Revision 11224
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/VegBank/plantconcept_/map.csv | ||
|---|---|---|
| 1 |
VegBank,VegCore,Filter,Comments |
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| 2 |
plantconcept_id,plantconcept_id,, |
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| 3 |
plantname_id,plantname_id,, |
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| 4 |
plantconcept_reference_id,*plantconcept_--plantconcept_reference_id,, |
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| 5 |
plantconcept_plantname,scientificName__for_nearest_taxon_concept,, |
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| 6 |
plantcode,*plantconcept_--plantcode,, |
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| 7 |
plantdescription,*plantconcept_--plantdescription,, |
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| 8 |
d_obscount,*plantconcept_--d_obscount,, |
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| 9 |
d_currentaccepted,*plantconcept_--d_currentaccepted,, |
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| 10 |
plantconcept_accessioncode,*plantconcept_--plantconcept_accessioncode,, |
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| 11 |
Kingdom,kingdom,, |
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| 12 |
Subkingdom,*Subkingdom,, |
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| 13 |
Superdivision,*Superdivision,, |
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| 14 |
Division,*Division,, |
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| 15 |
Subdivision,*Subdivision,, |
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| 16 |
Class,class,, |
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| 17 |
Subclass,*Subclass,, |
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| 18 |
Order,order,, |
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| 19 |
Family,family,, |
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| 20 |
Genus,genus,,includes genus author |
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| 21 |
Species,speciesBinomial,,full taxonomic name at that rank |
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| 22 |
Subspecies,EQUIV#to:Species#Subspecies,,full taxonomic name at that rank |
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| 23 |
Variety,EQUIV#to:Species#Variety,,full taxonomic name at that rank |
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| 24 |
Forma,EQUIV#to:Species#Forma,,full taxonomic name at that rank |
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| inputs/VegBank/plantconcept_/VegBIEN.csv | ||
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| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
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| 0 | 2 | |
| inputs/VegBank/plantconcept_/test.xml.ref | ||
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| 1 |
Put template: |
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| 2 |
<VegBIEN> |
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| 3 |
<_setDefault id="-1"> |
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| 4 |
<source_id><source><shortname>VegBank.new</shortname></source></source_id> |
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| 5 |
<path> |
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| 6 |
<_simplifyPath> |
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| 7 |
<next>parent_id</next> |
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| 8 |
<path> |
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| 9 |
<location> |
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| 10 |
<locationevent> |
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| 11 |
<locationevent fkey="parent_id"> |
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| 12 |
<taxonoccurrence> |
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| 13 |
<taxondetermination> |
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| 14 |
<taxonverbatim_id> |
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| 15 |
<taxonverbatim> |
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| 16 |
<taxonlabel_id> |
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| 17 |
<taxonlabel> |
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| 18 |
<parent_id> |
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| 19 |
<taxonlabel> |
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| 20 |
<parent_id> |
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| 21 |
<taxonlabel> |
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| 22 |
<rank>cultivar</rank> |
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| 23 |
<parent_id> |
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| 24 |
<taxonlabel> |
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| 25 |
<rank>forma</rank> |
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| 26 |
<parent_id> |
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| 27 |
<taxonlabel> |
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| 28 |
<rank>variety</rank> |
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| 29 |
<parent_id> |
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| 30 |
<taxonlabel> |
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| 31 |
<rank>subspecies</rank> |
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| 32 |
<parent_id> |
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| 33 |
<taxonlabel> |
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| 34 |
<rank>species</rank> |
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| 35 |
<parent_id> |
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| 36 |
<taxonlabel> |
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| 37 |
<rank>genus</rank> |
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| 38 |
<taxonepithet>$genus</taxonepithet> |
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| 39 |
<parent_id> |
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| 40 |
<taxonlabel> |
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| 41 |
<rank>family</rank> |
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| 42 |
<taxonepithet>$family</taxonepithet> |
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| 43 |
<parent_id> |
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| 44 |
<taxonlabel> |
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| 45 |
<rank>order</rank> |
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| 46 |
<taxonepithet>$order</taxonepithet> |
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| 47 |
<parent_id> |
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| 48 |
<taxonlabel> |
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| 49 |
<rank>class</rank> |
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| 50 |
<taxonepithet>$class</taxonepithet> |
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| 51 |
<parent_id> |
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| 52 |
<taxonlabel> |
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| 53 |
<rank>phylum</rank> |
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| 54 |
<parent_id> |
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| 55 |
<taxonlabel> |
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| 56 |
<rank>kingdom</rank> |
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| 57 |
<taxonepithet>$kingdom</taxonepithet> |
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</taxonlabel> |
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| 59 |
</parent_id> |
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| 60 |
</taxonlabel> |
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| 61 |
</parent_id> |
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| 62 |
</taxonlabel> |
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| 63 |
</parent_id> |
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| 64 |
</taxonlabel> |
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| 65 |
</parent_id> |
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| 66 |
</taxonlabel> |
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| 67 |
</parent_id> |
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| 68 |
</taxonlabel> |
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| 69 |
</parent_id> |
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| 70 |
</taxonlabel> |
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| 71 |
</parent_id> |
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| 72 |
</taxonlabel> |
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| 73 |
</parent_id> |
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| 74 |
</taxonlabel> |
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| 75 |
</parent_id> |
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| 76 |
</taxonlabel> |
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| 77 |
</parent_id> |
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| 78 |
</taxonlabel> |
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| 79 |
</parent_id> |
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| 80 |
</taxonlabel> |
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| 81 |
</parent_id> |
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| 82 |
<taxonomicname> |
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| 83 |
<_merge_prefix> |
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<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
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<value><_filter_genus><value>$genus</value></_filter_genus></value> |
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| 86 |
</_merge_prefix> |
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| 87 |
</taxonomicname> |
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| 88 |
</taxonlabel> |
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| 89 |
</taxonlabel_id> |
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| 90 |
<family>$family</family> |
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| 91 |
<genus>$genus</genus> |
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| 92 |
</taxonverbatim> |
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| 93 |
</taxonverbatim_id> |
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| 94 |
</taxondetermination> |
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| 95 |
</taxonoccurrence> |
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| 96 |
</locationevent> |
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| 97 |
</locationevent> |
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| 98 |
</location> |
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| 99 |
</path> |
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| 100 |
</_simplifyPath> |
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| 101 |
</path> |
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| 102 |
</_setDefault> |
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| 103 |
</VegBIEN> |
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| 104 |
Inserted 7 new rows into database |
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| inputs/VegBank/plantconcept_/unmapped_terms.csv | ||
|---|---|---|
| 1 |
plantconcept_id |
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| 2 |
plantname_id |
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| 3 |
*plantconcept_--plantconcept_reference_id |
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| 4 |
scientificName__for_nearest_taxon_concept |
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| 5 |
*plantconcept_--plantcode |
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| 6 |
*plantconcept_--plantdescription |
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| 7 |
*plantconcept_--d_obscount |
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| 8 |
*plantconcept_--d_currentaccepted |
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| 9 |
*plantconcept_--plantconcept_accessioncode |
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| 10 |
*Subkingdom |
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| 11 |
*Superdivision |
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| 12 |
*Division |
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| 13 |
*Subdivision |
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| 14 |
*Subclass |
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| 15 |
speciesBinomial |
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| inputs/VegBank/taxonobservation_/map.csv | ||
|---|---|---|
| 42 | 42 |
int_currplantcommon,vernacularName,, |
| 43 | 43 |
int_currplantcode,*taxonobservation_--int_currplantcode,, |
| 44 | 44 |
taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,, |
| 45 |
plantconcept_reference_id,*taxonobservation_--plantconcept_reference_id,,
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| 46 |
plantconcept_plantname,scientificName__for_nearest_taxon_concept,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
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| 47 |
plantcode,*taxonobservation_--plantcode,,
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| 48 |
plantdescription,*taxonobservation_--plantdescription,,
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| 49 |
d_obscount,*taxonobservation_--d_obscount,,
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| 50 |
d_currentaccepted,*taxonobservation_--d_currentaccepted,,
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| 51 |
plantconcept_accessioncode,*taxonobservation_--plantconcept_accessioncode,,
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| 52 |
Kingdom,kingdom,,
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| 53 |
Subkingdom,*Subkingdom,, |
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| 54 |
Superdivision,*Superdivision,, |
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| 55 |
Division,*Division,, |
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| 56 |
Subdivision,*Subdivision,, |
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| 57 |
Class,class,,
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| 58 |
Subclass,*Subclass,, |
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| 59 |
Order,order,,
|
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| 60 |
Family,family,,
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| 61 |
Genus,genus,,includes genus author
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| 62 |
Species,EQUIV#to:plantname#Species,,*taxonobservation_--full* taxonomic name at that rank
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| 63 |
Subspecies,EQUIV#to:plantname#Subspecies,,*taxonobservation_--full* taxonomic name at that rank
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| 64 |
Variety,EQUIV#to:plantname#Variety,,*taxonobservation_--full* taxonomic name at that rank
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| 65 |
Forma,EQUIV#to:plantname#Forma,,*taxonobservation_--full* taxonomic name at that rank
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| 45 |
*plantconcept_--plantconcept_reference_id,*plantconcept_--plantconcept_reference_id,,
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| 46 |
scientificName__for_nearest_taxon_concept,scientificName__for_nearest_taxon_concept,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
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| 47 |
*plantconcept_--plantcode,*plantconcept_--plantcode,,
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| 48 |
*plantconcept_--plantdescription,*plantconcept_--plantdescription,,
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| 49 |
*plantconcept_--d_obscount,*plantconcept_--d_obscount,,
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| 50 |
*plantconcept_--d_currentaccepted,*plantconcept_--d_currentaccepted,,
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| 51 |
*plantconcept_--plantconcept_accessioncode,*plantconcept_--plantconcept_accessioncode,,
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| 52 |
kingdom,kingdom,,
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| 53 |
*Subkingdom,*Subkingdom,,
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| 54 |
*Superdivision,*Superdivision,,
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| 55 |
*Division,*Division,,
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| 56 |
*Subdivision,*Subdivision,,
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| 57 |
class,class,,
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| 58 |
*Subclass,*Subclass,,
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| 59 |
order,order,,
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| 60 |
family,family,,
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| 61 |
genus,genus,,includes genus author
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| 62 |
speciesBinomial,EQUIV#to:plantname#Species,,full taxonomic name at that rank
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| 63 |
EQUIV#to:Species#Subspecies,EQUIV#to:plantname#Subspecies,,full taxonomic name at that rank
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| 64 |
EQUIV#to:Species#Variety,EQUIV#to:plantname#Variety,,full taxonomic name at that rank
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| 65 |
EQUIV#to:Species#Forma,EQUIV#to:plantname#Forma,,full taxonomic name at that rank
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| 66 | 66 |
plantname,DUPLICATE#of:plantconcept_plantname#plantname,,exact duplicate |
| 67 | 67 |
plantname_reference_id,*taxonobservation_--plantname_reference_id,, |
| 68 | 68 |
dateentered,*taxonobservation_--dateentered,, |
| inputs/VegBank/taxonobservation_/new_terms.csv | ||
|---|---|---|
| 31 | 31 |
int_currplantcommon,vernacularName,, |
| 32 | 32 |
int_currplantcode,*taxonobservation_--int_currplantcode,, |
| 33 | 33 |
taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,, |
| 34 |
plantconcept_reference_id,*taxonobservation_--plantconcept_reference_id,, |
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| 35 |
plantconcept_plantname,scientificName__for_nearest_taxon_concept,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is." |
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| 36 |
plantcode,*taxonobservation_--plantcode,, |
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| 37 |
plantdescription,*taxonobservation_--plantdescription,, |
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| 38 |
d_obscount,*taxonobservation_--d_obscount,, |
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| 39 |
d_currentaccepted,*taxonobservation_--d_currentaccepted,, |
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| 40 |
plantconcept_accessioncode,*taxonobservation_--plantconcept_accessioncode,, |
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| 41 | 34 |
plantname,DUPLICATE#of:plantconcept_plantname#plantname,,exact duplicate |
| 42 | 35 |
plantname_reference_id,*taxonobservation_--plantname_reference_id,, |
| 43 | 36 |
dateentered,*taxonobservation_--dateentered,, |
| inputs/VegBank/taxonobservation_/unmapped_terms.csv | ||
|---|---|---|
| 28 | 28 |
vernacularName |
| 29 | 29 |
*taxonobservation_--int_currplantcode |
| 30 | 30 |
*taxonobservation_--taxonobservation_accessioncode |
| 31 |
*taxonobservation_--plantconcept_reference_id
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| 31 |
*plantconcept_--plantconcept_reference_id
|
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| 32 | 32 |
scientificName__for_nearest_taxon_concept |
| 33 |
*taxonobservation_--plantcode
|
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| 34 |
*taxonobservation_--plantdescription
|
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| 35 |
*taxonobservation_--d_obscount
|
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| 36 |
*taxonobservation_--d_currentaccepted
|
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| 37 |
*taxonobservation_--plantconcept_accessioncode
|
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| 33 |
*plantconcept_--plantcode
|
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| 34 |
*plantconcept_--plantdescription
|
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| 35 |
*plantconcept_--d_obscount
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| 36 |
*plantconcept_--d_currentaccepted
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| 37 |
*plantconcept_--plantconcept_accessioncode
|
|
| 38 | 38 |
*Subkingdom |
| 39 | 39 |
*Superdivision |
| 40 | 40 |
*Division |
Also available in: Unified diff
inputs/VegBank/plantconcept_/: mapped columns, since this is now included in import_order.txt and therefore gets processed by the column-renaming runscripts. note that this means that in taxonobservation_/map.csv, the plantconcept_ input column names need to be changed to what they are mapped to.