Hi, I assume that you would like to map your EC numbers to reactions in BiGG reaction database to draft your genome scale model. If it is the case, then it is not really straightforward to do that. As far as I know, it does not really tell which EC numbers or which compounds participate in particular reaction when you download BiGG reaction database. I suggest to download some sbml models from BiGG and then map your EC list to EC numbers in those SBML files. Not all models from BiGG contain EC numbers for each of the reaction, but It may worth to map against saccharomyces iMM904, they have at least 600 ECnumbers that you can try.

BiGG is kind of "standard" representation of reactions and metabolites for genome scale model, but it is not always convenient to extract information from BiGG. Another less inconsistent naming system for reactions and metabolites that you can also use is KBase ID. Many genome scale models are using this format. But again, it is also not really easy to retrieve reactions from your EC list. This is a common problem in genome scale model when you want to build your model from your own annotation. You can download all reactions and metabolites from KBase here https://kbase.us/metabolic-modeling-faq/#How-can-I-download-all-the-biochemical-compounds-and-reactions-in-KBase . Depend on your organism but at least you will get the core metabolism which you can build up by adding more reactions manually.

In the worst case, you can also retrieve reactions from the most similar organism to your organism that have already modelled. Or if there is no closely related organism, there is Ecoli model.

I hope this help.

Cheers,

Hi Thanks for sharing the Reaction set from ModelSeed. But the issue is like the model which I am using don't have Model seed Identifier. So may be after mapping with Model Seed, I need to find another solution to map with the semi-curated model of mine!

Thanks Again!