Revision 5258
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/.TNRS/tnrs/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
|
| 18 | 18 |
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2",
|
| 19 | 19 |
Name_matched_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/2",Contains author based on matched name
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| 20 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/taxonconcept:[@fkey=canon_taxonconcept_id],else/.}/morphospecies",
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| 21 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/taxonconcept:[@fkey=canon_taxonconcept_id]}/identifyingtaxonomicname",
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| 22 | 20 |
Accepted_name_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/author, |
| 23 | 21 |
Accepted_name_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/family, |
| 24 | 22 |
Accepted_name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/1, |
| ... | ... | |
| 31 | 29 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/author,Contains author based on matched name |
| 32 | 30 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/family,Contains family based on matched name |
| 33 | 31 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus, |
| 32 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 33 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/else", |
|
| 34 | 34 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species, |
| 35 | 35 |
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
| 36 | 36 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 37 | 37 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2, |
| 38 |
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname, |
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| 39 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
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| 40 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/then", |
|
| 38 | 41 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname, |
| 39 | 42 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/verbatimrank, |
| 40 | 43 |
Accepted_name_lsid,,** No non-empty join mapping for OMIT ** |
| inputs/.TNRS/tnrs/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<taxondetermination> |
| 10 | 10 |
<taxonconcept_id> |
| 11 | 11 |
<taxonconcept> |
| 12 |
<identifyingtaxonomicname> |
|
| 13 |
<_join_words> |
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| 14 |
<1> |
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| 15 |
<_alt> |
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| 16 |
<1>$Name_matched</1> |
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| 17 |
<2> |
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| 18 |
<_join_words> |
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| 19 |
<1>$Name_matched_accepted_family</1> |
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| 20 |
<2>$Genus_matched</2> |
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| 21 |
<3>$Specific_epithet_matched</3> |
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| 22 |
<5> |
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| 23 |
<_join_words> |
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| 24 |
<1> |
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| 25 |
<_if name="if has infraspecificEpithet"> |
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| 26 |
<cond>$Infraspecific_epithet_matched</cond> |
|
| 27 |
<then>$Name_matched_rank</then> |
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| 28 |
</_if> |
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| 29 |
</1> |
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| 30 |
<2>$Infraspecific_epithet_matched</2> |
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| 31 |
</_join_words> |
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| 32 |
</5> |
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| 33 |
</_join_words> |
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| 34 |
</2> |
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| 35 |
</_alt> |
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| 36 |
</1> |
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| 37 |
<2>$Name_matched_author</2> |
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| 38 |
</_join_words> |
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| 39 |
</identifyingtaxonomicname> |
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| 40 | 12 |
<taxon_id> |
| 41 | 13 |
<taxon> |
| 42 | 14 |
<rank>cultivar</rank> |
| ... | ... | |
| 88 | 60 |
</parent_id> |
| 89 | 61 |
</taxon> |
| 90 | 62 |
</taxon_id> |
| 91 |
<taxonconcept fkey="canon_taxonconcept_id"> |
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| 92 |
<morphospecies>$Unmatched_terms</morphospecies> |
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| 93 |
<identifyingtaxonomicname>$Name_submitted</identifyingtaxonomicname> |
|
| 94 |
</taxonconcept> |
|
| 63 |
<identifyingtaxonomicname> |
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| 64 |
<_join_words> |
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| 65 |
<1> |
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| 66 |
<_alt> |
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| 67 |
<1>$Name_matched</1> |
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| 68 |
<2> |
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| 69 |
<_join_words> |
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| 70 |
<1>$Name_matched_accepted_family</1> |
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| 71 |
<2>$Genus_matched</2> |
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| 72 |
<3>$Specific_epithet_matched</3> |
|
| 73 |
<5> |
|
| 74 |
<_join_words> |
|
| 75 |
<1> |
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| 76 |
<_if name="if has infraspecificEpithet"> |
|
| 77 |
<cond>$Infraspecific_epithet_matched</cond> |
|
| 78 |
<then>$Name_matched_rank</then> |
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| 79 |
</_if> |
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| 80 |
</1> |
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| 81 |
<2>$Infraspecific_epithet_matched</2> |
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| 82 |
</_join_words> |
|
| 83 |
</5> |
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| 84 |
</_join_words> |
|
| 85 |
</2> |
|
| 86 |
</_alt> |
|
| 87 |
</1> |
|
| 88 |
<2>$Name_matched_author</2> |
|
| 89 |
</_join_words> |
|
| 90 |
</identifyingtaxonomicname> |
|
| 95 | 91 |
<_set_canon_taxonconcept> |
| 96 | 92 |
<canon_taxonconcept_id> |
| 97 | 93 |
<taxonconcept> |
| ... | ... | |
| 128 | 124 |
<2>$Infraspecific_epithet_matched</2> |
| 129 | 125 |
</_join_words> |
| 130 | 126 |
</subspecies> |
| 127 |
<taxonconcept fkey="canon_taxonconcept_id"> |
|
| 128 |
<identifyingtaxonomicname>$Name_submitted</identifyingtaxonomicname> |
|
| 129 |
<morphospecies>$Unmatched_terms</morphospecies> |
|
| 130 |
</taxonconcept> |
|
| 131 | 131 |
<taxonomicname>$Name_matched</taxonomicname> |
| 132 | 132 |
<verbatimrank>$Name_matched_rank</verbatimrank> |
| 133 | 133 |
</taxonconcept> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 160 | 160 |
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/7/_join_words:[1=""fm. ""]/2",
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| 161 | 161 |
cultivar,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""cult. ""]/2",
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| 162 | 162 |
scientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept:[creator_id/party:[creator_id=0]/organizationname=TNRS]}/identifyingtaxonomicname/_alt/2/_join_words/2",
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| 163 |
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/taxonconcept:[@fkey=canon_taxonconcept_id],else/.}/morphospecies",
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| 164 |
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/taxonconcept:[@fkey=canon_taxonconcept_id]}/identifyingtaxonomicname",
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| 165 | 163 |
acceptedScientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/author, |
| 166 | 164 |
acceptedClass,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/class, |
| 167 | 165 |
acceptedCultivar,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/_set_canon_taxonconcept/canon_taxonconcept_id/taxonconcept/cultivar, |
| ... | ... | |
| 202 | 200 |
forma,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/forma, |
| 203 | 201 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/genus, |
| 204 | 202 |
kingdom,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/kingdom, |
| 203 |
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 204 |
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/else", |
|
| 205 | 205 |
order,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/order, |
| 206 | 206 |
phylum,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/phylum, |
| 207 | 207 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/species, |
| ... | ... | |
| 209 | 209 |
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
| 210 | 210 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 211 | 211 |
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/subspecies/_alt/2/_join_words/2, |
| 212 |
verbatimScientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/identifyingtaxonomicname, |
|
| 213 |
verbatimScientificNameWithAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 214 |
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonconcept:[@fkey=canon_taxonconcept_id]/morphospecies/_if[@name=""if has verbatim name""]/then", |
|
| 212 | 215 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicname, |
| 213 | 216 |
scientificNameWithAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/taxonomicnamewithauthor, |
| 214 | 217 |
variety,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonconcept/variety, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 160 | 160 |
forma,"//*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept}/identifyingtaxonomicname",
|
| 161 | 161 |
cultivar,"//*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept}/identifyingtaxonomicname",
|
| 162 | 162 |
scientificNameAuthorship,"//*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/.,else/canon_taxonconcept_id/taxonconcept}/identifyingtaxonomicname",
|
| 163 |
morphospecies,"//*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/taxonconcept,else/.}/morphospecies",
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|
| 164 |
verbatimScientificNameWithAuthorship,"//*_id/taxonconcept/_if[@name=""if has verbatim name""]/{then/taxonconcept}/identifyingtaxonomicname",
|
|
| 165 | 163 |
acceptedScientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/author, |
| 166 | 164 |
acceptedClass,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/class, |
| 167 | 165 |
acceptedCultivar,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/cultivar, |
| ... | ... | |
| 202 | 200 |
forma,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/forma, |
| 203 | 201 |
genus,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/genus, |
| 204 | 202 |
kingdom,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/kingdom, |
| 203 |
verbatimScientificNameWithAuthorship,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 204 |
morphospecies,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/else", |
|
| 205 | 205 |
order,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/order, |
| 206 | 206 |
phylum,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/phylum, |
| 207 | 207 |
specificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/species, |
| ... | ... | |
| 209 | 209 |
infraspecificEpithet,"//taxonconcept/subspecies/_if[@name=""if has infraspecificEpithet""]/cond", |
| 210 | 210 |
taxonRank,"//taxonconcept/subspecies/_if[@name=""if has infraspecificEpithet""]/then", |
| 211 | 211 |
infraspecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/subspecies, |
| 212 |
verbatimScientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonconcept/identifyingtaxonomicname, |
|
| 213 |
verbatimScientificNameWithAuthorship,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 214 |
morphospecies,"//taxonconcept/morphospecies/_if[@name=""if has verbatim name""]/then", |
|
| 212 | 215 |
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonomicname, |
| 213 | 216 |
scientificNameWithAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/taxonomicnamewithauthor, |
| 214 | 217 |
variety,//taxonoccurrence/taxondetermination[]/*_id/taxonconcept/variety, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: TNRS input taxonconcept: Split single _if statement controlling where morphospecies goes into two _if statements for each case, so that other verbatim* terms don't need to have an _if statement in their mapping to the input taxonconcept