Revision 5948
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/test_taxonomic_names/Taxon/VegBIEN.csv | ||
|---|---|---|
| 3 | 3 |
scientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1", |
| 4 | 4 |
scientificNameID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
| 5 | 5 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 6 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 6 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| inputs/test_taxonomic_names/Taxon/test.xml.ref | ||
|---|---|---|
| 26 | 26 |
<taxonomicname>$scientificName</taxonomicname> |
| 27 | 27 |
</taxonlabel> |
| 28 | 28 |
</taxonlabel_id> |
| 29 |
<binomial>$scientificName</binomial>
|
|
| 29 |
<taxonname>$scientificName</taxonname>
|
|
| 30 | 30 |
</taxonverbatim> |
| 31 | 31 |
</taxonverbatim_id> |
| 32 | 32 |
</taxondetermination> |
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 45 | 45 |
darwin:Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4, |
| 46 | 46 |
darwin:ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 47 | 47 |
darwin:ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 48 |
darwin:ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 49 | 48 |
darwin:Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 50 | 49 |
darwin:Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 51 | 50 |
darwin:Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 51 |
darwin:ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 52 | 52 |
darwin:DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 53 | 53 |
darwin:MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 54 | 54 |
darwin:YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 34 | 34 |
InfraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
| 35 | 35 |
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 36 | 36 |
AuthorOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 37 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 38 | 37 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 39 | 38 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 40 | 39 |
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 40 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 41 | 41 |
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family, |
| 42 | 42 |
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 43 | 43 |
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2, |
| ... | ... | |
| 46 | 46 |
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family, |
| 47 | 47 |
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 48 | 48 |
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2, |
| 49 |
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/binomial, |
|
| 50 | 49 |
GBIFFamilyOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/family, |
| 51 | 50 |
GBIFGenusOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/genus, |
| 51 |
ScientificNameOriginal,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 52 | 52 |
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 53 | 53 |
CatalogNO,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 54 | 54 |
Locality,/location/locationnarrative/_merge/1, |
| inputs/GBIF/Specimen/test.xml.ref | ||
|---|---|---|
| 141 | 141 |
</taxonlabel> |
| 142 | 142 |
</taxonlabel_id> |
| 143 | 143 |
<author>$AuthorOfScientificName</author> |
| 144 |
<binomial>$ScientificName</binomial> |
|
| 145 | 144 |
<family>$Family</family> |
| 146 | 145 |
<genus>$Genus</genus> |
| 147 | 146 |
<specific_epithet>$SpecificEpithet</specific_epithet> |
| 147 |
<taxonname>$ScientificName</taxonname> |
|
| 148 | 148 |
</taxonverbatim> |
| 149 | 149 |
</taxonverbatim_id> |
| 150 | 150 |
</taxondetermination> |
| ... | ... | |
| 229 | 229 |
</taxonomicname> |
| 230 | 230 |
</taxonlabel> |
| 231 | 231 |
</taxonlabel_id> |
| 232 |
<binomial>$ScientificNameOriginal</binomial> |
|
| 233 | 232 |
<family>$GBIFFamilyOriginal</family> |
| 234 | 233 |
<genus>$GBIFGenusOriginal</genus> |
| 234 |
<taxonname>$ScientificNameOriginal</taxonname> |
|
| 235 | 235 |
</taxonverbatim> |
| 236 | 236 |
</taxonverbatim_id> |
| 237 | 237 |
</taxondetermination> |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 163 | 163 |
dwc_terms_scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author/_alt/1, |
| 164 | 164 |
conceptual_darwin_2003_1_0_ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author/_alt/2, |
| 165 | 165 |
dwc_dwcore_AuthorYearOfScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author/_alt/3, |
| 166 |
conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 167 |
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 168 |
dwc_terms_scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 169 | 166 |
conceptual_darwin_2003_1_0_Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 170 | 167 |
dwc_dwcore_Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 171 | 168 |
dwc_terms_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| ... | ... | |
| 175 | 172 |
conceptual_darwin_2003_1_0_Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 176 | 173 |
dwc_dwcore_SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 177 | 174 |
dwc_terms_specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 175 |
conceptual_darwin_2003_1_0_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 176 |
dwc_dwcore_ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 177 |
dwc_terms_scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 178 | 178 |
dwc_terms_dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value, |
| 179 | 179 |
conceptual_darwin_2003_1_0_DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 180 | 180 |
conceptual_darwin_2003_1_0_MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 41 | 41 |
taxonfit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
| 42 | 42 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 43 | 43 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 44 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/binomial,
|
|
| 44 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname,
|
|
| 45 | 45 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 46 | 46 |
Division,,** No join mapping for *Division ** |
| 47 | 47 |
Subclass,,** No join mapping for *Subclass ** |
| inputs/QMOR/Specimen/VegBIEN.csv | ||
|---|---|---|
| 55 | 55 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 56 | 56 |
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
| 57 | 57 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 58 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 59 | 58 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 60 | 59 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 61 | 60 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 61 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 62 | 62 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
| 63 | 63 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value, |
| 64 | 64 |
identificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
| schemas/vegbien.my.sql | ||
|---|---|---|
| 1244 | 1244 |
taxonlabel_id int(11) NOT NULL, |
| 1245 | 1245 |
verbatimrank text, |
| 1246 | 1246 |
taxonomicname text, |
| 1247 |
binomial text,
|
|
| 1247 |
taxonname text,
|
|
| 1248 | 1248 |
author text, |
| 1249 | 1249 |
family text, |
| 1250 | 1250 |
genus text, |
| ... | ... | |
| 1276 | 1276 |
|
| 1277 | 1277 |
|
| 1278 | 1278 |
-- |
| 1279 |
-- Name: COLUMN taxonverbatim.binomial; Type: COMMENT; Schema: public; Owner: -
|
|
| 1279 |
-- Name: COLUMN taxonverbatim.taxonname; Type: COMMENT; Schema: public; Owner: -
|
|
| 1280 | 1280 |
-- |
| 1281 | 1281 |
|
| 1282 | 1282 |
|
| schemas/vegbien.sql | ||
|---|---|---|
| 1802 | 1802 |
taxonlabel_id integer NOT NULL, |
| 1803 | 1803 |
verbatimrank text, |
| 1804 | 1804 |
taxonomicname text, |
| 1805 |
binomial text,
|
|
| 1805 |
taxonname text,
|
|
| 1806 | 1806 |
author text, |
| 1807 | 1807 |
family text, |
| 1808 | 1808 |
genus text, |
| ... | ... | |
| 1836 | 1836 |
|
| 1837 | 1837 |
|
| 1838 | 1838 |
-- |
| 1839 |
-- Name: COLUMN taxonverbatim.binomial; Type: COMMENT; Schema: public; Owner: -
|
|
| 1839 |
-- Name: COLUMN taxonverbatim.taxonname; Type: COMMENT; Schema: public; Owner: -
|
|
| 1840 | 1840 |
-- |
| 1841 | 1841 |
|
| 1842 |
COMMENT ON COLUMN taxonverbatim.binomial IS 'The taxonomic name without the author.';
|
|
| 1842 |
COMMENT ON COLUMN taxonverbatim.taxonname IS 'The taxonomic name without the author.';
|
|
| 1843 | 1843 |
|
| 1844 | 1844 |
|
| 1845 | 1845 |
-- |
| ... | ... | |
| 1884 | 1884 |
-- |
| 1885 | 1885 |
|
| 1886 | 1886 |
CREATE VIEW analytical_stem_view AS |
| 1887 |
SELECT datasource.organizationname AS "institutionCode", place.country, place.stateprovince AS "stateProvince", place.county, coordinates.latitude_deg AS "decimalLatitude", coordinates.longitude_deg AS "decimalLongitude", location.sourceaccessioncode AS "plotName", location.elevation_m AS "elevationInMeters", _m2_to_ha(location.area_m2) AS "plotArea_ha", method.name AS "samplingProtocol", aggregateoccurrence.collectiondate AS "dateCollected", accepted_taxonverbatim.family, accepted_taxonverbatim.genus, ((accepted_taxonverbatim.genus || ' '::text) || accepted_taxonverbatim.specific_epithet) AS "speciesBinomial", COALESCE(accepted_taxonverbatim.taxonomicname, accepted_taxonverbatim.binomial) AS "scientificName", accepted_taxonverbatim.author AS "scientificNameAuthorship", NULLIF(array_to_string(ARRAY[accepted_taxonlabel.taxonomicname, parsed_taxonverbatim.morphospecies], ' '::text), ''::text) AS "scientificNameWithMorphospecies", NULLIF(array_to_string(ARRAY[identifiedby.givenname, identifiedby.middlename, identifiedby.surname], ' '::text), ''::text) AS "identifiedBy", taxonoccurrence.growthform AS "growthForm", taxonoccurrence.iscultivated AS cultivated, taxonoccurrence.cultivatedbasis AS "cultivatedBasis", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.verbatimcollectorname AS "recordedBy", plantobservation.collectionnumber AS "recordNumber" FROM (((((((((((((((((((party datasource JOIN location ON ((location.creator_id = datasource.party_id))) LEFT JOIN locationplace USING (location_id)) LEFT JOIN place USING (place_id)) LEFT JOIN coordinates USING (coordinates_id)) JOIN locationevent USING (location_id)) LEFT JOIN method USING (method_id)) JOIN taxonoccurrence USING (locationevent_id)) JOIN taxondetermination USING (taxonoccurrence_id)) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) JOIN taxonverbatim datasource_taxonverbatim USING (taxonverbatim_id)) JOIN taxonlabel datasource_taxonlabel USING (taxonlabel_id)) JOIN taxonlabel parsed_taxonlabel ON ((parsed_taxonlabel.taxonlabel_id = datasource_taxonlabel.matched_label_id))) LEFT JOIN taxonverbatim parsed_taxonverbatim ON ((parsed_taxonverbatim.taxonlabel_id = parsed_taxonlabel.taxonlabel_id))) JOIN taxonlabel accepted_taxonlabel ON ((accepted_taxonlabel.taxonlabel_id = datasource_taxonlabel.canon_label_id))) JOIN taxonverbatim accepted_taxonverbatim ON ((accepted_taxonverbatim.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) WHERE ((datasource.creator_id = datasource.party_id) AND (NOT taxondetermination.isoriginal));
|
|
| 1887 |
SELECT datasource.organizationname AS "institutionCode", place.country, place.stateprovince AS "stateProvince", place.county, coordinates.latitude_deg AS "decimalLatitude", coordinates.longitude_deg AS "decimalLongitude", location.sourceaccessioncode AS "plotName", location.elevation_m AS "elevationInMeters", _m2_to_ha(location.area_m2) AS "plotArea_ha", method.name AS "samplingProtocol", aggregateoccurrence.collectiondate AS "dateCollected", accepted_taxonverbatim.family, accepted_taxonverbatim.genus, ((accepted_taxonverbatim.genus || ' '::text) || accepted_taxonverbatim.specific_epithet) AS "speciesBinomial", COALESCE(accepted_taxonverbatim.taxonomicname, accepted_taxonverbatim.taxonname) AS "scientificName", accepted_taxonverbatim.author AS "scientificNameAuthorship", NULLIF(array_to_string(ARRAY[accepted_taxonlabel.taxonomicname, parsed_taxonverbatim.morphospecies], ' '::text), ''::text) AS "scientificNameWithMorphospecies", NULLIF(array_to_string(ARRAY[identifiedby.givenname, identifiedby.middlename, identifiedby.surname], ' '::text), ''::text) AS "identifiedBy", taxonoccurrence.growthform AS "growthForm", taxonoccurrence.iscultivated AS cultivated, taxonoccurrence.cultivatedbasis AS "cultivatedBasis", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.verbatimcollectorname AS "recordedBy", plantobservation.collectionnumber AS "recordNumber" FROM (((((((((((((((((((party datasource JOIN location ON ((location.creator_id = datasource.party_id))) LEFT JOIN locationplace USING (location_id)) LEFT JOIN place USING (place_id)) LEFT JOIN coordinates USING (coordinates_id)) JOIN locationevent USING (location_id)) LEFT JOIN method USING (method_id)) JOIN taxonoccurrence USING (locationevent_id)) JOIN taxondetermination USING (taxonoccurrence_id)) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) JOIN taxonverbatim datasource_taxonverbatim USING (taxonverbatim_id)) JOIN taxonlabel datasource_taxonlabel USING (taxonlabel_id)) JOIN taxonlabel parsed_taxonlabel ON ((parsed_taxonlabel.taxonlabel_id = datasource_taxonlabel.matched_label_id))) LEFT JOIN taxonverbatim parsed_taxonverbatim ON ((parsed_taxonverbatim.taxonlabel_id = parsed_taxonlabel.taxonlabel_id))) JOIN taxonlabel accepted_taxonlabel ON ((accepted_taxonlabel.taxonlabel_id = datasource_taxonlabel.canon_label_id))) JOIN taxonverbatim accepted_taxonverbatim ON ((accepted_taxonverbatim.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) WHERE ((datasource.creator_id = datasource.party_id) AND (NOT taxondetermination.isoriginal));
|
|
| 1888 | 1888 |
|
| 1889 | 1889 |
|
| 1890 | 1890 |
-- |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 162 | 162 |
acceptedCultivar,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname", |
| 163 | 163 |
acceptedScientificNameAuthorship,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname", |
| 164 | 164 |
acceptedScientificNameAuthorship,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/author", |
| 165 |
acceptedTaxonName,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/binomial", |
|
| 166 | 165 |
acceptedFamily,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/family", |
| 167 | 166 |
acceptedGenus,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/genus", |
| 168 | 167 |
acceptedSpecificEpithet,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/specific_epithet", |
| 168 |
acceptedTaxonName,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonname", |
|
| 169 | 169 |
acceptedScientificName,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonomicname", |
| 170 | 170 |
acceptedTaxonRank,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/verbatimrank", |
| 171 | 171 |
taxonIsCanonical,"//taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/cond", |
| ... | ... | |
| 203 | 203 |
morphospecies,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonepithet, |
| 204 | 204 |
verbatimScientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonomicname, |
| 205 | 205 |
verbatimScientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/author, |
| 206 |
verbatimTaxonName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/binomial, |
|
| 207 | 206 |
verbatimFamily,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/family, |
| 208 | 207 |
verbatimGenus,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/genus, |
| 209 | 208 |
verbatimScientificName,"//taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 210 | 209 |
morphospecies,"//taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/then", |
| 211 | 210 |
verbatimSpecificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/specific_epithet, |
| 211 |
verbatimTaxonName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/taxonname, |
|
| 212 | 212 |
verbatimTaxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel/taxonverbatim/verbatimrank, |
| 213 | 213 |
family,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| 214 | 214 |
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| ... | ... | |
| 229 | 229 |
taxonNameOrEpithet,"//taxonlabel/taxonomicname/_if[@name=""if has taxonomic name""]/then", |
| 230 | 230 |
taxonomicStatus,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 231 | 231 |
scientificNameAuthorship,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/author, |
| 232 |
taxonName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/binomial, |
|
| 233 | 232 |
family,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/family, |
| 234 | 233 |
genus,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/genus, |
| 235 | 234 |
verbatimScientificName,"//taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 236 | 235 |
morphospecies,"//taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/else", |
| 237 | 236 |
specificEpithet,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/specific_epithet, |
| 237 |
taxonName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/taxonname, |
|
| 238 | 238 |
scientificName,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/taxonomicname, |
| 239 | 239 |
taxonRank,//taxonoccurrence/taxondetermination[]/*_id/taxonverbatim/verbatimrank, |
| 240 | 240 |
dateIdentified,//taxonoccurrence/taxondetermination[]/determinationdate/_*/date, |
| ... | ... | |
| 285 | 285 |
originalCultivar,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| 286 | 286 |
originalScientificNameAuthorship,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname, |
| 287 | 287 |
originalScientificNameAuthorship,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/author, |
| 288 |
originalTaxonName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/binomial, |
|
| 289 | 288 |
originalFamily,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/family, |
| 290 | 289 |
originalGenus,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/genus, |
| 291 | 290 |
originalSpecificEpithet,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/specific_epithet, |
| 291 |
originalTaxonName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 292 | 292 |
originalScientificName,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname, |
| 293 | 293 |
originalTaxonRank,//taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/verbatimrank, |
| 294 | 294 |
originalIdentificationQualifier,//taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit, |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 483 | 483 |
<3>$dwc_dwcore_AuthorYearOfScientificName</3> |
| 484 | 484 |
</_alt> |
| 485 | 485 |
</author> |
| 486 |
<binomial> |
|
| 487 |
<_alt> |
|
| 488 |
<0>$conceptual_darwin_2003_1_0_ScientificName</0> |
|
| 489 |
<1>$dwc_dwcore_ScientificName</1> |
|
| 490 |
<2>$dwc_terms_scientificName</2> |
|
| 491 |
</_alt> |
|
| 492 |
</binomial> |
|
| 493 | 486 |
<family> |
| 494 | 487 |
<_alt> |
| 495 | 488 |
<0>$conceptual_darwin_2003_1_0_Family</0> |
| ... | ... | |
| 511 | 504 |
<2>$dwc_terms_specificEpithet</2> |
| 512 | 505 |
</_alt> |
| 513 | 506 |
</specific_epithet> |
| 507 |
<taxonname> |
|
| 508 |
<_alt> |
|
| 509 |
<0>$conceptual_darwin_2003_1_0_ScientificName</0> |
|
| 510 |
<1>$dwc_dwcore_ScientificName</1> |
|
| 511 |
<2>$dwc_terms_scientificName</2> |
|
| 512 |
</_alt> |
|
| 513 |
</taxonname> |
|
| 514 | 514 |
</taxonverbatim> |
| 515 | 515 |
</taxonverbatim_id> |
| 516 | 516 |
<determinationdate> |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 49 | 49 |
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4, |
| 50 | 50 |
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 51 | 51 |
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 52 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 53 | 52 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 54 | 53 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 55 | 54 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 55 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 56 | 56 |
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 57 | 57 |
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| 58 | 58 |
YearIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 248 | 248 |
</taxonlabel> |
| 249 | 249 |
</taxonlabel_id> |
| 250 | 250 |
<author>$ScientificNameAuthor</author> |
| 251 |
<binomial>$ScientificName</binomial> |
|
| 252 | 251 |
<family>$Family</family> |
| 253 | 252 |
<genus>$Genus</genus> |
| 254 | 253 |
<specific_epithet>$Species</specific_epithet> |
| 254 |
<taxonname>$ScientificName</taxonname> |
|
| 255 | 255 |
</taxonverbatim> |
| 256 | 256 |
</taxonverbatim_id> |
| 257 | 257 |
<determinationdate> |
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 49 | 49 |
Specific epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
| 50 | 50 |
Autor (revised),/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 51 | 51 |
Autor (revised),/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 52 |
Species and morphotypes,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial,"Contains less than ""Specie+autor""" |
|
| 53 | 52 |
Family (revised),/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 54 | 53 |
Genera,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 55 | 54 |
Specific epithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 55 |
Species and morphotypes,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,"Contains less than ""Specie+autor""" |
|
| 56 | 56 |
Specie+autor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
| 57 | 57 |
Qualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
| 58 | 58 |
Field family,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family, |
| inputs/Madidi/Organism/test.xml.ref | ||
|---|---|---|
| 179 | 179 |
</taxonlabel> |
| 180 | 180 |
</taxonlabel_id> |
| 181 | 181 |
<author>$Autor (revised)</author> |
| 182 |
<binomial>$Species and morphotypes</binomial> |
|
| 183 | 182 |
<family>$Family (revised)</family> |
| 184 | 183 |
<genus>$Genera</genus> |
| 185 | 184 |
<specific_epithet>$Specific epithet</specific_epithet> |
| 185 |
<taxonname>$Species and morphotypes</taxonname> |
|
| 186 | 186 |
<taxonomicname>$Specie+autor</taxonomicname> |
| 187 | 187 |
</taxonverbatim> |
| 188 | 188 |
</taxonverbatim_id> |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 77 | 77 |
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank/_alt/1", |
| 78 | 78 |
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank/_alt/2", |
| 79 | 79 |
authors,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 80 |
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 81 | 80 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 82 | 81 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 83 | 82 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 83 |
SciName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 84 | 84 |
usdaRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank/_alt/1, |
| 85 | 85 |
infrarank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank/_alt/2, |
| 86 | 86 |
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname/_join/1, |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 224 | 224 |
</taxonlabel> |
| 225 | 225 |
</taxonlabel_id> |
| 226 | 226 |
<author>$authors</author> |
| 227 |
<binomial>$SciName</binomial> |
|
| 228 | 227 |
<family>$family</family> |
| 229 | 228 |
<genus>$genus</genus> |
| 230 | 229 |
<specific_epithet>$species</specific_epithet> |
| 230 |
<taxonname>$SciName</taxonname> |
|
| 231 | 231 |
<verbatimrank> |
| 232 | 232 |
<_alt> |
| 233 | 233 |
<1>$usdaRank</1> |
| inputs/CVS/Organism/VegBIEN.csv | ||
|---|---|---|
| 9 | 9 |
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 10 | 10 |
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1", |
| 11 | 11 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 12 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial,
|
|
| 12 |
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
|
|
| 13 | 13 |
locationAccuracy-m,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_deg/_noCV/value/_alt/1, |
| 14 | 14 |
publicLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
| 15 | 15 |
publicLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
| inputs/CVS/Organism/test.xml.ref | ||
|---|---|---|
| 30 | 30 |
<taxonomicname>$currentTaxonName sec Weakley 2006</taxonomicname> |
| 31 | 31 |
</taxonlabel> |
| 32 | 32 |
</taxonlabel_id> |
| 33 |
<binomial>$currentTaxonName sec Weakley 2006</binomial>
|
|
| 33 |
<taxonname>$currentTaxonName sec Weakley 2006</taxonname>
|
|
| 34 | 34 |
</taxonverbatim> |
| 35 | 35 |
</taxonverbatim_id> |
| 36 | 36 |
</taxondetermination> |
| inputs/.TNRS/tnrs_other/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 17 | 17 |
Accepted_name_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2", |
| 18 | 18 |
Accepted_name_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/author", |
| 19 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/binomial", |
|
| 20 | 19 |
Accepted_name_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/family/_nullIf:[null=Unknown]/value", |
| 20 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonname", |
|
| 21 | 21 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/verbatimrank", |
| 22 | 22 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| 23 | 23 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/taxonverbatim/verbatimrank", |
| ... | ... | |
| 37 | 37 |
Unmatched_terms,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonepithet, |
| 38 | 38 |
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonomicname, |
| 39 | 39 |
Author_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/author,Contains author in original string |
| 40 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/binomial, |
|
| 41 | 40 |
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/family,Contains family in original string (uncommon) |
| 42 | 41 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/genus, |
| 43 | 42 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 44 | 43 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/then", |
| 45 | 44 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/specific_epithet, |
| 45 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/taxonname, |
|
| 46 | 46 |
Infraspecific_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/verbatimrank, |
| 47 | 47 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family,Contains family based on matched name |
| 48 | 48 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| ... | ... | |
| 57 | 57 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
| 58 | 58 |
Taxonomic_status,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 59 | 59 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Contains author based on matched name |
| 60 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 61 | 60 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,Contains family based on matched name |
| 62 | 61 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 63 | 62 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 64 | 63 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/else", |
| 65 | 64 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 65 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 66 | 66 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
| 67 | 67 |
Accepted_name_lsid,,** No join mapping for *Accepted_name_lsid ** |
| 68 | 68 |
Accepted_name_species,,** No join mapping for *Accepted_name_species ** Also contains genus. Omitted because Accepted_name contains more info. |
| inputs/.TNRS/tnrs_other/test.xml.ref | ||
|---|---|---|
| 36 | 36 |
</taxonomicname> |
| 37 | 37 |
<taxonverbatim> |
| 38 | 38 |
<author>$Accepted_name_author</author> |
| 39 |
<binomial>$Accepted_name</binomial> |
|
| 40 | 39 |
<family> |
| 41 | 40 |
<_nullIf> |
| 42 | 41 |
<null>Unknown</null> |
| 43 | 42 |
<value>$Accepted_name_family</value> |
| 44 | 43 |
</_nullIf> |
| 45 | 44 |
</family> |
| 45 |
<taxonname>$Accepted_name</taxonname> |
|
| 46 | 46 |
<verbatimrank>$Accepted_name_rank</verbatimrank> |
| 47 | 47 |
</taxonverbatim> |
| 48 | 48 |
</taxonlabel> |
| ... | ... | |
| 107 | 107 |
<taxonomicname>$Name_submitted</taxonomicname> |
| 108 | 108 |
<taxonverbatim> |
| 109 | 109 |
<author>$Author_matched</author> |
| 110 |
<binomial>$Name_matched</binomial> |
|
| 111 | 110 |
<family>$Family_matched</family> |
| 112 | 111 |
<genus>$Genus_matched</genus> |
| 113 | 112 |
<morphospecies>$Unmatched_terms</morphospecies> |
| 114 | 113 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
| 114 |
<taxonname>$Name_matched</taxonname> |
|
| 115 | 115 |
<verbatimrank>$Infraspecific_rank</verbatimrank> |
| 116 | 116 |
</taxonverbatim> |
| 117 | 117 |
</taxonlabel> |
| ... | ... | |
| 151 | 151 |
</taxonlabel> |
| 152 | 152 |
</taxonlabel_id> |
| 153 | 153 |
<author>$Name_matched_author</author> |
| 154 |
<binomial>$Name_matched</binomial> |
|
| 155 | 154 |
<family>$Name_matched_accepted_family</family> |
| 156 | 155 |
<genus>$Genus_matched</genus> |
| 157 | 156 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
| 157 |
<taxonname>$Name_matched</taxonname> |
|
| 158 | 158 |
<verbatimrank>$Name_matched_rank</verbatimrank> |
| 159 | 159 |
</taxonverbatim> |
| 160 | 160 |
</taxonverbatim_id> |
| inputs/.TNRS/tnrs_accepted/VegBIEN.csv | ||
|---|---|---|
| 16 | 16 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
| 17 | 17 |
Accepted_name_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2", |
| 18 | 18 |
Accepted_name_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/author", |
| 19 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/binomial", |
|
| 20 | 19 |
Accepted_name_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/family/_nullIf:[null=Unknown]/value", |
| 20 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonname", |
|
| 21 | 21 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/verbatimrank", |
| 22 | 22 |
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]:[then=0]/cond",This table contains only accepted names (names that scrub to themselves) |
| 23 | 23 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| ... | ... | |
| 40 | 40 |
Unmatched_terms,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonepithet, |
| 41 | 41 |
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonomicname, |
| 42 | 42 |
Author_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/author,Contains author in original string |
| 43 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/binomial, |
|
| 44 | 43 |
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/family,Contains family in original string (uncommon) |
| 45 | 44 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/genus, |
| 46 | 45 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 47 | 46 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/then", |
| 48 | 47 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/specific_epithet, |
| 48 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/taxonname, |
|
| 49 | 49 |
Infraspecific_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/verbatimrank, |
| 50 | 50 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family,Contains family based on matched name |
| 51 | 51 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| ... | ... | |
| 60 | 60 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/cond/_has_taxonomic_name/rank", |
| 61 | 61 |
Taxonomic_status,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 62 | 62 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Contains author based on matched name |
| 63 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 64 | 63 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,Contains family based on matched name |
| 65 | 64 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 66 | 65 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 67 | 66 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/else", |
| 68 | 67 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 68 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 69 | 69 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
| 70 | 70 |
Accepted_name_lsid,,** No join mapping for *Accepted_name_lsid ** |
| 71 | 71 |
Accepted_name_species,,** No join mapping for *Accepted_name_species ** Also contains genus. Omitted because Accepted_name contains more info. |
| inputs/.TNRS/tnrs_accepted/test.xml.ref | ||
|---|---|---|
| 94 | 94 |
<taxonomicname>$Name_submitted</taxonomicname> |
| 95 | 95 |
<taxonverbatim> |
| 96 | 96 |
<author>$Author_matched</author> |
| 97 |
<binomial>$Name_matched</binomial> |
|
| 98 | 97 |
<family>$Family_matched</family> |
| 99 | 98 |
<genus>$Genus_matched</genus> |
| 100 | 99 |
<morphospecies>$Unmatched_terms</morphospecies> |
| 101 | 100 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
| 101 |
<taxonname>$Name_matched</taxonname> |
|
| 102 | 102 |
<verbatimrank>$Infraspecific_rank</verbatimrank> |
| 103 | 103 |
</taxonverbatim> |
| 104 | 104 |
</taxonlabel> |
| ... | ... | |
| 138 | 138 |
</taxonlabel> |
| 139 | 139 |
</taxonlabel_id> |
| 140 | 140 |
<author>$Name_matched_author</author> |
| 141 |
<binomial>$Name_matched</binomial> |
|
| 142 | 141 |
<family>$Name_matched_accepted_family</family> |
| 143 | 142 |
<genus>$Genus_matched</genus> |
| 144 | 143 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
| 144 |
<taxonname>$Name_matched</taxonname> |
|
| 145 | 145 |
<verbatimrank>$Name_matched_rank</verbatimrank> |
| 146 | 146 |
</taxonverbatim> |
| 147 | 147 |
</taxonverbatim_id> |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 52 | 52 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2, |
| 53 | 53 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
| 54 | 54 |
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4, |
| 55 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 56 | 55 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 57 | 56 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 58 | 57 |
Species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 58 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 59 | 59 |
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,Contains the binomial in addition to the authority |
| 60 | 60 |
DayIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| 61 | 61 |
MonthIdentified,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value", |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 247 | 247 |
</taxonomicname> |
| 248 | 248 |
</taxonlabel> |
| 249 | 249 |
</taxonlabel_id> |
| 250 |
<binomial>$ScientificName</binomial> |
|
| 251 | 250 |
<family>$Family</family> |
| 252 | 251 |
<genus>$Genus</genus> |
| 253 | 252 |
<specific_epithet>$Species</specific_epithet> |
| 253 |
<taxonname>$ScientificName</taxonname> |
|
| 254 | 254 |
<taxonomicname>$ScientificNameAuthor</taxonomicname> |
| 255 | 255 |
</taxonverbatim> |
| 256 | 256 |
</taxonverbatim_id> |
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 13 | 13 |
Accession Number,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 14 | 14 |
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[creator_id/party:[creator_id=0]/organizationname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1", |
| 15 | 15 |
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 16 |
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial,
|
|
| 16 |
Full Taxon Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
|
|
| 17 | 17 |
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 18 | 18 |
Accuracy,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_deg/_noCV/value/_alt/1, |
| 19 | 19 |
Lat (-=S),"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value", |
| inputs/NCU-NCSC/Specimen/test.xml.ref | ||
|---|---|---|
| 55 | 55 |
<taxonomicname>$Full Taxon Name</taxonomicname> |
| 56 | 56 |
</taxonlabel> |
| 57 | 57 |
</taxonlabel_id> |
| 58 |
<binomial>$Full Taxon Name</binomial>
|
|
| 58 |
<taxonname>$Full Taxon Name</taxonname>
|
|
| 59 | 59 |
</taxonverbatim> |
| 60 | 60 |
</taxonverbatim_id> |
| 61 | 61 |
</taxondetermination> |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 39 | 39 |
Subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/4, |
| 40 | 40 |
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 41 | 41 |
ScientificNameAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 42 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 43 | 42 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 44 | 43 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 45 | 44 |
species,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 45 |
ScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 46 | 46 |
Collector,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 47 | 47 |
CatalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 48 | 48 |
Locality,/location/locationnarrative/_merge/1, |
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 194 | 194 |
</taxonlabel> |
| 195 | 195 |
</taxonlabel_id> |
| 196 | 196 |
<author>$ScientificNameAuthor</author> |
| 197 |
<binomial>$ScientificName</binomial> |
|
| 198 | 197 |
<family>$family</family> |
| 199 | 198 |
<genus>$genus</genus> |
| 200 | 199 |
<specific_epithet>$species</specific_epithet> |
| 200 |
<taxonname>$ScientificName</taxonname> |
|
| 201 | 201 |
</taxonverbatim> |
| 202 | 202 |
</taxonverbatim_id> |
| 203 | 203 |
</taxondetermination> |
| inputs/VegBank/taxonobservation_/test.xml.ref | ||
|---|---|---|
| 177 | 177 |
<taxonomicname>$authorplantname</taxonomicname> |
| 178 | 178 |
</taxonlabel> |
| 179 | 179 |
</taxonlabel_id> |
| 180 |
<binomial>$authorplantname</binomial>
|
|
| 180 |
<taxonname>$authorplantname</taxonname>
|
|
| 181 | 181 |
</taxonverbatim> |
| 182 | 182 |
</taxonverbatim_id> |
| 183 | 183 |
</taxondetermination> |
| inputs/QMOR/Specimen/test.xml.ref | ||
|---|---|---|
| 229 | 229 |
</taxonlabel> |
| 230 | 230 |
</taxonlabel_id> |
| 231 | 231 |
<author>$scientificNameAuthorship</author> |
| 232 |
<binomial>$scientificName</binomial> |
|
| 233 | 232 |
<family>$family</family> |
| 234 | 233 |
<genus>$genus</genus> |
| 235 | 234 |
<specific_epithet>$specificEpithet</specific_epithet> |
| 235 |
<taxonname>$scientificName</taxonname> |
|
| 236 | 236 |
<verbatimrank>$taxonRank</verbatimrank> |
| 237 | 237 |
</taxonverbatim> |
| 238 | 238 |
</taxonverbatim_id> |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 162 | 162 |
acceptedCultivar,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""cult. ""]/2", |
| 163 | 163 |
acceptedScientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2", |
| 164 | 164 |
acceptedScientificNameAuthorship,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/author", |
| 165 |
acceptedTaxonName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/binomial", |
|
| 166 | 165 |
acceptedFamily,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/family", |
| 167 | 166 |
acceptedGenus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/genus", |
| 168 | 167 |
acceptedSpecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/specific_epithet", |
| 168 |
acceptedTaxonName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonname", |
|
| 169 | 169 |
acceptedScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonomicname", |
| 170 | 170 |
acceptedTaxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/verbatimrank", |
| 171 | 171 |
taxonIsCanonical,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]:[then=0]/cond", |
| ... | ... | |
| 203 | 203 |
morphospecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonepithet, |
| 204 | 204 |
verbatimScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonomicname, |
| 205 | 205 |
verbatimScientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/author, |
| 206 |
verbatimTaxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/binomial, |
|
| 207 | 206 |
verbatimFamily,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/family, |
| 208 | 207 |
verbatimGenus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/genus, |
| 209 | 208 |
verbatimScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 210 | 209 |
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/then", |
| 211 | 210 |
verbatimSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/specific_epithet, |
| 211 |
verbatimTaxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/taxonname, |
|
| 212 | 212 |
verbatimTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/verbatimrank, |
| 213 | 213 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/1/_taxon_family_require_std/family, |
| 214 | 214 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/1, |
| ... | ... | |
| 229 | 229 |
taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/3/_if[@name=""if has taxonomic name""]/then", |
| 230 | 230 |
taxonomicStatus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
| 231 | 231 |
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
| 232 |
taxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/binomial, |
|
| 233 | 232 |
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
| 234 | 233 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 235 | 234 |
verbatimScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
| 236 | 235 |
morphospecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/else", |
| 237 | 236 |
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
| 237 |
taxonName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 238 | 238 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
| 239 | 239 |
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
| 240 | 240 |
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_*/date/_dateRangeStart/value, |
| ... | ... | |
| 285 | 285 |
originalCultivar,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/8/_join_words:[1=""cult. ""]/2", |
| 286 | 286 |
originalScientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/2, |
| 287 | 287 |
originalScientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/author, |
| 288 |
originalTaxonName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/binomial, |
|
| 289 | 288 |
originalFamily,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/family, |
| 290 | 289 |
originalGenus,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/genus, |
| 291 | 290 |
originalSpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/specific_epithet, |
| 291 |
originalTaxonName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 292 | 292 |
originalScientificName,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname, |
| 293 | 293 |
originalTaxonRank,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/verbatimrank, |
| 294 | 294 |
originalIdentificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/taxonfit, |
Also available in: Unified diff
schemas/vegbien.sql: taxonverbatim: Renamed binomial to taxonname because this field is actually the taxonomic name without the author, not just the genus+specific epithet binomial