Determine the NCBITaxon ID for a species from the scientific name

This function returns the NCBITaxon ID for a species from the scientific name. It's probably easier just looking it up via a google search, and most of the ones used at the Allen Institute are listed here: https://github.com/AllenInstitute/GeneOrthology.

Usage

getNCBITaxon(
  species,
  ncbitaxon_obo = NULL,
  obo.file = "ncbitaxon.obo",
  obo.url =
    "https://raw.githubusercontent.com/obophenotype/ncbitaxon/refs/heads/master/subsets/taxslim.obo"
)

Arguments

species: Scientific name for one or more species. Not case sensitive, but make sure you spell it correctly or the function will return NA.
ncbitaxon_obo: Variable in ontologyIndex format read in from obo.file file.
obo.file: Location to look for or put the ncbitaxon.obo file, if ncbitaxon_obo is not provided
obo.url: URL to download obo.file from, if not already downloaded. We recommend keeping the default and only switching to "http://purl.obolibrary.org/obo/ncbitaxon.obo" if absolutely necessary.

Value

an AIT.anndata object with the updated/additional vector of highly variable genes