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SBRG / bigg_models

The BiGG Models website server
http://bigg.ucsd.edu
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bigg models don't have an SBO ID #337

Closed npusarla closed 4 years ago

matthiaskoenig commented 5 years ago

@npusarla Could you be more specific what the issue is and provide some additional information?

SBO Terms can be defined on many parts of a model, e.g., the model itself, the species, the reactions, geneProducts, ... . It would help if you describe what information you want to access precisely and what your use case is, i.e., provide some additional information on this issue. Which model did you look at? This information helps in seeing what is going on.

Best Matthias

npusarla commented 5 years ago

Hi! thanks for answering, I'm working with @zakandrewking , didn't realize someone would respond to this! In distinguishing between XML and JSON models, I noticed that json models did not have the SBO ID

draeger commented 5 years ago

Now it is becoming clearer. I assume you're aiming to define a new attribute to the model in JSON.

Maybe this could be a good chance to add an SBO id to an abstract superclass of all BiGG-JSON model components? In this way, you could add an SBO term to everything, including reactions (think about the SBO term for exchange, transport, demand, biomass, and so forth), metabolites (e.g., small molecule, complex, etc.), and so on?

zakandrewking commented 5 years ago

update: we will annotate JSON models with at least the SBO terms expected in Memote

Midnighter commented 4 years ago

Just a heads up that I had started some work to update the JSON schema for models in cobrapy. We should coordinate on this.

zakandrewking commented 4 years ago

yes, good idea. just tag me on the discussion wherever it happens (or on slack)