Where does MetaCyc_pathway_map come from?

[YuZhang-learner]

Dear Liu, Thank you for making such a good R package. I was using PICRUST2's Metacyc to predict 16S functionality and found that your example file has Metacyc's metacyc hierarchy MetaCyc_pathway_map. I would like to ask where is the source of this hierarchy file? Does it include all metabolic pathways on the MetACYC https://biocyc.org/ECOLI/class-tree?object=Pathways As far as I know, there may be a metabolic pathway on the website that belongs to a different category in the same hierarchy on the website, and your sample files seem to correspond one to one. Also, can all results of PicRust Metacyc be classified to different level using the MetaCyc_pathway_map file?

# MetaCyc pathway output
tmp_file_path <- system.file("extdata", "example_PICRUSt2_MetaCyc_path_abun_unstrat.tsv", package="file2meco")
pathway_table <- read.delim(tmp_file_path, row.names = 1)
data("MetaCyc_pathway_map")
tmp <- microtable$new(otu_table = pathway_table, tax_table = MetaCyc_pathway_map)
tmp$tidy_dataset()
tmp

[ChiLiubio]

Hi @YuZhang-learner ,

Please see these two topics in the biobakery forum (https://forum.biobakery.org/t/metacyc-pathway-hierarchical-structure-like-kegg-pathway-map-file/1883/4) and (https://forum.biobakery.org/t/metacyc-hierarchy-to-invetigate-identify-specific-pathways/1830). I documented why and how I created the mapping file. The "different category in the same hierarchy" issue can be also found in the topics. This file includes all metabolic pathways on the Metacyc. I have updated this file again about two months ago.

Best Chi

[YuZhang-learner]

Thanks.

[ChiLiubio]

Please feel free to tell me if you find any pathway missing in the mapping file. Thanks in advance.