Once a user has selected a network of interest, the model framework is loaded into the Network Viewer environment. Edges may then be selected and associated scientific evidence verified.
This tutorial outlines the steps necessary for accessing and reviewing the scientific evidence associated with edge relationships within this viewer panel.
Selecting A Model Initiates Display Within the Network Viewer Environment
By default, the node names are hidden and the legend is shown.
Click On "Labels" To Display All Node Names
Clicking on "Labels" will display or hide Labels, depending on wether they were hidden or visible.
Click On "Evidence" To Display The Number Of Evidence For Each Edge
The two numbers shown on each edge indicate the number of verified evidences out of the total number of evidences for an edge. Both evidence and labels can be shown at the same time.
Network Details Including Description Of The Model And Boundary Conditions Can Be Displayed In The Network Viewer
"Nodes" Drop-Down Menu Provides Quick Access to Nodes of Interest
Select "Nodes" button to display a list of all nodes found in the network.
Select Any Node From List to Highlight Associated Edge Connections
Click on any node to reveal additional information specific to the entity. The search tool may also be employed to quickly locate a node of interest.
Network Viewer Environment Updates To Display Information Pertinent to User-Selected Node
Select "Labels" button to display the names of nodes if if was not yet displayed.
"Selected-Node" Data Panel Provides Additional Node Details
Note: the [J] symbol indicates that the node evidence has been accepted during the Jamboree.
- Text list of all edges connected to the selected node are displayed for ease-of-navigation.
- Panel indicates list of additional networks in which the selected node may be found.
Select Any Edge From List to Highlight Associated Evidence
Click on any edge to reveal associated scientific evidence lines.
Network Viewer Environment Updates To Display Information Related to User-Selected Edge
"Selected-Edge" Data Panel Provides List of Associated Supporting Evidence
- Text list of all supporting evidence.
- Panel indicates list of remaining edges connected to original selected node.
Select Any Evidence Line From List to Highlight Supporting Scientific Literature Reference
Click on any evidence line to reveal details of associated scientific literature.
"Evidence Detail" Panel Displays Information Related to User-Selected Edge Evidence
- Evidence Detail panel indicates PubMed ID associated with the edge evidence, in addition to information regarding species and cellular context from the scientific study.
- Running icon means that there is already at least 1 vote on the evidence but no consensus was reached yet.
- Open lock icon indicates this evidence still needs approval or rejection via votes.
- A checkmark indicates approval of the evidence.
- A "X" indicates rejection of the evidence.
- A "?" indicates ambiguous evidences where some votes are in favor of approval and some votes in favor or rejection. These evidences are the primary focus of the jamboree discussions.
The green number indicates how many approval votes have been made, and the red number conversely how many rejection votes cast.
Select the Citation PubMed ID Hyperlink to Navigate To Referenced PubMed Abstract
Investigate Cited Scientific Literature
Browse associated scientific manuscript (abstract and/or manuscript full text, if available) to determine if publication supports the edge relationship as depicted in biological network.
When reviewing the scientific literature, please pay attention to the boundary conditions defined for the networks.
Two Button Verification Option Allow for Easy Edge Review
Select either button to "Approve" or "Reject" inclusion of the referenced literature to support the biological relationship as depicted by the network edge.
Selecting Either Option Generates a Feedback Form
Voting requires to fill up a feedback form:
1. Complete form to indicate relevance of referenced scientific study to the selected edge.
2. Provide any additional feedback (if applicable).
3. Submit form to save your vote.
Pop-Up Dialog Box Indicates Vote Was Saved Properly
Some Automatic Activity Checks Are Implemented
- If you try to vote twice on the same evidence, the following message will appear.
- There is a timer on the voting actions making sure there is a minimum time spent to actually review the evidence prior to voting. You will get the following message if you try to submit another vote within that time period (1 minute)
Select "Clone Evidence" Button to Duplicate an Evidence and Modify It
'Clone Evidence' will create a copy of the current evidence to allow small changes to the Evidence (e.g. changing species, cell/disease/tissue context or fixing the Reference). If you use Clone Evidence to fix a bad Evidence, please clone it the bad Evidence and then reject the original with a comment indicating why it is rejected. It is entirely reasonable that one could have the same basic Evidence that has slightly different context.
Change Relevant Fields to Create A New Evidence
'Clone Evidence' created a copy of the current evidence to allow small changes to the Evidence (e.g. changing species, cell/disease/tissue context or fixing the Reference). It is entirely reasonable that one could have the same basic Evidence that has slightly different context.
- Check the referenced article's citation
- Modify the context information where relevant
- Add a quotation from the article to support the new evidence
- Boundary conditions are given here as support to check appropriateness of context.
Alternatively, additional scientific literature in the public domain may provide more appropriate supporting evidence for the edge relationship of interest. Selecting the "New Evidence" button allows the user to incorporate his/her own literature suggestion.
Create New Supporting Literature Evidence From Scratch
- Click on "New Evidence"
- Enter PubMed ID of scientific study.
- Enter the referenced article's citation
- Indicate species in which study was conducted.
- Designate tissue in which study was conducted (if available).
- Designate disease context of study (if applicable).
- Designate cell line in which study was conducted (if available).
- Enter text quotation(s) in published manuscript supporting relevance of study to network edge.
- Save information as a new piece of supporting evidence.
A pop-up will notify you of the creation of the new evidence.
New Evidence Support Appears In the "Selected Edge" Panel
New evidence line appears in data panel, which may then be verified by other users.
New Evidence Support Appears In the "Community:Activity " Section And Can Be Deleted By The Creator As Long As No Vote Was Cast
The activity feed in the Community Section shows the newly created evidence "by you". As long as there has not been any vote on the evidence, and if you realized you made a mistake, you can delete the evidence.
Note that if you only want to bring slight modifications, it is best to clone the evidence and modify it prior to deletion, as it will disappear as soon as you click on "Delete".
Reputation points given for the evidence creation will be removed in case of deletion.
Deleted Evidence Disappears From Evidence List