The scripts aid in mapping of wikidata ids to taxonomic ids from 11 other databases (ott, gbif, ncbi, eol, itis, irmng, col, bold, worms, plazi, apni).
Ideally a big sparql query where a subject is a taxon and has a scientific name and optional mapping to to taxonomic ids from these 11 dbs, should have worked. Unfortunately, such a query times out on the wikidata sparql query service, because of enormous number of hits (>1 mio). Therefore, in this script, qlever's wikidata sparql endpoint was used (approach-1). Another crude way out is to map wd ids individually to each db and then joining them (approach-2).
A couple of R packages are required to run the scripts, mainly WikidataQueryServiceR, glue,dplyr, tidyverse, httr, rotl, taxizedb, and dbplyr.
Steps to perform:
a) Download the input:open tree of life taxonomy
b) Run the script Rscript --vanilla matchTaxonomy.R
The old output files can also be downloaded here 