About metabolic reaction finds its corresponding abbreviation

[NA NA]

Dear all,

    I want to know how my metabolic reaction finds its corresponding abbreviation in large quantities. Now I only know that I can find one by one in BIGG and I sincerely hope to get everyone’s help.

    I highly appreciate your recommendations. Thanks

[Chintan Joshi]

Hi NA,

This can be accomplished in different ways:

1. BiGG has an API that you can access using various methods. 

2. BiGG provides *.txt files that you can download.

Using either of these two methods will require you to write scripts to extract the information out. For e.g., if you have the enzyme names and want the corresponding BiGG identifiers of the reaction, you can parse through bigg_models_reactions.txt. However, often enzymes names might be written differently and you will not have an exact match. To overcome this, I will recommend using enzyme commission (EC) numbers, homologous gene names or gene symbols of the corresponding reactions to get the correct BiGG identifiers associated to the reactions. 

Best,

Chintan

[NA]

Hi Chintan，

     Thank you very much for your reply. Your opinion has helped me solve a lot of problems. I have another question I want to ask you, that is, I want to know where my abbreviation for metabolites can be found.Like the ones I listed below：

Abbreviation Description Charged formula gam6p[c] D-Glucosamine 6-phosphate C6H13NO8P cgly[c] Cys Gly C5H10N2O3S C5H10N2O3S

           Is this abbreviation universal, or is it based on one's own writing?

           Hope to get your reply, my good friend.

   sincerely，

   NA