FoodMicrobionet 3.1 is ready!

Posted on by

There are 44 studies and 2233 samples in this version of FoodMicrobionet. The samples belong to 9 major food groups and 76 different foods. There are 148 different combinations of food, nature, process, fermentation/spoilage. 3411 taxa have been identified at different taxonomic levels. This makes it by far the largest set of data on bacterial communities in foods (as of January 2019).

The ShinyFMBN app was also updated and provides better integration with external resources. The app is currently under embargo (pending revision of a manuscript). You will be able to access it on Mendeley data.

The app (version 1.2, which is compatible with R3.6 and the new installation procedure of Bioconductor packages), the database and a few other things are available at Mendeley data, and are connected to an article in IJFM-

You can cite this version as: Parente, E., De Filippis, F., Ercolini, D., Ricciardi, A., Zotta, T., 2019. Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database. International Journal of Food Microbiology, 305 (September 2019): 108249 DOI: 10.1016/j.ijfoodmicro.2019.108249.

2 thoughts on “FoodMicrobionet 3.1 is ready!”

  2. In the meantime: R 3.6 has been released and BioConductor has changed some of the commands needed to install/update packages. I will release a new version shortly. In the meantime, if you do not have all BioConductor packages installed/updated use this before running the app
    .cran_packages <- c("shiny", "DT", "tidyverse", "reshape2", "stringr", "tibble", "lubridate" ,"igraph") .bioc_packages <- c("BiocManager", "phyloseq") .inst <- .cran_packages %in% installed.packages() if(any(!.inst)) { install.packages(.cran_packages[!.inst]) } .inst <- .bioc_packages %in% installed.packages() if(any(!.inst)) { if(!"BiocManager" %in% installed.packages()) install.packages("BiocManager") BiocManager::install(.bioc_packages[2:length(.inst)]) } sapply(c(.cran_packages, .bioc_packages), require, character.only = TRUE) runApp("ShinyFMBN1_1")

Leave a Reply