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traitecoevo / APCalign

R package for accessing, matching and updating species names of Australian flora
https://traitecoevo.github.io/APCalign/
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scientificNameID and taxonID are distinct concepts #117

Closed ehwenk closed 1 year ago

ehwenk commented 1 year ago

I don't think it is a good idea to rename APC's taxonID's to ID and APNI's scientificNameID's to ID. These are distinct concepts, one linked to a scientific name (a name) and the other link to a taxon concept.

The scientificNameID's are what link the same scientific name between the APC & APNI.

Meanwhile only APC names have taxonID's, since only names on the APC are true taxon concepts. For AusTraits we now maintain columns with both taxonID and scientificNameID for this reason.

Referencing lines 45 & 83 in load_taxonomic_resources.R:


line 45: APC_tmp ... ID = taxonID,
line 83: taxonomic_resources[["APNI names"]] ...  dplyr::select(canonicalName, scientificName, ID = scientificNameID, nameType, taxonRank) %>%
ehwenk commented 1 year ago

Also no ID is being carried through to taxonomic_resources[["genera_APNI"]], so APNI listed genera don't have any identifier in any of the resources$ tibbles. I'm going to wait to fix this until we sort the names out

ehwenk commented 1 year ago

Looking further, this same confusion is being introduced on line 154 of update_taxonomy.R : taxonIDClean = scientificNameID,

We made these changes to the austraits.build workflow in Nov 22. See also:

https://github.com/traitecoevo/austraits.build/issues/608

ehwenk commented 1 year ago

See:

http://rs.tdwg.org/dwc/terms/taxonID : An identifier for the set of dwc:Taxon information. May be a global unique identifier or an identifier specific to the data set. http://rs.tdwg.org/dwc/terms/scientificNameID : An identifier for the nomenclatural (not taxonomic) details of a scientific name. http://rs.tdwg.org/dwc/terms/acceptedNameUsageID (the link between accepted names and synonyms, etc.): An identifier for the name usage (documented meaning of the name according to a source) of the currently valid (zoological) or accepted (botanical) taxon.

ehwenk commented 1 year ago

closed with https://github.com/traitecoevo/APCalign/commit/e0d342e0b20238f62ea34a18d5fe177ba33a0e59