ncbiTaxonomy: NCBI Taxonomy Database
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Details Value References See Also

Retrieve taxonomic classification from the Taxonomy database maintained by the National Center for Biotechnology Information (NCBI).

1	ncbiTaxonomy(x, quiet = FALSE)

`x`	Database connection parameters, either as object of class `dbPars` or `megapteraProj`. Alternatively, can be a character string giving the path to the megaptera file system (see `megapteraInit`).
`quiet`	Logical, indicating if diagnostic messages should be printed on screen.

The NCBI taxonomy database will be downloaded via FTP in "taxdump" format, unpacked, and translated into data frames. In a second step, the data frames will be stored in a postgreSQL database called "ncbitaxonomy". Any existing data will be overwritten in the process.

There is no versioning of the Taxonomy database like the release numbers of GenBank. The taxonomy FTP dump files are updated hourly so it might be reasonable to update them together with GenBank sequences data.

ncbiTaxonomy is called for its side effect (see Details).

NCBI Taxonomy Database website: http://www.ncbi.nlm.nih.gov/taxonomy

Federhen, Scott. 2012. The NCBI taxonomy database. Nucleic Acids Research 40: DI36-DI43.

stepA for extracting the taxonomic information relevant for a given megaptera project; dbUpdateTaxonomy and dbReadTaxonomy for storing and retrieving taxonomic information in a megaptera project database; dbSummaryTaxonomy for a short numerical summary of the project taxonomy.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.