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Completing the annotation of a model

MB
Maëva Beugin
Oct 24, 2023, 1:57 PM

Introduction

Do you have a metabolic model and want to improve the annotation of metabolites and reactions?
Metabolic models are sometimes lacking in annotation, particularly at the level of identifiers in recognised databases (BiGG, Rhea, ChEBI). For the model to be better recognised by Constellab and for the experiments to work optimally, it is preferable to add these identifiers for both the metabolites and the reactions.
Follow the steps below to get a more robust model in just a few clicks!

Prerequesites

Check that your model is in json format, if not go here to convert it.

If your model does not have a BiGG identifier or the literal name for metabolites, or a BiGG identifier for reactions, then this task will not be able to annotate your model. However, a live task could annotate it if you have a mapping table.

Steps to follow

  1. Upload your model
  2. Link it to the "Convert Model Annotation" task available in the "gws_gena" brick
  3. Fill parameters : you must indicate the type of identifier and the type of name of your metabolites and reactions (BiGG, literal name or other)
  4. Run your experiment
  5. Get your annotated model in output and a table summarising the number of identifiers added

You now have a better annotated model, which is therefore more robust and will be better recognised by Constellab when you continue your experiments!
This demonstration was done using this model from BiGG.
This demonstration was done using task from the brick gws_gena in version 0.5.2.