taxizedb

taxizedb - Tools for Working with Taxonomic Databases on your machine

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

taxize is a heavily used taxonomic toolbelt package in R - However, it makes web requests for nearly all methods. That is fine for most cases, but when the user has many, many names it is much more efficient to do requests to a local SQL database.

Data sources

Not all taxonomic databases are publicly available, or possible to mash into a SQLized version. Taxonomic DB’s supported:

• NCBI: text files are provided by NCBI, which we stitch into a sqlite db
• ITIS: they provide a sqlite dump, which we use here
• The PlantList: created from stitching together csv files. this source is no longer updated as far as we can tell. they say they’ve moved focus to the World Flora Online
• Catalogue of Life: created from Darwin Core Archive dump.
• GBIF: created from Darwin Core Archive dump. right now we only have the taxonomy table (called gbif), but will add the other tables in the darwin core archive later
• Wikidata: aggregated taxonomy of Open Tree of Life, GLoBI and Wikidata. On Zenodo, created by Joritt Poelen of GLOBI.
• World Flora Online: http://www.worldfloraonline.org/

Update schedule for databases:

• NCBI: since db_download_ncbi creates the database when the function is called, it’s updated whenever you run the function
• ITIS: since ITIS provides the sqlite database as a download, you can delete the old file and run db_download_itis to get a new dump; they I think update the dumps every month or so
• The PlantList: no longer updated, so you shouldn’t need to download this after the first download. hosted on Amazon S3
• Catalogue of Life: a GitHub Actions job runs once a day at 00:00 UTC, building the lastest COL data into a SQLite database thats hosted on Amazon S3
• GBIF: a GitHub Actions job runs once a day at 00:00 UTC, building the lastest GBIF data into a SQLite database thats hosted on Amazon S3
• Wikidata: last updated April 6, 2018. Scripts are available to update the data if you prefer to do it yourself.
• World Flora Online: since db_download_wfo creates the database when the function is called, it’s updated whenever you run the function

Links:

• NCBI: ftp://ftp.ncbi.nih.gov/pub/taxonomy/
• ITIS: https://www.itis.gov/downloads/index.html
• The PlantList - http://www.theplantlist.org/
• Catalogue of Life:
  • latest monthly edition via https://www.catalogueoflife.org/data/download
• GBIF: http://rs.gbif.org/datasets/backbone/
• Wikidata: https://zenodo.org/record/1213477
• World Flora Online: http://www.worldfloraonline.org/

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

All databases are SQLite.

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.

install

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

• Please report any issues, bugs or feature requests.
• License: MIT
• Get citation information for taxizedb in R with citation(package = 'taxizedb')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.