TaxSEA Database A dataset containing taxon sets. Each item in the list is a taxon set, and each member within a taxon set is a taxon.

Usage

data(TaxSEA_db)

Format

A list of vectors. Each vector contains character strings representing taxa as NCBI taxonomy IDs.

Source

See the README. BacDive sets: Schober et al. (2025) BacDive in 2025: the core database for prokaryotic strain data, via https://bacdive.dsmz.de.

Details

Set names start with their source: MiMeDB_, GutMGene_, GMRepoV2_, mBodyMap_, BacDive_ and so on.

The BacDive_ sets describe measured phenotypes of cultured strains (oxygen tolerance, Gram stain, substrate use, enzyme activities, growth temperature, salt and pH ranges and others), aggregated to species over every strain BacDive holds. They are built by the bacdive_harvester pipeline (https://github.com/feargalr/bacdive_harvester); see inst/scripts/make_BacDive_sets.R. Only sets with at least 3 members are included. Names read BacDive_<Family>_<value>, optionally followed by an assay context (e.g. _fermentation, _reduction) and _negative for species tested and found negative, e.g. BacDive_Oxygen_facultative_anaerobe, BacDive_Uses_nitrate_reduction.

Per-set provenance (source family, number of species and strains behind each set) and a record of the build (harvester release, BacDive client version, harvest dates) are shipped with the package:


system.file("extdata", "BacDive_set_provenance.tsv", package = "TaxSEA")
system.file("extdata", "BacDive_build_info.tsv", package = "TaxSEA")

Examples

data(TaxSEA_db)
all_sets <- names(TaxSEA_db)
GABA_producers<-TaxSEA_db[["MiMeDB_producers_of_GABA"]]