README.md

RheaReactions.jl

This is a simple package you can use to query Rhea reactions and associated annotations. Its primary use is in reconstructing metabolic models. It caches all requests by default, speeding up repeated calls where appropriate.

using RheaReactions # load module

get_reaction(11364) # Rhea reaction ID 11364

You can also get the metabolites associated with that reaction:

# [(coefficient, metabolite), ...] 
coeff_mets = get_reaction_metabolites(11364) # Rhea reaction ID 11364

And look at each metabolite individually:

coeff_mets[1][2] # metabolite

You can also look for all reactions that have a certain set of metabolite substrates and products. This function looks for all reactions that have both CHEBI:29985 (L-glutamate) and CHEBI:58359 (L-glutamine) on opposite sides of the reaction:

substrate_ids = [29985,]
product_ids = [58359,]
get_reactions_with_metabolites(
    substrate_ids,
    product_ids,
) # NB: not cached!

You can also look for Rhea reactions associated with a specific Uniprot ID:

get_reactions_with_uniprot_id("P30085")

You can look for all Rhea reaction IDs that map to a specific EC number:

get_reactions_with_ec("2.5.1.49")

Rhea reactions are typically broken into quartets.: one reference reaction, two directional reactions, and one bidirectional reaction. You can find all four reactions given any single reaction:

get_reaction_quartet(11364) # Rhea reaction ID 11364

You can test the package with:

] test

Troubleshooting

The cache can be source of subtle issues. If you get errors or unexpected behavior do:

1. clear_cache!(),
2. Restart the Julia session. If you still get errors, please file an issue!