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Revision 1052

Added by Aaron Marcuse-Kubitza almost 13 years ago

DwC mappings: Mapped datasource name to specimenreplicate.reference instead of location.reference

View differences:

inputs/NYBG/test/import.specimens.out.ref
1 
Inserted 82 new rows into database
1 
Inserted 80 new rows into database
inputs/NYBG/test/VegBIEN.specimens.xml.ref
7 7 
                    <locationevent>
8 8 
                        <location_id>
9 9 
                            <location>
10 
                                <elevation>350.0</elevation>
11 
                                <elevationrange>0.0</elevationrange>
12 
                                <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
13 10 
                                <locationdetermination>
14 11 
                                    <namedplace_id>
15 12 
                                        <namedplace>
......
39 36 
                                    <longitude>-71.40000000</longitude>
40 37 
                                </locationdetermination>
41 38 
                                <locationnarrative>Parque Nacional del Manu. R&#237;o Manu: Cocha Casha Station</locationnarrative>
39 
                                <elevation>350.0</elevation>
40 
                                <elevationrange>0.0</elevationrange>
42 41 
                            </location>
43 42 
                        </location_id>
44 43 
                        <commclass><commdetermination><commconcept_id><commconcept><commname_id><commname><commname>Floodplain forest</commname></commname></commname_id></commconcept></commconcept_id></commdetermination></commclass>
......
127 126 
                <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
128 127 
            </taxonoccurrence>
129 128 
        </taxonoccurrence_id>
130 
        <reference_id><reference/></reference_id>
129 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
130 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
131 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
132 
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
131 133 
        <catalognumber_dwc>00682023</catalognumber_dwc>
132 134 
        <collectionnumber>9877</collectionnumber>
133 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
134 135 
        <sourceaccessioncode>816590</sourceaccessioncode>
135 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
136 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
137 136 
    </specimenreplicate>
138 137 
    <specimenreplicate id="1">
139 138 
        <taxonoccurrence_id>
......
142 141 
                    <locationevent>
143 142 
                        <location_id>
144 143 
                            <location>
145 
                                <elevation>15.0</elevation>
146 
                                <elevationrange>0.0</elevationrange>
147 
                                <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
148 144 
                                <locationdetermination>
149 145 
                                    <namedplace_id>
150 146 
                                        <namedplace>
......
166 162 
                                    <longitude>-88.50000000</longitude>
167 163 
                                </locationdetermination>
168 164 
                                <locationnarrative>Belize Zoo, in savanna plot immediately behind zoo. Mile 31 on Western Highway</locationnarrative>
165 
                                <elevation>15.0</elevation>
166 
                                <elevationrange>0.0</elevationrange>
169 167 
                            </location>
170 168 
                        </location_id>
171 169 
                        <obsstartdate>1994-01-17</obsstartdate>
......
217 215 
                <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
218 216 
            </taxonoccurrence>
219 217 
        </taxonoccurrence_id>
220 
        <reference_id><reference/></reference_id>
218 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
219 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
220 
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
221 221 
        <catalognumber_dwc>200996</catalognumber_dwc>
222 222 
        <collectionnumber>545</collectionnumber>
223 223 
        <sourceaccessioncode>220541</sourceaccessioncode>
224 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
225 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
226 224 
    </specimenreplicate>
227 225 
</VegBIEN>
inputs/NYBG/maps/VegBIEN.specimens.csv
1 1 
NYBG:nybg_raw,VegBIEN:/specimenreplicate,Comments,Order
2 
Country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3 
StateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4 
County,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
2 5 
CoordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy/_noCV/value,,89
6 
BoundingBox,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
7 
Latitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/latitude/_alt/2/_nullIf:[null=0,type=float]/value",,81
8 
Longitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/longitude/_alt/2/_nullIf:[null=0,type=float]/value",,82
9 
Locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
3 10 
MaximumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
4 11 
MinimumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
5 
Country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
6 
StateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
7 
County,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
8 
BoundingBox,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
9 
Latitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/latitude/_alt/2/_nullIf:[null=0,type=float]/value",,81
10 
Longitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/longitude/_alt/2/_nullIf:[null=0,type=float]/value",,82
11 
Locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
12 12 
Habitat,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
13 13 
Vegetation,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
14 14 
Substrate,/*_id/taxonoccurrence/*_id/locationevent/landscapenarrative,,
......
35 35 
Phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
36 36 
Subspecies,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
37 37 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
38 
CatalogNumber,:[*_id/reference]/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
39 
CollectorNumber,:[*_id/reference]/collectionnumber/_alt/1,,22
40 
FieldNumber,:[*_id/reference]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
41 
Notes,:[*_id/reference]/description/_merge/1,,
42 
PlantFungusDescription,":[*_id/reference]/description/_merge/2/_label[label=""plant fungus""]/value",,
43 
UniqueNYInternalRecordNumber,:[*_id/reference]/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
44 
InstitutionCode,:[*_id/reference]/{museum_id/party/organizationname/_name/first},,11
45 
CollectionCode,":[*_id/reference]/{museum_id/party/organizationname/_name/last,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
38 
Notes,/description/_merge/1,,
39 
PlantFungusDescription,"/description/_merge/2/_label[label=""plant fungus""]/value",,
40 
InstitutionCode,/{museum_id/party/organizationname/_name/first},,11
41 
CollectionCode,"/{museum_id/party/organizationname/_name/last,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
42 
CatalogNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/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
43 
CollectorNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
44 
FieldNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
45 
UniqueNYInternalRecordNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/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
46 46 
BasisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
47 47 
ContinentOcean,,Brad: OMIT,59
48 48 
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
inputs/NYBG-CSV/test/import.specimens.out.ref
1 
Inserted 82 new rows into database
1 
Inserted 80 new rows into database
inputs/NYBG-CSV/test/VegBIEN.specimens.xml.ref
7 7 
                    <locationevent>
8 8 
                        <location_id>
9 9 
                            <location>
10 
                                <elevation>350.0</elevation>
11 
                                <elevationrange>0.0</elevationrange>
12 
                                <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
13 10 
                                <locationdetermination>
14 11 
                                    <namedplace_id>
15 12 
                                        <namedplace>
......
39 36 
                                    <longitude>-71.40</longitude>
40 37 
                                </locationdetermination>
41 38 
                                <locationnarrative>Parque Nacional del Manu. R&#237;o Manu: Cocha Casha Station</locationnarrative>
39 
                                <elevation>350.0</elevation>
40 
                                <elevationrange>0.0</elevationrange>
42 41 
                            </location>
43 42 
                        </location_id>
44 43 
                        <commclass><commdetermination><commconcept_id><commconcept><commname_id><commname><commname>Floodplain forest</commname></commname></commname_id></commconcept></commconcept_id></commdetermination></commclass>
......
127 126 
                <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
128 127 
            </taxonoccurrence>
129 128 
        </taxonoccurrence_id>
130 
        <reference_id><reference/></reference_id>
129 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
130 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
131 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
132 
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
131 133 
        <catalognumber_dwc>00682023</catalognumber_dwc>
132 134 
        <collectionnumber>9877</collectionnumber>
133 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
134 135 
        <sourceaccessioncode>816590</sourceaccessioncode>
135 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
136 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
137 136 
    </specimenreplicate>
138 137 
    <specimenreplicate id="1">
139 138 
        <taxonoccurrence_id>
......
142 141 
                    <locationevent>
143 142 
                        <location_id>
144 143 
                            <location>
145 
                                <elevation>15.0</elevation>
146 
                                <elevationrange>0.0</elevationrange>
147 
                                <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
148 144 
                                <locationdetermination>
149 145 
                                    <namedplace_id>
150 146 
                                        <namedplace>
......
166 162 
                                    <longitude>-88.50</longitude>
167 163 
                                </locationdetermination>
168 164 
                                <locationnarrative>Belize Zoo, in savanna plot immediately behind zoo. Mile 31 on Western Highway</locationnarrative>
165 
                                <elevation>15.0</elevation>
166 
                                <elevationrange>0.0</elevationrange>
169 167 
                            </location>
170 168 
                        </location_id>
171 169 
                        <obsstartdate>1994-01-17</obsstartdate>
......
217 215 
                <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
218 216 
            </taxonoccurrence>
219 217 
        </taxonoccurrence_id>
220 
        <reference_id><reference/></reference_id>
218 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
219 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
220 
        <reference_id><reference><shortname>NYBG</shortname></reference></reference_id>
221 221 
        <catalognumber_dwc>200996</catalognumber_dwc>
222 222 
        <collectionnumber>545</collectionnumber>
223 223 
        <sourceaccessioncode>220541</sourceaccessioncode>
224 
        <museum_id><party><organizationname>NY Herbarium</organizationname></party></museum_id>
225 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
226 224 
    </specimenreplicate>
227 225 
</VegBIEN>
inputs/NYBG-CSV/maps/VegBIEN.specimens.csv
1 1 
NYBG,VegBIEN:/specimenreplicate,Comments,Order
2 
Country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3 
StateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4 
County,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
2 5 
CoordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy,,89
6 
BoundingBox,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
7 
Latitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/latitude/_alt/2/_nullIf:[null=0,type=float]/value",,81
8 
Longitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/longitude/_alt/2/_nullIf:[null=0,type=float]/value",,82
9 
Locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
3 10 
MaximumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
4 11 
MinimumElevation,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
5 
Country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
6 
StateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
7 
County,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
8 
BoundingBox,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
9 
Latitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/latitude/_alt/2/_nullIf:[null=0,type=float]/value",,81
10 
Longitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/longitude/_alt/2/_nullIf:[null=0,type=float]/value",,82
11 
Locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
12 12 
Habitat,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
13 13 
Vegetation,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
14 14 
Substrate,/*_id/taxonoccurrence/*_id/locationevent/landscapenarrative,,
......
33 33 
Phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
34 34 
Subspecies,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
35 35 
Collector,/*_id/taxonoccurrence/verbatimcollectorname,,23
36 
CatalogNumber,:[*_id/reference]/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
37 
CollectorNumber,:[*_id/reference]/collectionnumber/_alt/1,,22
38 
FieldNumber,:[*_id/reference]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
39 
Notes,:[*_id/reference]/description/_merge/1,,
40 
PlantFungusDescription,":[*_id/reference]/description/_merge/2/_label[label=""plant fungus""]/value",,
41 
UniqueNYInternalRecordNumber,:[*_id/reference]/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
42 
InstitutionCode,:[*_id/reference]/{museum_id/party/organizationname/_name/first},,11
43 
CollectionCode,":[*_id/reference]/{museum_id/party/organizationname/_name/last,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
36 
Notes,/description/_merge/1,,
37 
PlantFungusDescription,"/description/_merge/2/_label[label=""plant fungus""]/value",,
38 
InstitutionCode,/{museum_id/party/organizationname/_name/first},,11
39 
CollectionCode,"/{museum_id/party/organizationname/_name/last,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
40 
CatalogNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
41 
CollectorNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
42 
FieldNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43 
UniqueNYInternalRecordNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/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
44 44 
BasisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15
45 45 
ContinentOcean,,Brad: OMIT,59
46 46 
DateLastModified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1
mappings/for_review/DwC-VegBIEN.specimens.csv
1 1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[bien.datasource=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2 
coordinatePrecision,//location/locationdetermination[]/coordsaccuracy,,89
3 
coordinatePrecision/_noCV/value,//location/locationdetermination[]/coordsaccuracy/_noCV/value,,89
4 
maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
5 
minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
6 
bien.datasource,//reference/shortname/_alt/1,,
7 2 
country,"//*_id/namedplace[placesystem=""area|country|territory""]/placename",Brad: Required; reject record if this field NULL,63
8 3 
stateProvince,"//*_id/namedplace[placesystem=""region|state|province""]/placename",,65
9 4 
county,//*_id/namedplace[placesystem=county]/placename,,66
5 
coordinatePrecision,//location/locationdetermination[]/coordsaccuracy,,89
6 
coordinatePrecision/_noCV/value,//location/locationdetermination[]/coordsaccuracy/_noCV/value,,89
10 7 
footprintWKT,//location/locationdetermination[]/footprintgeometry_dwc,,91
11 8 
decimalLatitude,//location/locationdetermination[]/latitude/_alt/1/_nullIf/value,,85
12 9 
verbatimLatitude,//location/locationdetermination[]/latitude/_alt/2/_nullIf/value,,81
......
14 11 
verbatimLongitude,//location/locationdetermination[]/longitude/_alt/2/_nullIf/value,,82
15 12 
locality,//location/locationnarrative/_alt/1,,68
16 13 
verbatimLocality,//location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
14 
maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
15 
minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
17 16 
habitat,//*/commname,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
18 17 
habitat/_merge/1,//*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
19 18 
habitat/_merge/2,//*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
......
43 42 
phylum,"//taxonoccurrence/taxondetermination[rolecode=identifier,plantlevel=Subkingdom]/*_id/plantconcept/*_id/*/plantname",,143
44 43 
infraspecificEpithet,"//taxonoccurrence/taxondetermination[rolecode=identifier,plantlevel=Subspecies]/*_id/plantconcept/*_id/*/plantname",,150
45 44 
recordedBy,//taxonoccurrence/verbatimcollectorname,,23
45 
fieldNotes,/description,,
46 
fieldNotes/_merge/1,/description/_merge/1,,
47 
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
48 
institutionCode,/{museum_id/party/organizationname/_name/first},,11
49 
collectionCode,"/{museum_id/party/organizationname/_name/last,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
50 
bien.datasource,//reference/shortname/_alt/1,,
46 51 
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
47 52 
recordNumber,/collectionnumber/_alt/1,,22
48 53 
collectionID,/collectionnumber/_alt/2,,9
49 54 
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
50 
fieldNotes,/description,,
51 
fieldNotes/_merge/1,/description/_merge/1,,
52 
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
53 55 
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
54 
institutionCode,/{museum_id/party/organizationname/_name/first},,11
55 
collectionCode,"/{museum_id/party/organizationname/_name/last,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
56 56 
acceptedNameUsage,,,135
57 57 
acceptedNameUsageID,,,128
58 58 
associatedMedia,,,36
mappings/DwC-VegBIEN.specimens.csv
1 1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[bien.datasource=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
2 
country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
3 
stateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
4 
county,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
2 5 
coordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy,,89
3 6 
coordinatePrecision/_noCV/value,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy/_noCV/value,,89
7 
footprintWKT,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
8 
decimalLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/latitude/_alt/1/_nullIf:[null=0,type=float]/value",,85
9 
verbatimLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/latitude/_alt/2/_nullIf:[null=0,type=float]/value",,81
10 
decimalLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/longitude/_alt/1/_nullIf:[null=0,type=float]/value",,86
11 
verbatimLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/longitude/_alt/2/_nullIf:[null=0,type=float]/value",,82
12 
locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/1,,68
13 
verbatimLocality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
4 14 
maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72
5 15 
minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71
6 
bien.datasource,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/reference/shortname/_alt/1,,
7 
country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63
8 
stateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65
9 
county,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66
10 
footprintWKT,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91
11 
decimalLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/latitude/_alt/1/_nullIf:[null=0,type=float]/value",,85
12 
verbatimLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/latitude/_alt/2/_nullIf:[null=0,type=float]/value",,81
13 
decimalLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/longitude/_alt/1/_nullIf:[null=0,type=float]/value",,86
14 
verbatimLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationdetermination[!namedplace_id]/longitude/_alt/2/_nullIf:[null=0,type=float]/value",,82
15 
locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationnarrative/_alt/1,,68
16 
verbatimLocality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
17 16 
habitat,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
18 17 
habitat/_merge/1,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
19 18 
habitat/_merge/2,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52
......
43 42 
phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143
44 43 
infraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/plantstatus/plantlevel=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150
45 44 
recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23
46 
catalogNumber,:[*_id/reference]/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
47 
recordNumber,:[*_id/reference]/collectionnumber/_alt/1,,22
48 
collectionID,:[*_id/reference]/collectionnumber/_alt/2,,9
49 
fieldNumber,:[*_id/reference]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
50 
fieldNotes,:[*_id/reference]/description,,
51 
fieldNotes/_merge/1,:[*_id/reference]/description/_merge/1,,
52 
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value",":[*_id/reference]/description/_merge/2/_label[label=""plant fungus""]/value",,
53 
occurrenceID,:[*_id/reference]/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
54 
institutionCode,:[*_id/reference]/{museum_id/party/organizationname/_name/first},,11
55 
collectionCode,":[*_id/reference]/{museum_id/party/organizationname/_name/last,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
45 
fieldNotes,/description,,
46 
fieldNotes/_merge/1,/description/_merge/1,,
47 
"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,
48 
institutionCode,/{museum_id/party/organizationname/_name/first},,11
49 
collectionCode,"/{museum_id/party/organizationname/_name/last,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
50 
bien.datasource,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/*_id/reference/shortname/_alt/1,,
51 
catalogNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
52 
recordNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
53 
collectionID,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
54 
fieldNumber,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
55 
occurrenceID,:[*_id/reference/shortname/_alt/2=$/_ignore/inLabel]/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
56 56 
acceptedNameUsage,,,135
57 57 
acceptedNameUsageID,,,128
58 58 
associatedMedia,,,36

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