FoodMicrobionet v1.0 web visualisation: user manual Disclaimer: the web visualisation has a limited set of functions and has the sole function of allowing inexperienced user to visually explore FoodMicrobionet and to perform a few basic search operations. To fully explore FoodMicrobionet it is advisable to import the nodes and edges tables into a network visualisation and analysis software such as Gephi (http://www.cytoscape.org/) or Cytoscape (http://www.cytoscape.org/). Supplementary files and nodes and edges specifications are released when a paper describing a given version of FoodMicrobionet is published. Please refer to this page: http://www2.unibas.it/parente/wordpress/?page_id=761 for further information. The web visualisation is available at: http://www2.unibas.it/parente/fmbn1_0web/ Please use one of the following browsers: Firefox Google Chrome Safari The visualisation was created from a Gephi project using the Sigmajs exporter plugin (v1.1.1) https://marketplace.gephi.org/plugin/sigmajs-‐exporter/ Start the visualisation: Access this URL in your browser: http://www2.unibas.it/parente/fmbn1_0web/ The visualisation will load typically in <10 seconds, but it depends on the speed of your connection
Although some of the functions are rather intuitive please read the instructions below before exploring the graph.
Edges (connections between samples and OTU nodes) represent the % occurrence of a given OTU in a sample. The size of the nodes is related to their weighted degree (i.e. to the sum of weights of all connection to the node) in the whole network. Therefore, large nodes represent OTUs which are "important" in all the dataset, but the actual abundance of a given OTU in a given sample is represented by the width of the edge. The colour of the nodes was attributed on the basis of the content of field <Custom 2> which stores information on Family (for OTU nodes) or food subgroup according to FoodEx classification (for sample nodes). Please refer to specifications for nodes table. A Yfan Hu layout algorithm was used to organize the graph. This pushes to the borders OTU nodes with few connections or with connections with low weights (i.e. OTU which occur at low abundances) and brings sample nodes close to the OTUs which dominate their bacterial community, and vice versa. As a consequence, the network is, to some degree, organized in areas which are dominated by nodes corresponding to a given food type and by the OTU which most frequently appear in that food. There are several areas in the visualisation:
Zooming in will eventually display node labels. Nodes can be selected by clicking: all connected nodes are shown and specific information for the selected node are displayed. When a node is selected an information pane appears on the right of the screen. Two examples for a OTU node (Pseudomonas fragi) and a sample node (a raw beef sample) are shown below. Please refer to nodes and edges specifications for information. Clickable links are provided to NCBI taxonomy (for OTU nodes) and to the original article in which the sample was described (for sample nodes). Please beware: the size of the nodes is not adjusted dynamically after the selection or search operations. This operation can only be performed with network visualisation software such as Gephi after a filtering and recalculation operation. Therefore only edge width provides a rough estimate of the abundance of an OTU in a given sample.
In addition, a clickable list of nodes connected to the selected node is provided at the bottom of the Information pane (scroll down to visualise). Search operations. Only limited search operations can be performed with the web visualisation. One option is typing in the search field and hitting return. This performs a search on the label field of all nodes. At least three characters (position within the label is not relevant) are needed and wildcards (*, ?) do not have effect on search. If a single hit is found the result is equivalent to clicking on a node (see above). If several hits are found, a list is displayed below the group selection area:
The first item of the list is displayed by default. Selecting another item will display the node and its connections. The OTU nodes are labelled with the name of the taxon corresponding to their identification level. If the node was identified only at the genus name only the genus name is shown etc. The sample nodes label always include the FoodID of the FoodEx classification (please refer to specifications for nodes table). FoodMicrobionet currently includes the following FoodIDs: A008K: Naturally leavened bread doughs (Group 21)
A01BP: Olives products (Group 17) A01QX: Cow, ox or bull fresh meat (Group 24) A024V: Cured ripened raw sausages (Group 2) A02LVNWC: Cow milk, semi skimmed (half fat) + starter (Group 81) A02LY: Cow milk, whole (Group 81) A02MC: Sheep milk (Group 64) A02MD: Buffalo milk (Group 135) A02NV: Kefir (milk and grain) (Group 11) A02QJ: Mozzarella, high-‐moisture (cow's milk, water buffalo milk) (Group 32) A02TY: Cheese, Fontina (curd, cheese) (Group 22) A02YH: Cheese, Canestrato Pugliese (curd, cheese) (Group 20) A02ZL: Cheese, Caciocavallo (curd, cheese) (Group 34) A02ZQ: Cheese, Grana Padano (curd, cheese) (Group 1) A02ZS: Cheese, Parmigiano Reggiano (curd) (Group 129) A048Y: Starter cultures, undefined (Group 58, Group 126) A049S; Bovine minced meat (Group 18) XX; Olive fermentation brine (Group 55) The Group selector can be used to select for members of the same family (OTU nodes) or food samples belonging to the same food subgroup on the basis of the colour of the node. Unfortunately the current version of the SigmaJS exporter does not create a list of group names. A list of the sample nodes, by FoodID, is shown above.
A clickable list of nodes belonging to a given group is shown in the information pane. Enjoy! The FoodMicrobionet team