Revision 3950
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS-CSV/test/import.organisms.xml.ref | ||
|---|---|---|
| 36 | 36 |
<linecover>$intercept_cm</linecover> |
| 37 | 37 |
<plantobservation> |
| 38 | 38 |
<authorplantcode>$individual_code</authorplantcode> |
| 39 |
<overallheight> |
|
| 40 |
<_alt> |
|
| 41 |
<0>$height_m</0> |
|
| 42 |
<1>$stem_height_m</1> |
|
| 43 |
</_alt> |
|
| 44 |
</overallheight> |
|
| 45 | 39 |
<sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode> |
| 46 | 40 |
<specimenreplicate> |
| 47 | 41 |
<_if name="if indirect voucher"> |
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 10 | 10 |
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.; Expanded for clarity",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.census_no,3 |
| 11 | 11 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank 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.",http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/volumeCanopy,3 |
| 12 | 12 |
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.; ""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#fieldNumber,53
|
| 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 |
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 | 13 |
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
|
| 16 | 14 |
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 |
| 17 | 15 |
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 |
| inputs/SALVIAS/test/import.organisms.xml.ref | ||
|---|---|---|
| 37 | 37 |
<notes>$Notes</notes> |
| 38 | 38 |
<plantobservation> |
| 39 | 39 |
<authorplantcode>$Ind</authorplantcode> |
| 40 |
<overallheight>$height_m</overallheight> |
|
| 41 | 40 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
| 42 | 41 |
<specimenreplicate> |
| 43 | 42 |
<_if name="if indirect voucher"> |
| inputs/SALVIAS/test/import.stems.xml.ref | ||
|---|---|---|
| 6 | 6 |
<aggregateoccurrence> |
| 7 | 7 |
<count>$NoInd</count> |
| 8 | 8 |
<plantobservation> |
| 9 |
<overallheight>$stem_height_m</overallheight> |
|
| 10 | 9 |
<sourceaccessioncode>$PlotObsID</sourceaccessioncode> |
| 11 | 10 |
<stemcount>$NoInd</stemcount> |
| 12 | 11 |
<stemobservation> |
| inputs/SALVIAS/maps/VegBIEN.stems.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:,Comments,Source,Order within table |
| 2 | 2 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,,http://rs.tdwg.org/dwc/terms/#individualCount,25 |
| 3 |
stem_height_m,/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 |
|
| 4 | 3 |
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
|
| 5 | 4 |
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,,http://rs.tdwg.org/dwc/terms/#individualCount,25 |
| 6 | 5 |
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 |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 11 | 11 |
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank 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.",http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/volumeCanopy,3 |
| 12 | 12 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,,http://rs.tdwg.org/dwc/terms/#fieldNotes,54 |
| 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
|
| 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 | 14 |
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
|
| 16 | 15 |
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 |
| 17 | 16 |
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 |
| mappings/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 52 | 52 |
volumeCanopy,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/volumeCanopy,3 |
| 53 | 53 |
fieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,,http://rs.tdwg.org/dwc/terms/#fieldNotes,54 |
| 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
|
| 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 | 55 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
|
| 57 | 56 |
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 |
| 58 | 57 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc",,http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
| mappings/for_review/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 52 | 52 |
volumeCanopy,//aggregateoccurrence/linecover,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/individualOrganismObservations/individualOrganismObservation/volumeCanopy,3 |
| 53 | 53 |
fieldNotes,//aggregateoccurrence/notes,,http://rs.tdwg.org/dwc/terms/#fieldNotes,54 |
| 54 | 54 |
fieldNumber,//plantobservation/authorplantcode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#fieldNumber,53
|
| 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 | 55 |
occurrenceID,//plantobservation/sourceaccessioncode,"""{"" sorts it with other _if[@name=specimenreplicate_via]s",http://rs.tdwg.org/dwc/terms/#occurrenceID,19
|
| 57 | 56 |
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 |
| 58 | 57 |
catalogNumber,"//plantobservation/specimenreplicate/_if[@name=""if indirect voucher""]/else/catalognumber_dwc",,http://rs.tdwg.org/dwc/terms/#catalogNumber,20 |
Also available in: Unified diff
mappings/VegCSV-VegBIEN.specimens.csv: height: Removed mapping to plantobservation.overallheight, since the height is a stem field rather than a plant field. Note that a height in the organisms table will be mapped to the height in a single stemobservation for that plant, with NULL sourceaccessioncode and authorstemcode. Note also that this change is possible because no mapped datasource yet provides a valid overallheight with multiple stems or that differs from its single stem's height. (Although SALVIAS sometimes provides both a stem height and an organism height, that height is always either the same, or the organism height is invalid. See <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS_issues#Some-organisms-have-one-stem-but-different-heights-in-the-organisms-and-stems-tables>.)