Download metabolic information from databases using the NCBI Taxonomy ID

Question

[ThaiosX195]

Hello everyone,

I would like to download metabolic data (pathways, metabolites, etc) of bacteria/virus species, starting from the NCBI Taxonomy ID. Do you know a script or a package in R or Python that could help me to find those information in databases like KEGG or MetaCyc or others?

Eg:

1354 (taxonomy ID) --> Enterococcus hirae --> KEGG/MetaCyc/other with R/Python --> Metabolic data download

Thank you so much in advance!

Matteo

[GenoMax]

Using EntrezDirect you can easily get the name of the organism

$ esearch -db taxonomy -query "1354[taxID]" | esummary | xtract -pattern DocumentSummary -element ScientificName
Enterococcus hirae

What you likely can't get (without getting a license for MetaCyc/KEGG) is bulk downloads of the metabolic data for that organism. That would likely go against the use policies for the tools mentioned.

http://bigg.ucsd.edu/ or https://img.jgi.doe.gov/ (requires an account) may be "no license" options you could look at.