yeastnet / Discussion / Help: Annotation of reactions

Annotation of reactions

Forum: Help

Creator: Naveen Venayak

Created: 2012-10-16

Updated: 2015-01-22

Naveen Venayak - 2012-10-16

Hi,

I was wondering if there is a file listing the reactions with their name, stoichiometry, etc, or if it must just be extracted from the model file?

Thank you

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Graham R - 2013-06-20

I can recommend using openCobra as mentioned in the README to pull out the reaction list or libSBML to parse the xml in through python.

I have a very similar question. Is there a good way to match reactions in the Yeast 7.00 model other reaction databases. For example is there a map of reaction ID codes S_0001 etc to known reaction codes, reaction IDs other widely used identifer, which I could use to match these reactions to something such as meta-cyc. The long names while very clear is seem very challenging to use for automatic matching.

cheers

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- Luca Barbanotti - 2015-01-22
  
  Hi Graham,
  
  I have similar problem too! I'm using Yeast 6.06 model with Cobra and Matlab and I need to sort all model's reaction for pathway, but "rxnReferences","rxnECNumbers" and "rxnNotes" fields are completely empty.
  
  Did you solve your problem? Probably EC numbers would be sufficient!
  Is there anyone who can help please?
  
  Thanks
  Luca
  
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