Revision 4073
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/QMOR/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 31 | 31 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/2, |
| 32 | 32 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 33 | 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 34 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 35 | 34 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 36 | 35 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 37 | 36 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| mappings/DwC2-VegBIEN.specimens.csv | ||
|---|---|---|
| 39 | 39 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber, |
| 40 | 40 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 41 | 41 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 42 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 43 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2, |
|
| 42 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
|
| 44 | 43 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 45 | 44 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 46 | 45 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| mappings/for_review/DwC2-VegBIEN.specimens.csv | ||
|---|---|---|
| 39 | 39 |
recordNumber,//specimenreplicate/collectionnumber, |
| 40 | 40 |
institutionCode,//party/organizationname, |
| 41 | 41 |
occurrenceID,//specimenreplicate/sourceaccessioncode, |
| 42 |
catalogNumber,"//taxonoccurrence/authortaxoncode/_if[@name=""if indirect voucher""]/else", |
|
| 43 | 42 |
recordNumber,//taxonoccurrence/authortaxoncode, |
| 44 | 43 |
establishmentMeans,//taxonoccurrence/iscultivated, |
| 45 | 44 |
establishmentMeans,//taxonoccurrence/isnative, |
| mappings/DwC.cs-VegBIEN.specimens.csv | ||
|---|---|---|
| 73 | 73 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 74 | 74 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 75 | 75 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 76 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 77 |
collectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 78 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
|
| 76 |
collectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 77 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
|
| 79 | 78 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 80 | 79 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 81 | 80 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| inputs/XAL/test/import.specimens.xml.ref | ||
|---|---|---|
| 257 | 257 |
</specimenreplicate> |
| 258 | 258 |
</plantobservation> |
| 259 | 259 |
</aggregateoccurrence> |
| 260 |
<authortaxoncode> |
|
| 261 |
<_alt> |
|
| 262 |
<1><_if name="if indirect voucher"><else>$CatalogNumber</else></_if></1> |
|
| 263 |
<2>$CollectorNumber</2> |
|
| 264 |
</_alt> |
|
| 265 |
</authortaxoncode> |
|
| 260 |
<authortaxoncode>$CollectorNumber</authortaxoncode> |
|
| 266 | 261 |
<taxondetermination> |
| 267 | 262 |
<isoriginal>true</isoriginal> |
| 268 | 263 |
<role>identifier</role> |
| inputs/XAL/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 32 | 32 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 33 | 33 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/1, |
| 34 | 34 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 35 |
CatalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 36 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 35 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 37 | 36 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 38 | 37 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 39 | 38 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/NY/test/import.specimens.xml.ref | ||
|---|---|---|
| 301 | 301 |
</aggregateoccurrence> |
| 302 | 302 |
<authortaxoncode> |
| 303 | 303 |
<_alt> |
| 304 |
<1><_if name="if indirect voucher"><else>$CatalogNumber</else></_if></1> |
|
| 305 |
<2> |
|
| 306 |
<_alt> |
|
| 307 |
<1>$CollectorNumber</1> |
|
| 308 |
<2>$FieldNumber</2> |
|
| 309 |
</_alt> |
|
| 310 |
</2> |
|
| 304 |
<1>$CollectorNumber</1> |
|
| 305 |
<2>$FieldNumber</2> |
|
| 311 | 306 |
</_alt> |
| 312 | 307 |
</authortaxoncode> |
| 313 | 308 |
<sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode> |
| inputs/NY/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 38 | 38 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/2,Usage inconsistent with DwC definition |
| 39 | 39 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 40 | 40 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 41 |
CatalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 42 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 43 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,Usage inconsistent with DwC definition |
|
| 41 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 42 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,Usage inconsistent with DwC definition |
|
| 44 | 43 |
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 45 | 44 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 46 | 45 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| inputs/UNCC/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 25 | 25 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/1, |
| 26 | 26 |
herbarium,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 27 | 27 |
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 28 |
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1,
|
|
| 28 |
collectno,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1,
|
|
| 29 | 29 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values |
| 30 | 30 |
cultivated,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values |
| 31 | 31 |
accession,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| inputs/ACAD/test/import.specimens.xml.ref | ||
|---|---|---|
| 92 | 92 |
</specimenreplicate> |
| 93 | 93 |
</plantobservation> |
| 94 | 94 |
</aggregateoccurrence> |
| 95 |
<authortaxoncode> |
|
| 96 |
<_alt> |
|
| 97 |
<1><_if name="if indirect voucher"><else>$catalogNumber</else></_if></1> |
|
| 98 |
<2>$recordNumber</2> |
|
| 99 |
</_alt> |
|
| 100 |
</authortaxoncode> |
|
| 95 |
<authortaxoncode>$recordNumber</authortaxoncode> |
|
| 101 | 96 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 102 | 97 |
<taxondetermination> |
| 103 | 98 |
<isoriginal>true</isoriginal> |
| inputs/ACAD/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 21 | 21 |
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/2, |
| 22 | 22 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 23 | 23 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 24 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 25 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
|
| 24 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
|
| 26 | 25 |
id,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 27 | 26 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 28 | 27 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| inputs/CVS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 10 | 10 |
authorObsCode,/location/locationevent/authoreventcode, |
| 11 | 11 |
obsStartDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value, |
| 12 | 12 |
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover, |
| 13 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/3,
|
|
| 13 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
|
|
| 14 | 14 |
currentTaxonName sec Weakley 2006,"/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", |
| 15 | 15 |
confidentialityStatus,,** No input mapping for confidentialityStatus ** |
| inputs/SALVIAS-CSV/test/import.organisms.xml.ref | ||
|---|---|---|
| 141 | 141 |
</aggregateoccurrence> |
| 142 | 142 |
<authortaxoncode> |
| 143 | 143 |
<_alt> |
| 144 |
<1> |
|
| 145 |
<_if name="if indirect voucher"> |
|
| 146 |
<cond> |
|
| 147 |
<_eq> |
|
| 148 |
<right>indirect</right> |
|
| 149 |
<left>$det_type</left> |
|
| 150 |
</_eq> |
|
| 151 |
</cond> |
|
| 152 |
<else> |
|
| 153 |
<_alt> |
|
| 154 |
<1>$coll_number</1> |
|
| 155 |
<2>$voucher_string</2> |
|
| 156 |
</_alt> |
|
| 157 |
</else> |
|
| 158 |
</_if> |
|
| 159 |
</1> |
|
| 160 |
<2>$individual_code</2> |
|
| 161 |
<3><_name><last>$orig_species</last></_name></3> |
|
| 144 |
<1>$individual_code</1> |
|
| 145 |
<2><_name><last>$orig_species</last></_name></2> |
|
| 162 | 146 |
</_alt> |
| 163 | 147 |
</authortaxoncode> |
| 164 | 148 |
<growthform> |
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 37 | 37 |
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag/_alt/2,Brad: see above |
| 38 | 38 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
| 39 | 39 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position |
| 40 |
det_type,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_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." |
|
| 41 |
coll_number,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
|
| 42 |
voucher_string,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_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." |
|
| 43 |
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,"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." |
|
| 44 |
orig_species,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/3/_name/last,Brad: OMIT |
|
| 40 |
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,"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." |
|
| 41 |
orig_species,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/last,Brad: OMIT |
|
| 45 | 42 |
habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
| 46 | 43 |
OBSERVATION_ID,/location/locationevent/taxonoccurrence/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." |
| 47 | 44 |
specific_authority,"/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",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss. |
| inputs/SALVIAS/test/import.organisms.xml.ref | ||
|---|---|---|
| 113 | 113 |
</aggregateoccurrence> |
| 114 | 114 |
<authortaxoncode> |
| 115 | 115 |
<_alt> |
| 116 |
<1> |
|
| 117 |
<_if name="if indirect voucher"> |
|
| 118 |
<cond> |
|
| 119 |
<_eq> |
|
| 120 |
<right>indirect</right> |
|
| 121 |
<left>$DetType</left> |
|
| 122 |
</_eq> |
|
| 123 |
</cond> |
|
| 124 |
<else> |
|
| 125 |
<_alt> |
|
| 126 |
<1>$coll_number</1> |
|
| 127 |
<2>$SourceVoucher</2> |
|
| 128 |
</_alt> |
|
| 129 |
</else> |
|
| 130 |
</_if> |
|
| 131 |
</1> |
|
| 132 |
<2>$Ind</2> |
|
| 133 |
<3> |
|
| 116 |
<1>$Ind</1> |
|
| 117 |
<2> |
|
| 134 | 118 |
<_name> |
| 135 | 119 |
<first>$OrigGenus</first> |
| 136 | 120 |
<last>$OrigSpecies</last> |
| 137 | 121 |
</_name> |
| 138 |
</3>
|
|
| 122 |
</2>
|
|
| 139 | 123 |
</_alt> |
| 140 | 124 |
</authortaxoncode> |
| 141 | 125 |
<growthform> |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 40 | 40 |
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other." |
| 41 | 41 |
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
| 42 | 42 |
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position |
| 43 |
DetType,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_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." |
|
| 44 |
coll_number,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string |
|
| 45 |
SourceVoucher,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_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." |
|
| 46 |
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,"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." |
|
| 47 |
OrigGenus,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/3/_name/first, |
|
| 48 |
OrigSpecies,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/3/_name/last,Brad: OMIT |
|
| 43 |
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,"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." |
|
| 44 |
OrigGenus,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/first, |
|
| 45 |
OrigSpecies,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/last,Brad: OMIT |
|
| 49 | 46 |
Habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
| 50 | 47 |
PlotObsID,/location/locationevent/taxonoccurrence/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." |
| 51 | 48 |
auth,"/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",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss. |
| inputs/U/test/import.specimens.xml.ref | ||
|---|---|---|
| 154 | 154 |
</specimenreplicate> |
| 155 | 155 |
</plantobservation> |
| 156 | 156 |
</aggregateoccurrence> |
| 157 |
<authortaxoncode> |
|
| 158 |
<_alt> |
|
| 159 |
<1><_if name="if indirect voucher"><else>$Barcode</else></_if></1> |
|
| 160 |
<2>$Number</2> |
|
| 161 |
</_alt> |
|
| 162 |
</authortaxoncode> |
|
| 157 |
<authortaxoncode>$Number</authortaxoncode> |
|
| 163 | 158 |
<sourceaccessioncode>$ID</sourceaccessioncode> |
| 164 | 159 |
<taxondetermination> |
| 165 | 160 |
<isoriginal>true</isoriginal> |
| inputs/U/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 19 | 19 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 20 | 20 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/2, |
| 21 | 21 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 22 |
Barcode,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 23 |
Number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
|
| 22 |
Number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
|
| 24 | 23 |
ID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 25 | 24 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 26 | 25 |
Detby,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| inputs/ARIZ/test/import.specimens.xml.ref | ||
|---|---|---|
| 323 | 323 |
</aggregateoccurrence> |
| 324 | 324 |
<authortaxoncode> |
| 325 | 325 |
<_alt> |
| 326 |
<1><_if name="if indirect voucher"><else>$CatalogNumberNumeric</else></_if></1> |
|
| 327 |
<2> |
|
| 328 |
<_alt> |
|
| 329 |
<1>$CollectorNumber</1> |
|
| 330 |
<2>$FieldNumber</2> |
|
| 331 |
</_alt> |
|
| 332 |
</2> |
|
| 326 |
<1>$CollectorNumber</1> |
|
| 327 |
<2>$FieldNumber</2> |
|
| 333 | 328 |
</_alt> |
| 334 | 329 |
</authortaxoncode> |
| 335 | 330 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
| inputs/ARIZ/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 43 | 43 |
FieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/2,Usage inconsistent with DwC definition |
| 44 | 44 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 45 | 45 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 46 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 47 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 48 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2,Usage inconsistent with DwC definition |
|
| 46 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 47 |
FieldNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,Usage inconsistent with DwC definition |
|
| 49 | 48 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 50 | 49 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 51 | 50 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| inputs/GBIF/test/import.specimens.xml.ref | ||
|---|---|---|
| 166 | 166 |
</specimenreplicate> |
| 167 | 167 |
</plantobservation> |
| 168 | 168 |
</aggregateoccurrence> |
| 169 |
<authortaxoncode><_if name="if indirect voucher"><else>$CatalogNO</else></_if></authortaxoncode> |
|
| 170 | 169 |
<taxondetermination> |
| 171 | 170 |
<isoriginal>true</isoriginal> |
| 172 | 171 |
<role>identifier</role> |
| inputs/GBIF/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 20 | 20 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
CollectionCD,/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 |
| 22 | 22 |
InstitutionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 23 |
CatalogNO,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 24 | 23 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 25 | 24 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 26 | 25 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/NCU-NCSC/test/import.specimens.xml.ref | ||
|---|---|---|
| 84 | 84 |
</specimenreplicate> |
| 85 | 85 |
</plantobservation> |
| 86 | 86 |
</aggregateoccurrence> |
| 87 |
<authortaxoncode><_if name="if indirect voucher"><else>$Barcode</else></_if></authortaxoncode> |
|
| 88 | 87 |
<iscultivated> |
| 89 | 88 |
<_map> |
| 90 | 89 |
<cultivated>t</cultivated> |
| inputs/NCU-NCSC/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 16 | 16 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 17 | 17 |
SeriesName,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_merge/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 18 | 18 |
Accession Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 19 |
Barcode,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 20 | 19 |
Cultivated?,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value/_map:[Yes=cultivated,No=wild]/value", |
| 21 | 20 |
Cultivated?,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value/_map:[Yes=cultivated,No=wild]/value", |
| 22 | 21 |
Accession Number,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| inputs/SpeciesLink/test/import.specimens.xml.ref | ||
|---|---|---|
| 471 | 471 |
<authortaxoncode> |
| 472 | 472 |
<_alt> |
| 473 | 473 |
<1> |
| 474 |
<_if name="if indirect voucher"> |
|
| 475 |
<else> |
|
| 476 |
<_alt> |
|
| 477 |
<0>$dwc_dwcore_CatalogNumber</0> |
|
| 478 |
<1>$conceptual_darwin_2003_1_0_CatalogNumber</1> |
|
| 479 |
<2>$dwc_terms_catalogNumber</2> |
|
| 480 |
</_alt> |
|
| 481 |
</else> |
|
| 482 |
</_if> |
|
| 483 |
</1> |
|
| 484 |
<2> |
|
| 485 | 474 |
<_alt> |
| 486 |
<1> |
|
| 487 |
<_alt> |
|
| 488 |
<0>$dwc_curatorial_CollectorNumber</0> |
|
| 489 |
<1>$conceptual_darwin_2003_1_0_CollectorNumber</1> |
|
| 490 |
</_alt> |
|
| 491 |
</1> |
|
| 492 |
<2>$dwc_terms_recordNumber</2> |
|
| 475 |
<0>$dwc_curatorial_CollectorNumber</0> |
|
| 476 |
<1>$conceptual_darwin_2003_1_0_CollectorNumber</1> |
|
| 493 | 477 |
</_alt> |
| 494 |
</2> |
|
| 478 |
</1> |
|
| 479 |
<2>$dwc_terms_recordNumber</2> |
|
| 495 | 480 |
</_alt> |
| 496 | 481 |
</authortaxoncode> |
| 497 | 482 |
<sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode> |
| inputs/SpeciesLink/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 73 | 73 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 74 | 74 |
institutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 75 | 75 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 76 |
CatalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 77 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 78 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 79 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
|
| 76 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 77 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
|
| 80 | 78 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 81 | 79 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 82 | 80 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| inputs/MO/test/import.specimens.xml.ref | ||
|---|---|---|
| 246 | 246 |
</specimenreplicate> |
| 247 | 247 |
</plantobservation> |
| 248 | 248 |
</aggregateoccurrence> |
| 249 |
<authortaxoncode> |
|
| 250 |
<_alt> |
|
| 251 |
<1><_if name="if indirect voucher"><else>$CatalogNumber</else></_if></1> |
|
| 252 |
<2>$CollectorNumber</2> |
|
| 253 |
</_alt> |
|
| 254 |
</authortaxoncode> |
|
| 249 |
<authortaxoncode>$CollectorNumber</authortaxoncode> |
|
| 255 | 250 |
<taxondetermination> |
| 256 | 251 |
<isoriginal>true</isoriginal> |
| 257 | 252 |
<role>identifier</role> |
| inputs/MO/maps/VegBIEN.specimens.csv | ||
|---|---|---|
| 29 | 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 |
| 30 | 30 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_alt/1, |
| 31 | 31 |
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/party/organizationname, |
| 32 |
CatalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 33 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 32 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 34 | 33 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/givenname/_namePart/first, |
| 35 | 34 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/middlename/_namePart/middle, |
| 36 | 35 |
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/party/surname/_namePart/last, |
| inputs/QMOR/test/import.specimens.xml.ref | ||
|---|---|---|
| 211 | 211 |
</specimenreplicate> |
| 212 | 212 |
</plantobservation> |
| 213 | 213 |
</aggregateoccurrence> |
| 214 |
<authortaxoncode><_if name="if indirect voucher"><else>$catalogNumber</else></_if></authortaxoncode> |
|
| 215 | 214 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 216 | 215 |
<taxondetermination> |
| 217 | 216 |
<isoriginal>true</isoriginal> |
| mappings/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 71 | 71 |
previousTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag, |
| 72 | 72 |
relativePlotX,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition, |
| 73 | 73 |
relativePlotY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition, |
| 74 |
voucherType,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left", |
|
| 75 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 76 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2, |
|
| 77 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/3, |
|
| 74 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1, |
|
| 75 |
scientificName,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2, |
|
| 78 | 76 |
growthForm,/location/locationevent/taxonoccurrence/growthform, |
| 79 | 77 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode, |
| 80 | 78 |
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", |
| mappings/for_review/VegCSV-VegBIEN.specimens.csv | ||
|---|---|---|
| 71 | 71 |
previousTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag:[../stemtag?[iscurrent=true]/iscurrent=false]/tag, |
| 72 | 72 |
relativePlotX,//stemobservation/xposition, |
| 73 | 73 |
relativePlotY,//stemobservation/yposition, |
| 74 |
voucherType,"//taxonoccurrence/authortaxoncode/_if[@name=""if indirect voucher""]/cond", |
|
| 75 |
catalogNumber,"//taxonoccurrence/authortaxoncode/_if[@name=""if indirect voucher""]/else", |
|
| 76 | 74 |
recordNumber,//taxonoccurrence/authortaxoncode, |
| 77 | 75 |
scientificName,//taxonoccurrence/authortaxoncode, |
| 78 | 76 |
growthForm,//taxonoccurrence/growthform, |
| mappings/DwC-VegBIEN.specimens.csv | ||
|---|---|---|
| 147 | 147 |
globalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 148 | 148 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 149 | 149 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 150 |
CatalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 151 |
catalogNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_if[@name=""if indirect voucher""]/else", |
|
| 152 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 153 |
collectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
|
| 154 |
RecordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
|
| 155 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/2, |
|
| 150 |
CollectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 151 |
collectorNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/1, |
|
| 152 |
RecordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
|
| 153 |
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2, |
|
| 156 | 154 |
EstablishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 157 | 155 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_map:[cultivated=t,wild=f,*=]/value", |
| 158 | 156 |
EstablishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
Also available in: Unified diff
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxonoccurrence: Removed catalogNumber mapping because the catalogNumber applies only to the specimen, not to the occurrence, especially in plots data