Revision 5014
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 46 | 46 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 47 | 47 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 48 | 48 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 49 |
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first/_alt/1,
|
|
| 50 |
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first/_alt/2,
|
|
| 51 |
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 49 |
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1/_alt/1,
|
|
| 50 |
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1/_alt/2,
|
|
| 51 |
infraname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 52 | 52 |
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 53 | 53 |
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1, |
| 54 | 54 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1, |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 78 | 78 |
<genus>$genus</genus> |
| 79 | 79 |
<species>$species</species> |
| 80 | 80 |
<subspecies> |
| 81 |
<_name>
|
|
| 82 |
<first>
|
|
| 81 |
<_join_words>
|
|
| 82 |
<1>
|
|
| 83 | 83 |
<_alt> |
| 84 | 84 |
<1>$usdaRank</1> |
| 85 | 85 |
<2>$infrarank</2> |
| 86 | 86 |
</_alt> |
| 87 |
</first>
|
|
| 88 |
<last>$infraname</last>
|
|
| 89 |
</_name>
|
|
| 87 |
</1>
|
|
| 88 |
<2>$infraname</2>
|
|
| 89 |
</_join_words>
|
|
| 90 | 90 |
</subspecies> |
| 91 | 91 |
<taxonomicname>$SciName</taxonomicname> |
| 92 | 92 |
<taxonomicnamewithauthor> |
| inputs/ACAD/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
ACAD,VegCore,Filter,Comments |
| 2 |
id,*occurrenceID,, |
|
| 3 |
basisOfRecord,*basisOfRecord,, |
|
| 4 |
identifiedBy,*identifiedBy,, |
|
| 5 |
collectionID,*collectionID,, |
|
| 6 |
class,*class,, |
|
| 7 |
geodeticDatum,*geodeticDatum,, |
|
| 8 |
reproductiveCondition,*reproductiveCondition,, |
|
| 9 |
decimalLongitude,*decimalLongitude,, |
|
| 10 |
institutionCode,*institutionCode,, |
|
| 11 |
continent,*continent,, |
|
| 12 |
recordedBy,*recordedBy,, |
|
| 13 |
county,*county,, |
|
| 14 |
order,*order,, |
|
| 15 |
georeferenceSources,*georeferenceSources,, |
|
| 16 |
language,*dcterms:language,, |
|
| 17 |
georeferenceVerificationStatus,*georeferenceVerificationStatus,, |
|
| 18 |
verbatimElevation,*verbatimElevation,, |
|
| 19 |
locationRemarks,*locationRemarks,, |
|
| 20 |
dateIdentified,*dateIdentified,, |
|
| 21 |
verbatimDepth,*verbatimDepth,, |
|
| 22 |
municipality,*municipality,, |
|
| 23 |
infraspecificEpithet,*infraspecificEpithet,, |
|
| 24 |
modified,*dcterms:modified,, |
|
| 25 |
type,*dcterms:type,, |
|
| 26 |
specificEpithet,*specificEpithet,, |
|
| 27 |
identificationRemarks,*identificationRemarks,, |
|
| 28 |
rightsHolder,*dcterms:rightsHolder,, |
|
| 29 |
recordNumber,*recordNumber,, |
|
| 30 |
eventDate,*eventDate,, |
|
| 31 |
rights,*dcterms:rights,, |
|
| 32 |
occurrenceRemarks,*occurrenceRemarks,, |
|
| 33 |
habitat,*habitat,, |
|
| 34 |
family,*family,, |
|
| 35 |
stateProvince,*stateProvince,, |
|
| 36 |
scientificNameAuthorship,*scientificNameAuthorship,, |
|
| 37 |
scientificName,*scientificName,, |
|
| 38 |
taxonRank,*taxonRank,, |
|
| 39 |
phylum,*phylum,, |
|
| 40 |
locality,*locality,, |
|
| 41 |
kingdom,*kingdom,, |
|
| 42 |
decimalLatitude,*decimalLatitude,, |
|
| 43 |
genus,*genus,, |
|
| 44 |
ownerInstitutionCode,*ownerInstitutionCode,, |
|
| 45 |
collectionCode,*collectionCode,, |
|
| 46 |
bibliographicCitation,*dcterms:bibliographicCitation,, |
|
| 47 |
catalogNumber,*catalogNumber,, |
|
| 48 |
country,*country,, |
|
| 49 |
dynamicProperties,*dynamicProperties,, |
|
| 2 |
id,occurrenceID,, |
|
| 3 |
basisOfRecord,basisOfRecord,, |
|
| 4 |
identifiedBy,identifiedBy,, |
|
| 5 |
collectionID,collectionID,, |
|
| 6 |
class,class,, |
|
| 7 |
geodeticDatum,geodeticDatum,, |
|
| 8 |
reproductiveCondition,reproductiveCondition,, |
|
| 9 |
decimalLongitude,decimalLongitude,, |
|
| 10 |
institutionCode,institutionCode,, |
|
| 11 |
continent,continent,, |
|
| 12 |
recordedBy,recordedBy,, |
|
| 13 |
county,county,, |
|
| 14 |
order,order,, |
|
| 15 |
georeferenceSources,georeferenceSources,, |
|
| 16 |
language,dcterms:language,, |
|
| 17 |
georeferenceVerificationStatus,georeferenceVerificationStatus,, |
|
| 18 |
verbatimElevation,verbatimElevation,, |
|
| 19 |
locationRemarks,locationRemarks,, |
|
| 20 |
dateIdentified,dateIdentified,, |
|
| 21 |
verbatimDepth,verbatimDepth,, |
|
| 22 |
municipality,municipality,, |
|
| 23 |
infraspecificEpithet,infraspecificEpithet,, |
|
| 24 |
modified,dcterms:modified,, |
|
| 25 |
type,dcterms:type,, |
|
| 26 |
specificEpithet,specificEpithet,, |
|
| 27 |
identificationRemarks,identificationRemarks,, |
|
| 28 |
rightsHolder,dcterms:rightsHolder,, |
|
| 29 |
recordNumber,recordNumber,, |
|
| 30 |
eventDate,eventDate,, |
|
| 31 |
rights,dcterms:rights,, |
|
| 32 |
occurrenceRemarks,occurrenceRemarks,, |
|
| 33 |
habitat,habitat,, |
|
| 34 |
family,family,, |
|
| 35 |
stateProvince,stateProvince,, |
|
| 36 |
scientificNameAuthorship,scientificNameAuthorship,, |
|
| 37 |
scientificName,scientificName,, |
|
| 38 |
taxonRank,taxonRank,, |
|
| 39 |
phylum,phylum,, |
|
| 40 |
locality,locality,, |
|
| 41 |
kingdom,kingdom,, |
|
| 42 |
decimalLatitude,decimalLatitude,, |
|
| 43 |
genus,genus,, |
|
| 44 |
ownerInstitutionCode,ownerInstitutionCode,, |
|
| 45 |
collectionCode,collectionCode,, |
|
| 46 |
bibliographicCitation,dcterms:bibliographicCitation,, |
|
| 47 |
catalogNumber,catalogNumber,, |
|
| 48 |
country,country,, |
|
| 49 |
dynamicProperties,dynamicProperties,, |
|
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 30 | 30 |
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/order, |
| 31 | 31 |
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/phylum, |
| 32 | 32 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 33 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
|
|
| 34 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 33 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
|
|
| 34 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 35 | 35 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 36 | 36 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1, |
| 37 | 37 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1, |
| ... | ... | |
| 50 | 50 |
county,/location/locationplace/*_id/placepath/county, |
| 51 | 51 |
stateProvince,/location/locationplace/*_id/placepath/stateprovince, |
| 52 | 52 |
verbatimElevation,/location/verbatimelevation, |
| 53 |
basisOfRecord,,** No join mapping for *basisOfRecord ** |
|
| 54 |
bibliographicCitation,,** No join mapping for *dcterms:bibliographicCitation ** |
|
| 55 |
dynamicProperties,,** No join mapping for *dynamicProperties ** |
|
| 56 |
geodeticDatum,,** No join mapping for *geodeticDatum ** |
|
| 57 |
georeferenceSources,,** No join mapping for *georeferenceSources ** |
|
| 58 |
georeferenceVerificationStatus,,** No join mapping for *georeferenceVerificationStatus ** |
|
| 59 |
identificationRemarks,,** No join mapping for *identificationRemarks ** |
|
| 60 |
language,,** No join mapping for *dcterms:language ** |
|
| 61 |
locationRemarks,,** No join mapping for *locationRemarks ** |
|
| 62 |
modified,,** No join mapping for *dcterms:modified ** |
|
| 63 |
municipality,,** No join mapping for *municipality ** |
|
| 64 |
occurrenceRemarks,,** No join mapping for *occurrenceRemarks ** |
|
| 65 |
ownerInstitutionCode,,** No join mapping for *ownerInstitutionCode ** |
|
| 66 |
reproductiveCondition,,** No join mapping for *reproductiveCondition ** |
|
| 67 |
rights,,** No join mapping for *dcterms:rights ** |
|
| 68 |
rightsHolder,,** No join mapping for *dcterms:rightsHolder ** |
|
| 69 |
type,,** No join mapping for *dcterms:type ** |
|
| 70 |
verbatimDepth,,** No join mapping for *verbatimDepth ** |
|
| 53 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
|
| 54 |
bibliographicCitation,,** No join mapping for dcterms:bibliographicCitation ** |
|
| 55 |
dynamicProperties,,** No join mapping for dynamicProperties ** |
|
| 56 |
geodeticDatum,,** No join mapping for geodeticDatum ** |
|
| 57 |
georeferenceSources,,** No join mapping for georeferenceSources ** |
|
| 58 |
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus ** |
|
| 59 |
identificationRemarks,,** No join mapping for identificationRemarks ** |
|
| 60 |
language,,** No join mapping for dcterms:language ** |
|
| 61 |
locationRemarks,,** No join mapping for locationRemarks ** |
|
| 62 |
modified,,** No join mapping for dcterms:modified ** |
|
| 63 |
municipality,,** No join mapping for municipality ** |
|
| 64 |
occurrenceRemarks,,** No join mapping for occurrenceRemarks ** |
|
| 65 |
ownerInstitutionCode,,** No join mapping for ownerInstitutionCode ** |
|
| 66 |
reproductiveCondition,,** No join mapping for reproductiveCondition ** |
|
| 67 |
rights,,** No join mapping for dcterms:rights ** |
|
| 68 |
rightsHolder,,** No join mapping for dcterms:rightsHolder ** |
|
| 69 |
type,,** No join mapping for dcterms:type ** |
|
| 70 |
verbatimDepth,,** No join mapping for verbatimDepth ** |
|
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 85 | 85 |
<phylum>$phylum</phylum> |
| 86 | 86 |
<species>$specificEpithet</species> |
| 87 | 87 |
<subspecies> |
| 88 |
<_name>
|
|
| 89 |
<first>$taxonRank</first>
|
|
| 90 |
<last>$infraspecificEpithet</last>
|
|
| 91 |
</_name>
|
|
| 88 |
<_join_words>
|
|
| 89 |
<1>$taxonRank</1>
|
|
| 90 |
<2>$infraspecificEpithet</2>
|
|
| 91 |
</_join_words>
|
|
| 92 | 92 |
</subspecies> |
| 93 | 93 |
<taxonomicname>$scientificName</taxonomicname> |
| 94 | 94 |
<taxonomicnamewithauthor> |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 68 | 68 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 69 | 69 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 70 | 70 |
specific_epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 71 |
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
|
|
| 72 |
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 71 |
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
|
|
| 72 |
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 73 | 73 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1, |
| 74 | 74 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2, |
| 75 | 75 |
specific_epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3, |
| ... | ... | |
| 79 | 79 |
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
| 80 | 80 |
orig_family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,Brad: OMIT |
| 81 | 81 |
orig_species,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,Brad: OMIT |
| 82 |
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/first,Brad: See comment above
|
|
| 83 |
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/last,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
|
|
| 82 |
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,Brad: See comment above
|
|
| 83 |
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/2,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
|
|
| 84 | 84 |
det_type,"/location/locationevent/taxonoccurrence/voucher/*_id/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." |
| 85 | 85 |
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string |
| 86 | 86 |
voucher_string,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| inputs/SALVIAS-CSV/Organism/test.xml.ref | ||
|---|---|---|
| 152 | 152 |
<genus>$genus</genus> |
| 153 | 153 |
<species>$specific_epithet</species> |
| 154 | 154 |
<subspecies> |
| 155 |
<_name>
|
|
| 156 |
<first>$infra_rank_1</first>
|
|
| 157 |
<last>$infra_ep_1</last>
|
|
| 158 |
</_name>
|
|
| 155 |
<_join_words>
|
|
| 156 |
<1>$infra_rank_1</1>
|
|
| 157 |
<2>$infra_ep_1</2>
|
|
| 158 |
</_join_words>
|
|
| 159 | 159 |
</subspecies> |
| 160 | 160 |
<taxonomicnamewithauthor> |
| 161 | 161 |
<_join_words> |
| ... | ... | |
| 189 | 189 |
</taxonpath_id> |
| 190 | 190 |
</taxondetermination> |
| 191 | 191 |
<verbatimcollectorname> |
| 192 |
<_name>
|
|
| 193 |
<first>$coll_firstname</first>
|
|
| 194 |
<last>$coll_lastname</last>
|
|
| 195 |
</_name>
|
|
| 192 |
<_join_words>
|
|
| 193 |
<1>$coll_firstname</1>
|
|
| 194 |
<2>$coll_lastname</2>
|
|
| 195 |
</_join_words>
|
|
| 196 | 196 |
</verbatimcollectorname> |
| 197 | 197 |
<voucher> |
| 198 | 198 |
<specimenreplicate_id> |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 61 | 61 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 62 | 62 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 63 | 63 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 64 |
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
|
|
| 65 |
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 64 |
infra_rank_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
|
|
| 65 |
infra_ep_1,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 66 | 66 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1, |
| 67 | 67 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/2, |
| 68 | 68 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/3, |
| ... | ... | |
| 73 | 73 |
OrigFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/family,Brad: OMIT |
| 74 | 74 |
OrigGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/genus, |
| 75 | 75 |
OrigSpecies,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/species,Brad: OMIT |
| 76 |
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/first,Brad: See comment above
|
|
| 77 |
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/last,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
|
|
| 76 |
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,Brad: See comment above
|
|
| 77 |
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/2,"Brad: This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
|
|
| 78 | 78 |
DetType,"/location/locationevent/taxonoccurrence/voucher/*_id/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." |
| 79 | 79 |
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Map instead as for voucher_string |
| 80 | 80 |
SourceVoucher,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| inputs/SALVIAS/plotObservations/test.xml.ref | ||
|---|---|---|
| 123 | 123 |
<genus>$Genus</genus> |
| 124 | 124 |
<species>$Species</species> |
| 125 | 125 |
<subspecies> |
| 126 |
<_name>
|
|
| 127 |
<first>$infra_rank_1</first>
|
|
| 128 |
<last>$infra_ep_1</last>
|
|
| 129 |
</_name>
|
|
| 126 |
<_join_words>
|
|
| 127 |
<1>$infra_rank_1</1>
|
|
| 128 |
<2>$infra_ep_1</2>
|
|
| 129 |
</_join_words>
|
|
| 130 | 130 |
</subspecies> |
| 131 | 131 |
<taxonomicnamewithauthor> |
| 132 | 132 |
<_join_words> |
| ... | ... | |
| 161 | 161 |
</taxonpath_id> |
| 162 | 162 |
</taxondetermination> |
| 163 | 163 |
<verbatimcollectorname> |
| 164 |
<_name>
|
|
| 165 |
<first>$coll_firstname</first>
|
|
| 166 |
<last>$coll_lastname</last>
|
|
| 167 |
</_name>
|
|
| 164 |
<_join_words>
|
|
| 165 |
<1>$coll_firstname</1>
|
|
| 166 |
<2>$coll_lastname</2>
|
|
| 167 |
</_join_words>
|
|
| 168 | 168 |
</verbatimcollectorname> |
| 169 | 169 |
<voucher> |
| 170 | 170 |
<specimenreplicate_id> |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 20 | 20 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family, |
| 21 | 21 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus, |
| 22 | 22 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 23 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 23 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 24 | 24 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 25 | 25 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1, |
| 26 | 26 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1, |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 127 | 127 |
dwc_dwcore_SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 128 | 128 |
dwc_terms_specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 129 | 129 |
conceptual_darwin_2003_1_0_Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1, |
| 130 |
dwc_dwcore_InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 131 |
dwc_terms_infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 130 |
dwc_dwcore_InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 131 |
dwc_terms_infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 132 | 132 |
conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 133 | 133 |
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 134 | 134 |
dwc_terms_scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| inputs/QMOR/Specimen/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/order, |
| 38 | 38 |
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/phylum, |
| 39 | 39 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 40 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
|
|
| 41 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 40 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
|
|
| 41 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 42 | 42 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 43 | 43 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1, |
| 44 | 44 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/2/_join_words/1, |
| inputs/QMOR/Specimen/test.xml.ref | ||
|---|---|---|
| 109 | 109 |
<phylum>$phylum</phylum> |
| 110 | 110 |
<species>$specificEpithet</species> |
| 111 | 111 |
<subspecies> |
| 112 |
<_name>
|
|
| 113 |
<first>$taxonRank</first>
|
|
| 114 |
<last>$infraspecificEpithet</last>
|
|
| 115 |
</_name>
|
|
| 112 |
<_join_words>
|
|
| 113 |
<1>$taxonRank</1>
|
|
| 114 |
<2>$infraspecificEpithet</2>
|
|
| 115 |
</_join_words>
|
|
| 116 | 116 |
</subspecies> |
| 117 | 117 |
<taxonomicname>$scientificName</taxonomicname> |
| 118 | 118 |
<taxonomicnamewithauthor> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 138 | 138 |
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/phylum, |
| 139 | 139 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species, |
| 140 | 140 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/1, |
| 141 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/first,
|
|
| 142 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_name/last,
|
|
| 141 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/1,
|
|
| 142 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/subspecies/_alt/2/_join_words/2,
|
|
| 143 | 143 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicname, |
| 144 | 144 |
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/1, |
| 145 | 145 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/taxonomicnamewithauthor/_first/2/_join_words/1/_first/1, |
| ... | ... | |
| 172 | 172 |
verbatimScientificName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonpath/taxonomicname, |
| 173 | 173 |
verbatimIdentificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit, |
| 174 | 174 |
recordedBy,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 175 |
recordedBy.givenName,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/first,
|
|
| 176 |
recordedBy.surName,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/last,
|
|
| 175 |
recordedBy.givenName,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/1,
|
|
| 176 |
recordedBy.surName,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join_words/2,
|
|
| 177 | 177 |
voucherType,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left", |
| 178 | 178 |
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 179 | 179 |
temperature,/location/locationevent/temperature_c, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Use new, more general _join_words() instead of _name()