This defines the valid taxonomic databases that can be used in taxon_db
objects and objects that use taxon_db objects, such as taxon_id and
taxon. db_ref$get can be used to see information for the databases. Users
can add their own custom databases to the list using db_ref$set. For each
database the following information is included:
The URL for the website associated with the database
A short description
The regular expression that defines valid taxon IDs
The ranks used in the database if specified
Examples
# List all database definitions
db_ref$get()
#> <taxon_db_def[8]>
#> _____________________ ncbi ______________________
#> url: http://www.ncbi.nlm.nih.gov/taxonomy
#> desc: NCBI Taxonomy Database
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _____________________________ gbif _____________________________
#> url: http://www.gbif.org/developer/species
#> desc: GBIF Taxonomic Backbone
#> id_regex: [0-9]+
#> rank_levels: kingdom < phylum < order < family < genus < species
#>
#> _________________________________ bold _________________________________
#> url: http://www.boldsystems.org
#> desc: Barcode of Life
#> id_regex: [0-9]+
#> rank_levels: phylum < class < order < family < subfamily < genus < spec…
#>
#> ___________________ col ___________________
#> url: http://www.catalogueoflife.org
#> desc: Catalogue of Life
#> id_regex: [a-z0-9]{32}
#> rank_levels:
#>
#> ______________ eol ______________
#> url: http://eol.org
#> desc: Encyclopedia of Life
#> id_regex: [0-9]+
#> rank_levels:
#>
#> ____________________ nbn ____________________
#> url: https://nbn.org.uk
#> desc: UK National Biodiversity Network
#> id_regex: [A-Z]{5}[0-9]{10}
#> rank_levels:
#>
#> ________________ tps ________________
#> url: http://www.tropicos.org/
#> desc: Tropicos
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _______________________ itis _______________________
#> url: http://www.itis.gov
#> desc: Integrated Taxonomic Information System
#> id_regex: [0-9]+
#> rank_levels:
# Get a specific database definition
db_ref$get('ncbi')
#> <taxon_db_def[1]>
#> _____________________ ncbi ______________________
#> url: http://www.ncbi.nlm.nih.gov/taxonomy
#> desc: NCBI Taxonomy Database
#> id_regex: [0-9]+
#> rank_levels:
# Add or overwrite a database definition
db_ref$set(
name = "my_new_database",
url = "http://www.my_tax_database.com",
desc = "I just made this up",
id_regex = ".*"
)
# Reset definitions to default values
db_ref$reset()