Revision 7166
Added by Aaron Marcuse-Kubitza almost 12 years ago
| inputs/.TNRS/tnrs_accepted/new_terms.csv | ||
|---|---|---|
| 1 |
Name_number,OMIT,,Identifies name only within one TNRS batch. Omitted because not globally unique. |
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| 2 |
Name_submitted,verbatimScientificName,, |
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| 3 |
Overall_score,matchedTaxonFit_fraction,,Assuming is a fraction based on the range of values |
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| 4 |
Name_matched,verbatimTaxonName,, |
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| 5 |
Name_matched,taxonName,, |
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| 6 |
Name_matched_rank,taxonRank,, |
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| 7 |
Name_matched_author,scientificNameAuthorship,,Contains author based on matched name |
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| 8 |
Name_matched_url,scientificNameID,, |
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| 9 |
Author_matched,verbatimScientificNameAuthorship,,Contains author in original string |
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| 10 |
Family_matched,verbatimFamily,,Contains family in original string (uncommon) |
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| 11 |
Family_score,matchedFamilyFit_fraction,, |
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| 12 |
Name_matched_accepted_family,family,,Contains family based on matched name |
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| 13 |
Genus_matched,verbatimGenus,, |
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| 14 |
Genus_matched,genus,, |
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| 15 |
Genus_score,matchedGenusFit_fraction,, |
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| 16 |
Specific_epithet_matched,verbatimSpecificEpithet,, |
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| 17 |
Specific_epithet_matched,specificEpithet,, |
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| 18 |
Specific_epithet_score,matchedSpeciesFit_fraction,, |
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| 19 |
Infraspecific_rank,verbatimTaxonRank,, |
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| 20 |
Infraspecific_epithet_matched,verbatimInfraspecificEpithet,, |
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| 21 |
Infraspecific_epithet_matched,infraspecificEpithet,, |
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| 22 |
Infraspecific_rank_2,UNUSED,, |
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| 23 |
Infraspecific_epithet_2_matched,UNUSED,, |
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| 24 |
Infraspecific_epithet_2_score,UNUSED,, |
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| 25 |
Unmatched_terms,morphospecies,, |
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| 26 |
Accepted_name,acceptedTaxonName,, |
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| 27 |
Accepted_name_author,acceptedScientificNameAuthorship,, |
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| 28 |
Accepted_name_rank,acceptedTaxonRank,, |
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| 29 |
Accepted_name_family,acceptedFamily,/_nullIf:[null=Unknown]/value, |
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| inputs/.TNRS/tnrs_accepted/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Time_submitted |
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| 2 |
*Name_score |
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| 3 |
*Author_score |
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| 4 |
verbatimInfraspecificEpithet |
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| 5 |
*Infraspecific_epithet_score |
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| 6 |
*Annotations |
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| 7 |
*Accepted_name_url |
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| 8 |
*Accepted_name_species |
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| 9 |
*Selected |
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| 10 |
*Source |
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| 11 |
*Warnings |
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| 12 |
*Accepted_name_lsid |
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| inputs/.TNRS/tnrs_accepted/create.sql | ||
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| 1 |
SELECT * |
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| 2 |
FROM tnrs |
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| 3 |
WHERE COALESCE( |
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| 4 |
"Name_submitted" = NULLIF(:schema.array_to_string(ARRAY[ |
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| 5 |
NULLIF("Accepted_name_family", 'Unknown')
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| 6 |
, "Accepted_name" |
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| 7 |
, "Accepted_name_author" |
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| 8 |
], ' '), '') |
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| 9 |
, false) |
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| 10 |
ORDER BY "Name_submitted" |
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| 11 |
; |
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| 12 |
|
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| 13 |
ALTER TABLE :table ADD PRIMARY KEY ("Name_submitted");
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| inputs/.TNRS/tnrs_accepted/header.csv | ||
|---|---|---|
| 1 |
Time_submitted,Name_number,Name_submitted,Overall_score,Name_matched,Name_matched_rank,Name_score,Name_matched_author,Name_matched_url,Author_matched,Author_score,Family_matched,Family_score,Name_matched_accepted_family,Genus_matched,Genus_score,Specific_epithet_matched,Specific_epithet_score,Infraspecific_rank,Infraspecific_epithet_matched,Infraspecific_epithet_score,Infraspecific_rank_2,Infraspecific_epithet_2_matched,Infraspecific_epithet_2_score,Annotations,Unmatched_terms,Taxonomic_status,Accepted_name,Accepted_name_author,Accepted_name_rank,Accepted_name_url,Accepted_name_species,Accepted_name_family,Selected,Source,Warnings,Accepted_name_lsid,Accepted_scientific_name |
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| inputs/.TNRS/tnrs_accepted/map.csv | ||
|---|---|---|
| 1 |
TNRS,VegCore,Filter,Comments |
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| 2 |
Time_submitted,*Time_submitted,, |
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| 3 |
Name_number,OMIT,,Identifies name only within one TNRS batch. Omitted because not globally unique. |
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| 4 |
Name_submitted,verbatimScientificName,, |
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| 5 |
Overall_score,matchedTaxonFit_fraction,,Assuming is a fraction based on the range of values |
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| 6 |
Name_matched,verbatimTaxonName,, |
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| 7 |
Name_matched,taxonName,, |
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| 8 |
Name_matched_rank,taxonRank,, |
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| 9 |
Name_score,*Name_score,, |
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| 10 |
Name_matched_author,scientificNameAuthorship,,Contains author based on matched name |
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| 11 |
Name_matched_url,scientificNameID,, |
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| 12 |
Author_matched,verbatimScientificNameAuthorship,,Contains author in original string |
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| 13 |
Author_score,*Author_score,, |
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| 14 |
Family_matched,verbatimFamily,,Contains family in original string (uncommon) |
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| 15 |
Family_score,matchedFamilyFit_fraction,, |
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| 16 |
Name_matched_accepted_family,family,,Contains family based on matched name |
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| 17 |
Genus_matched,verbatimGenus,, |
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| 18 |
Genus_matched,genus,, |
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| 19 |
Genus_score,matchedGenusFit_fraction,, |
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| 20 |
Specific_epithet_matched,verbatimSpecificEpithet,, |
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| 21 |
Specific_epithet_matched,specificEpithet,, |
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| 22 |
Specific_epithet_score,matchedSpeciesFit_fraction,, |
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| 23 |
Infraspecific_rank,verbatimTaxonRank,, |
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| 24 |
Infraspecific_epithet_matched,verbatimInfraspecificEpithet,, |
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| 25 |
Infraspecific_epithet_matched,infraspecificEpithet,, |
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| 26 |
Infraspecific_epithet_score,*Infraspecific_epithet_score,, |
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| 27 |
Infraspecific_rank_2,UNUSED,, |
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| 28 |
Infraspecific_epithet_2_matched,UNUSED,, |
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| 29 |
Infraspecific_epithet_2_score,UNUSED,, |
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| 30 |
Annotations,*Annotations,, |
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| 31 |
Unmatched_terms,morphospecies,, |
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| 32 |
Taxonomic_status,taxonomicStatus,, |
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| 33 |
Accepted_name,acceptedTaxonName,, |
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| 34 |
Accepted_name_author,acceptedScientificNameAuthorship,, |
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| 35 |
Accepted_name_rank,acceptedTaxonRank,, |
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| 36 |
Accepted_name_url,*Accepted_name_url,, |
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| 37 |
Accepted_name_species,*Accepted_name_species,,Also contains genus. Omitted because Accepted_name contains more info. |
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| 38 |
Accepted_name_family,acceptedFamily,/_nullIf:[null=Unknown]/value, |
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| 39 |
Selected,*Selected,, |
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| 40 |
Source,*Source,, |
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| 41 |
Warnings,*Warnings,, |
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| 42 |
Accepted_name_lsid,*Accepted_name_lsid,, |
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| 43 |
:true,taxonIsCanonical,,This table contains only accepted names (names that scrub to themselves) |
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| inputs/.TNRS/tnrs_accepted/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
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| 2 |
<VegBIEN> |
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| 3 |
<_setDefault id="-1"> |
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| 4 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
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| 5 |
<path> |
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| 6 |
<_simplifyPath> |
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| 7 |
<next>parent_id</next> |
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| 8 |
<path> |
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| 9 |
<location> |
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| 10 |
<locationevent> |
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| 11 |
<taxonoccurrence> |
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| 12 |
<taxondetermination> |
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| 13 |
<taxonverbatim_id> |
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| 14 |
<taxonverbatim> |
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| 15 |
<taxonlabel_id> |
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| 16 |
<taxonlabel> |
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| 17 |
<matched_label_id>0</matched_label_id> |
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| 18 |
<parent_id> |
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| 19 |
<taxonlabel> |
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| 20 |
<rank>$Name_matched_rank</rank> |
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| 21 |
<parent_id> |
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| 22 |
<taxonlabel> |
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| 23 |
<rank>cultivar</rank> |
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| 24 |
<parent_id> |
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| 25 |
<taxonlabel> |
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| 26 |
<rank>forma</rank> |
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| 27 |
<parent_id> |
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| 28 |
<taxonlabel> |
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| 29 |
<rank>variety</rank> |
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| 30 |
<parent_id> |
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| 31 |
<taxonlabel> |
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| 32 |
<rank>subspecies</rank> |
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| 33 |
<parent_id> |
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| 34 |
<taxonlabel> |
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| 35 |
<rank>species</rank> |
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| 36 |
<taxonepithet>$Specific_epithet_matched</taxonepithet> |
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| 37 |
<parent_id> |
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| 38 |
<taxonlabel> |
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| 39 |
<rank>genus</rank> |
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| 40 |
<matched_label_id> |
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| 41 |
<taxonlabel> |
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| 42 |
<source_id><source><shortname>NCBI</shortname></source></source_id> |
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| 43 |
<taxonomicname>$Genus_matched</taxonomicname> |
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| 44 |
</taxonlabel> |
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| 45 |
</matched_label_id> |
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| 46 |
<taxonepithet>$Genus_matched</taxonepithet> |
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| 47 |
<parent_id> |
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| 48 |
<taxonlabel> |
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| 49 |
<rank>family</rank> |
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| 50 |
<matched_label_id> |
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| 51 |
<taxonlabel> |
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| 52 |
<source_id><source><shortname>NCBI</shortname></source></source_id> |
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| 53 |
<taxonomicname>$Name_matched_accepted_family</taxonomicname> |
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| 54 |
</taxonlabel> |
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| 55 |
</matched_label_id> |
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| 56 |
<taxonepithet>$Name_matched_accepted_family</taxonepithet> |
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| 57 |
</taxonlabel> |
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| 58 |
</parent_id> |
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| 59 |
</taxonlabel> |
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| 60 |
</parent_id> |
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| 61 |
</taxonlabel> |
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| 62 |
</parent_id> |
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| 63 |
</taxonlabel> |
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| 64 |
</parent_id> |
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| 65 |
</taxonlabel> |
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| 66 |
</parent_id> |
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| 67 |
</taxonlabel> |
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| 68 |
</parent_id> |
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| 69 |
</taxonlabel> |
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| 70 |
</parent_id> |
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| 71 |
<taxonepithet>$Infraspecific_epithet_matched</taxonepithet> |
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| 72 |
</taxonlabel> |
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| 73 |
</parent_id> |
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| 74 |
<rank>$Name_matched_rank</rank> |
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| 75 |
<sourceaccessioncode>$Name_matched_url</sourceaccessioncode> |
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| 76 |
<taxonlabel fkey="matched_label_id"> |
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| 77 |
<matched_label_fit_fraction> |
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| 78 |
<_max> |
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| 79 |
<1>$Family_score</1> |
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| 80 |
<2>$Genus_score</2> |
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| 81 |
<3>$Specific_epithet_score</3> |
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| 82 |
<4>$Overall_score</4> |
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| 83 |
</_max> |
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| 84 |
</matched_label_fit_fraction> |
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| 85 |
<taxonomicname>$Name_submitted</taxonomicname> |
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| 86 |
<taxonverbatim> |
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| 87 |
<author>$Author_matched</author> |
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| 88 |
<family>$Family_matched</family> |
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| 89 |
<genus>$Genus_matched</genus> |
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| 90 |
<morphospecies>$Unmatched_terms</morphospecies> |
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| 91 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
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| 92 |
<taxonname>$Name_matched</taxonname> |
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| 93 |
<verbatimrank>$Infraspecific_rank</verbatimrank> |
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| 94 |
</taxonverbatim> |
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| 95 |
</taxonlabel> |
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| 96 |
<taxonomicname> |
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| 97 |
<_merge_prefix> |
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| 98 |
<prefix><_taxon_family_require_std><family>$Name_matched_accepted_family</family></_taxon_family_require_std></prefix> |
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| 99 |
<value> |
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| 100 |
<_join_words> |
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| 101 |
<1> |
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| 102 |
<_alt> |
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| 103 |
<1>$Name_matched</1> |
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| 104 |
<2> |
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| 105 |
<_join_words> |
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| 106 |
<2>$Genus_matched</2> |
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| 107 |
<3>$Specific_epithet_matched</3> |
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| 108 |
<5> |
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| 109 |
<_join_words> |
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| 110 |
<1> |
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| 111 |
<_if name="if has infraspecificEpithet"> |
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| 112 |
<cond>$Infraspecific_epithet_matched</cond> |
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| 113 |
<then>$Name_matched_rank</then> |
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| 114 |
</_if> |
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| 115 |
</1> |
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| 116 |
<2>$Infraspecific_epithet_matched</2> |
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| 117 |
</_join_words> |
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| 118 |
</5> |
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| 119 |
</_join_words> |
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| 120 |
</2> |
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| 121 |
</_alt> |
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| 122 |
</1> |
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| 123 |
<2>$Name_matched_author</2> |
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| 124 |
</_join_words> |
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| 125 |
</value> |
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| 126 |
</_merge_prefix> |
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| 127 |
</taxonomicname> |
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| 128 |
<taxonstatus>$Taxonomic_status</taxonstatus> |
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| 129 |
</taxonlabel> |
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| 130 |
</taxonlabel_id> |
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| 131 |
<author>$Name_matched_author</author> |
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| 132 |
<family>$Name_matched_accepted_family</family> |
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| 133 |
<genus>$Genus_matched</genus> |
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| 134 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
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| 135 |
<taxonname>$Name_matched</taxonname> |
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| 136 |
<verbatimrank>$Name_matched_rank</verbatimrank> |
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| 137 |
</taxonverbatim> |
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| 138 |
</taxonverbatim_id> |
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| 139 |
</taxondetermination> |
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| 140 |
</taxonoccurrence> |
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| 141 |
</locationevent> |
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| 142 |
</location> |
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| 143 |
</path> |
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| 144 |
</_simplifyPath> |
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| 145 |
</path> |
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| 146 |
</_setDefault> |
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| 147 |
</VegBIEN> |
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| 148 |
Inserted 14 new rows into database |
|
| inputs/.TNRS/tnrs_accepted/VegBIEN.csv | ||
|---|---|---|
| 1 |
TNRS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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| 2 |
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
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| 3 |
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists",This table contains only accepted names (names that scrub to themselves) |
|
| 4 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
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| 5 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/rank", |
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| 6 |
Accepted_name_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_nullIf:[null=Unknown]/value", |
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| 7 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
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| 8 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
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| 9 |
Accepted_name_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
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| 10 |
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", |
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| 11 |
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", |
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| 12 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/morphospecies/_if[@name=""if has accepted name""]/cond/_exists", |
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| 13 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/morphospecies/_if[@name=""if has accepted name""]/then", |
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| 14 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonname", |
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| 15 |
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", |
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| 16 |
: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) |
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| 17 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
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| 18 |
Specific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 19 |
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/cond/_exists",This table contains only accepted names (names that scrub to themselves) |
|
| 20 |
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
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| 21 |
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
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| 22 |
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/cond/_exists",This table contains only accepted names (names that scrub to themselves) |
|
| 23 |
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",Contains family based on matched name |
|
| 24 |
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",Contains family based on matched name |
|
| 25 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 26 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 27 |
Name_matched_url,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 28 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 29 |
Family_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/1", |
|
| 30 |
Genus_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/2", |
|
| 31 |
Specific_epithet_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/3", |
|
| 32 |
Overall_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/4",Assuming is a fraction based on the range of values |
|
| 33 |
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonomicname, |
|
| 34 |
Author_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/author,Contains author in original string |
|
| 35 |
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/family,Contains family in original string (uncommon) |
|
| 36 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/genus, |
|
| 37 |
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", |
|
| 38 |
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", |
|
| 39 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/specific_epithet, |
|
| 40 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/taxonname, |
|
| 41 |
Infraspecific_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/verbatimrank, |
|
| 42 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,Contains family based on matched name |
|
| 43 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 44 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
|
| 45 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 46 |
:true,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/2/_if[@name=""if has verbatim name""]/cond/_exists",This table contains only accepted names (names that scrub to themselves) |
|
| 47 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/2/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 48 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/2/_if[@name=""if has verbatim name""]/else", |
|
| 49 |
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 50 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 51 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 52 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,Contains author based on matched name |
|
| 53 |
Taxonomic_status,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
|
| 54 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Contains author based on matched name |
|
| 55 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,Contains family based on matched name |
|
| 56 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 57 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 58 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/else", |
|
| 59 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 60 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 61 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 62 |
Family_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/1", |
|
| 63 |
Genus_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/2", |
|
| 64 |
Specific_epithet_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/3", |
|
| 65 |
Overall_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/4",Assuming is a fraction based on the range of values |
|
| 66 |
Accepted_name_lsid,,** No join mapping for *Accepted_name_lsid ** |
|
| 67 |
Accepted_name_species,,** No join mapping for *Accepted_name_species ** Also contains genus. Omitted because Accepted_name contains more info. |
|
| 68 |
Accepted_name_url,,** No join mapping for *Accepted_name_url ** |
|
| 69 |
Annotations,,** No join mapping for *Annotations ** |
|
| 70 |
Author_score,,** No join mapping for *Author_score ** |
|
| 71 |
Infraspecific_epithet_2_matched,,** No non-empty join mapping for UNUSED ** |
|
| 72 |
Infraspecific_epithet_2_score,,** No non-empty join mapping for UNUSED ** |
|
| 73 |
Infraspecific_epithet_matched,,** No join mapping for verbatimInfraspecificEpithet ** |
|
| 74 |
Infraspecific_epithet_score,,** No join mapping for *Infraspecific_epithet_score ** |
|
| 75 |
Infraspecific_rank_2,,** No non-empty join mapping for UNUSED ** |
|
| 76 |
Name_number,,** No non-empty join mapping for OMIT ** Identifies name only within one TNRS batch. Omitted because not globally unique. |
|
| 77 |
Name_score,,** No join mapping for *Name_score ** |
|
| 78 |
Selected,,** No join mapping for *Selected ** |
|
| 79 |
Source,,** No join mapping for *Source ** |
|
| 80 |
Time_submitted,,** No join mapping for *Time_submitted ** |
|
| 81 |
Warnings,,** No join mapping for *Warnings ** |
|
| inputs/.TNRS/tnrs_other/header.csv | ||
|---|---|---|
| 1 |
Time_submitted,Name_number,Name_submitted,Overall_score,Name_matched,Name_matched_rank,Name_score,Name_matched_author,Name_matched_url,Author_matched,Author_score,Family_matched,Family_score,Name_matched_accepted_family,Genus_matched,Genus_score,Specific_epithet_matched,Specific_epithet_score,Infraspecific_rank,Infraspecific_epithet_matched,Infraspecific_epithet_score,Infraspecific_rank_2,Infraspecific_epithet_2_matched,Infraspecific_epithet_2_score,Annotations,Unmatched_terms,Taxonomic_status,Accepted_name,Accepted_name_author,Accepted_name_rank,Accepted_name_url,Accepted_name_species,Accepted_name_family,Selected,Source,Warnings,Accepted_name_lsid,Accepted_scientific_name |
|
| inputs/.TNRS/tnrs_other/map.csv | ||
|---|---|---|
| 1 |
TNRS,VegCore,Filter,Comments |
|
| 2 |
Time_submitted,*Time_submitted,, |
|
| 3 |
Name_number,OMIT,,Identifies name only within one TNRS batch. Omitted because not globally unique. |
|
| 4 |
Name_submitted,verbatimScientificName,, |
|
| 5 |
Overall_score,matchedTaxonFit_fraction,,Assuming is a fraction based on the range of values |
|
| 6 |
Name_matched,verbatimTaxonName,, |
|
| 7 |
Name_matched,taxonName,, |
|
| 8 |
Name_matched_rank,taxonRank,, |
|
| 9 |
Name_score,*Name_score,, |
|
| 10 |
Name_matched_author,scientificNameAuthorship,,Contains author based on matched name |
|
| 11 |
Name_matched_url,scientificNameID,, |
|
| 12 |
Author_matched,verbatimScientificNameAuthorship,,Contains author in original string |
|
| 13 |
Author_score,*Author_score,, |
|
| 14 |
Family_matched,verbatimFamily,,Contains family in original string (uncommon) |
|
| 15 |
Family_score,matchedFamilyFit_fraction,, |
|
| 16 |
Name_matched_accepted_family,family,,Contains family based on matched name |
|
| 17 |
Genus_matched,verbatimGenus,, |
|
| 18 |
Genus_matched,genus,, |
|
| 19 |
Genus_score,matchedGenusFit_fraction,, |
|
| 20 |
Specific_epithet_matched,verbatimSpecificEpithet,, |
|
| 21 |
Specific_epithet_matched,specificEpithet,, |
|
| 22 |
Specific_epithet_score,matchedSpeciesFit_fraction,, |
|
| 23 |
Infraspecific_rank,verbatimTaxonRank,, |
|
| 24 |
Infraspecific_epithet_matched,verbatimInfraspecificEpithet,, |
|
| 25 |
Infraspecific_epithet_matched,infraspecificEpithet,, |
|
| 26 |
Infraspecific_epithet_score,*Infraspecific_epithet_score,, |
|
| 27 |
Infraspecific_rank_2,UNUSED,, |
|
| 28 |
Infraspecific_epithet_2_matched,UNUSED,, |
|
| 29 |
Infraspecific_epithet_2_score,UNUSED,, |
|
| 30 |
Annotations,*Annotations,, |
|
| 31 |
Unmatched_terms,morphospecies,, |
|
| 32 |
Taxonomic_status,taxonomicStatus,, |
|
| 33 |
Accepted_name,acceptedTaxonName,, |
|
| 34 |
Accepted_name_author,acceptedScientificNameAuthorship,, |
|
| 35 |
Accepted_name_rank,acceptedTaxonRank,, |
|
| 36 |
Accepted_name_url,*Accepted_name_url,, |
|
| 37 |
Accepted_name_species,*Accepted_name_species,,Also contains genus. Omitted because Accepted_name contains more info. |
|
| 38 |
Accepted_name_family,acceptedFamily,/_nullIf:[null=Unknown]/value, |
|
| 39 |
Selected,*Selected,, |
|
| 40 |
Source,*Source,, |
|
| 41 |
Warnings,*Warnings,, |
|
| 42 |
Accepted_name_lsid,*Accepted_name_lsid,, |
|
| inputs/.TNRS/tnrs_other/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
|
| 4 |
<source_id><source><shortname>TNRS</shortname></source></source_id> |
|
| 5 |
<path> |
|
| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<locationevent> |
|
| 11 |
<taxonoccurrence> |
|
| 12 |
<taxondetermination> |
|
| 13 |
<taxonverbatim_id> |
|
| 14 |
<taxonverbatim> |
|
| 15 |
<taxonlabel_id> |
|
| 16 |
<taxonlabel> |
|
| 17 |
<matched_label_id> |
|
| 18 |
<taxonlabel> |
|
| 19 |
<rank>$Accepted_name_rank</rank> |
|
| 20 |
<taxonomicname> |
|
| 21 |
<_merge_prefix> |
|
| 22 |
<prefix> |
|
| 23 |
<_taxon_family_require_std> |
|
| 24 |
<family> |
|
| 25 |
<_nullIf> |
|
| 26 |
<null>Unknown</null> |
|
| 27 |
<value>$Accepted_name_family</value> |
|
| 28 |
</_nullIf> |
|
| 29 |
</family> |
|
| 30 |
</_taxon_family_require_std> |
|
| 31 |
</prefix> |
|
| 32 |
<value> |
|
| 33 |
<_join_words> |
|
| 34 |
<1>$Accepted_name</1> |
|
| 35 |
<2>$Accepted_name_author</2> |
|
| 36 |
</_join_words> |
|
| 37 |
</value> |
|
| 38 |
</_merge_prefix> |
|
| 39 |
</taxonomicname> |
|
| 40 |
<taxonverbatim> |
|
| 41 |
<author>$Accepted_name_author</author> |
|
| 42 |
<family> |
|
| 43 |
<_nullIf> |
|
| 44 |
<null>Unknown</null> |
|
| 45 |
<value>$Accepted_name_family</value> |
|
| 46 |
</_nullIf> |
|
| 47 |
</family> |
|
| 48 |
<morphospecies>$Unmatched_terms</morphospecies> |
|
| 49 |
<taxonname>$Accepted_name</taxonname> |
|
| 50 |
<verbatimrank>$Accepted_name_rank</verbatimrank> |
|
| 51 |
</taxonverbatim> |
|
| 52 |
</taxonlabel> |
|
| 53 |
</matched_label_id> |
|
| 54 |
<parent_id> |
|
| 55 |
<taxonlabel> |
|
| 56 |
<rank>$Name_matched_rank</rank> |
|
| 57 |
<parent_id> |
|
| 58 |
<taxonlabel> |
|
| 59 |
<rank>cultivar</rank> |
|
| 60 |
<parent_id> |
|
| 61 |
<taxonlabel> |
|
| 62 |
<rank>forma</rank> |
|
| 63 |
<parent_id> |
|
| 64 |
<taxonlabel> |
|
| 65 |
<rank>variety</rank> |
|
| 66 |
<parent_id> |
|
| 67 |
<taxonlabel> |
|
| 68 |
<rank>subspecies</rank> |
|
| 69 |
<parent_id> |
|
| 70 |
<taxonlabel> |
|
| 71 |
<rank>species</rank> |
|
| 72 |
<taxonepithet>$Specific_epithet_matched</taxonepithet> |
|
| 73 |
<parent_id> |
|
| 74 |
<taxonlabel> |
|
| 75 |
<rank>genus</rank> |
|
| 76 |
<taxonepithet>$Genus_matched</taxonepithet> |
|
| 77 |
<parent_id> |
|
| 78 |
<taxonlabel> |
|
| 79 |
<rank>family</rank> |
|
| 80 |
<taxonepithet>$Name_matched_accepted_family</taxonepithet> |
|
| 81 |
</taxonlabel> |
|
| 82 |
</parent_id> |
|
| 83 |
</taxonlabel> |
|
| 84 |
</parent_id> |
|
| 85 |
</taxonlabel> |
|
| 86 |
</parent_id> |
|
| 87 |
</taxonlabel> |
|
| 88 |
</parent_id> |
|
| 89 |
</taxonlabel> |
|
| 90 |
</parent_id> |
|
| 91 |
</taxonlabel> |
|
| 92 |
</parent_id> |
|
| 93 |
</taxonlabel> |
|
| 94 |
</parent_id> |
|
| 95 |
<taxonepithet>$Infraspecific_epithet_matched</taxonepithet> |
|
| 96 |
</taxonlabel> |
|
| 97 |
</parent_id> |
|
| 98 |
<rank>$Name_matched_rank</rank> |
|
| 99 |
<sourceaccessioncode>$Name_matched_url</sourceaccessioncode> |
|
| 100 |
<taxonlabel fkey="matched_label_id"> |
|
| 101 |
<matched_label_fit_fraction> |
|
| 102 |
<_max> |
|
| 103 |
<1>$Family_score</1> |
|
| 104 |
<2>$Genus_score</2> |
|
| 105 |
<3>$Specific_epithet_score</3> |
|
| 106 |
<4>$Overall_score</4> |
|
| 107 |
</_max> |
|
| 108 |
</matched_label_fit_fraction> |
|
| 109 |
<taxonomicname>$Name_submitted</taxonomicname> |
|
| 110 |
<taxonverbatim> |
|
| 111 |
<author>$Author_matched</author> |
|
| 112 |
<family>$Family_matched</family> |
|
| 113 |
<genus>$Genus_matched</genus> |
|
| 114 |
<morphospecies>$Unmatched_terms</morphospecies> |
|
| 115 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
|
| 116 |
<taxonname>$Name_matched</taxonname> |
|
| 117 |
<verbatimrank>$Infraspecific_rank</verbatimrank> |
|
| 118 |
</taxonverbatim> |
|
| 119 |
</taxonlabel> |
|
| 120 |
<taxonomicname> |
|
| 121 |
<_merge_prefix> |
|
| 122 |
<prefix><_taxon_family_require_std><family>$Name_matched_accepted_family</family></_taxon_family_require_std></prefix> |
|
| 123 |
<value> |
|
| 124 |
<_join_words> |
|
| 125 |
<1> |
|
| 126 |
<_alt> |
|
| 127 |
<1>$Name_matched</1> |
|
| 128 |
<2> |
|
| 129 |
<_join_words> |
|
| 130 |
<2>$Genus_matched</2> |
|
| 131 |
<3>$Specific_epithet_matched</3> |
|
| 132 |
<5> |
|
| 133 |
<_join_words> |
|
| 134 |
<1> |
|
| 135 |
<_if name="if has infraspecificEpithet"> |
|
| 136 |
<cond>$Infraspecific_epithet_matched</cond> |
|
| 137 |
<then>$Name_matched_rank</then> |
|
| 138 |
</_if> |
|
| 139 |
</1> |
|
| 140 |
<2>$Infraspecific_epithet_matched</2> |
|
| 141 |
</_join_words> |
|
| 142 |
</5> |
|
| 143 |
</_join_words> |
|
| 144 |
</2> |
|
| 145 |
</_alt> |
|
| 146 |
</1> |
|
| 147 |
<2>$Name_matched_author</2> |
|
| 148 |
</_join_words> |
|
| 149 |
</value> |
|
| 150 |
</_merge_prefix> |
|
| 151 |
</taxonomicname> |
|
| 152 |
<taxonstatus>$Taxonomic_status</taxonstatus> |
|
| 153 |
</taxonlabel> |
|
| 154 |
</taxonlabel_id> |
|
| 155 |
<author>$Name_matched_author</author> |
|
| 156 |
<family>$Name_matched_accepted_family</family> |
|
| 157 |
<genus>$Genus_matched</genus> |
|
| 158 |
<specific_epithet>$Specific_epithet_matched</specific_epithet> |
|
| 159 |
<taxonname>$Name_matched</taxonname> |
|
| 160 |
<verbatimrank>$Name_matched_rank</verbatimrank> |
|
| 161 |
</taxonverbatim> |
|
| 162 |
</taxonverbatim_id> |
|
| 163 |
</taxondetermination> |
|
| 164 |
</taxonoccurrence> |
|
| 165 |
</locationevent> |
|
| 166 |
</location> |
|
| 167 |
</path> |
|
| 168 |
</_simplifyPath> |
|
| 169 |
</path> |
|
| 170 |
</_setDefault> |
|
| 171 |
</VegBIEN> |
|
| 172 |
Inserted 12 new rows into database |
|
| inputs/.TNRS/tnrs_other/VegBIEN.csv | ||
|---|---|---|
| 1 |
TNRS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
Name_matched,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 3 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 4 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/rank", |
|
| 5 |
Accepted_name_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family/_nullIf:[null=Unknown]/value", |
|
| 6 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1", |
|
| 7 |
Accepted_name_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 8 |
Accepted_name_author,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2", |
|
| 9 |
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", |
|
| 10 |
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", |
|
| 11 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/morphospecies/_if[@name=""if has accepted name""]/cond/_exists", |
|
| 12 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/morphospecies/_if[@name=""if has accepted name""]/then", |
|
| 13 |
Accepted_name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/matched_label_id/_if[@name=""if is canonical name""]/else/taxonlabel/taxonverbatim/taxonname", |
|
| 14 |
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", |
|
| 15 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
|
| 16 |
Specific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 17 |
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname", |
|
| 18 |
Genus_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 19 |
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/_if[@name=""if is canonical name""]/then/matched_label_id/taxonlabel:[source_id/source/shortname=NCBI]/taxonomicname",Contains family based on matched name |
|
| 20 |
Name_matched_accepted_family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",Contains family based on matched name |
|
| 21 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 22 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank, |
|
| 23 |
Name_matched_url,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode, |
|
| 24 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank", |
|
| 25 |
Family_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/1", |
|
| 26 |
Genus_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/2", |
|
| 27 |
Specific_epithet_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/3", |
|
| 28 |
Overall_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/matched_label_fit_fraction/_if[@name=""if has taxondetermination""]/else/_max/4",Assuming is a fraction based on the range of values |
|
| 29 |
Name_submitted,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonomicname, |
|
| 30 |
Author_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/author,Contains author in original string |
|
| 31 |
Family_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/family,Contains family in original string (uncommon) |
|
| 32 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/genus, |
|
| 33 |
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", |
|
| 34 |
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", |
|
| 35 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/specific_epithet, |
|
| 36 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/taxonname, |
|
| 37 |
Infraspecific_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonlabel:[@fkey=matched_label_id]/taxonverbatim/verbatimrank, |
|
| 38 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,Contains family based on matched name |
|
| 39 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 40 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
|
| 41 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 42 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/2/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 43 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/2/_if[@name=""if has verbatim name""]/else", |
|
| 44 |
Infraspecific_epithet_matched,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 45 |
Name_matched_rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then", |
|
| 46 |
Infraspecific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 47 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,Contains author based on matched name |
|
| 48 |
Taxonomic_status,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonstatus, |
|
| 49 |
Name_matched_author,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,Contains author based on matched name |
|
| 50 |
Name_matched_accepted_family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,Contains family based on matched name |
|
| 51 |
Genus_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 52 |
Name_submitted,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/cond/_exists", |
|
| 53 |
Unmatched_terms,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/morphospecies/_if[@name=""if has verbatim name""]/else", |
|
| 54 |
Specific_epithet_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 55 |
Name_matched,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 56 |
Name_matched_rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank, |
|
| 57 |
Family_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/1", |
|
| 58 |
Genus_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/2", |
|
| 59 |
Specific_epithet_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/3", |
|
| 60 |
Overall_score,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/then/taxonfit/_max/4",Assuming is a fraction based on the range of values |
|
| 61 |
Accepted_name_lsid,,** No join mapping for *Accepted_name_lsid ** |
|
| 62 |
Accepted_name_species,,** No join mapping for *Accepted_name_species ** Also contains genus. Omitted because Accepted_name contains more info. |
|
| 63 |
Accepted_name_url,,** No join mapping for *Accepted_name_url ** |
|
| 64 |
Annotations,,** No join mapping for *Annotations ** |
|
| 65 |
Author_score,,** No join mapping for *Author_score ** |
|
| 66 |
Infraspecific_epithet_2_matched,,** No non-empty join mapping for UNUSED ** |
|
| 67 |
Infraspecific_epithet_2_score,,** No non-empty join mapping for UNUSED ** |
|
| 68 |
Infraspecific_epithet_matched,,** No join mapping for verbatimInfraspecificEpithet ** |
|
| 69 |
Infraspecific_epithet_score,,** No join mapping for *Infraspecific_epithet_score ** |
|
| 70 |
Infraspecific_rank_2,,** No non-empty join mapping for UNUSED ** |
|
| 71 |
Name_number,,** No non-empty join mapping for OMIT ** Identifies name only within one TNRS batch. Omitted because not globally unique. |
|
| 72 |
Name_score,,** No join mapping for *Name_score ** |
|
| 73 |
Selected,,** No join mapping for *Selected ** |
|
| 74 |
Source,,** No join mapping for *Source ** |
|
| 75 |
Time_submitted,,** No join mapping for *Time_submitted ** |
|
| 76 |
Warnings,,** No join mapping for *Warnings ** |
|
| inputs/.TNRS/tnrs_other/new_terms.csv | ||
|---|---|---|
| 1 |
Name_number,OMIT,,Identifies name only within one TNRS batch. Omitted because not globally unique. |
|
| 2 |
Name_submitted,verbatimScientificName,, |
|
| 3 |
Overall_score,matchedTaxonFit_fraction,,Assuming is a fraction based on the range of values |
|
| 4 |
Name_matched,verbatimTaxonName,, |
|
| 5 |
Name_matched,taxonName,, |
|
| 6 |
Name_matched_rank,taxonRank,, |
|
| 7 |
Name_matched_author,scientificNameAuthorship,,Contains author based on matched name |
|
| 8 |
Name_matched_url,scientificNameID,, |
|
| 9 |
Author_matched,verbatimScientificNameAuthorship,,Contains author in original string |
|
| 10 |
Family_matched,verbatimFamily,,Contains family in original string (uncommon) |
|
| 11 |
Family_score,matchedFamilyFit_fraction,, |
|
| 12 |
Name_matched_accepted_family,family,,Contains family based on matched name |
|
| 13 |
Genus_matched,verbatimGenus,, |
|
| 14 |
Genus_matched,genus,, |
|
| 15 |
Genus_score,matchedGenusFit_fraction,, |
|
| 16 |
Specific_epithet_matched,verbatimSpecificEpithet,, |
|
| 17 |
Specific_epithet_matched,specificEpithet,, |
|
| 18 |
Specific_epithet_score,matchedSpeciesFit_fraction,, |
|
| 19 |
Infraspecific_rank,verbatimTaxonRank,, |
|
| 20 |
Infraspecific_epithet_matched,verbatimInfraspecificEpithet,, |
|
| 21 |
Infraspecific_epithet_matched,infraspecificEpithet,, |
|
| 22 |
Infraspecific_rank_2,UNUSED,, |
|
| 23 |
Infraspecific_epithet_2_matched,UNUSED,, |
|
| 24 |
Infraspecific_epithet_2_score,UNUSED,, |
|
| 25 |
Unmatched_terms,morphospecies,, |
|
| 26 |
Accepted_name,acceptedTaxonName,, |
|
| 27 |
Accepted_name_author,acceptedScientificNameAuthorship,, |
|
| 28 |
Accepted_name_rank,acceptedTaxonRank,, |
|
| 29 |
Accepted_name_family,acceptedFamily,/_nullIf:[null=Unknown]/value, |
|
| inputs/.TNRS/tnrs_other/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*Time_submitted |
|
| 2 |
*Name_score |
|
| 3 |
*Author_score |
|
| 4 |
verbatimInfraspecificEpithet |
|
| 5 |
*Infraspecific_epithet_score |
|
| 6 |
*Annotations |
|
| 7 |
*Accepted_name_url |
|
| 8 |
*Accepted_name_species |
|
| 9 |
*Selected |
|
| 10 |
*Source |
|
| 11 |
*Warnings |
|
| 12 |
*Accepted_name_lsid |
|
| inputs/.TNRS/tnrs_other/create.sql | ||
|---|---|---|
| 1 |
SELECT * |
|
| 2 |
FROM tnrs |
|
| 3 |
WHERE NOT COALESCE( |
|
| 4 |
"Name_submitted" = NULLIF(:schema.array_to_string(ARRAY[ |
|
| 5 |
NULLIF("Accepted_name_family", 'Unknown')
|
|
| 6 |
, "Accepted_name" |
|
| 7 |
, "Accepted_name_author" |
|
| 8 |
], ' '), '') |
|
| 9 |
, false) |
|
| 10 |
ORDER BY "Name_submitted" |
|
| 11 |
; |
|
| 12 |
|
|
| 13 |
ALTER TABLE :table ADD PRIMARY KEY ("Name_submitted");
|
|
Also available in: Unified diff
Removed no longer used inputs/.TNRS/tnrs_accepted, tnrs_other. Use the tnrs_canon view instead.