Changed EC number in other databases

[FaribaRoshanzamir]

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:

• [ ] Tested my code on my own computer for running the model
• [ ] Done this analysis in the main branch of the repository
• [ ] Checked that a similar issue does not exist already

[mihai-sysbio]

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 👍🏻

[JonathanRob]

No, I'm not really aware of any automatic functionality that could be used to update this, unfortunately.

[haowang-bioinfo]

EC number changes but not frequently. @FaribaRoshanzamir please go ahead to update this if provided with evidence.

[mihai-sysbio]

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.