bacdive_abx: Antibiotics data from bacdive.org that is _not_ in the...

In scottdaniel/bacphene: Imports Bacterial Phenotype Data Into R

Antibiotics data from bacdive.org that is _not_ in the antibiogram format. Produced by getAbx.

Description

Antibiotics data from bacdive.org that is _not_ in the antibiogram format. Produced by getAbx.

Usage

bacdive_abx

Format

A data frame with the following columns:

'@ref'

The literature reference in the bacdive database.

ChEBI

ChEBI (Chemical entities of biological interest) identifier.

metabolite

Common name of the antibiotic.

'is antibiotic'

Should all be "yes" values.

'is sensitive'

Whether or not strain is sensitive to this antibiotic. Possible values are "yes", "no", and NA.

'is resistant'

Whether or not strain is resistant to this antibiotic. Possible values are "yes", "no", and NA.

ID

bacdive ID of strain.

taxon

The name of the taxon.

rank

The rank of the taxon.

type_strain

Whether or not the strain is the type strain for the species.

'doi/url'

DOI (Digital Object Identifier) for the reference.

'resistance conc.'

The concentration of antibiotic at which resistance was measured.

'sensitivity conc.'

The concentration of antibiotic at which sensitivity was measured.

'group ID'

Group ID of combined antibiotics i.e. bacteria was tested against multiple antibiotics at once.

'is intermediate'

Whether or not strain is intermediate sensitive to this antibiotic.

'intermediate conc.'

The concentration of antibiotic at which intermediate sensistivity was measured.

Note

Data frame also has the attribute "date_downloaded" for when the data was downloaded from bacdive.org.

scottdaniel/bacphene documentation built on March 25, 2023, 12:51 p.m.