Why is the number of compounds for a KEGG pathway different between the KEGG website and MetaboAnalyst?

In MetaboAnalyst, the KEGG pathways were obtained based on the KEGG REST APIs followed by manual curations. For some pathways, there may be a discrepancy in the number of compounds listed from KEGG directly compared to MetaboAnalyst (the compounds are primarily based on HMDB). This is because a KEGG pathway can contain compounds that have not been verified for that species or a generic compound, and there is no corresponding compound in HMDB. In most cases, these discrepancies should not affect data interpretation as we cannot measure those compounds anyway.

Hi, im curious about the pathway information from KEGG. so if it’s from the API, is it always updating/retrieving from the latest version? Or if not, which version of KEGG (and HMDB) is used?


This is how we obtained KEGG pathway information when we created the pathway libraries. The date or versions are described in the publications and should also be on the pathway library page.

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