get_taxa: Obtaining taxonomy for a SAFE dataset.

In ImperialCollegeLondon/safe_data: Interface to Data from the SAFE Project

Obtaining taxonomy for a SAFE dataset.

Description

This function generates a taxonomy table for a specified SAFE dataset record. Each row represent a taxon used in the data worksheets in the dataset and the table fields show the taxonomic hierarchy for those taxa.

Usage

get_taxa(obj)

Arguments

obj	A single record id, or an existing safedata dataframe.

Details

All SAFE datasets containing taxa must include worksheets providing taxonomy details, used to validate the taxa in the dataset against either or both of the GBIF or NCBI taxonomy database. All entries in these worksheet are validated against the databases before publication and are used to populate a taxonomic index for safedata datasets. The validated taxonomic index for a specific dataset is also available in the metadata for a record and this function converts that metadata into a taxonomy table for the dataset.

The returned table includes the fields worksheet_name, taxon_name, taxon_rank and taxon_status, along with the taxonomy database used to validate the taxon (taxon_auth). These fields provide the original taxonomy worksheet data included.

For more details on the structure of the taxon worksheets see: https://safedata-validator.readthedocs.io/en/latest/data_format/taxa.html # nolint

Value

A taxonomy table of classes "safe_taxa" and "data.frame".

Synonyms

The taxon table will include extra rows for worksheet taxa that are GBIF synonyms or are merged in the NCBI taxonomy. There will be a row giving the taxonomic hierarchy for the original taxon name provided with the dataset and an additional row providing the canonical taxon name. The worksheet name for these rows will be identical.

Taxonomic ranks

NCBI and GBIF differ in their use of taxonomic ranks: GBIF uses a reduced set of core 'backbone' ranks, where NCBI supports a wider range of ranks. The taxon hierarchy used for safedata reduces NCBI to the core GBIF backbone ranks but adds Superkingdom, which is used for bacterial and viral groups.

Especially note that the taxonomy used by GBIF and NCBI are **not congruent**: if the same taxon is included using both systems, it may well have substantially different ranks.

See Also

add_taxa

Examples

    set_example_safedata_dir()
    taxa <- get_taxa(1400562)
    set_example_safedata_dir(on=FALSE)

ImperialCollegeLondon/safe_data documentation built on Jan. 27, 2024, 9:51 a.m.