Why aren't all uploaded compound names/IDs matched even they are in HMDB or KEGG?

There are three common compound mapping functions

  1. In MetaboAnalyst Enrichment Analysis and Pathway Analysis modules. The main aim of the compound mapping function in MetaboAnalyst is to standardize the compound names for metabolite set enrichment analysis or pathway analysis. The focus is on those compounds defined in our Metabolite Sets or Pathway libraries in MetaboAnalyst. Please note, those unmapped compounds will not affect the results, as the statistics are calculated based on the universe defined by the libraries.

  2. In MetaboAnalyst, Other Utilities => Compound ID Conversion. This is based on common compounds obtained from HMDB, KEGG, RefMet, LipidMaps, and other sources. Please note, this is not developed as a general purpose mapping tools for all HMBD compounds.

  3. For general-purpose compound mapping, you can also try the MetabolomicsWorkbench
    RefMet Name Mapping tool

I’m finding an issue with compound ID name matching between uploading data in pathway/enrichment and the compound ID Conversion tool. I originally used the ID conversion tool to rename all metabolites that weren’t recognised; however when I upload that dataset into pathway analysis it’s picking up a lot of new metabolites that need renaming. How come the conversion tool automatically renames/recognises these metabolites but the pathways/enrichment doesn’t? Thanks.

This is a common question. Please read this post

Hey sorry no I don’t think that post is addressing my query. I use the “compound ID” feature first and sort out all my names, then when I upload the cleaned dataset a bunch of features aren’t recognised and need renaming (not picked up by the ‘Compound ID’ feature).

You are comparing two functions designed for different purposes. The post explains the reasons. Pay attention to my response with a screenshot.