This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Download metabolic information from databases using the NCBI Taxonomy ID

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

metabolism database r taxonomy ncbi
• 850 views • link
updated by Giulio • Giulio • written by ThaiosX195 • ThaiosX195

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.

• 0 views • link
written by GenoMax GenoMax

1 answer

Hi!

In both R and Python, you can now use the ariadne package to link taxids to KEGG and MetaCyc pathways and metabolites. It uses the KEGGREST API for KEGG and the Web of Life 2.0 mapping files for MetaCyc. While the former is up-to-date, the latter is an older version of MetaCyc before it became proprietary.

Happy to help with ariadne!

• 0 views • link
written by Giulio • Giulio

Log in to answer this question.

More posts like this