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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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Re-organization of aliases #111

Closed samseaver closed 5 years ago

samseaver commented 5 years ago

At the heart of this re-organization is the concept of obsolescence, or linked compounds and reactions. If compounds and reactions are supposed to be obsolete, in that they are already represented by another compound, then all of the aliases, synonyms and (in the case of reactions) enzyme classes of the obsolete compound are also assigned to the representative compound, and vie-versa.

This might seem like overkill, but it's necessary to simplify the workflow of merging and disambiguating compounds and reactions, which would mean either merging or separating the contents of the aliases field.

The old assignments are now stored in the Provenance folder, so we can still trace the source of each alias.

samseaver commented 5 years ago

Merging. The organizing of the aliases was discussed at a prior meeting.