Short term additions before lab release

[steve-federowicz]

• Add genome_id to model table
  • Using jons supplement for ecoli model genome_ids
  • Using links from old bigg website to figure out genome_ids for those models
• Add synonyms table using 'gene_synonyms' field of the genbank files
• Likely will need to use synonyms table to help in mapping GPRs from the older models on the old bigg site
• Make the cosmetic change of merging compartmentalized_component with model_component, so that there is only model_component that now contains a compartment_id
  • This will make the schema on draw.io identical to zaks schema

[zakandrewking]

• Make the cosmetic change of merging compartmentalized_component with model_component, so that there is only model_component that now contains a compartment_id
  • This will make the schema on draw.io identical to zaks schema

OK. this may be a small thing, but I think it's still important.

If we merge these, then the reaction matrix rows will be model-specific. In the current schema, the reaction matrix rows are universal, so there is less redundancy in the table. Better yet, you could take all the models away, and still have a universal database of reactions and metabolites! Pretty cool.

[steve-federowicz]

Ahhhh right, yea that makes sense. I updated the model schema.