# `fobitools` <img src='man/figures/logo.png' align="right" height="139" /> <!-- badges: start --> [](https://www.tidyverse.org/lifecycle/#stable) [](https://github.com/pcastellanoescuder/fobitools/actions) [](https://bioconductor.org/checkResults/release/bioc-LATEST/fobitools/) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/fobitools/) [](https://codecov.io/gh/pcastellanoescuder/fobitools?branch=main) [](https://github.com/pcastellanoescuder/fobitools/commits/main) [](https://www.gnu.org/licenses/gpl-3.0) [](https://doi.org/10.1093/databa/baaa033) <!-- badges: end --> This package provides a set of tools for interacting with [FOBI (Food-Biomarker Ontology)](https://github.com/pcastellanoescuder/FoodBiomarkerOntology). 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](https://github.com/pcastellanoescuder/fobitoolsGUI). This application implements most of `fobitools` functions in an user-friendly web interface and it is available at <http://webapps.nutrimetabolomics.com/fobitoolsGUI>. # 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: <https://doi.org/10.1093/databa/baaa033> # Code of Conduct Please note that the ‘fobitools’ project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.