NCBITaxonomy

This package provides an interface to the NCBI Taxonomy. When installed, it will download the latest version of the taxonomy files from the NCBI ftp service. To update the version of the taxonomy you use, you need to build the package again. This package is developed as part of the activities of the Viral Emergence Research Initiative (VERENA) consortium, with financial support from the Institut de Valorisation des Données (IVADO) at Université de Montréal.

Overview of capacities

• retrieval of names from the taxonomy
• listing of children and descendant taxa
• fuzzy matching of names
• taxonomic distance measurement based on Shimatani distance

How does it work?

Internally, the package relies on the files provided by NCBI to reconstruct the taxonomy – the README for what the files contain can be found here. Note that the files and their expected MD5 checksum are downloaded when the package is built, and the data are not extracted unless the checksum matches. The package will also check that the checksum on the server is different from the version on disk, to avoid downloading data for nothing.

Data are saved as arrow tables when the package is built, and these are loaded when the package is loaded with import or using, as DataFrames. These data frames are not exported, but they are used by the various function of the package. Note also that a number of fields are removed, and some tables are pre-merged - not at build time (so there is no information loss, and you are welcome to dig into the full data frame by reloading the arrow file), but at load time.

Please note that the taxonomy dump is a big download. If the NCBITAXONOMY_PATH is not set, it will be stored in the package folder under the .julia directory, which is a bad idea. We strongly recommend editing your configuration file.

The package will check that the local version of the taxonomy file is sufficiently recent (no older than about 30 days), and if this is not the case, will prompt the user to update to a more recent version.