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 withtaxizedb 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:
- NCBI Taxonomy
- ITIS
- World Flora Online (WFO)
- Catalogue of Life (COL)
- Global Biodiversity Information Facility (GBIF)
- Wikidata
Get in touchin 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The Plant List (TPL) has been replaced by World Flora Online.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 sotaxizedb can no longer facilitate new downloads. However, already downloaded database files can still be queried usingtaxizedb functions, for reproducibility.
Package API
This package for each data sources performs the following tasks:
- Downloaded taxonomic databases
db_download_* - Create
dplyrSQL backend viadbplyr::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 thesrc connections withdplyr, 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
Meta
- Pleasereport any issues, bugs or feature requests.
- License: MIT
- Get citation information for
taxizedbin R withcitation(package = 'taxizedb') - Please note that this package is released with aContributor Code of Conduct. By contributing to this project, you agree to abide by its terms.