Revision 4074
Added by Aaron Marcuse-Kubitza over 12 years ago
| mappings/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 53 | 53 |
volumeCanopy,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover, |
| 54 | 54 |
fieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 55 | 55 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode, |
| 56 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
|
|
| 56 |
individualID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
|
|
| 57 | 57 |
voucherType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left", |
| 58 | 58 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 59 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 60 | 59 |
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| 61 | 60 |
basalDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter, |
| 62 | 61 |
canopyForm,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| ... | ... | |
| 74 | 73 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
| 75 | 74 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2, |
| 76 | 75 |
growthForm,/location/locationevent/taxonoccurrence/growthform, |
| 77 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode,
|
|
| 76 |
individualID,/location/locationevent/taxonoccurrence/sourceaccessioncode,
|
|
| 78 | 77 |
computer.scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname", |
| 79 | 78 |
computer.taxonRank,"/location/locationevent/taxonoccurrence/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", |
| 80 | 79 |
computer.infraspecificEpithet,"/location/locationevent/taxonoccurrence/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/last", |
| mappings/for_review/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 53 | 53 |
volumeCanopy,//aggregateoccurrence/linecover, |
| 54 | 54 |
fieldNotes,//aggregateoccurrence/notes, |
| 55 | 55 |
recordNumber,//plantobservation/authorplantcode, |
| 56 |
occurrenceID,//plantobservation/sourceaccessioncode,
|
|
| 56 |
individualID,//plantobservation/sourceaccessioncode,
|
|
| 57 | 57 |
voucherType,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond", |
| 58 | 58 |
catalogNumber,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 59 |
occurrenceID,//specimenreplicate/sourceaccessioncode, |
|
| 60 | 59 |
stemCount,//plantobservation/stemcount, |
| 61 | 60 |
basalDiameter,//stemobservation/basaldiameter, |
| 62 | 61 |
canopyForm,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]/definedvalue", |
| ... | ... | |
| 74 | 73 |
recordNumber,//taxonoccurrence/authortaxoncode, |
| 75 | 74 |
scientificName,//taxonoccurrence/authortaxoncode, |
| 76 | 75 |
growthForm,//taxonoccurrence/growthform, |
| 77 |
occurrenceID,//taxonoccurrence/sourceaccessioncode,
|
|
| 76 |
individualID,//taxonoccurrence/sourceaccessioncode,
|
|
| 78 | 77 |
computer.scientificNameAuthorship,//plantconcept/plantname_id[rank=authority]/plantname, |
| 79 | 78 |
computer.taxonRank,//plantconcept/plantname_id[rank=subspecies]/plantname, |
| 80 | 79 |
computer.infraspecificEpithet,//plantconcept/plantname_id[rank=subspecies]/plantname, |
| mappings/VegCSV.self.stems.csv | ||
|---|---|---|
| 40 | 40 |
heightFirstBranch,heightFirstBranch |
| 41 | 41 |
identificationQualifier,identificationQualifier |
| 42 | 42 |
individualCount,individualCount |
| 43 |
individualID,individualID |
|
| 43 | 44 |
infraspecificEpithet,infraspecificEpithet |
| 44 | 45 |
kingdom,kingdom |
| 45 | 46 |
landform,landform |
| ... | ... | |
| 52 | 53 |
minimumDepthInMeters,minimumDepthInMeters |
| 53 | 54 |
minimumElevationInMeters,minimumElevationInMeters |
| 54 | 55 |
nitrogen,nitrogen |
| 55 |
occurrenceID,occurrenceID |
|
| 56 | 56 |
order,order |
| 57 | 57 |
organic,organic |
| 58 | 58 |
parentLocationID,parentLocationID |
| inputs/ARIZ/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 36 | 36 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/1, |
| 37 | 37 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2,Usage inconsistent with DwC definition |
| 38 | 38 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 39 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 40 | 39 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 41 | 40 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 42 | 41 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/1, |
| ... | ... | |
| 45 | 44 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 46 | 45 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
| 47 | 46 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,Usage inconsistent with DwC definition |
| 48 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 49 | 47 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 50 | 48 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 51 | 49 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/NCU-NCSC/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 12 | 12 |
Collect Date,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/2/_alt/3, |
| 13 | 13 |
Collect Date,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/2/_alt/3, |
| 14 | 14 |
Collect Date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_alt/3, |
| 15 |
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 16 | 15 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 17 | 16 |
SeriesName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 18 | 17 |
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 19 | 18 |
Cultivated?,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Yes=cultivated,No=wild]/value", |
| 20 | 19 |
Cultivated?,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Yes=cultivated,No=wild]/value", |
| 21 |
Accession Number,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 22 | 20 |
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=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", |
| 23 | 21 |
Alt E/W,,** No input mapping for Alt E/W ** |
| 24 | 22 |
Alt N/S,,** No input mapping for Alt N/S ** |
| inputs/SpeciesLink/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 62 | 62 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2, |
| 63 | 63 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 64 | 64 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 65 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 66 | 65 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 67 | 66 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 68 | 67 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| ... | ... | |
| 75 | 74 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 76 | 75 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
| 77 | 76 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
| 78 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 79 | 77 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 80 | 78 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 81 | 79 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| inputs/QMOR/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 25 | 25 |
eventDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/1, |
| 26 | 26 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 27 | 27 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 28 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 29 | 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 30 | 29 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 31 | 30 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2, |
| 32 | 31 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 33 | 32 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 34 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 35 | 33 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 36 | 34 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 37 | 35 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| mappings/VegCSV.self.organisms.csv | ||
|---|---|---|
| 40 | 40 |
heightFirstBranch,heightFirstBranch |
| 41 | 41 |
identificationQualifier,identificationQualifier |
| 42 | 42 |
individualCount,individualCount |
| 43 |
individualID,individualID |
|
| 43 | 44 |
infraspecificEpithet,infraspecificEpithet |
| 44 | 45 |
kingdom,kingdom |
| 45 | 46 |
landform,landform |
| ... | ... | |
| 52 | 53 |
minimumDepthInMeters,minimumDepthInMeters |
| 53 | 54 |
minimumElevationInMeters,minimumElevationInMeters |
| 54 | 55 |
nitrogen,nitrogen |
| 55 |
occurrenceID,occurrenceID |
|
| 56 | 56 |
order,order |
| 57 | 57 |
organic,organic |
| 58 | 58 |
parentLocationID,parentLocationID |
| mappings/VegCSV.self.specimens.csv | ||
|---|---|---|
| 40 | 40 |
heightFirstBranch,heightFirstBranch |
| 41 | 41 |
identificationQualifier,identificationQualifier |
| 42 | 42 |
individualCount,individualCount |
| 43 |
individualID,individualID |
|
| 43 | 44 |
infraspecificEpithet,infraspecificEpithet |
| 44 | 45 |
kingdom,kingdom |
| 45 | 46 |
landform,landform |
| ... | ... | |
| 52 | 53 |
minimumDepthInMeters,minimumDepthInMeters |
| 53 | 54 |
minimumElevationInMeters,minimumElevationInMeters |
| 54 | 55 |
nitrogen,nitrogen |
| 55 |
occurrenceID,occurrenceID |
|
| 56 | 56 |
order,order |
| 57 | 57 |
organic,organic |
| 58 | 58 |
parentLocationID,parentLocationID |
| mappings/DwC-VegBIEN.specimens.csv | ||
|---|---|---|
| 123 | 123 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2, |
| 124 | 124 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 125 | 125 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 126 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 127 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 128 |
OccurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 129 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 130 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 131 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 132 | 126 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 133 | 127 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 134 | 128 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| ... | ... | |
| 155 | 149 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 156 | 150 |
EstablishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 157 | 151 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 158 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 159 |
Id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 160 |
OccurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 161 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 162 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 163 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 164 | 152 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 165 | 153 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 166 | 154 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| inputs/MT/test/import.specimens.xml.ref | ||
|---|---|---|
| 51 | 51 |
<aggregateoccurrence> |
| 52 | 52 |
<count>$individualCount</count> |
| 53 | 53 |
<plantobservation> |
| 54 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 55 | 54 |
<specimenreplicate> |
| 56 | 55 |
<collectioncode_dwc> |
| 57 | 56 |
<_merge> |
| ... | ... | |
| 80 | 79 |
<value>$establishmentMeans</value> |
| 81 | 80 |
</_map> |
| 82 | 81 |
</isnative> |
| 83 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 84 | 82 |
<taxondetermination> |
| 85 | 83 |
<isoriginal>true</isoriginal> |
| 86 | 84 |
<role>identifier</role> |
| inputs/MT/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 5 | 5 |
collectionID,/location/authorlocationcode/_alt/4/_merge/2/_merge/2, |
| 6 | 6 |
continent,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,country,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=continent]/placename", |
| 7 | 7 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 8 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 9 | 8 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 10 | 9 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2, |
| 11 | 10 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 12 | 11 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 13 | 12 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 14 | 13 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 15 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 16 | 14 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
| 17 | 15 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=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", |
| 18 | 16 |
locality,/location/locationnarrative/_merge/1, |
| inputs/NY/test/import.specimens.xml.ref | ||
|---|---|---|
| 284 | 284 |
</userdefined_id> |
| 285 | 285 |
<definedvalue>$Sex</definedvalue> |
| 286 | 286 |
</definedvalue> |
| 287 |
<sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode> |
|
| 288 | 287 |
<specimenreplicate> |
| 289 | 288 |
<catalognumber_dwc><_if name="if indirect voucher"><else>$CatalogNumber</else></_if></catalognumber_dwc> |
| 290 | 289 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| ... | ... | |
| 305 | 304 |
<2>$FieldNumber</2> |
| 306 | 305 |
</_alt> |
| 307 | 306 |
</authortaxoncode> |
| 308 |
<sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode> |
|
| 309 | 307 |
<taxondetermination> |
| 310 | 308 |
<isoriginal>true</isoriginal> |
| 311 | 309 |
<role>identifier</role> |
| inputs/NY/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 31 | 31 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/1, |
| 32 | 32 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2,Usage inconsistent with DwC definition |
| 33 | 33 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 34 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 35 | 34 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 36 | 35 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 37 | 36 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/1, |
| ... | ... | |
| 40 | 39 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 41 | 40 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
| 42 | 41 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,Usage inconsistent with DwC definition |
| 43 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 44 | 42 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 45 | 43 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 46 | 44 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/UNCC/test/import.specimens.xml.ref | ||
|---|---|---|
| 159 | 159 |
</notes> |
| 160 | 160 |
<plantobservation> |
| 161 | 161 |
<authorplantcode>$collectno</authorplantcode> |
| 162 |
<sourceaccessioncode>$accession</sourceaccessioncode> |
|
| 163 | 162 |
<specimenreplicate> |
| 164 | 163 |
<collectionnumber>$collectno</collectionnumber> |
| 165 | 164 |
<institution_id><party><organizationname>$herbarium</organizationname></party></institution_id> |
| ... | ... | |
| 198 | 197 |
</value> |
| 199 | 198 |
</_map> |
| 200 | 199 |
</isnative> |
| 201 |
<sourceaccessioncode>$accession</sourceaccessioncode> |
|
| 202 | 200 |
<taxondetermination> |
| 203 | 201 |
<isoriginal>true</isoriginal> |
| 204 | 202 |
<role>identifier</role> |
| inputs/UNCC/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 21 | 21 |
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/6/_label[label=""loaned to""]/value", |
| 22 | 22 |
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_merge/7/_label[label=""in or out""]/value", |
| 23 | 23 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/1, |
| 24 |
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 25 | 24 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/1, |
| 26 | 25 |
herbarium,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 27 | 26 |
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 28 | 27 |
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
| 29 | 28 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values |
| 30 | 29 |
cultivated,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values |
| 31 |
accession,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 32 | 30 |
SciName,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=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", |
| 33 | 31 |
authors,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=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", |
| 34 | 32 |
infraname,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=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", |
| inputs/ACAD/test/import.specimens.xml.ref | ||
|---|---|---|
| 77 | 77 |
<aggregateoccurrence> |
| 78 | 78 |
<plantobservation> |
| 79 | 79 |
<authorplantcode>$recordNumber</authorplantcode> |
| 80 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 81 | 80 |
<specimenreplicate> |
| 82 | 81 |
<catalognumber_dwc><_if name="if indirect voucher"><else>$catalogNumber</else></_if></catalognumber_dwc> |
| 83 | 82 |
<collectioncode_dwc> |
| ... | ... | |
| 93 | 92 |
</plantobservation> |
| 94 | 93 |
</aggregateoccurrence> |
| 95 | 94 |
<authortaxoncode>$recordNumber</authortaxoncode> |
| 96 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 97 | 95 |
<taxondetermination> |
| 98 | 96 |
<isoriginal>true</isoriginal> |
| 99 | 97 |
<role>identifier</role> |
| inputs/ACAD/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 14 | 14 |
eventDate,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/1, |
| 15 | 15 |
eventDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/1, |
| 16 | 16 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2, |
| 17 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 18 | 17 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 19 | 18 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 20 | 19 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2, |
| ... | ... | |
| 22 | 21 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 23 | 22 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 24 | 23 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
| 25 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 26 | 24 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 27 | 25 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 28 | 26 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/SALVIAS-CSV/test/import.organisms.xml.ref | ||
|---|---|---|
| 58 | 58 |
</else> |
| 59 | 59 |
</_if> |
| 60 | 60 |
</catalognumber_dwc> |
| 61 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
|
| 62 | 61 |
</specimenreplicate> |
| 63 | 62 |
<stemobservation> |
| 64 | 63 |
<basaldiameter>$basal_diam</basaldiameter> |
| inputs/SALVIAS-CSV/maps/VegCSV.organisms.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS-CSV,VegCSV[DwC],Comments |
| 2 |
OBSERVATION_ID,occurrenceID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 2 |
OBSERVATION_ID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 3 | 3 |
PLOT_ID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 4 | 4 |
plot_code,parentPlotName,"Brad: Same as plotCode, above" |
| 5 | 5 |
census_no,censusNumber,"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." |
| 6 |
census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows: |
|
| 7 |
----- |
|
| 8 |
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count |
|
| 9 |
FROM ""SALVIAS-CSV"".organisms |
|
| 10 |
WHERE subplot IS NOT NULL AND census_date IS NOT NULL |
|
| 11 |
GROUP BY ""PLOT_ID"", subplot |
|
| 12 |
HAVING count(DISTINCT census_date) > 1 |
|
| 6 |
census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
|
|
| 7 |
-----
|
|
| 8 |
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
|
|
| 9 |
FROM ""SALVIAS-CSV"".organisms
|
|
| 10 |
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
|
|
| 11 |
GROUP BY ""PLOT_ID"", subplot
|
|
| 12 |
HAVING count(DISTINCT census_date) > 1
|
|
| 13 | 13 |
-----" |
| 14 | 14 |
subplot,plotName, |
| 15 | 15 |
individual_code,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot." |
| inputs/SALVIAS-CSV/maps/VegCSV.organisms.full.csv | ||
|---|---|---|
| 21 | 21 |
stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare." |
| 22 | 22 |
cf_aff,identificationQualifier,"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." |
| 23 | 23 |
no_of_individuals,individualCount,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| 24 |
OBSERVATION_ID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 24 | 25 |
stem_liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank. |
| 25 |
OBSERVATION_ID,occurrenceID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 26 | 26 |
PLOT_ID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 27 | 27 |
plot_code,parentPlotName,"Brad: Same as plotCode, above" |
| 28 |
census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows: |
|
| 29 |
----- |
|
| 30 |
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count |
|
| 31 |
FROM ""SALVIAS-CSV"".organisms |
|
| 32 |
WHERE subplot IS NOT NULL AND census_date IS NOT NULL |
|
| 33 |
GROUP BY ""PLOT_ID"", subplot |
|
| 34 |
HAVING count(DISTINCT census_date) > 1 |
|
| 28 |
census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
|
|
| 29 |
-----
|
|
| 30 |
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
|
|
| 31 |
FROM ""SALVIAS-CSV"".organisms
|
|
| 32 |
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
|
|
| 33 |
GROUP BY ""PLOT_ID"", subplot
|
|
| 34 |
HAVING count(DISTINCT census_date) > 1
|
|
| 35 | 35 |
-----" |
| 36 | 36 |
subplot,plotName, |
| 37 | 37 |
tag2,previousTag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 3 | 3 |
det_type,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 4 | 4 |
coll_number,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
| 5 | 5 |
voucher_string,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 6 |
census_date,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows: |
|
| 7 |
----- |
|
| 8 |
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count |
|
| 9 |
FROM ""SALVIAS-CSV"".organisms |
|
| 10 |
WHERE subplot IS NOT NULL AND census_date IS NOT NULL |
|
| 11 |
GROUP BY ""PLOT_ID"", subplot |
|
| 12 |
HAVING count(DISTINCT census_date) > 1 |
|
| 6 |
census_date,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
|
|
| 7 |
-----
|
|
| 8 |
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
|
|
| 9 |
FROM ""SALVIAS-CSV"".organisms
|
|
| 10 |
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
|
|
| 11 |
GROUP BY ""PLOT_ID"", subplot
|
|
| 12 |
HAVING count(DISTINCT census_date) > 1
|
|
| 13 | 13 |
-----" |
| 14 | 14 |
no_of_individuals,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| 15 | 15 |
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover, |
| ... | ... | |
| 20 | 20 |
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 21 | 21 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
| 22 | 22 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 23 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 24 | 23 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter, |
| 25 | 24 |
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
| 26 | 25 |
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
| inputs/REMIB/test/import.specimens.xml.ref | ||
|---|---|---|
| 146 | 146 |
</_date> |
| 147 | 147 |
</collectiondate> |
| 148 | 148 |
<plantobservation> |
| 149 |
<sourceaccessioncode>$accession_number</sourceaccessioncode> |
|
| 150 | 149 |
<specimenreplicate> |
| 151 | 150 |
<collectioncode_dwc>$acronym</collectioncode_dwc> |
| 152 | 151 |
<sourceaccessioncode>$accession_number</sourceaccessioncode> |
| 153 | 152 |
</specimenreplicate> |
| 154 | 153 |
</plantobservation> |
| 155 | 154 |
</aggregateoccurrence> |
| 156 |
<sourceaccessioncode>$accession_number</sourceaccessioncode> |
|
| 157 | 155 |
<taxondetermination> |
| 158 | 156 |
<isoriginal>true</isoriginal> |
| 159 | 157 |
<role>identifier</role> |
| inputs/REMIB/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 15 | 15 |
coll_day,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_alt/1/_date/day/_nullIf:[null=0,type=float]/value", |
| 16 | 16 |
coll_month,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_alt/1/_date/month/_nullIf:[null=0,type=float]/value", |
| 17 | 17 |
coll_year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_alt/1/_date/year/_nullIf:[null=0,type=float]/value", |
| 18 |
accession_number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 19 | 18 |
acronym,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 20 | 19 |
accession_number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 21 |
accession_number,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 22 | 20 |
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname", |
| 23 | 21 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
| 24 | 22 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=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", |
| inputs/SALVIAS/test/import.organisms.xml.ref | ||
|---|---|---|
| 60 | 60 |
</else> |
| 61 | 61 |
</_if> |
| 62 | 62 |
</catalognumber_dwc> |
| 63 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
|
| 64 | 63 |
</specimenreplicate> |
| 65 | 64 |
<stemobservation> |
| 66 | 65 |
<definedvalue fkey="tablerecord_id"> |
| inputs/SALVIAS/test/import.stems.xml.ref | ||
|---|---|---|
| 6 | 6 |
<aggregateoccurrence> |
| 7 | 7 |
<plantobservation> |
| 8 | 8 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
| 9 |
<specimenreplicate><sourceaccessioncode>$PlotObsID</sourceaccessioncode></specimenreplicate> |
|
| 10 | 9 |
<stemcount>$NoInd</stemcount> |
| 11 | 10 |
<stemobservation> |
| 12 | 11 |
<basaldiameter>$basal_diam</basaldiameter> |
| ... | ... | |
| 79 | 78 |
</locationevent> |
| 80 | 79 |
</location> |
| 81 | 80 |
</VegBIEN> |
| 82 |
Inserted 26 new rows into database |
|
| 81 |
Inserted 24 new rows into database |
|
| inputs/SALVIAS/maps/VegCSV.stems.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegCSV[DwC],Comments |
| 2 | 2 |
stem_id,, |
| 3 | 3 |
origrecord_id_stems,, |
| 4 |
PlotObsID,occurrenceID,
|
|
| 4 |
PlotObsID,individualID,
|
|
| 5 | 5 |
NoInd,stemCount, |
| 6 | 6 |
basal_diam,basalDiameter, |
| 7 | 7 |
stem_dbh,diameterBreastHeight, |
| inputs/SALVIAS/maps/VegCSV.stems.full.csv | ||
|---|---|---|
| 6 | 6 |
gentry_dbh,diameterBreastHeightGentry, |
| 7 | 7 |
stem_height_m,height, |
| 8 | 8 |
stem_height_first_branch_m,heightFirstBranch, |
| 9 |
PlotObsID,individualID, |
|
| 9 | 10 |
stem_liana_infestation,lianaInfestation, |
| 10 |
PlotObsID,occurrenceID, |
|
| 11 | 11 |
stem_tag2,previousTag, |
| 12 | 12 |
NoInd,stemCount, |
| 13 | 13 |
stem_notes,stemNotes, |
| inputs/SALVIAS/maps/VegCSV.organisms.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegCSV[DwC],Comments |
| 2 |
PlotObsID,occurrenceID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 2 |
PlotObsID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
|
|
| 3 | 3 |
PlotID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 4 | 4 |
PlotCode,parentPlotName,"Brad: Same as plotCode, above" |
| 5 | 5 |
census_no,censusNumber,"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." |
| inputs/SALVIAS/maps/VegCSV.organisms.full.csv | ||
|---|---|---|
| 27 | 27 |
ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 28 | 28 |
cfaff,identificationQualifier,"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." |
| 29 | 29 |
NoInd,individualCount,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
| 30 |
PlotObsID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 30 | 31 |
liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank. |
| 31 |
PlotObsID,occurrenceID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 32 | 32 |
PlotID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above." |
| 33 | 33 |
PlotCode,parentPlotName,"Brad: Same as plotCode, above" |
| 34 | 34 |
Line,plotName, |
| inputs/SALVIAS/maps/VegBIEN.stems.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:,Comments |
| 2 | 2 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
| 3 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
|
| 4 | 3 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| 5 | 4 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter, |
| 6 | 5 |
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 29 | 29 |
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 30 | 30 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
| 31 | 31 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 32 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
|
| 33 | 32 |
canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
| 34 | 33 |
canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
| 35 | 34 |
liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank. |
| inputs/U/test/import.specimens.xml.ref | ||
|---|---|---|
| 146 | 146 |
<notes>$Notes</notes> |
| 147 | 147 |
<plantobservation> |
| 148 | 148 |
<authorplantcode>$Number</authorplantcode> |
| 149 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 150 | 149 |
<specimenreplicate> |
| 151 | 150 |
<catalognumber_dwc><_if name="if indirect voucher"><else>$Barcode</else></_if></catalognumber_dwc> |
| 152 | 151 |
<collectionnumber>$Number</collectionnumber> |
| ... | ... | |
| 155 | 154 |
</plantobservation> |
| 156 | 155 |
</aggregateoccurrence> |
| 157 | 156 |
<authortaxoncode>$Number</authortaxoncode> |
| 158 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
|
| 159 | 157 |
<taxondetermination> |
| 160 | 158 |
<isoriginal>true</isoriginal> |
| 161 | 159 |
<role>identifier</role> |
| inputs/U/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 15 | 15 |
Collyy,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_alt/1/_date/year/_nullIf:[null=0,type=float]/value", |
| 16 | 16 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 17 | 17 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2, |
| 18 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 19 | 18 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 19 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/2, |
| 21 | 20 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 22 | 21 |
Number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
| 23 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 24 | 22 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 25 | 23 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 26 | 24 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/ARIZ/test/import.specimens.xml.ref | ||
|---|---|---|
| 306 | 306 |
</userdefined_id> |
| 307 | 307 |
<definedvalue>$Sex</definedvalue> |
| 308 | 308 |
</definedvalue> |
| 309 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
|
| 310 | 309 |
<specimenreplicate> |
| 311 | 310 |
<catalognumber_dwc><_if name="if indirect voucher"><else>$CatalogNumberNumeric</else></_if></catalognumber_dwc> |
| 312 | 311 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| ... | ... | |
| 327 | 326 |
<2>$FieldNumber</2> |
| 328 | 327 |
</_alt> |
| 329 | 328 |
</authortaxoncode> |
| 330 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
|
| 331 | 329 |
<taxondetermination> |
| 332 | 330 |
<isoriginal>true</isoriginal> |
| 333 | 331 |
<role>identifier</role> |
| inputs/NCU-NCSC/test/import.specimens.xml.ref | ||
|---|---|---|
| 76 | 76 |
<aggregateoccurrence> |
| 77 | 77 |
<collectiondate><_date><date>$Collect Date</date></_date></collectiondate> |
| 78 | 78 |
<plantobservation> |
| 79 |
<sourceaccessioncode>$Accession Number</sourceaccessioncode> |
|
| 80 | 79 |
<specimenreplicate> |
| 81 | 80 |
<catalognumber_dwc><_if name="if indirect voucher"><else>$Barcode</else></_if></catalognumber_dwc> |
| 82 | 81 |
<collectioncode_dwc>$SeriesName</collectioncode_dwc> |
| ... | ... | |
| 112 | 111 |
</value> |
| 113 | 112 |
</_map> |
| 114 | 113 |
</isnative> |
| 115 |
<sourceaccessioncode>$Accession Number</sourceaccessioncode> |
|
| 116 | 114 |
<taxondetermination> |
| 117 | 115 |
<isoriginal>true</isoriginal> |
| 118 | 116 |
<role>identifier</role> |
| inputs/SpeciesLink/test/import.specimens.xml.ref | ||
|---|---|---|
| 417 | 417 |
</_alt> |
| 418 | 418 |
</definedvalue> |
| 419 | 419 |
</definedvalue> |
| 420 |
<sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode> |
|
| 421 | 420 |
<specimenreplicate> |
| 422 | 421 |
<catalognumber_dwc> |
| 423 | 422 |
<_if name="if indirect voucher"> |
| ... | ... | |
| 479 | 478 |
<2>$dwc_terms_recordNumber</2> |
| 480 | 479 |
</_alt> |
| 481 | 480 |
</authortaxoncode> |
| 482 |
<sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode> |
|
| 483 | 481 |
<taxondetermination> |
| 484 | 482 |
<isoriginal>true</isoriginal> |
| 485 | 483 |
<role>identifier</role> |
| inputs/QMOR/test/import.specimens.xml.ref | ||
|---|---|---|
| 197 | 197 |
</userdefined_id> |
| 198 | 198 |
<definedvalue>$sex</definedvalue> |
| 199 | 199 |
</definedvalue> |
| 200 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 201 | 200 |
<specimenreplicate> |
| 202 | 201 |
<catalognumber_dwc><_if name="if indirect voucher"><else>$catalogNumber</else></_if></catalognumber_dwc> |
| 203 | 202 |
<collectioncode_dwc> |
| ... | ... | |
| 211 | 210 |
</specimenreplicate> |
| 212 | 211 |
</plantobservation> |
| 213 | 212 |
</aggregateoccurrence> |
| 214 |
<sourceaccessioncode>$id</sourceaccessioncode> |
|
| 215 | 213 |
<taxondetermination> |
| 216 | 214 |
<isoriginal>true</isoriginal> |
| 217 | 215 |
<role>identifier</role> |
| mappings/VegCSV.self.plots.csv | ||
|---|---|---|
| 40 | 40 |
heightFirstBranch,heightFirstBranch |
| 41 | 41 |
identificationQualifier,identificationQualifier |
| 42 | 42 |
individualCount,individualCount |
| 43 |
individualID,individualID |
|
| 43 | 44 |
infraspecificEpithet,infraspecificEpithet |
| 44 | 45 |
kingdom,kingdom |
| 45 | 46 |
landform,landform |
| ... | ... | |
| 52 | 53 |
minimumDepthInMeters,minimumDepthInMeters |
| 53 | 54 |
minimumElevationInMeters,minimumElevationInMeters |
| 54 | 55 |
nitrogen,nitrogen |
| 55 |
occurrenceID,occurrenceID |
|
| 56 | 56 |
order,order |
| 57 | 57 |
organic,organic |
| 58 | 58 |
parentLocationID,parentLocationID |
| mappings/DwC2-VegBIEN.specimens.csv | ||
|---|---|---|
| 32 | 32 |
fieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 33 | 33 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode, |
| 34 | 34 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 35 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 36 | 35 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 37 | 36 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 38 | 37 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2, |
| ... | ... | |
| 42 | 41 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
| 43 | 42 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 44 | 43 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 45 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 46 | 44 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 47 | 45 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 48 | 46 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| mappings/for_review/DwC2-VegBIEN.specimens.csv | ||
|---|---|---|
| 32 | 32 |
fieldNotes,//aggregateoccurrence/notes, |
| 33 | 33 |
recordNumber,//plantobservation/authorplantcode, |
| 34 | 34 |
sex,"//plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 35 |
occurrenceID,//plantobservation/sourceaccessioncode, |
|
| 36 | 35 |
catalogNumber,"//specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 37 | 36 |
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 |
| 38 | 37 |
collectionID,//specimenreplicate/collectioncode_dwc, |
| ... | ... | |
| 42 | 41 |
recordNumber,//taxonoccurrence/authortaxoncode, |
| 43 | 42 |
establishmentMeans,//taxonoccurrence/iscultivated, |
| 44 | 43 |
establishmentMeans,//taxonoccurrence/isnative, |
| 45 |
occurrenceID,//taxonoccurrence/sourceaccessioncode, |
|
| 46 | 44 |
identifiedBy,//taxonoccurrence/taxondetermination[role=identifier]/*_id/party/givenname, |
| 47 | 45 |
identifiedBy,//taxonoccurrence/taxondetermination[role=identifier]/*_id/party/middlename, |
| 48 | 46 |
identifiedBy,//taxonoccurrence/taxondetermination[role=identifier]/*_id/party/surname, |
| mappings/DwC.cs-VegBIEN.specimens.csv | ||
|---|---|---|
| 61 | 61 |
collectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/1, |
| 62 | 62 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2, |
| 63 | 63 |
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 64 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 65 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 66 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode, |
|
| 67 | 64 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 68 | 65 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 69 | 66 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2, |
| ... | ... | |
| 77 | 74 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
| 78 | 75 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 79 | 76 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 80 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 81 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 82 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
|
| 83 | 77 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 84 | 78 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 85 | 79 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
Also available in: Unified diff
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: Split occurrenceID into occurrenceID and individualID, where individualID refers to the plant in plots data and occurrenceID refers to the specimen in specimens data. This prevents plant sourceaccessioncodes from being mapped to the specimenreplicate, which was messing up stems mappings for the parent plantobservation. It also avoids mapping the specimenreplicate sourceaccessioncode to additional tables where it isn't needed. (Note that occurrenceID is needed for location to ensure that each specimen gets its own location to make locationdeterminations on. Everything else is directly or indirectly scoped by location when its own sourceaccessioncode isn't specified.)