MOTIVATION: Metabolomics is an emerging 'omics' science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements. RESULTS: We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks. AVAILABILITY AND IMPLEMENTATION: The new graphite version (1.24) is available on Bioconductor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Metabolomics is an emerging 'omics' science involving the characterization of metabolites and metabolism in biological systems. Few bioinformatic tools have been developed for the visualization, exploration and analysis of metabolomic data within the context of metabolic pathways: some of them became rapidly obsolete and are no longer supported, others are based on a single database. A systematic collection of existing annotations has the potential of considerably boosting the investigation and contextualization of metabolomic measurements. RESULTS: We have released a major update of our Bioconductor package graphite which explicitly tracks small molecules within pathway topologies and their interactions with proteins. The package gathers the information stored in eight major databases, oriented both at genes and at metabolites, across 14 different species. Depending on user preferences, all pathways can be retrieved as gene-only, gene metabolite or metabolite-only networks. AVAILABILITY AND IMPLEMENTATION: The new graphite version (1.24) is available on Bioconductor. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Fuhai Li; Andrew P Michelson; Randi Foraker; Ming Zhan; Philip R O Payne Journal: BMC Med Inform Decis Mak Date: 2021-01-07 Impact factor: 2.796
Authors: Jan Stanstrup; Corey D Broeckling; Rick Helmus; Nils Hoffmann; Ewy Mathé; Thomas Naake; Luca Nicolotti; Kristian Peters; Johannes Rainer; Reza M Salek; Tobias Schulze; Emma L Schymanski; Michael A Stravs; Etienne A Thévenot; Hendrik Treutler; Ralf J M Weber; Egon Willighagen; Michael Witting; Steffen Neumann Journal: Metabolites Date: 2019-09-23