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CADDIS Volume 5

CADDIS Volume 5. Causal Databases: Learn about Interactive Conceptual Diagrams (ICDs)

In CADDIS, conceptual diagrams are used as visual tools for structuring causal assessments of stream biological impairmentHelpimpairmentA detrimental effect on the biological integrity of a waterbody that prevents attainment of the designated use.s. They are developed as part of Step 2 (List Candidate Causes) of the Stressor Identification process.

These diagrams illustrate hypothesized pathways by which human activities, sources and stressors may lead to biotic responses. The ICD application builds upon this role for these diagrams by linking supporting literature to hypothesized causal pathways. These diagrams then serve as front-end for searching an online citation database of this literature-based information.

By organizing literature evidence along the causal pathways in conceptual diagrams, the ICD application shows where evidence for different pathways is strongest, weak or lacking. It can help structure your causal assessment and aid in communicating and defending assessment results, by linking evidence to causal pathways in your conceptual diagram.

Literature evidence already entered into the ICD database can give you a better understanding of how sources, stressors and responses may operate in your system. The database allows you to quickly and efficiently access scientific literature relevant to specific cause-effect linkages.

The ICD application provides:

  1. A set of U.S. EPA-constructed conceptual diagrams illustrating human activities, sources and stressors, and potential biotic responses (collectively referred to as shapes). These diagrams can be used to search the ICD literature database for peer-reviewed scientific literature supporting linkages among selected shapes.
     
  2. An online graphical editor that allows users to create new (or modify existing) diagrams and link new or existing references to them.
     
  3. A collaborative workspace, whereby users can grant other users the ability to view and revise diagrams they have created.

As you use the ICD application, please keep in mind that it is meant to be a collaborative environment. At any time, the creator of a diagram can allow all registered users to view and comment on any of their diagrams. Thus, you should assume that any comments you make on a diagram can be seen by all registered users of the ICD application.

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What you are able to do in the ICD application is determined by two closely related concepts: your user role, and the mode of the application in which you’re operating.

There are three user roles defined in the ICD:

  • Public users are any users who do not register in the ICD application. They have access to View mode of the ICD application, for EPA-constructed diagrams.
     
  • Registered users are any users that self-register in (and then log in to) the ICD application. They have access to View and Edit modes of the application, for all diagrams that have been set as registered user-viewable by the diagrams’ creators.
     
  • Admin users are registered users that have been granted administrative privileges. As with other registered users, admin users are not able to view any diagrams that have not been designated as registered user-viewable by the diagrams’ creators.

Your user role determines which of the ICD application’s two modes you can access.
For more information see the Viewing ICDs and Editing ICDs tabs above and the Complete ICD User Guide (Helpful Links box at right).

  • View mode allows you to select shapes within an open diagram and obtain citations for supporting literature - that is, references suggesting that linkages among the selected shapes can occur.
     
  • Edit mode allows you to modify existing diagrams, create new diagrams, and link new or existing supporting literature to those diagrams. It also allows you to designate other registered users as collaborators, granting them permission to view and/or modify any diagram you create (even if it is not designated as viewable by all registered users).

To register for the ICD application:

  • If you have an EPA LAN account, go to the EPA Web Application Access site and log in using your LAN id and password. You need to request access to the CADDIS community, so click Community Access >> Request Access to Communities, check CADDIS in the list, and click Save Groups. You will receive an email when access to the CADDIS community is granted, and you can then log in to the ICD application as a registered user, using your LAN id and password.
     
  • If you do not have an EPA LAN account, click the Self Register link on the EPA Web Application Access site. Complete the Self-Registration form, using Kate Schofield as the EPA Contact Name, schofield.kate@epa.gov as the EPA Contact's Email Address, and (703) 347-8533 as the EPA Contact's Phone Number. Under "Select the Community or Application for which you are requesting access" choose CADDIS, then accept the EPA Privacy & Security Notice and click Submit. You will receive an email when access to the CADDIS community is granted, and you can then log in to the ICD application as a registered user, using the user name and password you provided during registration.

Remember - you only need to register once. Once you have successfully registered (and been granted access to the CADDIS community), you can simply log in to the ICD application on all subsequent visits. For more information on registering for and logging in to the ICD application, see the ICD User Guide (Helpful Links box at right).

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Once you have registered for and logged in to the ICD application (or have decided remain a public user and not register; see ICD User Roles and Modes tab for more detail), you are ready to start using the tool. View mode of the ICD application allows you to select shapes within a diagram and view scientific literature that provides support for linkages among those shapes. Public users can view EPA-constructed diagrams; registered users can view any diagrams that they have created, that they have been designated as collaborators on, or that have been set as registered user-viewable by their creators.

To get started in View mode, click the Open Diagram button, select the diagram you wish to open and click Open.

  • Initially some shapes in the diagram may be hidden, indicating that parent-child relationships have been assigned among shapes. A black triangle under a shape indicates that there are additional shapes (i.e., child shapes) associated with that shape (i.e., the parent shape). To show all shapes in a diagram, click Show All; to show only the child shapes under a specific parent, click the black triangle under that parent.
     
  • When shapes are hidden in View mode, arrows and lines will not be displayed; to view all arrows and lines, click Show All to make sure all shapes are displayed.
     
  • The large EPA diagrams in the ICD application (composite ICD, metals ICD, and sediment ICD) were drawn without arrows and lines, given the scope of these diagrams and the number of shapes they contain. By selecting shapes and highlighting the shapes linked to them (see below), you can still "view" potential causal pathways among these shapes, even without arrows explicitly included.

You can select any shape within the diagram by single-clicking it.

  • The first shape you select will highlight blue.
     
  • Any shapes linked to the shape you selected (by literature evidence entered into the ICD database) will highlight purple.
     
  • If a shape linked to your selected shape is hidden (i.e., it is a hidden child shape), its visible parent shape will outline in orange; show that parent's child shapes (i.e., click on the black triangle under that shape) to see any purple child shapes.
     
  • You then can select any purple shape to view citations for papers supporting a linkage between the shapes you’ve selected. If no shapes highlight purple, it means that no literature supporting linkages between the shape you selected and any other shapes has yet been entered into the database—not necessarily that these linkages do not occur, or have not been observed anywhere in the scientific literature.
     
  • Once you select a second shape (i.e., a first purple shape), the shape-highlighting will change: your second selected shape also will highlight blue, and shapes linked to that second shape will highlight purple. You can continue to select purple shapes in this manner, to view supporting literature for multiple pair-wise linkages.
     
  • To deselect any shape you've selected, click it again (it will return to its original color); click Deselect All to clear your search (i.e., deselect all shapes) and begin again.

Once you have selected your shapes, click on the References panel icon reference icon to view supporting citations.

  • The References panel will list the shapes you’ve selected (Selected Shapes, top sub-panel), references supporting pair-wise linkages among these shapes (Selected Linkages, middle sub-panel), and any references you’ve saved from all the searches you conducted in a given session (Saved References, bottom sub-panel).
     
  • Buttons at the bottom of the Selected Linkages panel allow you to save references into to the Saved References sub-panel. Any references you save into the Saved References sub-panel will remain there, even if you clear your search (by clicking Deselect All on the View mode toolbar) and begin again.
     
  • Buttons at the bottom of the Saved References sub-panel allow you to download selected references from this panel.

A brief description of features on the View mode toolbar (Figure 1) follows; for more information on viewing diagrams in the ICD application see the ICD User Guide (Helpful Links box at right).

Figure 1. View mode toolbar in the ICD application.Figure 1. View mode toolbar in the ICD application.

ICD iconsIcons in View toolbar

  • Inset icon: Pan around the open diagram by zooming in and dragging the blue window around the Inset (you also can use the Esc key to show/hide the Inset)
     
  • Open Diagram: Open a diagram
     
  • Legend: View a legend of the shapes used in the EPA-constructed diagrams
     
  • Collapse/Expand: Vertically collapse a diagram and remove any unoccupied white space/Vertically expand a diagram and include any unoccupied white space (typically used when child shapes are hidden)
     
  • Hide All/Show All: Hide all child shapes (shapes designated as sub-categories of another shape)/Show all child shapes (i.e., view all shapes in diagram)
     
  • Deselect All: Reset the shape selection process by deselecting all currently selected shapes
     
  • View as Image: View an image of the diagram as it currently appears on the screen
     
  • Log In/Log Out: Log in to the ICD application/Log out of the ICD application
     
  • Register: Register in the ICD application (only need to do this once; after that, can just log in)
     
  • Help icon: Access the ICD User Guide for more detailed help with using the ICDs
     
  • Search icon: Conduct a text-based keyword search of references (rather than a diagram-based search)
     
  • References Panel icon: View/Hide the References panel, which shows you selected shapes and supporting references for linkages among those shapes

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Once you have registered for and logged in to the ICD application, the Edit tab will appear on the top left of the toolbar (public users will not see the Edit tab). To get started in Edit mode, click on the Edit tab. This will bring up the Home: Diagram Settings screen (Figure 2), which will allow you to open existing diagrams, create a new diagram, designate collaborators for any diagram you create, and change any diagram settings (e.g., description, keywords, viewer settings) for any diagram you create. You also can bring up this screen by clicking on the Home button, at the top left of the Edit mode toolbar.

  • To create a new diagram, click the Create New Diagram button and fill in the required fields (descriptions of these fields can be viewed by mousing over the help icons next to these fields on the Home: Diagram Settings screen).
     
  • To open an existing diagram, browse or search the existing diagrams, select a diagram (i.e., so that it appears in the Diagram List window), then click the Open Diagram icon to the right of the diagram list.
     
  • To designate collaborators (i.e., registered users who can make changes to your diagram), select users from the Registered Users window (bottom right) and either double click on or drag-and-drop users to add them to the Collaborators window; then click the Recategorize Diagram icon (to the left of the Collaborators window) to save these changes before proceeding.
     
  • To change diagram view settings, check the appropriate boxes and click the Recategorize Diagram icon (registered users will only be able to select the Registered and Check out diagram options).
    • If you check Registered, all registered users will be able to view and comment on your diagram. They will not be able to modify the diagram and save it under the existing diagram name, but they will be able to save it as a new diagram, of which they are the creator.
       
    • If you check Check out diagram, you will be able to save changes to the existing diagram, using the same diagram name—that is, the Save button on the Edit mode toolbar will be enabled. This feature is to ensure that multiple collaborators can not make simultaneous changes to a diagram. If you are the diagram creator or a designated collaborator, and you wish to save changes to the diagram you’re opening, you must check the Check out diagram box and then click the Recategorize Diagram icon. If you don't check out the diagram, the Save button will be disabled on the Edit mode toolbar and you will not be able to save "over" the diagram you're opening. If you want collaborators to be able to make changes to the same diagram, you also must remember to check the diagram back in (i.e., uncheck the Check out diagram box and click the Recategorize Diagram icon) once you are done making your edits.
       
  • To change any diagram descriptors (e.g., diagram name or description), select the diagram in the Diagram List window, make any changes in the Diagram Descriptors fields, and click the Recategorize Diagram icon to save your changes.
     
  • To view all previous versions of a given diagram, select the diagram in the Diagram List window and click the Diagram History icon.
     
  • To delete a diagram, select the diagram in the Diagram List window and click the Delete Diagram icon.

Keep in mind that most of the options discussed above are available only if you are the diagram creator or a designated collaborator. For example, the Diagram History, Recategorize Diagram, and Delete Diagram icons will not appear and the Collaborators window and Diagram Descriptors fields will be shaded out when you select a diagram you did not create or on which you are not a designated collaborator. To access these features you must first save the selected diagram as a new diagram (using Save As).

Figure 2. Home: Diagram Settings screen, in Edit mode of the ICD application.Figure 2. Home: Diagram Settings screen, in Edit mode of the ICD application.


Once you have created a new or opened an existing diagram, you are ready to start creating or editing your diagram.

  • To add a shape to the diagram, click on any shape icon on the toolbar, then click anywhere on the diagram canvas to place that shape. Fill in shape information in the Shape Attributes screen: its label (the text which appears in the shape), any direction for that label (increasing, decreasing, or a change in), and any parent shape designation (the shape that your new shape is a sub-cateogry or child of, if any).
     
    • The ability to establish parent-child relationships was created for large, complicated diagrams (e.g., the composite EPA diagram) that users may occasionally want to view in less detailed form. This functionality will be evolving in future versions of the ICD, so we generally recommend that you do not create any parent-child relationships in your own diagrams.
       
  • To add an arrow or line, click on the arrow or line icon on the toolbar. Click once on the canvas at the point you wish to start the arrow or line, to begin drawing; click a second time at the point you wish to end the arrow or line, to stop drawing.
     
  • To delete a shape or a line, mouse over the shape or line so that the highlighting dots appear, and then press the Delete key.
     
  • To link supporting references to your diagram, click Add Linkage on the Edit mode toolbar, select the shapes you want to create a linkage between (you can select more than two shapes, but only if you want to link the first shape you selected to all subsequent shapes, or create links between all shape-pair combinations of the selected shapes). Once you have selected your shapes, click Save Linkage on the Edit mode toolbar.
     
  • Fill in the required information on the Save New Linkage screen. You can search citations already entered in the ICD literature database using the Find Citation field, as well as add new citations individually (click Enter new citation) or by uploading references from your reference manager software (click Upload new citation(s)). To select a citation, either double-click it in the Existing Citation window or drag-and-drop it into the Selected Citations window. Click Save to save the linkage.
     
  • To save changes you’ve made to the diagram, either click Save (if you are the diagram creator or a designated collaborator) or Save As (to save the diagram as a new diagram, with you as the creator).

A brief description of features on the Edit mode toolbar (Figure 3) follows; for more information on viewing diagrams in the ICD application see the ICD User Guide (Helpful Links box at right).

Figure 3. Edit mode toolbar in the ICD application.Figure 3. Edit mode toolbar in the ICD application.

iconsIcons in Edit toolbar

  • Inset icon: Pan around the open diagram by zooming in and dragging the blue window around the Inset (you also can use the Esc key to show/hide the Inset)
     
  • Home: Open the Home: Diagram Settings screen, from which you can create a new diagram, search for and open an existing diagram, and designate collaborators or modify other diagram settings for diagrams you create
     
  • Save: Save any changes made to the open diagram
     
  • Save As: Save the open diagram as a new diagram
     
  • Close: Close the open diagram
     
  • Shape, Arrow and Line icons: Add a shape, arrow or line to the open diagram
     
  • Hide/Show: Hide/Show all arrows and lines
     
  • Tiers: Designate tiers (horizontal layers) of the diagram as collapsible or non-collapsible
     
  • Select/End: Select multiple shapes (e.g., to move or delete them)/End the Select function
     
  • Copy/End: Copy a shape and all its attributes, for pasting into the open diagram/End the Copy function
     
  • Align/End: Select and vertically align multiple shapes/End the Align function
     
  • Add Linkage/Save Linkage: Link a supporting reference to pair-wise linkages between shapes
     
  • Comment icon: Submit a comment on the open diagram
     
  • Help icon: Access the ICD User Guide

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