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Revision 1428

Added by Aaron Marcuse-Kubitza almost 13 years ago

VegBIEN: Merged aggregateoccurrence.verbatimcollectorname and specimenreplicate.verbatimcollectorname into taxonoccurrence

View differences:

mappings/DwC-VegBIEN.specimens.no_empty.csv
79 79 
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
80 80 
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
81 81 
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
82 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
82 85 
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
83 86 
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
84 87 
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
......
89 92 
Remarks,/description/_merge/2,,158
90 93 
TaxonRemarks,/description/_merge/2,,158
91 94 
taxonRemarks,/description/_merge/2,,158
92 
Collector,/verbatimcollectorname,,23
93 
RecordedBy,/verbatimcollectorname,,23
94 
recordedBy,/verbatimcollectorname,,23
95 95 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
96 96 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
97 97 
GlobalUniqueIdentifier,":[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
mappings/for_review/DwC2-VegBIEN.specimens.csv
29 29 
class,"//taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",,144
30 30 
phylum,"//taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
31 31 
kingdom,"//taxonoccurrence/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
32 
recordedBy,//taxonoccurrence/verbatimcollectorname,,23
32 33 
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
33 34 
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
34 35 
fieldNotes,/description/_merge/1,,
35 36 
taxonRemarks,/description/_merge/2,,158
36 
recordedBy,/verbatimcollectorname,,23
37 37 
catalogNumber,/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
38 38 
occurrenceID,/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
39 39 
recordNumber,/collectionnumber/_alt/1,,22
inputs/NYBG/test/VegBIEN.specimens.xml.ref
91 91 
                        </plantconcept>
92 92 
                    </plantconcept_id>
93 93 
                </taxondetermination>
94 
                <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
94 95 
            </taxonoccurrence>
95 96 
        </taxonoccurrence_id>
96 97 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
97 98 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
98 
        <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
99 99 
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
100 100 
        <catalognumber_dwc>00682023</catalognumber_dwc>
101 101 
        <sourceaccessioncode>816590</sourceaccessioncode>
......
168 168 
                        </plantconcept>
169 169 
                    </plantconcept_id>
170 170 
                </taxondetermination>
171 
                <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
171 172 
            </taxonoccurrence>
172 173 
        </taxonoccurrence_id>
173 174 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
174 
        <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
175 175 
        <datasource_id><party><organizationname>NYBG</organizationname></party></datasource_id>
176 176 
        <catalognumber_dwc>200996</catalognumber_dwc>
177 177 
        <sourceaccessioncode>220541</sourceaccessioncode>
inputs/NYBG/maps/VegBIEN.specimens.csv
81 81 
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
82 82 
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
83 83 
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
84 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
85 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
86 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 87 
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
85 88 
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
86 89 
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
......
92 95 
Remarks,/description/_merge/2,,158
93 96 
TaxonRemarks,/description/_merge/2,,158
94 97 
taxonRemarks,/description/_merge/2,,158
95 
Collector,/verbatimcollectorname,,23
96 
RecordedBy,/verbatimcollectorname,,23
97 
recordedBy,/verbatimcollectorname,,23
98 98 
CatalogNumber,":[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
99 99 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
100 100 
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_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
inputs/MOBOT/test/VegBIEN.specimens.xml.ref
72 72 
                        </plantconcept>
73 73 
                    </plantconcept_id>
74 74 
                </taxondetermination>
75 
                <verbatimcollectorname>Wiggins</verbatimcollectorname>
75 76 
            </taxonoccurrence>
76 77 
        </taxonoccurrence_id>
77 78 
        <collectioncode_dwc>Tropicos</collectioncode_dwc>
78 
        <verbatimcollectorname>Wiggins</verbatimcollectorname>
79 79 
        <datasource_id><party><organizationname>MOBOT</organizationname></party></datasource_id>
80 80 
        <catalognumber_dwc>1</catalognumber_dwc>
81 81 
        <collectionnumber>10572</collectionnumber>
......
161 161 
                        </plantconcept>
162 162 
                    </plantconcept_id>
163 163 
                </taxondetermination>
164 
                <verbatimcollectorname>J.D. &amp; E.G. Chapman</verbatimcollectorname>
164 165 
            </taxonoccurrence>
165 166 
        </taxonoccurrence_id>
166 167 
        <collectioncode_dwc>Tropicos</collectioncode_dwc>
167 
        <verbatimcollectorname>J.D. &amp; E.G. Chapman</verbatimcollectorname>
168 168 
        <datasource_id><party><organizationname>MOBOT</organizationname></party></datasource_id>
169 169 
        <catalognumber_dwc>2</catalognumber_dwc>
170 170 
        <collectionnumber>6723</collectionnumber>
inputs/MOBOT/maps/src.join.specimens.csv
79 79 
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
80 80 
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
81 81 
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
82 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
82 85 
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
83 86 
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
84 87 
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
......
89 92 
Remarks,/description/_merge/2,,158
90 93 
TaxonRemarks,/description/_merge/2,,158
91 94 
taxonRemarks,/description/_merge/2,,158
92 
Collector,/verbatimcollectorname,,23
93 
RecordedBy,/verbatimcollectorname,,23
94 
recordedBy,/verbatimcollectorname,,23
95 95 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
96 96 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
97 97 
GlobalUniqueIdentifier,":[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
inputs/MOBOT/maps/VegBIEN.specimens.csv
79 79 
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
80 80 
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
81 81 
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
82 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
82 85 
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
83 86 
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
84 87 
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
......
89 92 
Remarks,/description/_merge/2,,158
90 93 
TaxonRemarks,/description/_merge/2,,158
91 94 
taxonRemarks,/description/_merge/2,,158
92 
Collector,/verbatimcollectorname,,23
93 
RecordedBy,/verbatimcollectorname,,23
94 
recordedBy,/verbatimcollectorname,,23
95 95 
CatalogNumber,":[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
96 96 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
97 97 
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_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
inputs/SALVIAS/maps/VegBIEN.organisms.csv
23 23 
census_no,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
24 24 
Habit,"/aggregateoccurrence/growthform/_map:[_closed=1,./{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: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
25 25 
intercept_cm,/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank 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."
26 
coll_firstname,/aggregateoccurrence/verbatimcollectorname/_name/first,Brad: See comment above
27 
coll_lastname,/aggregateoccurrence/verbatimcollectorname/_name/last,"Brad: Correct for VegBank. 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."
28 26 
census_date,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date,
29 27 
infra_rank_1,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first",
30 28 
auth,"/taxondetermination[role=computer]:[iscurrent=true]/*_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: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
......
36 34 
OrigGenus,"/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/_name/first",
37 35 
OrigSpecies,"/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/_name/last",Brad: OMIT
38 36 
OrigFamily,"/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,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT
37 
coll_firstname,/verbatimcollectorname/_name/first,Brad: See comment above
38 
coll_lastname,/verbatimcollectorname/_name/last,"Brad: Correct for VegBank. 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."
39 39 
GenAuth,,
40 40 
IsMorpho,,
41 41 
OrigAuth,,
inputs/GBIF/test/VegBIEN.specimens.xml.ref
58 58 
                        </plantconcept>
59 59 
                    </plantconcept_id>
60 60 
                </taxondetermination>
61 
                <verbatimcollectorname>PRINGLE</verbatimcollectorname>
61 62 
            </taxonoccurrence>
62 63 
        </taxonoccurrence_id>
63 64 
        <collectioncode_dwc>Type herbarium, Gottingen (GOET)</collectioncode_dwc>
64 
        <verbatimcollectorname>PRINGLE</verbatimcollectorname>
65 65 
        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
66 66 
        <catalognumber_dwc>3390</catalognumber_dwc>
67 67 
    </specimenreplicate>
......
123 123 
                        </plantconcept>
124 124 
                    </plantconcept_id>
125 125 
                </taxondetermination>
126 
                <verbatimcollectorname>ANDERSSON</verbatimcollectorname>
126 127 
            </taxonoccurrence>
127 128 
        </taxonoccurrence_id>
128 129 
        <collectioncode_dwc>Type herbarium, Gottingen (GOET)</collectioncode_dwc>
129 
        <verbatimcollectorname>ANDERSSON</verbatimcollectorname>
130 130 
        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
131 131 
        <catalognumber_dwc>3395</catalognumber_dwc>
132 132 
    </specimenreplicate>
inputs/GBIF/maps/src.join.specimens.csv
83 83 
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
84 84 
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
85 85 
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
86 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
87 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
88 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
86 89 
CollectionCD,/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
87 90 
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
88 91 
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
......
94 97 
Remarks,/description/_merge/2,,158
95 98 
TaxonRemarks,/description/_merge/2,,158
96 99 
taxonRemarks,/description/_merge/2,,158
97 
Collector,/verbatimcollectorname,,23
98 
RecordedBy,/verbatimcollectorname,,23
99 
recordedBy,/verbatimcollectorname,,23
100 100 
CatalogNO,":[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
101 101 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
102 102 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
inputs/GBIF/maps/VegBIEN.specimens.csv
83 83 
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
84 84 
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
85 85 
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
86 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
87 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
88 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
86 89 
CollectionCD,/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
87 90 
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
88 91 
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
......
94 97 
Remarks,/description/_merge/2,,158
95 98 
TaxonRemarks,/description/_merge/2,,158
96 99 
taxonRemarks,/description/_merge/2,,158
97 
Collector,/verbatimcollectorname,,23
98 
RecordedBy,/verbatimcollectorname,,23
99 
recordedBy,/verbatimcollectorname,,23
100 100 
CatalogNO,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
101 101 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
102 102 
catalogNumber,":[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
inputs/UArizona/test/VegBIEN.specimens.xml.ref
74 74 
                        </plantconcept>
75 75 
                    </plantconcept_id>
76 76 
                </taxondetermination>
77 
                <verbatimcollectorname>J. Freeland</verbatimcollectorname>
77 78 
            </taxonoccurrence>
78 79 
        </taxonoccurrence_id>
79 80 
        <collectioncode_dwc>ARIZ</collectioncode_dwc>
80 81 
        <description>Much branched shrub with long white thorns and pale yellow catkins.</description>
81 
        <verbatimcollectorname>J. Freeland</verbatimcollectorname>
82 82 
        <datasource_id><party><organizationname>UArizona</organizationname></party></datasource_id>
83 83 
        <catalognumber_dwc>104</catalognumber_dwc>
84 84 
        <sourceaccessioncode>Herbarium:ARIZ:dbsn104</sourceaccessioncode>
......
152 152 
                        </plantconcept>
153 153 
                    </plantconcept_id>
154 154 
                </taxondetermination>
155 
                <verbatimcollectorname>M. F. Wojciechowski &amp; M. J. Sanderson</verbatimcollectorname>
155 156 
            </taxonoccurrence>
156 157 
        </taxonoccurrence_id>
157 158 
        <collectioncode_dwc>ARIZ</collectioncode_dwc>
158 
        <verbatimcollectorname>M. F. Wojciechowski &amp; M. J. Sanderson</verbatimcollectorname>
159 159 
        <datasource_id><party><organizationname>UArizona</organizationname></party></datasource_id>
160 160 
        <catalognumber_dwc>198483</catalognumber_dwc>
161 161 
        <sourceaccessioncode>Herbarium:ARIZ:dbsn198483</sourceaccessioncode>
inputs/UArizona/maps/src.join.specimens.csv
80 80 
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
81 81 
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
82 82 
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
83 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
85 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 86 
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
84 87 
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
85 88 
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
......
90 93 
Remarks,/description/_merge/2,,158
91 94 
TaxonRemarks,/description/_merge/2,,158
92 95 
taxonRemarks,/description/_merge/2,,158
93 
Collector,/verbatimcollectorname,,23
94 
RecordedBy,/verbatimcollectorname,,23
95 
recordedBy,/verbatimcollectorname,,23
96 96 
CatalogNumberNumeric,":[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
97 97 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
98 98 
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_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
inputs/UArizona/maps/VegBIEN.specimens.csv
80 80 
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
81 81 
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
82 82 
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
83 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
85 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 86 
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
84 87 
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
85 88 
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
......
90 93 
Remarks,/description/_merge/2,,158
91 94 
TaxonRemarks,/description/_merge/2,,158
92 95 
taxonRemarks,/description/_merge/2,,158
93 
Collector,/verbatimcollectorname,,23
94 
RecordedBy,/verbatimcollectorname,,23
95 
recordedBy,/verbatimcollectorname,,23
96 96 
CatalogNumberNumeric,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
97 97 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
98 98 
GlobalUniqueIdentifier,":[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
inputs/SpeciesLink/test/VegBIEN.specimens.xml.ref
161 161 
                        </plantconcept>
162 162 
                    </plantconcept_id>
163 163 
                </taxondetermination>
164 
                <verbatimcollectorname>Nadruz  M.</verbatimcollectorname>
164 165 
            </taxonoccurrence>
165 166 
        </taxonoccurrence_id>
166 167 
        <collectioncode_dwc>JBRJ_RBdna</collectioncode_dwc>
167 
        <verbatimcollectorname>Nadruz  M.</verbatimcollectorname>
168 168 
        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
169 169 
        <catalognumber_dwc>1355</catalognumber_dwc>
170 170 
        <sourceaccessioncode>103390850</sourceaccessioncode>
inputs/SpeciesLink/maps/src.join.specimens.csv
79 79 
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
80 80 
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
81 81 
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
82 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
82 85 
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
83 86 
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
84 87 
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
......
89 92 
Remarks,/description/_merge/2,,158
90 93 
TaxonRemarks,/description/_merge/2,,158
91 94 
taxonRemarks,/description/_merge/2,,158
92 
Collector,/verbatimcollectorname,,23
93 
RecordedBy,/verbatimcollectorname,,23
94 
recordedBy,/verbatimcollectorname,,23
95 95 
CatalogNumber,":[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
96 96 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
97 97 
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_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
inputs/SpeciesLink/maps/VegBIEN.specimens.csv
79 79 
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
80 80 
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
81 81 
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
82 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
83 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
84 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
82 85 
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
83 86 
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
84 87 
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
......
89 92 
Remarks,/description/_merge/2,,158
90 93 
TaxonRemarks,/description/_merge/2,,158
91 94 
taxonRemarks,/description/_merge/2,,158
92 
Collector,/verbatimcollectorname,,23
93 
RecordedBy,/verbatimcollectorname,,23
94 
recordedBy,/verbatimcollectorname,,23
95 95 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
96 96 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
97 97 
GlobalUniqueIdentifier,":[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
inputs/UNC-NCSC/maps/VegBIEN.specimens.csv
85 85 
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
86 86 
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
87 87 
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
88 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
89 
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
90 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
88 91 
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
89 92 
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
90 93 
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
......
96 99 
Remarks,/description/_merge/2,,158
97 100 
TaxonRemarks,/description/_merge/2,,158
98 101 
taxonRemarks,/description/_merge/2,,158
99 
Collector,/verbatimcollectorname,,23
100 
RecordedBy,/verbatimcollectorname,,23
101 
recordedBy,/verbatimcollectorname,,23
102 102 
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
103 103 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
104 104 
catalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_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
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref
53 53 
                <definedvalue>1</definedvalue>
54 54 
            </definedvalue>
55 55 
            <growthform>tree</growthform>
56 
            <verbatimcollectorname>Vasquez</verbatimcollectorname>
57 56 
        </aggregateoccurrence>
58 57 
        <taxondetermination>
59 58 
            <role>computer</role>
......
102 101 
                </plantconcept>
103 102 
            </plantconcept_id>
104 103 
        </taxondetermination>
104 
        <verbatimcollectorname>Vasquez</verbatimcollectorname>
105 105 
    </taxonoccurrence>
106 106 
    <taxonoccurrence id="1">
107 107 
        <locationevent_id>
......
156 156 
                <definedvalue>1</definedvalue>
157 157 
            </definedvalue>
158 158 
            <growthform>tree</growthform>
159 
            <verbatimcollectorname>Vasquez</verbatimcollectorname>
160 159 
        </aggregateoccurrence>
161 160 
        <taxondetermination>
162 161 
            <role>computer</role>
......
205 204 
                </plantconcept>
206 205 
            </plantconcept_id>
207 206 
        </taxondetermination>
207 
        <verbatimcollectorname>Vasquez</verbatimcollectorname>
208 208 
    </taxonoccurrence>
209 209 
</VegBIEN>
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
29 29 
census_no,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
30 30 
habit,"/aggregateoccurrence/growthform/_map:[T=tree,H=hemiepiphyte,L=liana,E=epiphyte,S=shrub,Hb=herb]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
31 31 
intercept_cm,/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank 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."
32 
coll_firstname,/aggregateoccurrence/verbatimcollectorname/_name/first,Brad: See comment above
33 
coll_lastname,/aggregateoccurrence/verbatimcollectorname/_name/last,"Brad: Correct for VegBank. 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."
34 32 
infra_rank_1,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first",
35 33 
specific_authority,"/taxondetermination[role=computer]:[iscurrent=true]/*_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: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
36 34 
infra_ep_1,"/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last",
......
40 38 
cf_aff,"/taxondetermination[role=identifier]/{taxonFit,*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/middle}","Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
41 39 
orig_species,"/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/_name/last",Brad: OMIT
42 40 
orig_family,"/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,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT
41 
coll_firstname,/verbatimcollectorname/_name/first,Brad: See comment above
42 
coll_lastname,/verbatimcollectorname/_name/last,"Brad: Correct for VegBank. 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."
43 43 
collector_code,,Brad: OMIT
44 44 
comments,,Brad: OMIT
45 45 
fam_status,,Brad: OMIT. This will be determined later by using TNRS.
schemas/vegbien.my.sql
131 131 
    occurrencestatus_dwc text DEFAULT 'present' NOT NULL,
132 132 
    method_id int(11),
133 133 
    linecover double precision,
134 
    verbatimcollectorname text,
135 134 
    growthform text
136 135 
);
137 136 

  		




  ......




  2058
  2057
  
    
    taxonoccurrence_id int(11) NOT NULL,


  		




  2059
  2058
  
    
    collectionnumber text,


  		




  2060
  2059
  
    
    specimen_id int(11),


  		




  2061
  
  
    
    description text,


  		




  2062
  
  
    
    verbatimcollectorname text


  		




  
  2060
  
    
    description text


  		




  2063
  2061
  
    
);


  		




  2064
  2062
  
    

  		




  2065
  2063
  
    

  		




  ......




  2285
  2283
  
    
CREATE TABLE taxonoccurrence (


  		




  2286
  2284
  
    
    taxonoccurrence_id int(11) NOT NULL,


  		




  2287
  2285
  
    
    locationevent_id int(11),


  		




  2288
  
  
    
    accessioncode text


  		




  
  2286
  
    
    accessioncode text,


  		




  
  2287
  
    
    verbatimcollectorname text


  		




  2289
  2288
  
    
);


  		




  2290
  2289
  
    

  		




  2291
  2290
  
    

  		












  

    
      schemas/vegbien.sql
    
  





  216
  216
  
    
    occurrencestatus_dwc occurrencestatus_dwc DEFAULT 'present'::occurrencestatus_dwc NOT NULL,


  		




  217
  217
  
    
    method_id integer,


  		




  218
  218
  
    
    linecover double precision,


  		




  219
  
  
    
    verbatimcollectorname text,


  		




  220
  219
  
    
    growthform taxonclass,


  		




  221
  220
  
    
    CONSTRAINT aggregateoccurrence_plantobservation_count_1 CHECK (((plantobservation_id IS NULL) OR (NOT (count IS DISTINCT FROM 1))))


  		




  222
  221
  
    
);


  		




  ......




  2415
  2414
  
    
    taxonoccurrence_id integer NOT NULL,


  		




  2416
  2415
  
    
    collectionnumber text,


  		




  2417
  2416
  
    
    specimen_id integer,


  		




  2418
  
  
    
    description text,


  		




  2419
  
  
    
    verbatimcollectorname text


  		




  
  2417
  
    
    description text


  		




  2420
  2418
  
    
);


  		




  2421
  2419
  
    

  		




  2422
  2420
  
    

  		




  ......




  2672
  2670
  
    
CREATE TABLE taxonoccurrence (


  		




  2673
  2671
  
    
    taxonoccurrence_id integer NOT NULL,


  		




  2674
  2672
  
    
    locationevent_id integer,


  		




  2675
  
  
    
    accessioncode text


  		




  
  2673
  
    
    accessioncode text,


  		




  
  2674
  
    
    verbatimcollectorname text


  		




  2676
  2675
  
    
);


  		




  2677
  2676
  
    

  		




  2678
  2677
  
    

  		












  

    
      mappings/VegX-VegBIEN.organisms.csv
    
  





  88
  88
  
    
/simpleUserdefined[name=censusNo]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue",


  		




  89
  89
  
    
/simpleUserdefined[name=growthForm]/value,/aggregateoccurrence/growthform,


  		




  90
  90
  
    
/simpleUserdefined[name=interceptCm]/value,/aggregateoccurrence/linecover,


  		




  91
  
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/givenName",/aggregateoccurrence/verbatimcollectorname/_name/first,


  		




  92
  
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/surName",/aggregateoccurrence/verbatimcollectorname/_name/last,


  		




  93
  91
  
    
/simpleUserdefined[name=collectionDate]/value,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate,


  		




  94
  92
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Rank","/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first",


  		




  95
  93
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[role=computer]:[iscurrent=true]/*_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",


  		




  ......




  108
  106
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=cl])/Name","/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,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",


  		




  109
  107
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=phyl_div])/Name","/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",


  		




  110
  108
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=identifier]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=reg])/Name","/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",


  		




  
  109
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/givenName",/verbatimcollectorname/_name/first,


  		




  
  110
  
    
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID->/parties/party/individualName/surName",/verbatimcollectorname/_name/last,


  		












  

    
      mappings/DwC.self.specimens.csv
    
  





  79
  79
  
    
phylum,phylum


  		




  80
  80
  
    
Kingdom,Kingdom


  		




  81
  81
  
    
kingdom,kingdom


  		




  
  82
  
    
Collector,Collector


  		




  
  83
  
    
RecordedBy,RecordedBy


  		




  
  84
  
    
recordedBy,recordedBy


  		




  82
  85
  
    
CollectionCode,CollectionCode


  		




  83
  86
  
    
collectionCode,collectionCode


  		




  84
  87
  
    
Sex,Sex


  		




  ......




  89
  92
  
    
Remarks,Remarks


  		




  90
  93
  
    
TaxonRemarks,TaxonRemarks


  		




  91
  94
  
    
taxonRemarks,taxonRemarks


  		




  92
  
  
    
Collector,Collector


  		




  93
  
  
    
RecordedBy,RecordedBy


  		




  94
  
  
    
recordedBy,recordedBy


  		




  95
  95
  
    
CatalogNumber,CatalogNumber


  		




  96
  96
  
    
catalogNumber,catalogNumber


  		




  97
  97
  
    
GlobalUniqueIdentifier,GlobalUniqueIdentifier


  		












  

    
      mappings/DwC2.ci-VegBIEN.specimens.csv
    
  





  59
  59
  
    
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


  		




  60
  60
  
    
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


  		




  61
  61
  
    
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


  		




  
  62
  
    
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23


  		




  
  63
  
    
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23


  		




  62
  64
  
    
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


  		




  63
  65
  
    
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


  		




  64
  66
  
    
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


  		




  ......




  67
  69
  
    
fieldNotes,/description/_merge/1,,


  		




  68
  70
  
    
TaxonRemarks,/description/_merge/2,,158


  		




  69
  71
  
    
taxonRemarks,/description/_merge/2,,158


  		




  70
  
  
    
RecordedBy,/verbatimcollectorname,,23


  		




  71
  
  
    
recordedBy,/verbatimcollectorname,,23


  		




  72
  72
  
    
CatalogNumber,":[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


  		




  73
  73
  
    
catalogNumber,":[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


  		




  74
  74
  
    
OccurrenceID,":[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


  		












  

    
      mappings/DwC2-VegBIEN.specimens.csv
    
  





  29
  29
  
    
class,"/*_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,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",,144


  		




  30
  30
  
    
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


  		




  31
  31
  
    
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


  		




  
  32
  
    
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23


  		




  32
  33
  
    
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


  		




  33
  34
  
    
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


  		




  34
  35
  
    
fieldNotes,/description/_merge/1,,


  		




  35
  36
  
    
taxonRemarks,/description/_merge/2,,158


  		




  36
  
  
    
recordedBy,/verbatimcollectorname,,23


  		




  37
  37
  
    
catalogNumber,":[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


  		




  38
  38
  
    
occurrenceID,":[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


  		




  39
  39
  
    
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22


  		












  

    
      mappings/for_review/VegX-VegBIEN.organisms.csv
    
  





  88
  88
  
    
/simpleUserdefined[name=censusNo]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]/definedvalue",


  		




  89
  89
  
    
/simpleUserdefined[name=growthForm]/value,//aggregateoccurrence/growthform,


  		




  90
  90
  
    
/simpleUserdefined[name=interceptCm]/value,//aggregateoccurrence/linecover,


  		




  91
  
  
    
//individualName/givenName,//aggregateoccurrence/verbatimcollectorname/_name/first,


  		




  92
  
  
    
//individualName/surName,//aggregateoccurrence/verbatimcollectorname/_name/last,


  		




  93
  91
  
    
/simpleUserdefined[name=collectionDate]/value,//specimenreplicate/collectiondate,


  		




  94
  92
  
    
//*s/taxonConcept[@code=TaxonomicRankBelowSubspeciesEnum]/Rank,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first",


  		




  95
  93
  
    
//*s/taxonConcept[@code=auth]/Name,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",


  		




  ......




  108
  106
  
    
//*s/taxonConcept[@code=cl]/Name,"/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname",


  		




  109
  107
  
    
//*s/taxonConcept[@code=phyl_div]/Name,"/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",


  		




  110
  108
  
    
//*s/taxonConcept[@code=reg]/Name,"/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",


  		




  
  109
  
    
//individualName/givenName,/verbatimcollectorname/_name/first,


  		




  
  110
  
    
//individualName/surName,/verbatimcollectorname/_name/last,


  		












  

    
      mappings/DwC-VegBIEN.specimens.csv
    
  





  79
  79
  
    
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


  		




  80
  80
  
    
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


  		




  81
  81
  
    
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


  		




  
  82
  
    
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23


  		




  
  83
  
    
RecordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23


  		




  
  84
  
    
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23


  		




  82
  85
  
    
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


  		




  83
  86
  
    
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


  		




  84
  87
  
    
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


  		




  ......




  89
  92
  
    
Remarks,/description/_merge/2,,158


  		




  90
  93
  
    
TaxonRemarks,/description/_merge/2,,158


  		




  91
  94
  
    
taxonRemarks,/description/_merge/2,,158


  		




  92
  
  
    
Collector,/verbatimcollectorname,,23


  		




  93
  
  
    
RecordedBy,/verbatimcollectorname,,23


  		




  94
  
  
    
recordedBy,/verbatimcollectorname,,23


  		




  95
  95
  
    
CatalogNumber,":[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


  		




  96
  96
  
    
catalogNumber,":[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


  		




  97
  97
  
    
GlobalUniqueIdentifier,":[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


  		












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