Combined antibiogram dataset from NCBI, ENA, BV-BRC, and more

The antibiograms.tsv.zip dataset collects antibiograms found in NCBI, ENA and BV-BRC. Each row corresponds to an antibiotic susceptibility test (AST) for a given sample against a specific antibiotic. The dataset is a table with 14 columns:

biosample. A unique identifier for the sample from the NCBI BioSample database.

sra_biosample. If given, a space-separated list of sample identifiers from the NCBI SRA Sample Database.

species. The species the sample belongs to, and, in some cases, with subspecies information.

antibiotic. The name of the antibiotic against which the sample is tested.

phenotype. The interpreted phenotype from the AST standard used during testing.

measurement_sign. If given, corresponds to the sign of the raw result from the AST. Its interpretation depends on the typing method.

measurement_value. If given, corresponds to the value of the raw result from the AST. Its interpretation depends on the typing method.

measurement_units. If given, corresponds to the units of the raw result from the AST.

typing_method. Name of the technique used for AST.

typing_platform. Name of the platform used for AST.

standard. Testing standard used for the interpretation of the phenotype.

genomes. Space-separated list of genome identifiers from the NCBI Genome Database (starting with GCA_ or GCF_), the BV-BRC Genome Database (starting with BVBRC_), or the ENA FTP Site (starting with ftp://ftp.sra.ebi.ac.uk/vol1/analysis/).

reads. Space-separated list of read run identifiers from the NCBI SRA database.

read_type. Space-separated list with the same length as the reads column, storing the type of read of each corresponding read run.

The gn-genomes.zip file contains some extra genomes with associated AST metadata found in metadata.xlsx file within it.