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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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What data should be included in a compartment-free Biochemistry object? #16

Closed mmundy42 closed 7 years ago

mmundy42 commented 9 years ago

Currently a Biochemistry object has the following data:

Questions:

  1. With reactions defined in a compartment-free notation, are compartments still needed in the Biochemistry or can they only be included in Model Templates?
  2. Do we need to define source files for cues, compoundSets, and reactionSets so they can be included in the Biochemistry?
  3. Does the Biochemistry object need to include compound_aliases and reaction_aliases or do the aliases only need to be available via SOLR?
janakagithub commented 9 years ago

Does the Biochemistry object need to include compound_aliases and reaction_aliases or do the aliases only need to be available via SOLR I would want to see the compound and reaction aliases intact in the biochemistry object. When we use biochemistry object for analysis, in most cases, it is through aliases that we recognize the compounds and reactions

chian commented 9 years ago

In theory, compartments can go provided old models can link back to the old biochemistry. I would prefer to see them to go and for us to go all compartment free.

Sent from my iPhone

On Sep 1, 2015, at 1:11 AM, Mike Mundy notifications@github.com wrote:

Currently a Biochemistry object has the following data:

compounds reactions compartments cues compoundSets reactionSets compound_aliases reaction_aliases Questions:

With reactions defined in a compartment-free notation, are compartments still needed in the Biochemistry or can they only be included in Model Templates? Do we need to define source files for cues, compoundSets, and reactionSets so they can be included in the Biochemistry? Does the Biochemistry object need to include compound_aliases and reaction_aliases or do the aliases only need to be available via SOLR? — Reply to this email directly or view it on GitHub.

JamesJeffryes commented 7 years ago

This is out of date and was discussed at the jam session so I'm closing this issue