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EDIorg / taxonomyCleanr

R package for cleaning taxonomic data.
https://ediorg.github.io/taxonomyCleanr/
MIT License
12 stars 3 forks source link

TaxaDB #43

Open kzollove opened 3 years ago

kzollove commented 3 years ago

Utilize taxaDB instead of the WebAPI

This should help speed up resolve_sci_taxa and resolve_comm_taxa functions

atn38 commented 2 years ago

@kzollove what do you think about the different sets of providers that taxadb and taxize support and what that means for taxonomyCleanr? context: I'm running into some issues since R EML switched to taxadb and thinking about next steps here.

kzollove commented 2 years ago

Hi @atn38! This issue has not been in my radar for a while. Admittedly, I have hardly cracked the surface. Having checked just now, I see that neither WORRMS nor "Tropicos - Missouri Botanical Garden" is not on the taxadb list of providers. Since those are currently supported by taxonomyCleanr, that poses (yet another) roadblock for making this switch.

I imagine if we decided to spearhead the transition to taxadb, we would elect to still make those taxonomies available through taxize...

atn38 commented 2 years ago

yea -- WORRMS is the big missing piece from taxadb for me. What you suggested sounds like one way to go.

clnsmth commented 2 years ago

Indeed @kzollove @atn38. Authorities not supported by taxadb could be maintained/implemented as REST API calls.