taxizedb

taxizedb - Tools for Working with Taxonomic Databases

Docs: https://docs.ropensci.org/taxizedb/

taxizedb is an R package for interacting with taxonomic databases. Its functionality can be divided in two parts: 1. You can download the databases to your platform 2. You can query the downloaded databases to retrieve taxonomic information.

This two step approach is different from tools which interact with web services for each query, and has a number of advantages:

Once you download a database you can work with it offline
Once you download a database querying it is super fast
As long as you store your database files all the queries in your analysis will be fully reproducible

Data sources

When you download a database with taxizedb it will automatically convert it to SQLite and then all query functions will interact with this SQLite database. However, not all taxonomic databases are publicly available, or can be converted to SQLite. The following databases are supported:

Get in touch in the issues with any ideas on new data sources.

Data sources - legacy support

The Plant List (TPL) has been replaced by World Flora Online. The website seems to be down so taxizedb can no longer facilitate new downloads. However, already downloaded database files can still be queried using taxizedb functions, for reproducibility.

Package API

This package for each data sources performs the following tasks:

Downloaded taxonomic databases db_download_*
Create dplyr SQL backend via dbplyr::src_dbi - src_*
Query and get data back into a data.frame - sql_collect
Manage cached database files - tdb_cache
Retrieve immediate descendents of a taxon - children
Retrieve the taxonomic hierarchies from local database - classification
Retrieve all taxa descending from a vector of taxa - downstream
Convert species names to taxon IDs - name2taxid
Convert taxon IDs to species names - taxid2name
Convert taxon IDs to ranks - taxid2rank

You can use the src connections with dplyr, etc. to do operations downstream. Or use the database connection to do raw SQL queries.

Installation

CRAN version

install.packages("taxizedb")

dev version

remotes::install_github("ropensci/taxizedb")

Citation

To cite taxizedb in publications use:

Chamberlain S, Arendsee Z, Stirling T (2023). taxizedb: Tools for Working with ‘Taxonomic’ Databases. R package version 0.3.1. https://doi.org/10.5281/zenodo.1158055