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 this source is no longer updated as far as we can tell.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The PlantList: no longer updated, so you shouldn’t need to download this after the first download.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 http://www.catalogueoflife.org/DCA_Export/archive.php
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.
![[ICO]](/icons/blank.gif){kind=icon}
![[PARENTDIR]](/icons/back.gif){kind=icon}
![[TXT]](/icons/text.gif){kind=icon}
