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Improve annotation of metabolites in models #964

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JHL-452b opened this issue Jan 14, 2025 · 0 comments
Open
1 task

Improve annotation of metabolites in models #964

JHL-452b opened this issue Jan 14, 2025 · 0 comments

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@JHL-452b
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JHL-452b commented Jan 14, 2025

Current behavior:

As discussed in #728 , we had added SMILEs and Inchi to the metabolites in Human-GEM (./data/modelCuration/metabolites_SMILES_Inchi.tsv). This metabolite information allows us to enhance the metabolite annotation for Human-GEM by comparing it with other metabolite databases.
In this way, I found a total of 5946 matching items that should be included in metabolites.tsv. The distribution of these successfully matched items is as follows:

metBiGGID metKEGGID metHMDBID metChEBIID metPubChemID metLipidMapsID metMetaNetXID
New matched items 3 379 1915 844 1546 797

You can find more details in this New_metabolites.xls. It should be noted that the metabolite IDs in the MetaNetX database have been updated, and the previously matched metabolite IDs are no longer applicable. Thus, I updated the MetaNetX ID in the last column of the table.

Proposed changes:

  • Add new annotation for metabolites and update the metabolites.tsv.
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