Apply previous manual changes made to metabolic_reactions.tsv

[ggsun]

This PR makes changes to the metabolism process such that all relevant manual changes that were previously made to the metabolic_reactions.tsv file (previously called reactions.tsv, see link for complete list) are applied to the new version of the file pulled from EcoCyc in a repeatable, robust way. For this purpose I added a metabolic_reactions_modified.tsv file that lists out the rows in metabolic_reactions.tsv that should be replaced, with an extra column to explain the intents of those changes. This PR also includes the addition of equilibrium complexes as possible catalysts of metabolic reactions, which was previously done manually by directly editing the reactions.tsv file.

All of these changes do not solve issue #1077 so further investigation would be needed to address this.

[tahorst]

Looks good! I like all the different types of flat file modifications we can make now. Do you think there are any issues with compound classes being too general or too specific with the new EcoCyc flat files? Seems like most of these changes to metabolic reactions are compound class -> specific instance or specific instance -> compound class.

[ggsun]

Looks good! I like all the different types of flat file modifications we can make now. Do you think there are any issues with compound classes being too general or too specific with the new EcoCyc flat files? Seems like most of these changes to metabolic reactions are compound class -> specific instance or specific instance -> compound class.

Yeah, it looks like there isn't a clear rule on where they're using specific instances vs compound classes. Might be useful to ask for another file that lists out the hierarchy between all these individual instances and classes so we can more systematically handle this.