Taxa Lookup

Taxa Lookup ({taxalook}) is a database and repository containing tabular information on species including their places of occurrence (e.g. countries, continents), their natural habitats (e.g. freshwater) they are occurring in and other information.

Usage

You can use the R-package {taxalook} to query the database directly from R OR you can download the data from its Zenodo-Repository.

From R

Installation

remotes::install_github('andschar/taxalook')

Example

You can query one or multiple taxa (or even all the taxa in the database by not supplying a string) and you can add specific information on the taxa depending on your requirements (e.g. habitat = TRUE).

require(taxalook)

tax = c('Pimephales promelas', 'Daphnia magna')

tl_query(tax) # Only taxalook identifier and taxon name
tl_query(tax, what = 'taxonomy') # Taxonomy information
tl_query(tax, what = 'id') # Identifiers to other databases
tl_query(tax, what = 'group') # Taxa convenient grouping
tl_query(tax, what = 'habitat') # Habitat information
tl_query(tax, what = 'continent') # Continent occurrence information
tl_query(tax, what = 'country') # Country occurrence information

Raw Data only

All the data tables are stored in the sub-directory data as tab-separated (i.e. .tsv) and non-quoted files.

table	description
tl_continent	On which continent does a taxon occur ?
tl_country	In which country does a taxon occur ?
tl_group	To which group (e.g. algae, invertebrate) does a taxon belong to ?
tl_habitat	In which habitat does a taxon occur ?
tl_id	Table containing identifiers from other databases (e.g. GBIF, WORMS)
tl_taxonomy	Taxonomic classification

The tables can be merged via the unique key column tl_id.

Contribute

The information here is by no means complete and users are highly encouraged to contribute information to this database. Missing entries, wrong entries, more detailed information, you name it. Please signal issues via the Issue tracker.