Question in Microbiome Modeling Toolbox -- Get Metabolites Full Name

[Xinyi Chen]

Hello,

I am using mgpipe function from the Microbiome Modeling Toolbox in Linux Cluster but change the abundance file to another one. I used AGORA2 Infofile as the reference file, and mgpipe function for species level model (used createPanModels beforehand). 

After getting the secreted metabolites, I want to extract the secreted metabolites full name instead of metID for future plots. I do find the metabolites in https://vmh.life/, but it seems like I cannot download the whole file containing every metabolite. Or is there a function that I can use to get the metabolite full name? 

Thank you so much for all the help! 

Best regards,

Xinyi

[Xinyi Chen]

Hello,

I hope this message finds you well.

I just wanted to follow up on my previous inquiry regarding extracting the full names of secreted metabolites after using the mgpipe function in the Microbiome Modeling Toolbox. I was able to retrieve the metabolites through the usual process, but I am still having trouble obtaining the full names rather than the metIDs.

I noticed that while I can find the metabolites on VMH Life, it appears there isn't an easy way to download a full list containing all metabolites. I wanted to check if there is an alternative method or function within the toolbox, or perhaps an API, that would allow me to easily retrieve these full names for future analysis and plotting.

Any insights or suggestions would be greatly appreciated!

Thank you once again for your time and support!

Best regards,
Xinyi

[Farid Zare]

Hi Xinyi,

Please follow this link: https://www.vmh.life/#human/all, click on the second ribbon, "Metabolites Found," and you will find a download button at the bottom right of the widget, which includes all metabolites and their full names.

Regards,
Farid

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Farid Zare MSc

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Member of Recon4IMD & COBRA toolbox

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[Ines Thiele]

Hello 

Model.metNames

Contains the full names. Pls refer to the cobra v3 nature protocol for content of fields in the model structure.

Best ines 

Sent from my iPhone

On 5 Mar 2025, at 14:44, Farid Zare <farid.z...@gmail.com> wrote:



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[Almut Heinken]

Hello,

you can also load the metabolite database into Matlab by typing:

database = loadVMHDatabase;

If you run the following code, you can translate the metabolite IDs into the names.

Best regards,

Almut

for i=2:size(netSecretionFluxes,1)
    met = strrep(netSecretionFluxes{i,1},'EX_','');
    met = strrep(met,'[fe]','');
    met = database.metabolites{find(strcmp(database.metabolites(:,1),met)),2};
    netSecretionFluxes{i,1} = met;
end

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