Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine learning pipelines. My own searches usually yield only databases that curate mutations related to drug resistance class ("resistant, possibly resistant, susceptible), but not quantitative information in a standardized form like the Stanford database.

  • $\begingroup$ There are thousands of phenotypic variables. The most commonly documented is that of growth rates (or colony size). Also you can have 2^n genotypes for an organism with n genes, assuming there are only two alleles of a gene. Whole genome single and double knockouts experiments have been donee for yeast and E.coli, afaik, but I am not aware of a database. These experiments just measure the growth and fitness. $\endgroup$
    Oct 19, 2015 at 9:28


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