Hi Levi, I recently just put together a new package called orthogene <https://github.com/neurogenomics/orthogene> (currently under review by bioc) that has a convenience function for flexibly mapping species identifiers to any ID types (including NCBI taxa IDs): map_species()
It may not be as comprehensive as GenomeInfoDbData, but might still be useful. Best, Brian ___________ Brian Schilder PhD Candidate UK Dementia Research Institute at Imperial College London Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab Profile | bit.ly/imperial_profile <https://bit.ly/imperial_profile> LinkedIn | linkedin.com/in/brian-schilder <https://www.linkedin.com/in/brian-schilder/> Twitter | twitter.com/BMSchilder <http://www.twitter.com/BMSchilder> Lab | neurogenomics.co.uk <http://neurogenomics.co.uk/> UK DRI | www.ukdri.ac.uk <http://www.ukdri.ac.uk/> > On 8 Aug 2021, at 19:10, Levi Waldron <lwaldron.resea...@gmail.com> wrote: > > Does anyone else do mapping between NCBI taxids, names, and ranks? We do > this in curatedMetagenomicData and soon other packages, currently using > external files that lack provenance and versioning, so Ludwig Geistlinger > was looking for Bioconductor annotation resources. The closest he found was > in GenomeInfoDbData <https://bioconductor.org/packages/GenomeInfoDbData> but > this has only genus and species, and some quirks like Bacteria being listed > as a genus: > >> library(GenomeInfoDbData) >> data(specData) >> head(specData) > tax_id genus species > 1 1 all <NA> > 2 1 root <NA> > 3 2 Bacteria <NA> > 4 6 Azorhizobium <NA> > 5 7 Azorhizobium caulinodans > 6 9 Buchnera aphidicola >> dim(specData) > [1] 2521271 3 >> subset(specData, c(genus == "Escherichia" & species == "coli"))$tax_id > [1] 562 > > Any thoughts from the GenomeInfoDbData maintainer ("Bioconductor Maintainer > <maintainer at bioconductor.org>") about a pull request either to a) update > specData to add additional columns for all taxonomic levels, or b) creating > a new object? Or, another approach altogether? See > https://github.com/waldronlab/curatedMetagenomicData/issues/245. > > -- > > Levi Waldron > > Associate Professor > > Department of Epidemiology and Biostatistics > > CUNY Graduate School of Public Health and Health Policy > > Institute for Implementation Science in Population Health > > 55 W 125th St, New York NY 10035 > > https://waldronlab.io > > Join the microbiome Virtual International Forum: https://microbiome-vif.org > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel