3.a Search for AOPs
Task 1: Search or list the content of the centralized database
1- Start Effectopedia. The welcome screen shows the initial options for using Effectopedia.
2- From the welcome screen choose the first option "Explore the current status of existing adverse outcome pathways"
3- In the Search tab of the interface click on List button
Task 2: Load an AOP in the pathway viewer
1- Click on the first Pathway title to load the Estrogen Binding Mediated Population Reduction pathway in the viewer
2- By default the pathway is loaded in browsing mode. Press left mouse button on the canvas and move it to display different parts of the diagram
3- Use Zoom in () and Zoom Out () buttons to scale the pathway
Task 3: Load an AOP from file
1- Use Open button to load the Example1.aopzin the viewer. This file is part of https://learning.aopkb.org/pluginfile.php/215/mod_page/content/11/examples.zip file so you need to locate the folder where you have extracted your examples. (Note that a single file can contain more than one AOP and the last viewed one is automatically displayed).
2- This file contains newer version of the Estrogen Receptor Binding AOP compared to the one you have viewed in Task 2.
3- Scroll down to the diagram until you find the chemicals triggering the AOP and the molecular initiating event.
4- Switch Effectopedia from Drag to Edit mode for the next steps of the task.
5- Double click on the link (orange circle) between the 4-n Amylaniline (green box) and Binding to ER (box No2). The Edit screen below should appear. This is the editor/viewer for the link (shown in the central panel) connecting a chemical (shown in the left panel) to molecular initiating event (shown in the right panel). The link describes the mechanism which causes certain chemical structures to bind to Estrogen receptor and triggering cascade of biological responses.
6- Explore the information about the link. You can expand or collapse the Chemical Structure and Molecular Initiating Event panels using the little left and right arrows at the top of the divider
7- Explore the information about the Molecular Initiating Event.
8- In the Chemical Structure (left panel), look at the Associated Molecular Initiating Events.
9- Double click on Binding to ER (in the Associated Molecular Initiating Events). This will load the dedicated editor for the molecular initiating events. You can use this method of navigation to explore the components of the pathway. Alternatively if you double click on the title of each element, the system does open the dedicated editor for this element. You can also go back to the viewer (i.e. back to full view of the AOP diagram) and double click on any other element to load its editor.
10- In the MIE Binding to ER, scroll down to the Associated Test section and double click on Trout CytortER Assay. The screen below appears. This is a description of an assay which provides information on how the test is performed and tested substances;this is where actual data for tested chemicals can be entered. The screen capture below shows the information for two tested chemicals (red curves) in the assay along with data for a reference chemical (Estradiol, blue curve)
Below is a live demonstration on how you can use Effectopedia to search for AOPs, key events and chemicals and display the results in the pathway viewer: