ModelSEED / Model-SEED-core

The Model SEED is a tool for building, curating, and analyzing gonome-scale metabolic models. Visit the Model SEED homepage for installation instructions and full feature documentation.
http://bionet.mcs.anl.gov/index.php/Model_SEED_Homepage
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Feature request: source of annotation for reactions #153

Open samseaver opened 12 years ago

samseaver commented 12 years ago

Again, I don't know what you are implementing, but the two sources of annotations for each reaction are genes, and EC numbers. While the REACTION_MODEL table has a PEGS field, it doesn't have an EZYMES field.

This essentially means that for the new EC numbers that get merged into the ENZYMES field in the REACTION table, I've currently no easy way of knowing a posterior which database/model the particular ENZYMES numbers from from.

I've got an interim hack, where I add my own two letter code depending on the source, and I filter these out when parsing the ENZYMES and PEGS field, this isn't ideal, but it allows me to see which genes and EC numbers, for example, from from a BioCyc database or comes from KEGG.