I often work with plant species check lists and have been using the 'taxize' R package to programmatically compile information on higher taxonomic ranks (above-genus) in these lists. To do this, I use the 'tax_name' function to query online databases and extract higher taxonomic ranks for each species in the list. However, there are often conflicts in generic names (between plants and various animal groups) - is there a way to constrain my database queries to plants only? I have sifted through all the documentation I could find, but haven't come up with a solution.
Hi Adriaan,
Looking in the guts of the function I don't think this can be easily done, but I thought it must be possible some other way, as you can search ITIS by kingdom on its website. That lead to the ritis package, and I think this might do what you want.
library(ritis)
#search for a plant only in Plantae, finds Quercus
itis_search(q = "nameWOInd:Quercus AND kingdom:Plantae" )
#search for a plant in Animalia, nothing returned
itis_search(q = "nameWOInd:Quercus AND kingdom:Animalia" )
#search for a genus used for both animals and plants, different authorities returned
itis_search(q = "nameWOInd:Baileya AND kingdom:Animalia" )
itis_search(q = "nameWOInd:Baileya AND kingdom:Plantae" )
I'm not sure how you'd go about doing this for NCBI, but I hope that is at least partly helpful!
Malcolm
Hi Malcolm
I haven't come across the 'ritis' package - will definitely give it a bash! Looks like it will do what I'm hoping for.
Thanks very much!
Adriaan
Not sure if it's possible with taxize, but if you're primarily interested in plants try the Taxonomic Name Resolution Service (TNRS: http://tnrs.iplantcollaborative.org/).
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