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Taxon name #3

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retog opened this issue Mar 13, 2024 · 4 comments
Open

Taxon name #3

retog opened this issue Mar 13, 2024 · 4 comments

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@retog
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retog commented Mar 13, 2024

Only species have a property with their name without parents and authority.
Only species have a property with their name without parents and authority.
Should find a description of all fields in CSV;
dwc:taxonID
dwc:parentNameUsageID
dwc:acceptedNameUsageID
dwc:originalNameUsageID
dwc:scientificNameID
dwc:datasetID
dwc:taxonomicStatus
dwc:taxonRank
dwc:scientificName
dwc:scientificNameAuthorship
col:notho
dwc:genericName
dwc:infragenericEpithet
dwc:specificEpithet
dwc:infraspecificEpithet
dwc:cultivarEpithet
dwc:nameAccordingTo
dwc:namePublishedIn
dwc:nomenclaturalCode
dwc:nomenclaturalStatus
dwc:taxonRemarks
dcterms:references

@retog
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retog commented Mar 16, 2024

https://dwc.tdwg.org/terms/

scientificName: The full scientific name, with authorship and date information if known. When forming part of a dwc:Identification, this should be the name in lowest level taxonomic rank that can be determined. This term should not contain identification qualifications, which should instead be supplied in the dwc:identificationQualifier term.

This seems to be true for species, subspecies and varietis, but not for rank genus.

@nleanba
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nleanba commented Jul 13, 2024

The Taxon.tsv is missing a filed containing the uninomial name for taxa above rank genus. This may be fixed by using a different export format

@nleanba
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nleanba commented Jul 13, 2024

The ColIDP Format has the following columns in the NameUsage.tsv file:

  • col:ID
  • col:alternativeID
  • col:nameAlternativeID
  • col:sourceID
  • col:parentID
  • col:basionymID
  • col:status
  • col:scientificName
  • col:authorship
  • col:rank
  • col:notho
  • col:originalSpelling
  • col:uninomial
  • col:genericName
  • col:infragenericEpithet
  • col:specificEpithet
  • col:infraspecificEpithet
  • col:cultivarEpithet
  • col:combinationAuthorship
  • col:combinationAuthorshipID
  • col:combinationExAuthorship
  • col:combinationExAuthorshipID
  • col:combinationAuthorshipYear
  • col:basionymAuthorship
  • col:basionymAuthorshipID
  • col:basionymExAuthorship
  • col:basionymExAuthorshipID
  • col:basionymAuthorshipYear
  • col:namePhrase
  • col:nameReferenceID
  • col:publishedInYear
  • col:publishedInPage
  • col:publishedInPageLink
  • col:gender
  • col:genderAgreement
  • col:etymology
  • col:code
  • col:nameStatus
  • col:accordingToID
  • col:accordingToPage
  • col:accordingToPageLink
  • col:referenceID
  • col:scrutinizer
  • col:scrutinizerID
  • col:scrutinizerDate
  • col:extinct
  • col:temporalRangeStart
  • col:temporalRangeEnd
  • col:environment
  • col:species these seem not to be used -\
  • col:section
  • col:subgenus
  • col:genus
  • col:subtribe
  • col:tribe
  • col:subfamily
  • col:family
  • col:superfamily
  • col:suborder
  • col:order
  • col:subclass
  • col:class
  • col:subphylum
  • col:phylum
  • col:kingdom these seem not to be used -/
  • col:ordinal
  • col:branchLength
  • col:link
  • col:nameRemarks
  • col:remarks

@nleanba
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nleanba commented Jul 24, 2024

It might also be possible to "hack" uninomial names:

PREFIX dwc: <http://rs.tdwg.org/dwc/terms/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

CONSTRUCT {
  ?taxon dwc:scientificName ?scientificName ;
         dwc:scientificNameAuthorship ?author ;
         dwc:rank ?rank ;
         ?rankIri ?uninomen .
} WHERE {
  BIND(<https://www.catalogueoflife.org/data/taxon/87BXZ> as ?taxon)
  ?taxon dwc:scientificName ?scientificName ;
         dwc:scientificNameAuthorship ?author ;
         dwc:rank ?rank .
  BIND(IRI(CONCAT("http://rs.tdwg.org/dwc/terms/", ?rank)) as ?rankIri)
  BIND(STRBEFORE(?scientificName, CONCAT(" ", ?author)) as ?uninomen)
}

But this seems rather fragile.

@retog opinions?

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