OrganizationName/_name/last
5
ScientificName,"/taxonImportance/stemCount/stemLocation/{taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName,taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/*_ID/plantConcept:[*_ID/reference]/*_ID/*/plantName}"
6
Kingdom,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Kingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
7
Phylum,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subkingdom]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
8
Class,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Class]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
9
Order,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Order]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
10
Family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
11
Genus,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
12
Species,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
13
Subspecies,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
14
ScientificNameAuthor,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/reference/referenceContributor/*_ID/referenceParty/{givenName,surname}"
15
IdentifiedBy,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]:[interpretationType=Author,originalInterpretation=false,currentInterpretation=true]/*_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}"
16
YearIdentified,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/year"
17
MonthIdentified,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/month"
18
DayIdentified,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,!*_ID/plantConcept/plantStatus]/interpretationDate/_date/day"
19
FieldNumber,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber
20
Collector,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/{givenName/_namePart/first,middleName/_namePart/middle,surName/_namePart/last}"
21
YearCollected,/*_ID/observation/obsStartDate/_date/year
22
MonthCollected,/*_ID/observation/obsStartDate/_date/month
23
DayCollected,/*_ID/observation/obsStartDate/_date/day
24
Country,"/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""area|country|territory""])/placeName"
25
StateProvince,"/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""region|state|province""])/placeName"
26
County,/*_ID/observation/*_ID/plot/place(/*_ID/namedPlace[placeSystem=county])/placeName
27
Locality,/*_ID/observation/*_ID/plot/place/*_ID/namedPlace/placeDescription
28
Longitude,/*_ID/observation/*_ID/plot/realLongitude
29
Latitude,/*_ID/observation/*_ID/plot/realLatitude
30
CoordinatePrecision,/*_ID/observation/*_ID/plot/locationAccuracy
31
BoundingBox,/*_ID/observation/*_ID/plot/dsgpoly
32
MinimumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"
33
MaximumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"
34
MinimumDepth,/*_ID/observation/waterDepth/min
35
MaximumDepth,/*_ID/observation/waterDepth/max
36
Sex,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=sex]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
37
Notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes
38
Habitat,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=habitat]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
39
PlantFungusDescription,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=plantFungusDescription]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
40
Substrate,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=substrate]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
41
Vegetation,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=vegetation]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
42
UniqueNYInternalRecordNumber,"/{taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=epoch,*_ID/plantConcept,*_ID/party]/museumAccessionNumber,*_ID/observation/*_ID/plot:[confidentialityStatus=0]/authorPlotCode}"
mappings/SALVIAS-VegBank.plots.csv
1
SALVIAS,VegBank:/observation
2
project,/*_ID/project/projectName
3
plot_code,"/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode,authorObsCode}"
4
major_geo,/*_ID/plot/place(/*_ID/namedPlace[placeSystem=continent])/placeName
5
country,"/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""area|country|territory""])/placeName"
6
pol1,"/*_ID/plot/place(/*_ID/namedPlace[placeSystem=""region|state|province""])/placeName"
7
pol2,/*_ID/plot/place(/*_ID/namedPlace[placeSystem=county])/placeName
8
locality_description,/*_ID/plot/place/*_ID/namedPlace/placeDescription
9
lat_decimal,/*_ID/plot/realLatitude
10
long_decimal,/*_ID/plot/realLongitude
11
elev_m,/*_ID/plot/elevation
12
elev_max_m,"/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"
13
elev_min_m,"/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"
14
temp_c,"/definedValue[*_ID/userDefined[tableName=observation,userDefinedName=temperatureC]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
15
precip_mm,"/definedValue[*_ID/userDefined[tableName=observation,userDefinedName=precipitationMm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
16
slope_aspect,/*_ID/plot/slopeAspect
17
slope_gradient,/*_ID/plot/slopeGradient
18
clay_percent,/soilObs/soilClay
19
silt_percent,/soilObs/soilSilt
20
sand_percent,/soilObs/soilSand
21
organic_percent,/soilObs/soilOrganic
22
pH,/soilObs/soilPH
23
soil_N,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilNitrogen]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
24
soil_P,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilPhosphorus]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
25
soil_C,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCarbon]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
26
soil_K,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilPotassium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
27
soil_Mg,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilMagnesium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
28
soil_Ca,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCalcium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
29
soil_Na,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilSodium]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
30
soil_acidity,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilAcidity]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
31
soil_base,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilBase]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
32
soil_cation_cap,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilCationCap]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
33
soil_conductivity,"/soilObs/definedValue[*_ID/userDefined[tableName=soilObs,userDefinedName=soilConductivity]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
34
soil_texture,/soilObs/soilTexture
35
holdridge_life_zone,/commClass/commInterpretation/*_ID/commConcept/commDescription
36
life_zone_code,/commClass/commInterpretation/commconcept_ID/*_ID/observation/commClass/commInterpretation/*_ID/commConcept/*_ID/*/commName
37
plot_methodology,/methodNarrative
38
plot_area_ha,/*_ID/plot/area
39
date_start,/obsStartDate
40
date_finish,/obsEndDate
mappings/SALVIAS-VegBank.organisms.csv
1
SALVIAS,VegBank:/taxonObservation
2
OBSERVATION_ID,"/{taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=false,interpretationDate=epoch,*_ID/plantConcept,*_ID/party]/museumAccessionNumber,*_ID/observation/*_ID/plot:[confidentialityStatus=0]/authorPlotCode}"
3
plot_code,/*_ID/observation/*_ID/plot/PARENT_ID/plot:[confidentialityStatus=0]/authorPlotCode
4
census_no,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=censusNo]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
5
census_date,/*_ID/observation/obsStartDate
6
subplot,"/*_ID/observation/{*_ID/plot:[confidentialityStatus=0]/authorPlotCode,authorObsCode}"
7
individual_code,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=individualCode]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
8
tag1,/taxonImportance/stemCount/stemLocation/stemCode
9
tag2,/taxonImportance/stemCount/stemLocation/stemCode
10
x_position,/taxonImportance/stemCount/stemLocation/stemXPosition
11
y_position,/taxonImportance/stemCount/stemLocation/stemYPosition
12
coll_number,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collectionNumber
13
coll_lastname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/surName
14
coll_firstname,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/collector_ID/party/givenName
15
det_type,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=determinationType]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
16
family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
17
genus,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Genus]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
18
specific_epithet,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
19
specific_authority,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Species]/*_ID/plantConcept/*_ID/plantName/reference_ID/reference/shortName"
20
infra_rank_1,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/first"
21
infra_ep_1,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=computer,*_ID/plantConcept/plantStatus/plantLevel=Subspecies]:[interpretationType=""Computer (automated)"",originalInterpretation=false,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName/_name/last"
22
cf_aff,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=cfAff]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
23
habit,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/definedValue[*_ID/userDefined[tableName=taxonInterpretation,userDefinedName=habit]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
24
no_of_individuals,/taxonImportance/*/stemCount
25
cover_percent,/taxonImportance/cover
26
intercept_cm,"/taxonImportance/definedValue[*_ID/userDefined[tableName=taxonImportance,userDefinedName=interceptCm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
27
height_m,/taxonImportance/stemCount/stemHeight
28
ht_first_branch_m,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=heightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
29
stem_tag1,/taxonImportance/stemCount/stemLocation/stemCode
30
stem_tag2,/taxonImportance/stemCount/stemLocation/stemCode
31
stem_dbh,/taxonImportance/stemCount/stemDiameter
32
basal_diam,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemBasalDiameter]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
33
stem_height_m,/taxonImportance/stemCount/stemHeight
34
stem_height_first_branch_m,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemHeightFirstBranchM]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
35
stem_canopy_form,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemCanopyForm]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
36
stem_canopy_position,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemCanopyPosition]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
37
stem_liana_infestation,"/taxonImportance/stemCount/stemLocation/definedValue[*_ID/userDefined[tableName=stemLocation,userDefinedName=stemLianaInfestation]:[userDefinedType=varchar]]:[@fkey=tableRecord_ID]/definedValue"
38
notes,/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=collector]/notes
39
orig_family,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Family]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"
40
orig_species,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[ROLE_ID/aux_Role/roleCode=identifier,*_ID/plantConcept/plantStatus/plantLevel=Species]:[interpretationType=Author,originalInterpretation=true,currentInterpretation=true,interpretationDate=epoch,*_ID/party]/*_ID/plantConcept:[plantStatus:[plantConceptStatus=accepted,startDate=epoch,*_ID/party],*_ID/reference]/*_ID/*/plantName"

Also available in: Unified diff