Revision 3780
Added by Aaron Marcuse-Kubitza over 12 years ago
| VegBIEN.specimens.csv | ||
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| 1 | 1 |
NY[DwC],VegBIEN:,Comments,Order |
| 2 |
MaximumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value",,72 |
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MinimumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/elevation/_alt/2/_avg/min/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace[""\bca\.?""=]/value/_nullIf:[null=.]/value",,71 |
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MinimumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/elevationrange/_range/from/_units:[default=m,to=m,to=]/value/_rangeStart/value/_replace[""\bca\.?""=]/value/_nullIf:[null=.]/value",,71 |
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MaximumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/1",,72 |
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MinimumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/2/_rangeEnd/value/_replace[""\bca\.?""=]/value/_nullIf:[null=.]/value",,71 |
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| 2 | 7 |
CoordinatePrecision,/specimenreplicate/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89 |
| 3 | 8 |
BoundingBox,/specimenreplicate/*_id/locationevent/*_id/location/locationdetermination/footprintgeometry_dwc,,91 |
| 4 | 9 |
Latitude,"/specimenreplicate/*_id/locationevent/*_id/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value",,81 |
| ... | ... | |
| 11 | 16 |
Substrate,"/specimenreplicate/*_id/locationevent/*_id/location/locationnarrative/_merge/1/_merge/2/_label[label=""substrate""]/value",,68 |
| 12 | 17 |
Vegetation,"/specimenreplicate/*_id/locationevent/*_id/location/locationnarrative/_merge/1/_merge/3/_label[label=""vegetation""]/value",,68 |
| 13 | 18 |
Habitat,"/specimenreplicate/*_id/locationevent/*_id/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52 |
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MinimumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/{./{elevation/_alt/2/_avg/min,elevationrange/_range/from}/_units:[default=m,to=m,to=]/value/_rangeStart/value,elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/2/_rangeEnd/value}/_replace[""\bca\.?""=]/value/_nullIf:[null=.]/value",,71
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MaximumElevation,"/specimenreplicate/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value,elevationrange/_range/to/_units:[default=m,to=m,to=]/value/_alt/1}",,72
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UniqueNYInternalRecordNumber,/specimenreplicate/*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1,"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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InstitutionCode,/specimenreplicate/*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1,, |
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CollectionCode,/specimenreplicate/*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2,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 |
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CatalogNumber,/specimenreplicate/*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3,"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 |
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DayCollected,"/specimenreplicate/*_id/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44 |
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MonthCollected,"/specimenreplicate/*_id/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44 |
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YearCollected,"/specimenreplicate/*_id/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44 |
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DayCollected,"/specimenreplicate/*_id/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44 |
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MonthCollected,"/specimenreplicate/*_id/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44 |
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YearCollected,"/specimenreplicate/*_id/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44 |
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| 16 | 29 |
MaximumDepth,"/specimenreplicate/*_id/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value",,75 |
| 17 | 30 |
MinimumDepth,"/specimenreplicate/*_id/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value",,74 |
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DayCollected,"/specimenreplicate/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
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MonthCollected,"/specimenreplicate/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
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YearCollected,"/specimenreplicate/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
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CatalogNumber,/specimenreplicate/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 |
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CollectionCode,/specimenreplicate/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 |
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| 21 | 33 |
CollectorNumber,/specimenreplicate/collectionnumber/_alt/1/_alt/1,,22 |
| 22 | 34 |
FieldNumber,/specimenreplicate/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53 |
| 23 | 35 |
Sex,"/specimenreplicate/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 |
| 24 | 36 |
Notes,/specimenreplicate/description/_merge/1/_merge/1,, |
| 25 | 37 |
PlantFungusDescription,"/specimenreplicate/description/_merge/1/_merge/2/_label[label=""plant fungus""]/value",, |
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InstitutionCode,/specimenreplicate/institution_id/party/organizationname,, |
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UniqueNYInternalRecordNumber,/specimenreplicate/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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| 26 | 40 |
DayIdentified,"/specimenreplicate/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,120 |
| 27 | 41 |
MonthIdentified,"/specimenreplicate/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,120 |
| 28 | 42 |
YearIdentified,"/specimenreplicate/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,120 |
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IdentifiedBy,"/specimenreplicate/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
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IdentifiedBy,/specimenreplicate/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/givenname/_namePart/first,Brad: Bob: does this look correct for VegBank?,119 |
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IdentifiedBy,/specimenreplicate/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/middlename/_namePart/middle,Brad: Bob: does this look correct for VegBank?,119 |
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IdentifiedBy,/specimenreplicate/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/surname/_namePart/last,Brad: Bob: does this look correct for VegBank?,119 |
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| 30 | 46 |
ScientificName,"/specimenreplicate/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname","Brad: Bob, Nick, please is this mapping OK?",134 |
| 31 | 47 |
ScientificNameAuthor,"/specimenreplicate/taxondetermination[role=identifier]:[isoriginal=true,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: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153 |
| 32 | 48 |
Subspecies,"/specimenreplicate/taxondetermination[role=identifier]:[isoriginal=true,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",,150 |
| ... | ... | |
| 38 | 54 |
Phylum,"/specimenreplicate/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 |
| 39 | 55 |
Kingdom,"/specimenreplicate/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 |
| 40 | 56 |
Collector,/specimenreplicate/verbatimcollectorname,,23 |
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CatalogNumber,"/specimenreplicate/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","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
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CollectionCode,"/specimenreplicate/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",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
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InstitutionCode,"/specimenreplicate/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
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UniqueNYInternalRecordNumber,"/specimenreplicate/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","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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| 45 | 57 |
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord ** |
| 46 | 58 |
DateLastModified,,** No non-empty join mapping for DateLastModified ** |
| 47 | 59 |
IndividualCount,,** No non-empty join mapping for IndividualCount ** |
Also available in: Unified diff
mappings/DwC2-VegBIEN.specimens.csv: Expanded {} expressions using expand_braces, so that each distinct output for the same input is on its own line, improving readability. This will also help enable search-and-replace reversing of XPaths for the re-rooting to location.