Open FaribaRoshanzamir opened 2 years ago
I came across this one accidentally, but I am wondering if there is any automatic way to do these checkings and update the model once in a while?
That's a very good question - I vaguely remember discussions about it, but I could not find any implementation of this functionality. Perhaps @JonathanRob, @haowang-bioinfo or even @pecholley remember something.
If you @mihai-sysbio will update it on the Metabolic atlas
Metabolic Atlas strives to be a perfect mirror of the model content, so if a change on the website is expected, it should come from a change in the model.
We can update this one manually, for now.
Please go ahead @FaribaRoshanzamir 👍🏻
No, I'm not really aware of any automatic functionality that could be used to update this, unfortunately.
EC number changes but not frequently. @FaribaRoshanzamir please go ahead to update this if provided with evidence.
GECKO 3 contains a function to getECfromDatabases
via KEGG mapping. Perhaps this is a good opportunity to bulk update the EC codes, and also reduce the missing values by about ~1900 entries.
Description of the issue:
Protoporphyrin ferrochelatase enzyme (FECH) was classified as EC 4.99.1.1 but now it's classified as 4.98.1.1. This change is already updated in several databases including the Enzyme database, KEGG, MetaCyc. I came across this one accidentally, but I am wondering if there is any automatic way to do these checkings and update the model once in a while?
Expected feature/value/output:
We can update this one manually, for now. If you @mihai-sysbio will update it on the Metabolic atlas, I think we should keep the old EC number as well.
Current feature/value/output:
Reproducing these results:
I hereby confirm that I have:
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branch of the repository