Revision 5338
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/.TNRS/tnrs/VegBIEN.csv | ||
|---|---|---|
| 37 | 37 |
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/family,Contains family in original string (uncommon) |
| 38 | 38 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/genus, |
| 39 | 39 |
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname, |
| 40 |
Specific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=species]/taxonname", |
|
| 41 |
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=genus]/taxonname", |
|
| 42 |
Family_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=family]/taxonname",Contains family in original string (uncommon) |
|
| 43 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/taxonname, |
|
| 44 |
Infraspecific_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/verbatimrank, |
|
| 45 | 40 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/species, |
| 46 | 41 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/cond/_exists", |
| 47 | 42 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/then", |
| ... | ... | |
| 61 | 56 |
Genus_score,,** No non-empty join mapping for OMIT ** |
| 62 | 57 |
Infraspecific_epithet_2_matched,,** No non-empty join mapping for UNUSED ** |
| 63 | 58 |
Infraspecific_epithet_2_score,,** No non-empty join mapping for UNUSED ** |
| 59 |
Infraspecific_epithet_matched,,** No join mapping for verbatimInfraspecificEpithet ** |
|
| 64 | 60 |
Infraspecific_epithet_score,,** No non-empty join mapping for OMIT ** |
| 65 | 61 |
Infraspecific_rank_2,,** No non-empty join mapping for UNUSED ** |
| 66 | 62 |
Name_matched_url,,** No non-empty join mapping for OMIT ** |
| inputs/.TNRS/tnrs/test.xml.ref | ||
|---|---|---|
| 156 | 156 |
<family>$Family_matched</family> |
| 157 | 157 |
<genus>$Genus_matched</genus> |
| 158 | 158 |
<identifyingtaxonomicname>$Name_submitted</identifyingtaxonomicname> |
| 159 |
<parent_id> |
|
| 160 |
<taxonconcept> |
|
| 161 |
<parent_id> |
|
| 162 |
<taxonconcept> |
|
| 163 |
<rank>cultivar</rank> |
|
| 164 |
<parent_id> |
|
| 165 |
<taxonconcept> |
|
| 166 |
<rank>forma</rank> |
|
| 167 |
<parent_id> |
|
| 168 |
<taxonconcept> |
|
| 169 |
<rank>variety</rank> |
|
| 170 |
<parent_id> |
|
| 171 |
<taxonconcept> |
|
| 172 |
<rank>subspecies</rank> |
|
| 173 |
<parent_id> |
|
| 174 |
<taxonconcept> |
|
| 175 |
<rank>species</rank> |
|
| 176 |
<taxonname>$Specific_epithet_matched</taxonname> |
|
| 177 |
<parent_id> |
|
| 178 |
<taxonconcept> |
|
| 179 |
<rank>genus</rank> |
|
| 180 |
<taxonname>$Genus_matched</taxonname> |
|
| 181 |
<parent_id> |
|
| 182 |
<taxonconcept> |
|
| 183 |
<rank>family</rank> |
|
| 184 |
<taxonname>$Family_matched</taxonname> |
|
| 185 |
</taxonconcept> |
|
| 186 |
</parent_id> |
|
| 187 |
</taxonconcept> |
|
| 188 |
</parent_id> |
|
| 189 |
</taxonconcept> |
|
| 190 |
</parent_id> |
|
| 191 |
</taxonconcept> |
|
| 192 |
</parent_id> |
|
| 193 |
</taxonconcept> |
|
| 194 |
</parent_id> |
|
| 195 |
</taxonconcept> |
|
| 196 |
</parent_id> |
|
| 197 |
</taxonconcept> |
|
| 198 |
</parent_id> |
|
| 199 |
<taxonname>$Infraspecific_epithet_matched</taxonname> |
|
| 200 |
<verbatimrank>$Infraspecific_rank</verbatimrank> |
|
| 201 |
</taxonconcept> |
|
| 202 |
</parent_id> |
|
| 203 | 159 |
<species>$Specific_epithet_matched</species> |
| 204 | 160 |
<taxonname>$Unmatched_terms</taxonname> |
| 205 | 161 |
<taxonomicname>$Name_matched</taxonomicname> |
| ... | ... | |
| 217 | 173 |
</path> |
| 218 | 174 |
</_simplifyPath> |
| 219 | 175 |
</VegBIEN> |
| 220 |
Inserted 13 new rows into database |
|
| 176 |
Inserted 10 new rows into database |
|
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 205 | 205 |
verbatimFamily,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/family, |
| 206 | 206 |
verbatimGenus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/genus, |
| 207 | 207 |
verbatimScientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname, |
| 208 |
verbatimCultivar,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=cultivar]/taxonname", |
|
| 209 |
verbatimForma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=forma]/taxonname", |
|
| 210 |
verbatimVariety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=variety]/taxonname", |
|
| 211 |
verbatimSubspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=subspecies]/taxonname", |
|
| 212 |
verbatimSpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=species]/taxonname", |
|
| 213 |
verbatimGenus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=genus]/taxonname", |
|
| 214 |
verbatimFamily,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=family]/taxonname", |
|
| 215 |
verbatimOrder,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=order]/taxonname", |
|
| 216 |
verbatimClass,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=class]/taxonname", |
|
| 217 |
verbatimPhylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=phylum]/taxonname", |
|
| 218 |
verbatimKingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonconcept[rank=_val]/parent_id""]/taxonconcept[rank=kingdom]/taxonname", |
|
| 219 |
verbatimInfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/taxonname, |
|
| 220 |
verbatimTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/parent_id/taxonconcept/verbatimrank, |
|
| 221 | 208 |
verbatimSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/species, |
| 222 | 209 |
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/cond/_exists", |
| 223 | 210 |
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/taxonname/_if[@name=""if has verbatim name""]/then", |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 205 | 205 |
verbatimFamily,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/family, |
| 206 | 206 |
verbatimGenus,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/genus, |
| 207 | 207 |
verbatimScientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/identifyingtaxonomicname, |
| 208 |
verbatimCultivar,//taxonconcept/parent_id[rank=cultivar]/taxonname, |
|
| 209 |
verbatimForma,//taxonconcept/parent_id[rank=forma]/taxonname, |
|
| 210 |
verbatimVariety,//taxonconcept/parent_id[rank=variety]/taxonname, |
|
| 211 |
verbatimSubspecies,//taxonconcept/parent_id[rank=subspecies]/taxonname, |
|
| 212 |
verbatimSpecificEpithet,//taxonconcept/parent_id[rank=species]/taxonname, |
|
| 213 |
verbatimGenus,//taxonconcept/parent_id[rank=genus]/taxonname, |
|
| 214 |
verbatimFamily,//taxonconcept/parent_id[rank=family]/taxonname, |
|
| 215 |
verbatimOrder,//taxonconcept/parent_id[rank=order]/taxonname, |
|
| 216 |
verbatimClass,//taxonconcept/parent_id[rank=class]/taxonname, |
|
| 217 |
verbatimPhylum,//taxonconcept/parent_id[rank=phylum]/taxonname, |
|
| 218 |
verbatimKingdom,//taxonconcept/parent_id[rank=kingdom]/taxonname, |
|
| 219 |
verbatimInfraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/parent_id/taxonconcept/taxonname, |
|
| 220 |
verbatimTaxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/parent_id/taxonconcept/verbatimrank, |
|
| 221 | 208 |
verbatimSpecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/species, |
| 222 | 209 |
verbatimScientificNameWithAuthorship,"//taxonconcept/taxonname/_if[@name=""if has verbatim name""]/cond/_exists", |
| 223 | 210 |
morphospecies,"//taxonconcept/taxonname/_if[@name=""if has verbatim name""]/then", |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: verbatim* taxonconcept: Don't create hierarchy of parent taxonconcepts, because the parsed names (rather than the names for the matched taxonconcept) are from the input taxonomic name, rather than from the official tree of life used by TNRS. Otherwise, if a taxonomic name provides e.g. no family (common), a separate genus taxonconcept would have been created with no parent_id, which would not compare equal to the matched taxonconcept's genus with a parent_id. Continue to store the parsed family, genus, species in the family, genus, species cached fields, because the parsed family is often different from the matched taxonconcept's family when e.g. no family is provided in the taxonomic name.