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Revision 1540

Added by Aaron Marcuse-Kubitza almost 13 years ago

mappings/DwC2-VegBIEN.specimens.csv: Mapped establishmentMeans, which contains growthform, iscultivated, isnative, etc. combined

View differences:

inputs/UNCC/maps/VegBIEN.specimens.csv
17 17 
collector1,/*_id/taxonoccurrence/verbatimcollectorname/_merge/2,,23
18 18 
collector2,/*_id/taxonoccurrence/verbatimcollectorname/_merge/3,,23
19 19 
collector3,/*_id/taxonoccurrence/verbatimcollectorname/_merge/4,,23
20 
cultivated,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values,30
20 21 
herbarium,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
21 22 
comment1,/description/_merge/1/_merge/1,,
22 23 
comment2,/description/_merge/1/_merge/2,,
......
27 28 
inorout,"/description/_merge/1/_merge/7/_label[label=""in or out""]/value",,
28 29 
accession,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
29 30 
collectno,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
30 
cultivated,,"** No join mapping for establishmentMeans/_map:[Y=cultivated,N=wild,*=]/value ** Ignore other values"
31 31 
filler,,"Where used, same as family"
32 32 
flower,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
33 33 
fruit,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
inputs/NCU-NCSC/test/VegBIEN.specimens.xml.ref
48 48 
                        </plantconcept>
49 49 
                    </plantconcept_id>
50 50 
                </taxondetermination>
51 
                <growthform/>
52 
                <iscultivated>f</iscultivated>
53 
                <isnative/>
51 54 
            </taxonoccurrence>
52 55 
        </taxonoccurrence_id>
53 56 
        <collectioncode_dwc>NCU</collectioncode_dwc>
......
108 111 
                        </plantconcept>
109 112 
                    </plantconcept_id>
110 113 
                </taxondetermination>
114 
                <growthform/>
115 
                <iscultivated>f</iscultivated>
116 
                <isnative/>
111 117 
            </taxonoccurrence>
112 118 
        </taxonoccurrence_id>
113 119 
        <collectioncode_dwc>WEWO</collectioncode_dwc>
inputs/NCU-NCSC/maps/VegBIEN.specimens.csv
7 7 
Long (-=W),"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/2/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",,82
8 8 
Collect Date,"/*_id/taxonoccurrence/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/3",,44
9 9 
Full Taxon Name,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname","Brad: Bob, Nick, please is this mapping OK?",134
10 
Cultivated?,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value/_map:[Yes=cultivated,No=wild]/value",,30
10 11 
SeriesName,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
11 12 
Barcode,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
12 13 
Accession Number,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
13 14 
Alt E/W,,
14 15 
Alt N/S,,
15 
Cultivated?,,"** No join mapping for establishmentMeans/_map:[Yes=cultivated,No=wild]/value ** "
16 16 
Elevation,,** No join mapping for VerbatimElevation **
17 17 
FIPS,,FIPS county code
18 18 
Format,,** No join mapping for PreparationType **
mappings/DwC2-VegBIEN.specimens.csv
31 31 
phylum,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
32 32 
kingdom,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
33 33 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
34 
establishmentMeans,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
34 35 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
35 36 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
36 37 
fieldNotes,/description/_merge/1,,
......
72 73 
earliestEraOrLowestErathem,,,103
73 74 
earliestPeriodOrLowestSystem,,,105
74 75 
endDayOfYear,,,47
75 
establishmentMeans,,,30
76 76 
eventID,,,41
77 77 
eventRemarks,,,55
78 78 
eventTime,,Brad: OMIT,45
mappings/DwC.ci-VegBIEN.specimens.csv
109 109 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
110 110 
collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
111 111 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
112 
EstablishmentMeans,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
113 
establishmentMeans,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
112 114 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
113 115 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
114 116 
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
......
169 171 
EarliestEraOrLowestErathem,,,103
170 172 
EarliestPeriodOrLowestSystem,,,105
171 173 
EndDayOfYear,,,47
172 
EstablishmentMeans,,,30
173 174 
EventID,,,41
174 175 
EventRemarks,,,55
175 176 
EventTime,,Brad: OMIT,45
......
310 311 
earliestEraOrLowestErathem,,,103
311 312 
earliestPeriodOrLowestSystem,,,105
312 313 
endDayOfYear,,,47
313 
establishmentMeans,,,30
314 314 
eventID,,,41
315 315 
eventRemarks,,,55
316 316 
eventTime,,Brad: OMIT,45
mappings/for_review/DwC2-VegBIEN.specimens.csv
31 31 
phylum,"//taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
32 32 
kingdom,"//taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
33 33 
recordedBy,//taxonoccurrence/verbatimcollectorname,,23
34 
establishmentMeans,"/*_id/taxonoccurrence/{growthform/_map,iscultivated/_map,isnative/_map}/value",,30
34 35 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
35 36 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
36 37 
fieldNotes,/description/_merge/1,,
......
72 73 
earliestEraOrLowestErathem,,,103
73 74 
earliestPeriodOrLowestSystem,,,105
74 75 
endDayOfYear,,,47
75 
establishmentMeans,,,30
76 76 
eventID,,,41
77 77 
eventRemarks,,,55
78 78 
eventTime,,Brad: OMIT,45
mappings/DwC-VegBIEN.specimens.csv
109 109 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
110 110 
collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
111 111 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
112 
EstablishmentMeans,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
113 
establishmentMeans,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
112 114 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
113 115 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
114 116 
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
mappings/DwC.cs-VegBIEN.specimens.csv
54 54 
kingdom,"/*_id/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
55 55 
collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
56 56 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
57 
establishmentMeans,"/*_id/taxonoccurrence/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
57 58 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
58 59 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
59 60 
fieldNotes,/description/_merge/1,,
......
100 101 
earliestEraOrLowestErathem,,,103
101 102 
earliestPeriodOrLowestSystem,,,105
102 103 
endDayOfYear,,,47
103 
establishmentMeans,,,30
104 104 
eventID,,,41
105 105 
eventRemarks,,,55
106 106 
eventTime,,Brad: OMIT,45

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