Package: fobitools 1.21.0

Pol Castellano-Escuder

fobitools: Tools for Manipulating the FOBI Ontology

A set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.

Authors:Pol Castellano-Escuder [aut, cre], Alex Sánchez-Pla [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fobitools/json (API)

# Install 'fobitools' in R:
install.packages('fobitools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pcastellanoescuder/fobitools/issues

Datasets:
  • fobi - FOBI Table File - Jul 23, 2021
  • fobi_terms - FOBI's 'ontology_index' object - Jul 23, 2021
  • foods - FOBI Foods Table File - Feb 02, 2021
  • idmap - FOBI Identifier Map File - Jul 18, 2021

On BioConductor:fobitools-1.21.0(bioc 3.24)fobitools-1.20.0(bioc 3.23)

massspectrometrymetabolomicssoftwarevisualizationbiomedicalinformaticsgraphandnetworkannotationcheminformaticspathwaysgenesetenrichmentbiological-intrerpretationbiological-knowledgebiological-significance-analysisenrichment-analysisfood-biomarker-ontologyknowledge-graphnutritionobofoundryontologytext-mining

4.90 score 1 stars 7 scripts 7 exports 112 dependencies

Last updated from:40cda2ba39. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE249
linux-devel-x86_64NOTE395
source / vignettesOK367
linux-release-x86_64NOTE405
macos-release-arm64NOTE196
macos-oldrel-arm64NOTE161
windows-develNOTE302
windows-releaseNOTE295
windows-oldrelNOTE275
wasm-releaseOK238

Exports:%>%annotate_foodsfobi_graphid_convertmseaoraparse_fobi

Dependencies:base64encBHBiocParallelbitbit64blobcachemclasscliclisymbolscodetoolscowplotcpp11crayondata.tableDBIdiagramdigestdplyrdtte1071englishevdfarverfastmapfastmatchfffgseaformatRfutile.loggerfutile.optionsfuturefuture.applygenericsggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragtablehmsigraphipredisobandjsonliteKernSmoothlabelinglambda.rlatticelavalexiconlifecyclelistenvmagrittrMASSMatrixmemoisemgsubNLPnnetnumDerivontologyIndexparallellypillarpkgconfigpolyclipprettyunitsprodlimprogressprogressrproxypurrrqdapRegexR6RColorBrewerRcppRcppArmadilloRecordLinkagerlangrpartRSQLiteS7scalesshapeslamsnowSQUAREMstringistringrsurvivalsystemfontssyuzhettextcleantextshapetibbletictoctidygraphtidyrtidyselecttweenrtzdbutf8vctrsviridisviridisLitevroomwithrxtablezoo

Use case: LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice
Installation | Load packages | Download the data from Metabolomics Workbench | Sumary of the study (ST000291) | Download data | Scraping metabolite names and identifiers with rvest | Prepare features and metadata | Statistical analysis with POMA | Create a SummarizedExperiment object | Preprocessing | Limma model | Convert PubChem IDs to FOBI IDs | Enrichment analysis | Over representation analysis (ORA) | MSEA | MSEA plot with ggplot2 | Network of metabolites found in MSEA | Limitations | Session Information | References
Rendered fromMW_ST000291_enrichment.Rmdusingknitr::rmarkdown

Last update: 2024-11-27
Started: 2021-05-08

Use case: Amino Acid Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine
Installation | Load packages | Download the data from Metabolomics Workbench | Sumary of the study (ST000629) | Download data | Prepare features and metadata | Statistical analysis with POMA | Create a SummarizedExperiment object | Preprocessing | Limma model | Convert metabolite names to KEGG identifiers with MetaboAnalyst web server | Convert KEGG IDs to FOBI IDs | Enrichment analysis | Over representation analysis (ORA) | MSEA | MSEA plot with ggplot2 | Network of metabolites found in MSEA | Limitations | Session Information | References
Rendered fromMW_ST000629_enrichment.Rmdusingknitr::rmarkdown

Last update: 2024-11-27
Started: 2021-05-10

Dietary text annotation
Installation | Load packages | Load food items from a food frequency questionnaire (FFQ) sample data | Automatic dietary text anotation | The similarity argument | Network visualization of the annotated terms | How do I know which compounds are associated with my study food items? | Limitations | Session Information | References
Rendered fromDietary_data_annotation.Rmdusingknitr::rmarkdown

Last update: 2022-01-12
Started: 2021-01-13

Simple food over representation analysis (ORA)
Installation | Load fobitools | metaboliteUniverse and metaboliteList | Network visualization of metaboliteList terms | Session Information | References
Rendered fromfood_enrichment_analysis.Rmdusingknitr::rmarkdown

Last update: 2022-01-12
Started: 2021-01-13