microbetag : building a thorough database of genome-scale KO annotations

In this repository we keep internal data for the microbetag microbial co-occurrence network annotator. microbetag makes use of 2-column files for each genome, indicating the KO term found and a KEGG module in which this terms takes part into. As a single KO term might participates in more than one KEGG modules, the same KO might be more than once in an annotation file. chem_xref.tar.gz The MNXref namespace The identifier of a chemical compound in an external resource [XREF] The corresponding identifier in the MNXref namespace [MNX_ID] The description given by the external resource [STRING] MNXref 4.0 release notes: - The third column (evidence tag for the mapping) was suppressed - The descriptions were completed - Deprecated identifiers were moved into they own table below gtdb_modelseed_gems.zip for all the GTDB genomes their corresponding PATRIC annotations were gathered. Then, using modelseedpy we constructed their genome scale metabolic reconstructions gtdb_kofam_scan_per_module.tar.gz all representative genomes of GTDB (v.202) were parsed and their corresponding `.faa` files were retrieved from the NCBI FTP. Then the kofam_scan tool was used to annotate them and finally a manual script was used to keep KOs of each genome per module. SeedSet.pkl.gz A pickle file with the seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page. Example: PATRIC SeedSet373.172 [cpd00891, cpd00136, cpd00199, cpd01772, cpd00...397278.5 [cpd00891, cpd00136, cpd01772, cpd02698, cpd08... NonSeedSet.pkl.gz A pickle file with the non seeds of each GEM included in the gtdb_modelseed_gems.zip file and related to the KEGG MODULES based on the seedId_keggId_module.tsv file you can find on microbetag's GitHub page. Example: PATRIC NonSeedSet64187.548 [cpd00508, cpd00869, cpd00774, cpd03830, cpd00...74426.1719 [cpd00204, cpd00447, cpd20171, cpd03470, cpd00... seeds_per_genome.pkl.gz A pickle file with a binary representation of the seeds per genome . Example: cpd00493 cpd00296 cpd11431 cpd00063 cpd15717 ... 2162051.4 1 0 0 1 0 0 0 0 0 0 ... nonseeds_per_genome.pkl.gz Like above for non-seeds. phen_classes.zip A list of pickle files with the re-trained classes of phenDB for the prediction of functional traits on a genome.