The Network View displays knowledge networks of one or multiple genes selected from the previous views.
– The entry gene (your genes of interest which were selected in one of the prior Views) is displayed as a blue circle with with a double border and a double helix inside.
– Evidences/concepts are represented as Nodes on the interactive graph, each with a type (such as “gene”, “protein”, “SNP”, etc.).
– Edges (node relationships), also have types (such as “encodes”, “published_in” and “occurs_in”) and are used to connect nodes. KnetMiner uses various different data points to initially only show the most relevant nodes and relationships based on your search.
– Dotted lines indicate text-mined and similar evidences (and should generally be taken with a grain of salt – read the Evidence within the edge and connecting nodes by opening the orange Info Box on the right and then clicking on the edge/node).
– Nodes connected with solid lines were imported directly from databases and score more reliably. We encourage using both relationship types and always reading related evidences.
Most node types also link to their accessions (at the bottom of the Info Box), allowing for more in depth search, confirmation and citing of both individual resources and KnetMiner.
Main Controls
Main buttons (from top left to top right)
Top of interface: Button Description
| Graph Explorer | Used to add and modify Nodes and Edges in the graph. See more below. |
| Circular | Change to Circular (avsfd) layout (citation) |
| fCoSe | Change to fCoSe layout (Citation) |
| Refresh layout | Re-runs the currently selected layout |
| Reset to initial graph state | Repositions the graph to to the state it was created in |
| Remove disconnected | Removes all floating nodes (nodes without edges) |
| Toggle Grouping Optionsy | Toggles advanced Grouping Options on and off |
| Save | Save the network to your account |
| Search network | Search for keywords within the network |
| Download icon | Download in either Tabular or Cytoscape JSON formats |
| Save to your workspace on KnetSpace | Saves your current KnetWork for sharing and further editing |
Button of interface: Button Description
| Shortcuts | Displays a list of shortcuts available in Network view. |
| Settings | Modify settings based on your preferences. |
| Export graph | Download the graph as Image, in Tabular format or in Cytoscape Desktop format |
| + (plus) | Zooms into graph (alternatively use mouse-wheel) |
| – (minus) | Zooms out of graph (alternatively use mouse-wheel) |
| Fullscreen toggle | Closes surrounding UI and shrinks them, focussing on the network |
| Lit Review | Opens the AI literature review feature |
Global Graph Explorer
The graph explorer allows you to add/remove nodes and edges from the graph.
Use the double arrows in line with the green Graph Explorer text to collapse the graph explorer into slim mode. Use the arrow on the left side to close the Graph Explorer.
Switching between Node and Edge mode can be done by clicking on the tabs at the top.
The ‘cards’ in the Graph Explorer have between two and three states:
1. Two states when the initial graph showed 0/x for the specific card. In this case clicking the card will add all available nodes of that type to the graph, then remove them all on the next click.
2. Three states when the initial graph showed >0/x for the specific card. In this case there are three toggles: firstly adding all the remainder, then removing all, followed by going back to the the initial state (of when the graph was just made).
Clicking the settings cog on a card allows you to change the node/edge size and toggle on/off the label.
Edges have identical logic.
Clicking on a node in the graph changes the Graph Explorer to display Local Mode
Local Graph Explorer
Clicking on one or multiple individual nodes, brings up the Local Graph Explorer. Here, at the top of the Grapg Explorer, you can toggle Labels and Highlights on/off, dismiss the selected node(s), dismiss all other (unselected) nodes, or perform one of two power features: Dismiss unselected nodes of this type, or Dismiss all nodes not of this type.
As with the Global Graph Explorer explained above, locally, the Graph Explorer still shows Linked Nodes and edges, but this time they are local to the node(s) selected and therefore only show a subset of directly attached Nodes and Edges.
Info Box
The Info Box can be found by either clicking the orange Info Box button pinned to the right of the screen, or by clicking on a publication in the graph.
The Info Box shows all data related to a node in a graph, in a neatly structured way, with link-outs to where the data can be accessed. The format of the Info Box will depend on the node being accessed.
Context menu
Right-clicking on a node or node grouping in the interface will bring up the context menu. Here lie additional features like turning on/off highlighting, Dismissing nodes and Group/ungrouping nodes. Selecting two nodes also allow you to highlight the shortest path between the nodes.
Search functionality
Searching can be achieved by using the top right Search Network field. Be careful not to use Search at the very top of the KnetMiner interface – as this Searches the whole platform.
Searching for a keyword will highlight the keyword(s) throughout the Info Box.
Press enter, or click the magnifying glass to search. At the top you can filter for evidence types. Color denotes whether the node is currently visible in the graph: green meaning that it is, and red that it is not. Select one or multiple nodes and then Show in Graph to add/select the graph and close the Search interface. The highlights will remain so long as the keywords remain in the search box at the top of the interface.
Table View
The Table View allows you to view the currently visible graph as a table. This can also be changed to the full current graph by going to Settings in the bottom menu and unticking ‘Show only visible nodes in Table View’.
Not all node types are available in the table view, instead it’s intended design is to navigate Nodes with significant data, filter results and help you prioritise nodes in the graph.
The currently selected table can also be downloaded by clicking the Download TSV button in the top header.
Filters can also be applied by clicking the various filter buttons in the table header.
Lit Review
Clicking on the Literature Review button opens a popup allowing for configuration. The feature works best using a maximum of three genes, however it is possible to use more.
Focus topics are similar to keywords, and work to guide the Large Language Model.
Publications: All/ Visible allow you to choose to use all the publications within the current graph, or only the currently visible publications. This will also affect the No of publications to use, which is set to the lower value of either 50 or the amount of available publications, but can be adjusted to your own preference.
Summary type allows for choosing between Short, Medium and Long summaries. We suggest using Medium in majority of the cases, as it is a strong middleground and doesn’t push the limits of the model.
Limits:
No account: daily limit of 0.
Registered, Free resource: daily limit of 2.
Registered, Paid resource: daily limit of 20.
Custom API key:
Generate your own OpenAI API key and paste it into the Custom API key field. We will hold and securely encrypt this key for you to continue using in KnetMiner. Nobody else can see or use your key.
You must at least be registered to use this feature.
Export graph
Exporting the graph allows you to download it in three different formats:
Image Download, Tabular Download, Cytoscape Download.
The Image Downloader brings up a popup configurator where you can choose a name for the exported file and a format for downloading the image: split, with seperate graph and Legend, or to download them pre-combined.
The download allows for PNG and JPG downloading.
The Tabular Downloader downloads the graph as a .tsv.
Downloading in Cytoscape format requires some setup, which can be
found here. Note that this is Cytoscape desktop format, not Cytoscape.js format.
More functionality
– Lasso tool and multi-select: hold shift to multi-select nodes on screen, or shift+(left mouse drag) to select using the lasso tool.
– Shortest path: shortest semantic pathways are auto-computed and displayed linking back to the seed gene(s) whenever interacting with any nodes in the graph. This can be disabled in the Settings cog at the bottom of the screen (Autohighlight Semantic Motifs). To calculate the shortest path (non-semantically) between two nodes, multi-select two nodes, right click and select ‘Autohighlight Semantic Motifs’.
Additional info
Gene names are displayed with their species name prefixed, generally in two-letter capital+lowercase format.
– For example: Triticum aestivum = Ta, so gene CHS in wheat would be called TaCHS.
– This is only available pending data availability.
