A cross-institutional, FAIR VIVO for Metabolomics

Michael Conlon, Kevin S. Hanson, Taeber Rapczak, Naomi Braun, Christopher P. Barnes

Keywords: FAIR data principles, metabolomics, Triple Pattern Fragments

TL;DR: The NIH Metabolomics Consortium is creating a VIVO to improve findability and accessibility of metabolomics data

Abstract:

Metabolomics is the scientific study of metabolites present within an organism, cell, or tissue. A metabolite is the intermediate end product of metabolism. The term metabolite is usually restricted to small molecules. Metabolomic studies involve the identification of metabolites in biological samples, often by processes involving mass spectroscopy. Datasets from such studies may involve the identification of several thousand compounds leaving tens of thousands unidentified. These data sets are valuable for scientific reuse. The National Institutes of Health in the United States has established a National Metabolomics Data Repository known as the Metabolomics Workbench (www.metabolicsworkbench.org) to provide access to datasets resulting from NIH-funded work. In Europe, the European Molecular Biology Laboratory also provides a data registry.

VIVO is being used to create investigator-centric metadata regarding datasets and publications in metabolomics. The initial work is focused on investigators participating in the NIH Common Fund Metabolomics Program. Future work could include other metabolomics investigators. The VIVO for metabolomics will provide metadata to the consortium web site http://metabolomics.info which provides information of interest to all metabolomics investigators, as well as a Triple Pattern Fragments (TPF) endpoint for discovery of metadata regarding metabolomic investigations. The work will improve the findability of metabolomics datasets, as each will be an entity with a profile page, discoverable via popular search engines. Each entry will link directly to the metabolomics workbench, improving accessibility. Much work remains in the metabolomics community on interoperability between repositories -- a long term goal is to support the use of a wide range of metabolomic software tools on the widest possible range of metabolomics datasets. This will require coordination across repositories and development and implementation of common representations. Significant additional work remains on reuse to develop and implement standards for the representation of identification information, quantification, and naming of metabolites.

ORCID: 0000-0002-1304-8447

Submission Type: poster