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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Convert BiGG to EC numbers #26

Closed acenieuw closed 6 years ago

acenieuw commented 6 years ago

Dear Daniel,

I stumbled upon this sentence in the CarveMe publication:

"However, when comparing the total coverage of unique EC numbers, one can observe that BiGG lags behind modelSEED and KEGG."

I was wondering how you converted BiGG Ids to EC numbers. We have tried to convert BiGG to EC numbers via MetaNetX Ids but this way, we were only ably to convert about 25% of the BiGG reactions.

Really interested how you did it! :-)

Kind regards,

Carina

cdanielmachado commented 6 years ago

Dear Carina,

Yes, I extracted them from MetaNetX, and you are right, a large fraction of BiGG reactions do not have an assigned EC number in MetaNetX, which might be one of the reasons why it has lower coverage EC numbers than modelSEED and KEGG.

This probably results in an underestimation of the true coverage of BiGG, that's why we compared the total number of reactions as well.

Best regards, Daniel