Here we keep all the external links for the ModelSEED Biochemistry Database, the synonyms of the compounds and reactions, and the EC number of the reactions.
We believe that all the file names are self-explanatory with the
exception of Source_Classifiers.txt. Here we classify the sources of
our biochemistry in three tiers:
- Primary Database: This is only KEGG and MetaCyc, the two sources of the structural data we used to perform our initial merger
- Secondary Database: This is any other database that was integrated based on aliases, including names
- Published Model: This is data from any published metabolic reconstruction
In the "Source" column for the biochemistry database, we use these three classifiers in succeeding order, and a fourth classifier for any new compounds or reactions that do not come from these three sources: "User".