Data and script for parsing BioSample antibiogram data
The repo contains
biosample_result-4.xml.zip - a zipped XML format file which is the result of a search of the NCBI BioSample database, downloaded in March 2023
multiple_XML_antibiotgrams.Rmd - a R markdown script for parsing the NCBI XML file
ncbi_antibiograms_20230312.tsv.zip - a zipped tsv file of the results of the multiple_XML_antibiotgrams.Rmd script. A database of antibiogram results from strains with public deposited genome sequences linked to BioSample IDs
Please use the data for your analysis if you like but be aware that I make no guarantees of accuracy!