title: MetaMapR: pathway independent metabolomic network analysis incorporating unknowns.
abstract: Metabolic network mapping is a widely used approach for integration of metabolomic experimental results with biological domain knowledge. However, current approaches can be limited by biochemical domain or pathway knowledge which results in sparse disconnected graphs for real world metabolomic experiments. MetaMapR integrates enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate richly connected metabolic networks. This open source, web-based or desktop software, written in the R programming language, leverages KEGG and PubChem databases to derive associations between metabolites even in cases where biochemical domain or molecular annotations are unknown. Network calculation is enhanced through an interface to the Chemical Translation System, which allows metabolite identifier translation between >200 common biochemical databases. Analysis results are presented as interactive visualizations or can be exported as high-quality graphics and numerical tables which can be imported into common network analysis and visualization tools.
  
  
  METHODS
  Freely available at http://dgrapov.github.io/MetaMapR/. Requires R and a modern web browser. Installation instructions, tutorials and application examples are available at http://dgrapov.github.io/MetaMapR/.
  
  
  BACKGROUND
  ofiehn@ucdavis.edu.
authors.affiliation: National Institutes of Health West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA 95616, USA and.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Grapov
authors.affiliation: National Institutes of Health West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA 95616, USA and.
authors.forename: Kwanjeera
authors.initials: K
authors.lastname: Wanichthanarak
authors.affiliation: National Institutes of Health West Coast Metabolomics Center, Genome Center, University of California Davis, Davis CA 95616, USA and King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia.
authors.forename: Oliver
authors.initials: O
authors.lastname: Fiehn
mesh_terms: D053858:Metabolic Networks and Pathways; D055432:Metabolomics / Q000379:methods*; D012984:Software; D064878:Web Browser
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