Grant Number:	1U24DK141185-01 Interpret this number
Primary Investigator:	Subramaniam, Shankar
Organization:	University Of California, San Diego
Project Title:	Metabolomics Workbench - National Metabolomics Data Repository
Fiscal Year:	2024

PROJECT SUMMARY/ABSTRACT The Metabolomics Workbench (MW) – National Metabolomics Data Repository (NMDR) is a unique data resource that serves the biomedical research community. It was started through the NIH Common Fund Metabolomics Initiative over a decade ago and has developed into a one-of-its-kind metabolomics data repository and resource. Projects ranging from independent investigator studies involving metabolic measurements (funded through R21 or R01 mechanisms) to large national initiatives, including several Common Fund-driven metabolomics studies, find their home in the NMDR. The NMDR contains almost 3000 studies, some very large, containing more than 1000 human subjects. The metabolomics data generated by the researchers can be submitted through easy and facile mechanisms that have evolved over the years by the MW. The MW-NMDR is widely regarded as one of the most FAIR (findable, accessible, interoperable, usable) data resources of its kind. The sunset associated with the Common Fund Projects has mandated the need for mechanisms to sustain data, such as the NMDR, and the RFA offers the mechanism for this perpetuation for the community. This proposal will address two essential aspects needed for the metabolomics resource. The first and primary objective of the MW-NMDR proposal is the continuation of the repository and resource along with the evolution of all features currently present in the infrastructure. The MW-NMDR receives approximately 50 study submissions, some very large, each month and offers mechanisms for easy upload of the data followed by curation by the MW team. It is subsequently transferred into a relational database along with the metadata to make the data discoverable. These mechanisms require continuous maintenance and updating. The MW also houses a metabolite structure database and RefMet, the reference metabolite classification and annotation system, which facilitates data harmonization. The metabolite database and RefMet require continuous updating, an essential task for the MW. The outreach and engagement of the biomedical research community is another need of the MW-NMDR; continuing this effort with additional mechanisms is a key objective.The second objective of the MW-NMDR proposal is the enhancement of the infrastructure through multiple mechanisms. First, the dramatic growth in the data warrants easy discovery mechanisms. Towards this, we will develop a graph database and query system, which will enable researchers to pose complex queries/filters to discover data and access them. We will develop a Neo4j graph database along with an interactive graph visualization interface that will facilitate dynamical queries in a cascading manner. This will obviate the need for a researcher to learn sophisticated computer skills. Second, we will develop a simple and accessible human subjects’ clinical metadata model to help create specified cohorts and the associated metabolomics data. Third, we plan to provide data in multiple formats using tools and interfaces. Finally, we will develop further the cloud aspects of MW-NMDR and provide AI-ML-ready datasets.





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