Welcome to fobitoolsGUI!

Overview

fobitoolsGUI is a web-based tool based on the fobitools R package. This user-friendly web interface provides a set of tools for interacting with FOBI (Food-Biomarker Ontology). A collection of basic manipulation tools for biological significance analysis, graph visualization and text mining strategies for annotating nutritional data are provided here:

• FOBI graph static visualization
• FOBI graph dynamic visualization
• Extract FOBI information in a downloadable table
• Compound ID conversion (among metabolite names, FOBI, ChemSpider, KEGG, PubChemCID, InChIKey, InChICode and HMDB IDs)
• Biological significance analysis using ORA and MSEA methods:
  • Chemical class enrichment analysis: ORA and MSEA using FOBI chemical classes as metabolite sets
  • Food enrichment analysis: ORA and MSEA using FOBI food groups as metabolite sets
• Text mining algorithm for annotating free-text dietary data

fobitoolsGUI is hosted at our own server, freely available at http://webapps.nutrimetabolomics.com/fobitoolsGUI.

Run fobitoolsGUI locally

Step 1: Install package dependencies

Open a RStudio console and run:

# CRAN packages

installifnot <- function(pckgName){
  if (!(require(pckgName, character.only = TRUE))) {
    install.packages(pckgName, dep = TRUE)
    require(pckgName, character.only = TRUE)
  }
}

pk1 <- c("shiny", "DT", "dplyr", "readxl", "readr", "ontologyIndex", "igraph",
         "plotly", "ggplot2", "shinythemes", "shinyWidgets", "networkD3", "BiocManager")

for (i in 1:length(pk1)){
  installifnot(pk1[i])
}

# Bioconductor packages

BiocManager::install(c("fobitools", "BioNet"))

Step 2: Launch fobitoolsGUI locally

Once all dependencies have been installed run the following command and enjoy the fobitoolsGUI!

shiny::runGitHub("nutrimetabolomics/fobitoolsGUI")

Citation

Pol Castellano-Escuder, Raúl González-Domínguez, David S Wishart, Cristina Andrés-Lacueva, Alex Sánchez-Pla, FOBI: an ontology to represent food intake data and associate it with metabolomic data, Database, Volume 2020, 2020, baaa033. DOI: https://doi.org/10.1093/databa/baaa033

Code of Conduct

Please note that the 'fobitoolsGUI' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.