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Importing and Working with Data from the Metabolomics Workbench

Learn how to import and work with data from the Metabolomics Workbench in Pathway Tools, facing challenges and utilizing solutions. The Metabolomics Workbench repository houses numerous clinical studies, particularly focused on humans, with diverse metabolites. Pathway Tools offers visualization tools for extracted data. Explore the process of mapping compound identifiers and leveraging the Metabolomics Workbench REST API with examples like a study on Chronic Fatigue Syndrome.

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Importing and Working with Data from the Metabolomics Workbench

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  1. Importing and Working with Data from the Metabolomics Workbench • Peter E. Midfordecocyc.org • SRI International biocyc.org • metacyc.org

  2. Overview • What is the Metabolomics Workbench? • Challenges of working with Metabolomics Workbench studies • Importing into Pathway Tools (currently Desktop)

  3. What is the Metabolomics Workbench? • Metabolomics Consortium Data Repository and Coordinating Center • Funded by NIH Common Fund • Repository has 604 releasedStudies, across 57 species • weighted towards Humans and mammal model organisms • Hundreds more studies under embargo • RefMet is a vocabulary of compounds (and Isobaric mixtures) • 11681 identifiers for compounds and isobaric mixtures • Also a structure database andsmall collection of metabolomics analysis tools

  4. Adding Metabolomics Workbench Import to Pathway Tools • Challenges • Mapping compound identifiers from study data to MetaCyc identifiers • Used MOL files from Workbench Compound Database to generate InChI strings for RefMet terms to match against MetaCyc • Many complex clinical studies • Replicates • Multiple treatment levels/factors • Uses Metabolomics Workbench REST API

  5. Example: Chronic Fatigue Syndrome • Naviaux, et al. Metabolic features of chronic fatigue syndrome. PNAS 2016 September, 113 (37) E5472-E5480. • Metabolite comparison across: • CFS female (n=23) • CFS male (n=22) • No disease female (n=21) • No disease male (n=18) • 449 metabolites reported, 131 recognized

  6. Dashboard? • Current recommendation – save the data file and reload into the Dashboard.

  7. Summary • Metabolomics Workbench includes a growing repository of metabolomics studies • Many of these are human clinical studies with lots of replicates and a wide range of reported compounds, many lacking information about their role in metabolism • Pathway Tools provides several ways to visualize metabolite data extracted from Metabolomics Workbench studies

  8. Acknowledgements • SRI • Peter Karp, Suzanne Paley • Funding sources: • National Cancer Institute

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