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Revision 4194

mappings/VegCore-VegBIEN.csv: Mapped verbatimScientificName to taxonoccurrence.authortaxoncode as an alternative to scientificName

View differences:

inputs/XAL/specimens/VegBIEN.csv
33 33
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
34 34
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
35 35
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"This historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber (http://rs.tdwg.org/dwc/terms/#recordNumber). It is also unused: `grep -F ""<darwin:FieldNumber>"" inputs/XAL/src/digir.specimens.xml` returns no lines."
36
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
36
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
37 37
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
38 38
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
39 39
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
inputs/NY/specimens/VegBIEN.csv
37 37
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
38 38
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
39 39
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,Usage inconsistent with DwC definition
40
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
40
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
41 41
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
42 42
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
43 43
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
inputs/UNCC/specimens/VegBIEN.csv
24 24
herbarium,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
25 25
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
26 26
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
27
SciName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
27
SciName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
28 28
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values
29 29
cultivated,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values
30 30
SciName,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
inputs/ACAD/specimens/VegBIEN.csv
20 20
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
21 21
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
22 22
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,
23
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
23
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
24 24
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
25 25
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
26 26
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
inputs/CVS/1.organisms/VegBIEN.csv
10 10
authorObsCode,/location/locationevent/authoreventcode,
11 11
obsStartDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,
12 12
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,
13
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
13
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
14 14
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
inputs/SALVIAS-CSV/1.organisms/VegBIEN.csv
37 37
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: These are important, fundamental values of many tree plots"
38 38
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position
39 39
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"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."
40
orig_species,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/last,Brad: OMIT
40
orig_species,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_name/last,Brad: OMIT
41 41
habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
42 42
OBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
43 43
specific_authority,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: This is the author of the scientificName.
inputs/SALVIAS/1.organisms/VegBIEN.csv
40 40
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: These are important, fundamental values of many tree plots"
41 41
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position
42 42
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"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."
43
OrigGenus,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/first,
44
OrigSpecies,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/last,Brad: OMIT
43
OrigGenus,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_name/first,
44
OrigSpecies,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_name/last,Brad: OMIT
45 45
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait.; According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
46 46
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
47 47
auth,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: This is the author of the scientificName.
inputs/ARIZ/specimens/VegBIEN.csv
44 44
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
45 45
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
46 46
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,Usage inconsistent with DwC definition
47
ScientificNameAuthor,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1,Contains the binomial in addition to the authority
48
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
47
ScientificNameAuthor,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_alt/1,Contains the binomial in addition to the authority
48
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2/_alt/2,
49 49
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
50 50
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
51 51
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
inputs/GBIF/specimens/VegBIEN.csv
20 20
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
21 21
CollectionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
22 22
InstitutionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
23
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
23
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
24 24
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
25 25
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
26 26
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
inputs/NCU-NCSC/specimens/VegBIEN.csv
15 15
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
16 16
SeriesName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
17 17
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
18
Full Taxon Name,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
18
Full Taxon Name,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
19 19
Cultivated?,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Yes=cultivated,No=wild]/value",
20 20
Cultivated?,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Yes=cultivated,No=wild]/value",
21 21
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
inputs/SpeciesLink/specimens/VegBIEN.csv
90 90
SELECT count(*) FROM ""SpeciesLink"".specimens
91 91
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
92 92
-----"
93
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
94
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
93
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
94
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
95 95
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
96 96
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
97 97
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
inputs/MO/specimens/VegBIEN.csv
30 30
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
31 31
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
32 32
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
33
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
33
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
34 34
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
35 35
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
36 36
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
inputs/QMOR/specimens/VegBIEN.csv
30 30
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2,
31 31
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname,
32 32
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
33
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
33
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
34 34
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname/_namePart/first,
35 35
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename/_namePart/middle,
36 36
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname/_namePart/last,
mappings/VegCore-VegBIEN.csv
86 86
relativePlotX,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,
87 87
relativePlotY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,
88 88
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,
89
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
89
verbatimScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1,
90
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
90 91
growthForm,/location/locationevent/taxonoccurrence/growthform,
91 92
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value",
92 93
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value",
mappings/Veg+-VegBIEN.csv
249 249
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,
250 250
AuthorPlantCode,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/3,
251 251
authorPlantCode,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/3,
252
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
253
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
252
VerbatimScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1,
253
verbatimScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1,
254
ScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
255
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
254 256
GrowthForm,/location/locationevent/taxonoccurrence/growthform,
255 257
growthForm,/location/locationevent/taxonoccurrence/growthform,
256 258
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
mappings/Veg+.cs-VegBIEN.csv
124 124
collectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
125 125
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,
126 126
authorPlantCode,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/3,
127
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
127
verbatimScientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1,
128
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,
128 129
growthForm,/location/locationevent/taxonoccurrence/growthform,
129 130
habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
130 131
verbatimGrowthForm,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=*]/value","According to <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.habit>, <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS#Habit>"
mappings/for_review/VegCore-VegBIEN.csv
86 86
relativePlotX,//stemobservation/xposition,
87 87
relativePlotY,//stemobservation/yposition,
88 88
recordNumber,//taxonoccurrence/authortaxoncode,
89
verbatimScientificName,//taxonoccurrence/authortaxoncode,
89 90
scientificName,//taxonoccurrence/authortaxoncode,
90 91
growthForm,//taxonoccurrence/growthform,
91 92
establishmentMeans,//taxonoccurrence/iscultivated,

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