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A utility to study and analyse cancer-associated metabolites using knowledge graphs

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CanGraph is a python program that allows you to extract information about a newly discovered or existing metabolite from the following databases:

Human Metabolome DB 👨🏽

Detailed information on small molecule metabolites found in the human body

DrugBank 💉

Detailed drug data with comprehensive drug target information

Exposome Explorer 🔎

Dedicated to biomarkers of exposure to environmental risk factors for disease, specially cancers

WikiData 📊

The free knowledge base with 99,190,630 data items that anyone can edit

SMPDB 🛤️

Small Molecule Pathways, over 70% of which not found in any other db

MeSH and MetaNetX 📍

Unified NameSpace for metabolites and Medical Subject Headings.

For this purpose, CanGraph accepts any of the following inputs:

• InChI: The International Chemical Identifier for the metabolite, which can be calculated using Open Source Software and identifies a metabolite with 99.99% accuracy based on its structure

• InChIKey: The Hashed, shortened version of the InChI, sometimes used for efficiency

• Name: A commonly accepted name for the metabolite; preferably, IUPAC’s standarized name

• HMDB_ID: The Metabolite’s Identifier in the Human Metabolome Database

• ChEBI_ID: The Metabolite’s Identifier in the ChEBI Database

which must be provided as explained in CanGraph’s README

Acknowledgements

This research was funded by the Agence Nationale de la Recherche Project number ANR-19-CE45-0021 (New approaches to bridge the gap between genome-scale metabolic networks and untargeted metabolomics – MetClassNet) and the Deutsche ForschungsGemeinschaft Project number 431572533 (MetClassNet: new approaches to bridge the gap between genome-scale metabolic networks and untargeted metabolomics )

You can check MetClassNet’s Official Website here

Most of the work for this project has been carried out at the International Agency for Research on Cancer’s OncoMetaBolomics Team