Revision 3945
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS-CSV/test/import.organisms.xml.ref | ||
|---|---|---|
| 44 | 44 |
</overallheight> |
| 45 | 45 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
| 46 | 46 |
<specimenreplicate> |
| 47 |
<_if name="if direct voucher"> |
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| 47 |
<_if name="if indirect voucher">
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|
| 48 | 48 |
<cond> |
| 49 | 49 |
<_eq> |
| 50 | 50 |
<right>indirect</right> |
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 13 | 13 |
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/height,4 |
| 14 | 14 |
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare.",http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/height,4 |
| 15 | 15 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/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.; ""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
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| 16 |
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct 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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17 |
|
| 17 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/else/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
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| 18 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/else/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
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| 16 |
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
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coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
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voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
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| 19 | 19 |
no_of_individuals,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,"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.",http://rs.tdwg.org/dwc/terms/#individualCount,25 |
| 20 | 20 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter,Expanded for clarity,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.basal_diam,37 |
| 21 | 21 |
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. ,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.stem_canopy_form,40 |
| inputs/SALVIAS/test/import.organisms.xml.ref | ||
|---|---|---|
| 40 | 40 |
<overallheight>$height_m</overallheight> |
| 41 | 41 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
| 42 | 42 |
<specimenreplicate> |
| 43 |
<_if name="if direct voucher"> |
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| 43 |
<_if name="if indirect voucher">
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|
| 44 | 44 |
<cond> |
| 45 | 45 |
<_eq> |
| 46 | 46 |
<right>indirect</right> |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 13 | 13 |
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.; ""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#fieldNumber,53
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| 14 | 14 |
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/height,4 |
| 15 | 15 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/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.; ""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
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| 16 |
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct 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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17 |
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| 17 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/else/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
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| 18 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/else/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
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| 16 |
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
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coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
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SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
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| 19 | 19 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,"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.",http://rs.tdwg.org/dwc/terms/#individualCount,25 |
| 20 | 20 |
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. ,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.stem_canopy_form,40 |
| 21 | 21 |
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. ,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.stem_canopy_position,41 |
| mappings/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 54 | 54 |
fieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#fieldNumber,53
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| 55 | 55 |
height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/overallheight,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/height,4 |
| 56 | 56 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
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voucherType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/cond/_eq:[right=indirect]/left","values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17 |
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catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/else/catalognumber_dwc",,http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
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voucherType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
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| 58 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc",,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
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| 59 | 59 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,,http://rs.tdwg.org/dwc/terms/#individualCount,25 |
| 60 | 60 |
basalDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter,Expanded for clarity,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.basal_diam,37 |
| 61 | 61 |
canopyForm,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.stem_canopy_form,40 |
| mappings/for_review/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 54 | 54 |
fieldNumber,//plantobservation/authorplantcode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#fieldNumber,53
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| 55 | 55 |
height,//plantobservation/overallheight,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/height,4 |
| 56 | 56 |
occurrenceID,//plantobservation/sourceaccessioncode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
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voucherType,"//plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/cond","values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17 |
|
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catalogNumber,"//plantobservation/specimenreplicate/_if[@name=""if direct voucher""]/else/catalognumber_dwc",,http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
|
| 57 |
voucherType,"//plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/cond","values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
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catalogNumber,"//plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc",,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
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| 59 | 59 |
individualCount,//plantobservation/stemcount,,http://rs.tdwg.org/dwc/terms/#individualCount,25 |
| 60 | 60 |
basalDiameter,//stemobservation/basaldiameter,Expanded for clarity,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.basal_diam,37 |
| 61 | 61 |
canopyForm,"//stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]/definedvalue",,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.stem_canopy_form,40 |
Also available in: Unified diff
mappings/VegCSV-VegBIEN.specimens.csv: catalogNumber direct voucher _if statement: Changed @name to "if indirect voucher", so that it's logical consistent with the else branch following it. It was previously "if direct voucher" because the _if statement only contained a case for direct vouchers, and the else branch was being used in place of a _not() function.