json cobra specification

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ronan.mt...@gmail.com

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Oct 20, 2022, 12:39:58 PM10/20/22
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Hi All,
I'd like to export metabolic networks in json format to explore connecting escher with the cobra toolbox. Do any of yee know of a document that gives a specification of a metabolic network in json format, ideally with examples?
Regards,
Ronan

Moritz Beber

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Oct 20, 2022, 4:27:42 PM10/20/22
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Hi Ronan,

There is a JSON schema that details the structure of a metabolic model. No claim to perfection but you can find the current version here https://github.com/opencobra/cobrapy/blob/devel/src/cobra/io/schema_v1.json

As for examples, you can load any model of your choosing in cobrapy and store it using save_json_model https://cobrapy.readthedocs.io/en/latest/autoapi/cobra/io/json/index.html#cobra.io.json.save_json_model

Best,
Moritz
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