I have found a small (but nefarious) error in the samples table which affects selection of samples in the app if samples with id>1472 are included. This apparently escaped previous testing. You can find the fix here (in the meantime I will upload an update in Mendeley data).
The paper describing FoodMicrobionet v 3.1 is now available:
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.
Check it out, there are several important novelties. Don’t forget to read the supplementary material and to access the datasets and scripts on Mendeley datasets.
You can download it for free at https://authors.elsevier.com/a/1ZDuwcF3i1Aey until August 3 2019.
Among other features, the new version on ShinyFMBN can produce (and save) a number of summary tables and plots. A few examples are listed below (for Mozzarella cheese, if you are interested: FMBN features 6 studies on this delicious cheese). Again, if you are interested to see features in the export tab, send me an E-mail and I will see what I can do.
There are more than 4000 samples in version 3.2 of FoodMicrobionet.
More will be added until the end of September. After that, development will be stopped for lack of funding and time and the new version is scheduled to be released on February 14th, 2020, together with a revised app and a few service scripts.
|Food type (L1)||Count|
|Animal and vegetable fats and oils and primary derivatives thereof||52|
|Eggs and egg products||21|
|Fish, seafood, amphibians, reptiles and invertebrates||183|
|Fruit and fruit products||135|
|Grains and grain-based products||54|
|Major isolated ingredients, additives, flavours, baking and processing aids||72|
|Meat and meat products||899|
|Milk and dairy products||2048|
|Vegetables and vegetable products||427|
I am working on version 3.2 of FoodMicrobionet (which will include 70+ studies and 3500+ samples) and version 2 of the Shiny app. However, these versions will not be made public anytime soon and will only be shared with partners with whom I have research collaborations. If you are interested in collaborating in the development of FoodMicrobionet or in the submissions of research projects related to FoodMicrobionet contact me.
New data and scripts, including version 1.2 of the ShinyFMBN app are available at Mendeley data.
This is a new script for converting *_agg.RDS or *_physeq.Rdata files created using the ShinyFMBN app (v1.1 or later) in OTU, taxonomy and sample metadata tables suitable for use with the Marker Data Profiling analysis pipeline of Microbiome Analyst (https://www.microbiomeanalyst.ca). Click here to download. Please beware: I am too old to be willing to write foolproof scripts and try to predict the vagaries of lazy users. If you are a fool (and/or don’t read/follow the instructions provided as comments in the script) the script will not work. Period.
Dr. Sandrine Guillou has kindly invited me to give a talk at IAFP’s European Symposium on Food Safety in Nantes. Il will be speaking in symposium S4 (Network Analysis to Better Decipher Functions and Dynamics of Food Microbial Ecosystems) and the title of my talk is: “Shining Light on Networks in Food Microbiomes: FoodMicrobionet and the ShinyFMBN App“. You can download the presentation here. While we wait for the review of the manuscript I have submitted, you can cite FMBN 3.1 using this talk: Parente, E., Ricciardi, A., Zotta, T. 2019. Shining Light on Networks in Food Microbiomes: FoodMicrobionet and the ShinyFMBN App. Proceedings of IAFP’s European Symposium on Food Safety, Nantes, April 24-26, 2019.
FMBN2.0.3. Minor changes: Changed FoodId for study 11 (A01QX->A049Q). Added number of reads for some samples. Removed a few duplicates in lineages. Expanded the definition for llabel. Table specifications are here. Project table is here. Edge and nodes tables are here. Accessibility is now much improved, using R scripts: With very little effort you can extract files for analysis from the edge and node tables using this R script and produce graphical and statistical analyses using this one. Read the instructions carefully. You can cite this version and the scripts using this paper.
FMBN2.0.2. Minor changes: Fixed problems with inconsistent lineages for a few OTU nodes. Major changes: Revised specification for node and edges tables: now you can use Custom1 to 3 fields for more efficient filtering and application of styles. A web visualisation of the filtered network (weighted degree >17) is available here. This version will allow a better integration with the Bipartite package of R and with the CoNet app of Cytoscape. A .pdf version (187 Mb) of the filtered network (weighted degree>17) is available here. A .pdf version (10.9 Mb) of the “robust” network (identification at the genus level or above, edges with abundance <0.1% removed) is available here.