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# `fobitools` <img src='man/figures/logo.png' align="right" height="139" /> <!-- badges: start --> [![Lifecycle: stable](]( [![Actions Status](]( [![Bioc release status](]( [![Bioc devel status](]( [![Codecov test coverage](]( [![Last Commit](]( [![License: GPL v3](]( [![DOI](]( <!-- badges: end --> This package 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: - Graph visualization of FOBI - Parse FOBI information from OBO to a readable table format - Compound ID conversion (among metabolite names, FOBI, ChemSpider, KEGG, PubChemCID, InChIKey, InChICode and HMDB IDs) - Biological significance analysis via 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 `fobitools` also offers a Shiny app version called [fobitoolsGUI]( This application implements most of `fobitools` functions in an user-friendly web interface and it is available at <>. # Installation To install Bioconductor version use: ``` r # install.packages("BiocManager") BiocManager::install("fobitools") ``` If you need the GitHub version (not recommended unless you know what you are doing), use: ``` r # install.packages("devtools") devtools::install_github("pcastellanoescuder/fobitools") ``` ## 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: <> # Code of Conduct Please note that the ‘fobitools’ project is released with a [Contributor Code of Conduct]( By contributing to this project, you agree to abide by its terms.