Help:Contents

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Before You Start

We ask that all users abide by the AOP Wiki Editing & Comments Policy. In order to comment on existing AOPs, Key Events, and Key Event Relationships, you need to first create an account. If you have not done so, instructions are available. The process for making comments is described in detail here: Using Talk pages for collaborative AOP development and evaluation of AOPs. To author or edit AOPs still requires membership in an OECD AOP development project. Helpful information for authors is available here: Special Considerations for AOP-Wiki Authors.

https://aopkb.org/aopwiki/index.php?title=Special:UserLogin&returnto=Help%3AContents&type=signup

Main Types of Data

  • Adverse Outcome Pathway - or Mode of Action, the way chemicals act on an organism, leading to an adverse outcome
    • Molecular Initiating Event - Key Event representing the initial perturbation of the system by a chemical
      • Chemical Initiator - the actor (subject) in an AOP or MoA that perturbs the pathway represented by the MIE
    • Key Event - the building block for MoAs and AOPs
    • Adverse Outcome - or Endpoint, the adverse consequences at the organism or population level that would potentially be of regulatory concern.
    • Key Event Relationship - Describes the relationship between two key events or a key event and an adverse outcome

Common Terms

  • Widget page: this is a tool that automatically keeps information consistent across pages. When you edit an AOP in the widget, changes will show up on any page where the AOP is referenced.
  • Wiki page: the page you are looking at is an example of a wiki page. The wiki page is where you can view AOPs and enter text, and is where researchers will go to find out information about an AOP or its elements.

Setting Up Your Profile

Preferences.png

After you have created an account, you will be able to edit pages. Most users will probably want to "watch" any page that they edit. If you follow the "Preferences" link in the top right corner, you can set it to automatically add a watch whenever you edit a page. You can then turn the watch off for pages you do not wish to track. You can also elect to receive emails when a watched page is edited in your user preferences. Finally, you may wish to have a signature other than your user name for when you sign comments on a talk page.

If you need to change your password, please see the help page for changing your password.

More information is available on setting these and other preferences.

Quick Start

This section is intended to give a quick overview of the process. Please follow the heading links for each section to find detailed information. Warning: The following symbols have special meaning in MediaWiki and thus, cannot be used in any input fields: [, ], {, }, | Use of these symbols in text sections should be restricted to cases where the associated wiki format is desired. For more information, see the tutorials for wiki formatting, wiki tables and wiki templates.

To create a new AOP

  1. In the Sidebar, under actions, click the Create new AOP link
  2. Enter a unique Short Title and a descriptive Long Title for your AOP.
  3. Click the "Create AOP" button after specifying a new name.
  4. You will be taken to a widget page to create a new AOP. Populate the widget page by clicking on the 'Add' button for each entry.
  5. When done creating the new AOP, click the 'Return to Wiki' button at the top of the widget page.

To edit AOP wiki pages

  1. All sections except those contained under the "Summary of the AOP" heading are for text entry. If you manually enter text in this section, it will get automatically altered or deleted in subsequent edits using the widgets. See below for more details about editing text sections.
  2. Any changes you wish to make to the "Summary of the AOP" sections should be made using the widget page. Clicking on the link under the "Summary of the AOP" heading will take you to a widget where you can edit individual sections. Detailed instructions for each widget are on the Help:Edit AOP page.

To edit Key Event wiki pages

  1. If you wish to edit a Key Event wiki page, click on its link under from the "Summary of the AOP" section.
  2. On the wiki page, all sections except those contained under the "Key Event Overview" heading are for text entry. If you manually enter text in this section, it will get automatically altered or deleted in subsequent edits using the widgets. See below for more details about editing text sections.
  3. Any changes you wish to make to the "Key Event Overview" sections should be made using the widget page. Detailed instructions for each widget are on the Help:Edit AOP page.

To edit Molecular Initiating Event wiki pages

As a subcategory of key events, the MIE pages have the same template. See instructions in Key Event section for more details. There are two things to keep in mind for MIEs:

  1. In the overview section, a subsection for 'chemical initiators' will be present. Please use the widget (linked under the Key Event Overview heading) to add chemicals.
  2. An additional text entry section is included for providing evidence linking the chemicals listed in the overview section to this MIE.

To edit Adverse Outcome wiki pages

As a subcategory of key events, the AO pages have the same template. See instructions in Key Event section for more details. There are two things to keep in mind for AOs:

  1. In the overview section, a subsection for 'affected organs' will be present. Please use the widget (linked under the Key Event Overview heading) to add organs.
  2. An additional text entry section is included for providing regulatory examples using the adverse outcome.

To edit Key Event Relationship wiki pages

  1. If you wish to edit a Key Event Relationship wiki page, click on its link under from the "Summary of the AOP" section.
  2. All sections except those contained under the "Key Event Relationship Overview" heading are for text entry. If you manually enter text in this section, it will get automatically altered or deleted in subsequent edits using the widgets. See below for more details about editing text sections.
  3. You should use the widget to make changes to the "Key Event Relationship Overview" section. Detailed instructions for each widget are on the Help:Edit Key Event Relationship page.

Editing tips for text entry sections

To add text to any section, click the "[Edit]" link to the right hand side of the section header for that section. Type your notes in the resulting text box and click the save page button at the bottom. Don't delete the ==Heading== line at the top as that creates the header line. Type your desired text for that section beneath it.

Pre-existing text in template

Some sections include italicized text providing the type of information expected in this section based on the OECD guidance document. This text can be deleted once you begin adding content and should be deleted prior to submitting the AOP for OECD consideration. This text can be easily recognized by the <em>..</em> tags surrounding it.

Common Formatting Options

Below are a few tips for commonly desired formatting options within the text entry sections. Additional options are available.

  • To separate paragraphs, you must include a blank line between them in the edit box.
  • To create subheadings within a section precede the section with ===Heading=== (note 3 equal signs vs. two above) on a line by itself. Additional nesting of subheadings just requires increasing the number of equal signs by one.
  1. To create a numbered list, begin each line with the '#' symbol
  • To create a bulleted list, begin each line with the '*' symbol
  • Hovering over the icons at the top of the edit window will provide a brief description of what they do.
    • The first two provide you the ability to Bold and Italicize text. Just replace the highlighted text leaving all single quote marks around the text.
    • The next two create hyperlinks to other wiki pages and external pages respectively. Just replace the highlighted text leaving all "[" & "]" marks around the text.
    • The second icon from the right will include your wiki signature. Please use this to sign any contributions you make to a "Talk" page.

Including images in text sections

Including a table in text sections

General information on wiki widgets

Summary (for AOP) and Overview (all other pages) sections are intended for programmatic editing using the widgets in each subsection. If you manually enter text in this section, it will get automatically altered or deleted in subsequent edits using the widgets. If you need to make changes and can't determine how to do it through the widgets, contact us at aopwiki@googlegroups.com, and we will help you make the necessary changes.

In cases where a heading does not have a widget yet, check out our Upcoming Features page to see where it stands in the queue. New buttons will be added as soon as the widgets are developed.

  1. To add a new item in the Summary/Overview section:
    1. Click the "Add Item to Table" button.
    2. Fill out the appropriate boxes in the pop up box. Hovering over the "i" beside each label will provide a brief description of the associated text box. Detailed descriptions of each widget are available on the detailed help page for each page type. Follow the links for the appropriate section above.
    3. The evidence field is never required and can be skipped if you don't have a rating. Once you've filled out the information. Click the Submit button.

Note that the Overview sections on non-AOP pages will have some tables that have no edit widgets associated. These provide links to associated wiki pages and should only be edited via the corresponding AOP page. Otherwise, the relationships among the pages can be lost.

Using Talk pages for collaborative AOP development and evaluation of AOPs

Before commenting on AOPs, please read the AOP Wiki Editing & Comments Policy. To see or add comments on an existing page, click on the Discussion tab in the top left of the wiki page. All KEs and KERs will have a basic comment page and new comments can be added at the top of bottom of the page. For AOP pages, there are two formats that a Discussion page will have based on whether or not the AOP has entered the OECD review process or not. AOPs that have not entered the OECD review process will have a simple comment page as for the KEs and KERs. AOPs that are undergoing (or have undergone) OECD review will have two sections, one for general comments, and one for listed the formal OECD reviews. In those cases, please add your general comments as shown below:

= General Comments =
All general comments should be entered here.

= Formal Reviews Managed by the OECD =
Don't add any text after this heading.

Special Considerations for AOP-Wiki Authors

  • The widget pages now require a separate login, but the same credentials are used for both. We are still looking for a single sign on solution.
  • The names for the AOPs & Events are now specified in the Title section on each page. If you make changes there, we will propagate them for you to the other pages. Please do not rename pages using the popup widgets. The edit button is for changing the Essentiality, Evidence, or Quantitative considerations only.
  • The next release will streamline this process, and we hope to have these updates out by summer of 2015.

General Wiki Help

Frequently Asked Questions

You may find the answer to your specific question on our FAQ page.