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 http://webapps.nutrimetabolomics.com/fobitoolsGUI.
Installation
To install Bioconductor version use:
# install.packages("BiocManager")
BiocManager::install("fobitools")If you need the GitHub version (not recommended unless you know what you are doing), use:
# 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. By contributing to this project, you agree to abide by its terms.
