Revision 7190
Added by Aaron Marcuse-Kubitza almost 12 years ago
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 18 | 18 |
Number of subplot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2", |
| 19 | 19 |
Inventory code,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| 20 | 20 |
Observations,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 21 |
Tree number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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|
| 21 |
Tree number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 22 | 22 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 23 | 23 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 24 | 24 |
Trunk,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 51 | 51 |
campus,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/5/_label[label=""campus""]/value", |
| 52 | 52 |
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/6/_label[label=""loaned to""]/value", |
| 53 | 53 |
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/7/_label[label=""in or out""]/value", |
| 54 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 54 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 55 | 55 |
accession,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1] |
| 56 | 56 |
|
| 57 | 57 |
[1] Using the following query: |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 66 | 66 |
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
| 67 | 67 |
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not." |
| 68 | 68 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
| 69 |
individual_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"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."
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|
| 69 |
individual_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,"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."
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|
| 70 | 70 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,"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." |
| 71 | 71 |
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." |
| 72 | 72 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 24 | 24 |
YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 25 | 25 |
IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 26 | 26 |
FieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 27 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 27 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 28 | 28 |
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" |
| 29 | 29 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1", |
| 30 | 30 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric |
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 23 | 23 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 24 | 24 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 25 | 25 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 26 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 26 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 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 | 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 29 | 29 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 57 | 57 |
</_alt> |
| 58 | 58 |
</notes> |
| 59 | 59 |
<plantobservation> |
| 60 |
<collectionnumber>$CollectorNumber</collectionnumber>
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| 60 |
<authorplantcode>$CollectorNumber</authorplantcode>
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| 61 | 61 |
<specimenreplicate> |
| 62 | 62 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 63 | 63 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 109 | 109 |
intercept_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m, |
| 110 | 110 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value, |
| 111 | 111 |
fieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 112 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 112 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 113 | 113 |
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" |
| 114 | 114 |
individualObservationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/1, |
| 115 | 115 |
individualID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2, |
| inputs/TRT/Specimen/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
<taxonoccurrence> |
| 59 | 59 |
<aggregateoccurrence> |
| 60 | 60 |
<plantobservation> |
| 61 |
<collectionnumber>$recordNumber</collectionnumber>
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| 61 |
<authorplantcode>$recordNumber</authorplantcode>
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| 62 | 62 |
<definedvalue fkey="tablerecord_id"> |
| 63 | 63 |
<userdefined_id> |
| 64 | 64 |
<userdefined> |
| inputs/TRTE/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 22 | 22 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 23 | 23 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 109 | 109 |
intercept_m,//aggregateoccurrence/linecover_m, |
| 110 | 110 |
intercept_cm,//aggregateoccurrence/linecover_m/_cm_to_m/value, |
| 111 | 111 |
fieldNotes,//aggregateoccurrence/notes, |
| 112 |
recordNumber,//plantobservation/collectionnumber,
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| 112 |
recordNumber,//plantobservation/authorplantcode,
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| 113 | 113 |
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" |
| 114 | 114 |
individualObservationID,//plantobservation/sourceaccessioncode, |
| 115 | 115 |
individualID,//plantobservation/sourceaccessioncode, |
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
darwin:YearCollected,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 16 | 16 |
darwin:IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 17 | 17 |
darwin:Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 18 |
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 18 |
darwin:CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 19 | 19 |
darwin: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" |
| 20 | 20 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
darwin:CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| inputs/NCU/Specimen/VegBIEN.csv | ||
|---|---|---|
| 18 | 18 |
CityLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_alt/2, |
| 19 | 19 |
CollectionDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 20 | 20 |
Description,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 21 |
firstCollectorRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"Actually the collector's number, not remarks"
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| 21 |
firstCollectorRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,"Actually the collector's number, not remarks"
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| 22 | 22 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 23 | 23 |
CollectionGUID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 24 | 24 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| inputs/NCU/Specimen/test.xml.ref | ||
|---|---|---|
| 40 | 40 |
<collectiondate>$CollectionDate</collectiondate> |
| 41 | 41 |
<notes>$Description</notes> |
| 42 | 42 |
<plantobservation> |
| 43 |
<collectionnumber>$firstCollectorRemarks</collectionnumber>
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| 43 |
<authorplantcode>$firstCollectorRemarks</authorplantcode>
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| 44 | 44 |
<specimenreplicate> |
| 45 | 45 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 46 | 46 |
<collectioncode_dwc>$CollectionGUID</collectioncode_dwc> |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 22 | 22 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 23 | 23 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 48 | 48 |
<taxonoccurrence> |
| 49 | 49 |
<aggregateoccurrence> |
| 50 | 50 |
<plantobservation> |
| 51 |
<collectionnumber>$recordNumber</collectionnumber>
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| 51 |
<authorplantcode>$recordNumber</authorplantcode>
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| 52 | 52 |
<specimenreplicate> |
| 53 | 53 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc> |
| 54 | 54 |
<collectioncode_dwc> |
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 22 | 22 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 23 | 23 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 24 | 24 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 25 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 25 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 26 | 26 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 27 | 27 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 28 | 28 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 53 | 53 |
<taxonoccurrence> |
| 54 | 54 |
<aggregateoccurrence> |
| 55 | 55 |
<plantobservation> |
| 56 |
<collectionnumber>$recordNumber</collectionnumber>
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| 56 |
<authorplantcode>$recordNumber</authorplantcode>
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| 57 | 57 |
<specimenreplicate> |
| 58 | 58 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc> |
| 59 | 59 |
<collectioncode_dwc> |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 67 | 67 |
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not." |
| 68 | 68 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover_m/_cm_to_m/value,"Brad: This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
| 69 | 69 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 70 |
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"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."
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|
| 70 |
Ind,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,"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."
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|
| 71 | 71 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,"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." |
| 72 | 72 |
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." |
| 73 | 73 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
| inputs/SALVIAS/plotObservations/test.xml.ref | ||
|---|---|---|
| 55 | 55 |
<linecover_m><_cm_to_m><value>$intercept_cm</value></_cm_to_m></linecover_m> |
| 56 | 56 |
<notes>$Notes</notes> |
| 57 | 57 |
<plantobservation> |
| 58 |
<collectionnumber>$Ind</collectionnumber>
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| 58 |
<authorplantcode>$Ind</authorplantcode>
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| 59 | 59 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
| 60 | 60 |
<specimenreplicate> |
| 61 | 61 |
<catalognumber_dwc> |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
Collmm,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 17 | 17 |
Collyy,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 18 | 18 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 19 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
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| 19 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
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| 20 | 20 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 22 | 22 |
ID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| inputs/U/Specimen/test.xml.ref | ||
|---|---|---|
| 68 | 68 |
</collectiondate> |
| 69 | 69 |
<notes>$Notes</notes> |
| 70 | 70 |
<plantobservation> |
| 71 |
<collectionnumber>$Number</collectionnumber>
|
|
| 71 |
<authorplantcode>$Number</authorplantcode>
|
|
| 72 | 72 |
<specimenreplicate> |
| 73 | 73 |
<catalognumber_dwc>$Barcode</catalognumber_dwc> |
| 74 | 74 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 22 | 22 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 23 | 23 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
|
|
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
|
|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| inputs/QFA/Specimen/test.xml.ref | ||
|---|---|---|
| 48 | 48 |
<taxonoccurrence> |
| 49 | 49 |
<aggregateoccurrence> |
| 50 | 50 |
<plantobservation> |
| 51 |
<collectionnumber>$recordNumber</collectionnumber>
|
|
| 51 |
<authorplantcode>$recordNumber</authorplantcode>
|
|
| 52 | 52 |
<specimenreplicate> |
| 53 | 53 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc> |
| 54 | 54 |
<collectioncode_dwc> |
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 22 | 22 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 23 | 23 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
|
|
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
|
|
| 25 | 25 |
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" |
| 26 | 26 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 27 | 27 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| inputs/JBM/Specimen/test.xml.ref | ||
|---|---|---|
| 42 | 42 |
<taxonoccurrence> |
| 43 | 43 |
<aggregateoccurrence> |
| 44 | 44 |
<plantobservation> |
| 45 |
<collectionnumber>$recordNumber</collectionnumber>
|
|
| 45 |
<authorplantcode>$recordNumber</authorplantcode>
|
|
| 46 | 46 |
<definedvalue fkey="tablerecord_id"> |
| 47 | 47 |
<userdefined_id> |
| 48 | 48 |
<userdefined> |
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 22 | 22 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 23 | 23 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
|
|
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
|
|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| inputs/UBC/Specimen/test.xml.ref | ||
|---|---|---|
| 48 | 48 |
<taxonoccurrence> |
| 49 | 49 |
<aggregateoccurrence> |
| 50 | 50 |
<plantobservation> |
| 51 |
<collectionnumber>$recordNumber</collectionnumber>
|
|
| 51 |
<authorplantcode>$recordNumber</authorplantcode>
|
|
| 52 | 52 |
<specimenreplicate> |
| 53 | 53 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc> |
| 54 | 54 |
<collectioncode_dwc> |
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 22 | 22 |
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 23 | 23 |
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
|
|
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
|
|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| inputs/HIBG/Specimen/test.xml.ref | ||
|---|---|---|
| 48 | 48 |
<taxonoccurrence> |
| 49 | 49 |
<aggregateoccurrence> |
| 50 | 50 |
<plantobservation> |
| 51 |
<collectionnumber>$recordNumber</collectionnumber>
|
|
| 51 |
<authorplantcode>$recordNumber</authorplantcode>
|
|
| 52 | 52 |
<specimenreplicate> |
| 53 | 53 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc> |
| 54 | 54 |
<collectioncode_dwc> |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 59 | 59 |
dwc_curatorial_IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 60 | 60 |
dwc_terms_individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 61 | 61 |
conceptual_darwin_2003_1_0_Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 62 |
dwc_terms_recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/1,
|
|
| 63 |
conceptual_darwin_2003_1_0_FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 62 |
dwc_terms_recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/1,
|
|
| 63 |
conceptual_darwin_2003_1_0_FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 64 | 64 |
----- |
| 65 | 65 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
| 66 | 66 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
|
| 67 | 67 |
-----" |
| 68 |
dwc_curatorial_FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 68 |
dwc_curatorial_FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 69 | 69 |
----- |
| 70 | 70 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
| 71 | 71 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
|
| 72 | 72 |
-----" |
| 73 |
dwc_terms_fieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 73 |
dwc_terms_fieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/2,"Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec)
|
|
| 74 | 74 |
----- |
| 75 | 75 |
SELECT count(*) FROM ""SpeciesLink"".specimens |
| 76 | 76 |
WHERE COALESCE(""dwc_curatorial_FieldNumber"", ""dwc_terms_fieldNumber"", ""conceptual_darwin_2003_1_0_FieldNumber"") != ""dwc_terms_recordNumber""
|
| 77 | 77 |
-----" |
| 78 |
conceptual_darwin_2003_1_0_CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/3,
|
|
| 79 |
dwc_curatorial_CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/3,
|
|
| 78 |
conceptual_darwin_2003_1_0_CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/3,
|
|
| 79 |
dwc_curatorial_CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_alt/3,
|
|
| 80 | 80 |
conceptual_darwin_2003_1_0_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" |
| 81 | 81 |
dwc_dwcore_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" |
| 82 | 82 |
dwc_terms_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" |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 108 | 108 |
</count> |
| 109 | 109 |
<notes>$conceptual_darwin_2003_1_0_Notes</notes> |
| 110 | 110 |
<plantobservation> |
| 111 |
<collectionnumber>
|
|
| 111 |
<authorplantcode>
|
|
| 112 | 112 |
<_alt> |
| 113 | 113 |
<1>$dwc_terms_recordNumber</1> |
| 114 | 114 |
<2> |
| ... | ... | |
| 125 | 125 |
</_alt> |
| 126 | 126 |
</3> |
| 127 | 127 |
</_alt> |
| 128 |
</collectionnumber>
|
|
| 128 |
</authorplantcode>
|
|
| 129 | 129 |
<definedvalue fkey="tablerecord_id"> |
| 130 | 130 |
<userdefined_id> |
| 131 | 131 |
<userdefined> |
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
plotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| 22 | 22 |
observationDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 23 | 23 |
pctCover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
| 24 |
collectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
|
|
| 24 |
collectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
|
|
| 25 | 25 |
observationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 26 | 26 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
| 27 | 27 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_split:[separator="", ""]/value", |
| inputs/bien_web/observation/test.xml.ref | ||
|---|---|---|
| 18 | 18 |
<collectiondate>$observationDate</collectiondate> |
| 19 | 19 |
<cover_fraction><_percent_to_fraction><value>$pctCover</value></_percent_to_fraction></cover_fraction> |
| 20 | 20 |
<plantobservation> |
| 21 |
<collectionnumber>$collectionNumber</collectionnumber>
|
|
| 21 |
<authorplantcode>$collectionNumber</authorplantcode>
|
|
| 22 | 22 |
<specimenreplicate> |
| 23 | 23 |
<institution_id> |
| 24 | 24 |
<sourcelist> |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 20 | 20 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
| 21 | 21 |
PlantFungusDescription,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/2/_label[label=""plant fungus""]/value", |
| 22 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,Usage inconsistent with DwC definition
|
|
| 22 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,Usage inconsistent with DwC definition
|
|
| 23 | 23 |
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" |
| 24 | 24 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 25 | 25 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 92 | 92 |
</_join> |
| 93 | 93 |
</notes> |
| 94 | 94 |
<plantobservation> |
| 95 |
<collectionnumber>$FieldNumber</collectionnumber>
|
|
| 95 |
<authorplantcode>$FieldNumber</authorplantcode>
|
|
| 96 | 96 |
<definedvalue fkey="tablerecord_id"> |
| 97 | 97 |
<userdefined_id> |
| 98 | 98 |
<userdefined> |
| inputs/Madidi/Organism/test.xml.ref | ||
|---|---|---|
| 20 | 20 |
<aggregateoccurrence> |
| 21 | 21 |
<notes>$Observations</notes> |
| 22 | 22 |
<plantobservation> |
| 23 |
<collectionnumber>$Tree number</collectionnumber>
|
|
| 23 |
<authorplantcode>$Tree number</authorplantcode>
|
|
| 24 | 24 |
<specimenreplicate><catalognumber_dwc>$Specimen</catalognumber_dwc></specimenreplicate> |
| 25 | 25 |
<stemobservation> |
| 26 | 26 |
<authorstemcode>$Trunk</authorstemcode> |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 73 | 73 |
</_join> |
| 74 | 74 |
</notes> |
| 75 | 75 |
<plantobservation> |
| 76 |
<collectionnumber>$collectno</collectionnumber>
|
|
| 76 |
<authorplantcode>$collectno</authorplantcode>
|
|
| 77 | 77 |
<specimenreplicate> |
| 78 | 78 |
<institution_id> |
| 79 | 79 |
<sourcelist> |
| inputs/SALVIAS-CSV/Organism/test.xml.ref | ||
|---|---|---|
| 54 | 54 |
</definedvalue> |
| 55 | 55 |
<linecover_m><_cm_to_m><value>$intercept_cm</value></_cm_to_m></linecover_m> |
| 56 | 56 |
<plantobservation> |
| 57 |
<collectionnumber>$individual_code</collectionnumber>
|
|
| 57 |
<authorplantcode>$individual_code</authorplantcode>
|
|
| 58 | 58 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
| 59 | 59 |
<specimenreplicate> |
| 60 | 60 |
<catalognumber_dwc> |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 67 | 67 |
<count>$IndividualCount</count> |
| 68 | 68 |
<notes>$FieldNotes</notes> |
| 69 | 69 |
<plantobservation> |
| 70 |
<collectionnumber>$CollectorNumber</collectionnumber>
|
|
| 70 |
<authorplantcode>$CollectorNumber</authorplantcode>
|
|
| 71 | 71 |
<definedvalue fkey="tablerecord_id"> |
| 72 | 72 |
<userdefined_id> |
| 73 | 73 |
<userdefined> |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
IndividualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 17 | 17 |
convertednotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 18 | 18 |
notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 19 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,
|
|
| 19 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,
|
|
| 20 | 20 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/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 |
| 22 | 22 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| inputs/TRTE/Specimen/test.xml.ref | ||
|---|---|---|
| 48 | 48 |
<taxonoccurrence> |
| 49 | 49 |
<aggregateoccurrence> |
| 50 | 50 |
<plantobservation> |
| 51 |
<collectionnumber>$recordNumber</collectionnumber>
|
|
| 51 |
<authorplantcode>$recordNumber</authorplantcode>
|
|
| 52 | 52 |
<specimenreplicate> |
| 53 | 53 |
<catalognumber_dwc>$catalogNumber</catalognumber_dwc> |
| 54 | 54 |
<collectioncode_dwc> |
Also available in: Unified diff
schemas/vegbien.sql: plantobservation: Renamed collectionnumber to authorplantcode since this number, which identifies the plant, is actually different from the collectionnumber that identifies the specimen collected from it. This distinction is meaningful for plots data, but generally not for specimens data.