Help

Before you start

Resources

Please read the AOP Wiki Editing & Comments Policy.

General guidance on assembling AOP information in the AOP-Wiki is available in the OECD AOP Users' Handbook.

Check out the new online training course available here:  https://aopwiki.org/training/. We have launched a training wiki (https://training.aopwiki.org/) to allow users to learn the new system before making changes on the new production wiki. You do not need to be an author on this wiki to be granted author status on the training wiki, but all information in the training wiki is purged periodically and no mechanism exists to migrate information from that system to this one. If you would like to request author privileges on the training wiki, please contact us at aopwiki@googlegroups.com.

Help is available anytime by clicking the Help link at the bottom of the page and by using the context sensitive help throughout the site.  

Training Course Available

An Online course has been developed to promote knowledge of and participation in the AOP process, including submissions to the AOP Wiki. The course was designed and developed by etioLogic, LLC for the Human Toxicology Project Consortium and is now hosted on the "Animal-Free Safety Assessment (AFSA) Collaboration" website (AFSAcollaboration.org) and is freely available to any and every one. The course can be downloaded as zip files from (Download)  or run directly online by clicking on the links below.

For an overview and historical perspective of the AOP framework click here: https://aopwiki.org/training/aops/ For training on the AOP-Wiki: https://aopwiki.org/training/wiki/

For questions or suggestions regarding the course, please contact the course sponsor via the e-mail address available in the Read Me file at  (Read Me):   

Thanks to the Human Toxicology Project Consortium for sponsoring this new resource to support AOP development and to etioLogic for assembling this course. 

Requesting Access to Create and Edit AOPs

Read-access to all content is available without need to create a user profile, login ID, or password.

Any user can provide comments on all wiki content by creating an account and logging into the wiki.  To set up an account, click on “sign up” in the upper right-hand corner of the home page.  Enter a valid e-mail address and create a password. Click on the link you receive in a confirmation e-mail. Creation of an account provides access needed to submit comments via the “Discussion” pages associated with each page in the AOP-wiki, but does not grant full author rights.

To obtain author access to the AOP-Wiki, users must first create a user profile/account in the AOP-wiki as described above.  Once you have an account, author access can be obtained in one of two ways:

  • Option 1 – Approval of an AOP-development project with the OECD AOP Development Workplan:  Author access to the AOP-Wiki may be obtained by submitting an AOP-development proposal to the OECD AOP development Programme workplan. A link to the AOP project proposal form   and instructions can be found at  http://www.oecd.org/chemicalsafety/testing/adverse-outcome-pathways-molecular-screening-and-toxicogenomics.htm.   Project proposals are reviewed twice per year. Once a project has been approved,  author access will automatically be granted to the project leader and any additional project team members listed on the project proposal.
  • Option 2 -  Obtain access via the Society for Advancement of AOPs (SAAOP):  The SAAOP will review author requests for AOPs at early stages of development when the authors would prefer to refine the AOP prior to submitting a proposal for the OECD program. For this option, the requester should provide a brief description of their intended contribution that preferably includes a graphical diagram of the proposed AOP. If the author request is to expand information on existing objects, the specific  KEs and KERs should be listed along with a brief description of the proposed changes and certification that edits will be coordinated with AOP authors using those KEs and KERs. Author access applications submitted to the SAAOP are typically reviewed within 2 weeks of submission. 

Whichever option is chosen, the user should fill out the author request form here:  https://aopwiki.org/wiki_accesses/new. Requesters should certify that all users have read and agree with the “rights and responsibilities” for wiki authors. For option 2, the requester should upload a file containing the additional information described above.  After completing step one, the requester will select existing AOP users for all project team members requesting access. More detailed instructions are available in the Help section accessible via the Help link at the bottom of the page or via the following direct link: https://aopwiki.org/info_pages/2#Requesting Author Access.

Frequently Asked Questions

We are collecting solutions to all problems users nave noticed on our Frequently Asked Questions page:  https://aopwiki.org/info_pages/4. Please check there for answers if you have any problems. If you do not see your answer posted, email aopwiki@googlegroups.com, and we will work with you to solve the problem.

Citing the AOP-Wiki

Entire AOP-Wiki

Reference:  Society for Advancement of AOPs. [year]. AOP-Wiki. [Cited date]. Available from http://aopwiki.org.

Text citation:  (Society for Advancement of AOPs, [year])

URL citation.  (aopwiki.org)

Specific AOP, Event, or Relationship Pages

Cite the page-specific URL

AOP Pages*: https://aopwiki.org/aops/[AOP ID number]; e.g., https://aopwiki.org/aops/25 

Event pages:  https://aopwiki.org/events/[Event page ID number]; e.g., https://aopwiki.org/events/285 

Relationship pages:  https://aopwiki.org/relationships/[Relationship ID number]; e.g., https://aopwiki.org/relationships/94

* Note - before citing a specific AOP page, please check the "author status" field to determine whether it is open for citation. If the status reads "under development, not open for comment, do not cite", the page should not be cited without permission from the contact author. 

Citing a Snapshot

  • Because the content on AOP-Wiki pages may evolve over time, to cite the content as it was observed on a given date, please create and cite a snapshot.
  • After creating the snapshot, cite the URL associated with that snapshot; e.g., https://aopwiki.org/aopwiki/snapshot/html_file/25-2020-08-14T12:40:08+00:00.html 
  • Note, you must be logged in as an AOP author to create a snapshot.  If you do not have author access to the AOP-Wiki, please contact aopwiki@googlegroups.com to request a snapshot.  Please specify the AOP page you would like a snapshot of (all linked Event and Relationship pages will be included) and a short title for your snapshot and request that the URL for the snapshot be sent to you.

Contributing to the AOP Wiki

Create a new AOP!

Step 1: Create an AOP Wiki User Account

  • If you already have an account(e.g. for commenting on existing AOPs), skip this step.

Step 2: Get author rights for your AOP Wiki User Account

  • Option 1: Submit a proposal to the OECD AOP Development Program
  • Option 2: Submit an AOP idea to the Society for the Advancement of AOPs

Step 3: Start creating your AOP!

  • Sign in using your AOP Wiki User Account (after receiving author privileges)
  • On the AOP page, press the "New AOP" button
  • Follow the recommendations in the AOP Developer's Handbook

Creating a Wiki Account

First a new user has to self-register at the AOP Wiki site by clicking the "sign up" link in the top banner of the AOP Wiki main page:

In the next page, the new user has to give his Email-Address (which will then also be the user name) and a password:

The password must include at least one lowercase letter, one uppercase letter, one number and one special character (e.g. !@#$%^&*-).

The new user will receive an Email with instructions to activate his account.

Once the email has been validated, a signed in user can submit comments via the “Discussion” pages associated with each page in the AOP-wiki. For full author rights, see the section below.

Requesting Author Access

The procedure to get write access to the AOP Wiki consists of two steps:

1) Create a user account

2) Request author access

Create a user account

See instructions for creating a user account here:

Please note: This account does not yet automatically entitle the new user to edit or add information in the Wiki!

Request author access

Author access can be obtained in one of two ways:

  • Option 1 – Approval of an AOP-development project with the OECD AOP Development Workplan:  Author access to the AOP-Wiki may be obtained by submitting an AOP-development proposal to the OECD AOP development Programme workplan. A link to the AOP project proposal form   and instructions can be found at  http://www.oecd.org/chemicalsafety/testing/adverse-outcome-pathways-molecular-screening-and-toxicogenomics.htm.   Project proposals are reviewed twice per year. Once a project has been approved, author access will automatically be granted to any verified member of the project team by noting the OECD project on the author request form.
  • Option 2 -  Obtain access via the Society for Advancement of AOPs (SAAOP):  The SAAOP will review author requests for AOPs at early stages of development when the authors would prefer to refine the AOP prior to submitting a proposal for the OECD program. For this option, the requester should provide a brief description of their intended contribution that preferably includes a graphical diagram of the proposed AOP. If the author request is to expand information on existing objects, the specific  KEs and KERs should be listed along with a brief description of the proposed changes and certification that edits will be coordinated with AOP authors using those KEs and KERs. Author access applications submitted to the SAAOP are typically reviewed within 2 weeks of submission.

 Regardless of whether you obtain access for an OECD project or through the SAAOP, you must Submit a new Wiki access request.

  • SAAOP requests - include a form that briefly describes the SOP to developed.
  • OECD requests - simply include the title or identifier for your OECD approved AOP development project.
  1. On the top nav bar, click on your username to bring up a drop down list of options. Click 'request author access' to bring up a new form entitled, "AOP-Wiki Developer Access Request Form." 
  2. Click the check boxes to accept the “rights and responsibilities” and whether or not this is an OECD project. Fill in the information regarding OECD project title and project leader email or click 'Browse' to upload a file containing your AOP proposal for Option 2 requests. Click 'Create form' to create a new request.  
  3. To add users to the request, after creating the form, click 'Add user.' You will be brought to a new page entitled "New Wiki Access User" which you can search by last name. Select a user and click 'Add user' to add the user to the request. The system will alert you if you attempt to add a user who is already an AOP-Wiki author.
  4. Once you have the information and users you would like added to the request form, click 'Submit form' to submit your form to the wiki author committee. When your request is processed, you will receive an email.

Creating & Editing AOPS

AOP Pages

The main page listing all AOPs can be located by clicking 'AOPs' in the navigation menu on the top of all pages. This page lists all AOPs in the Wiki with information about their ID, Title, Point of Contact, Author Status, SAAOP Status, MIE and AO, OECD Status, and OECD Project number.

To order AOPs by ID, Title, Point of Contact, Author Status, SAAOP Status, MIE and AO, OECD Status, or OECD Project number, click on one of these headings at the top of the AOPs list. You should see an up arrow next to the field which you sorted by indicating sort by ascending order, or a down error indicating sort by descending order.

To view AOPs by OECD status, click on the button 'With OECD Status' at the top of the page. This will bring you to a page entitled, "AOPs With OECD Status" listing AOPs categorized by OECD status. To view AOPs by SAAOP status, click on the button 'With SAAOP Status' at the top of the page. This will bring you to a page entitled, "AOPs With SAAOP Status" listing AOPs categorized by OECD status. Clicking on 'Recent AOPs' will bring a list of AOPs that have been recently added to the AOP-Wiki.

The AOP list may be searched by title, keyword or by ID. To search for a specific AOP by title, in the dialog box entitled 'Search AOPs..' type in the full title for the AOP you wish to find and click 'Search.'  A list of AOP Title search Results will be returned. To search for an AOP by keyword, in the dialog box entitled 'Search AOPs..' type in keyword(s) for the AOP you wish to find and click 'Search.' AOP Full text search results will be returned. To search for a specific AOP by ID, in the dialog box entitled 'Find by ID' type in the numeric ID for the AOP you wish to find and click 'Find by ID.' You will be redirected to the AOP page matching that identifier.

Instructions for creating and editing an individual AOP page are  located here .

Key Event Pages

The main page listing all KEs can be located by clicking 'Key Events' in the navigation menu on the top of all pages. This page lists all KEs in the Wiki with information about their ID, Title, Short name, and level of Biological Organization.

The KE list may be searched by titleor by ID. To search for a specific KE by title, in the dialog box entitled 'Search Key Events..' type in the full title for the KE you wish to find and click 'Search.'  A list of KE Title search Results will be returned. To search for a specific KE by ID, in the dialog box entitled 'Find by ID' type in the numeric ID for the KE you wish to find and click 'Find by ID.' You will be redirected to the KE page matching that identifier.

Instructions for creating and editing an individual KE page are  located here .

Key Event Relationship Pages

The main page listing all KERs can be located by clicking 'KE Relationships' in the navigation menu on the top of all pages. This page lists all KEs in the Wiki with information about their ID, Upstream event, Relationship type, and Downstream event.

The KER list may be searched by title or by ID. To search for a specific KE by title, in the dialog box entitled 'Search relationships..' type in the name of either the Upstream event or the Downstream event and click 'Search.'  A list of KE Title search Results will be returned. To search for a specific KER by ID, in the dialog box entitled 'Find by ID' type in the numeric ID for the KER you wish to find and click 'Find by ID.' You will be redirected to the KER page matching that identifier.

Instructions for creating and editing an individual KER page are  located here .

Stressor Pages

The main page listing all Stressors can be located by clicking 'Stressors' in the navigation menu on the top of all pages. This page lists all Stressors in the Wiki by Name and ID.

The Stressor list may be searched by name or by ID. To search for a specific stressor by name, in the dialog box entitled 'Search stressors..' type in the name of either the stressor or the individual chemical you wish to find and click 'Search.'  A list of Stressor name search results and Chemical name search results will be returned. To search for a specific Stressor by ID, in the dialog box entitled 'Find by ID' type in the numeric ID for the Stressor you wish to find and click 'Find by ID.' You will be redirected to the Stressor page matching that identifier.

Instructions for creating and editing an individual stressor page are located here

Adding Pictures or Attachments to Text Sections

Abrief text description is provided below.  Follow this link for a version that includes screenshots:  Adding Picture or Attachments to Text Sections (including screenshots).

The formatting toolbar at the top of each text edit field includes icons for inserting either a link to a file or embedding an image. To use these tools, however, you must first upload the file to the server (unless the file is already available on the web).  In order to do this, you need to click on the "Add pictures" button at the top of the page.

On the subsequent page, you will click on the button labelled "New picture" at the top of the page and upload the desired file from your local computer.  The Image Title should contain a short but informative label for your file.  This is particularly important for non-image files because the content will not be displayed on the page listing the files.  Once you've uploaded the desired file, right click on the file when looking at the list of all files for that AOP/KE/Relationship and select the "Copy link location" or "Copy image location" depending on the type of file you uploaded (see below for an example of a PDF file). After you have copied the link for the desired file, return to the AOP/KE/Relationship edit page insert your file link.  The process is slightly different for an image vs. a file. 

To insert a link to a file, type the text you wish to display for the link.  In the example below, "Table 2" was typed into the appropriate location in the edit box. Highlight the text you just typed and click the "Link" icon in the formatting bar as shown above.  In the dialog box that opens, paste the link you copied in the previous step.  Advanced options are available but not necessary.  Simply click OK unless you wish to set additional settings.  When you click the "Update AOP" button, you will now have a hyperlink associated with the text you entered at the appropriate place in your text field.

When inserting an image, you do not need to type any text.  Just place your cursor at the desired location in the text box and click the "Image" link in the formatting bar as shown above.  In the dialog box that opens, paste the link to the image file you uploaded in the earlier step.  The inserted image will now shown on the web page itself. This dialog box also has additional options should you wish to set them, but you can just click OK once you've pasted the link.

Request a new term

Most terms are populated in the Wiki by selection of exisiting terms from drop down menus. There may be instances where a term you wish to use has not been used before. In this case, an AOP contributor can request a new term.

To request a new term, click on you username in the upper right hand corner of the nav bar. From the drop down list, select 'request new term.'  You will be brought to a new page entitled "New Term Request" where you can name the term, select a term type, and justification that this term needs to be added. Click 'Create Term request' to send the request form to administrators. For terms that link to external vocabularies such as taxon terms, cell terms, organ terms, biological processes, and biological objects; administrators will locate and identify matching terms from public databases and vocabularies that match the user's request. If your term is accepted, you will be sent an email notification.

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Contact for Help

If you have any questions that are not addressed below please contact us at:

       aopwiki@googlegroups.com.

User Profile & Preferences

Edit User Profile

To edit your user profile, click on your username in the upper right hand corner of the page. This will bring up a drop down list of options, choose 'my profile.'  You will be directed to a new page with your user profile.

To edit the text fields of your profile (First Name, Last Name, Affiliation, etc.), under these fields click 'Edit.' You will be brought to a page entitled "Editing Profile."  Edit the text fields and click 'Update profile' to save your changes. You will be returned to the user profile page.

Change password

To change your password, navigate to your user profile as directed in the previous Help topic. Click 'Change your password or email' and you will be directed to a new page entitled "Edit User."  Type in your current password, new password, and retype the new password as confirmation. Passwords must be an 8 character minimum and contain at least one uppercase letter, one lowercase letter, and one special char (ex. !@#$%^&*-).  Click 'update password and/or email' to save your changes.

To edit your email address, make changes to the email address text field, and type in your current password. Click 'update password and/or email' to save your changes. Check your email, where you should see an email asking you to verify your new email address. Follow the confirm link in the email to verify. You need to log in to the AOP-Wiki site using your changed email/password in order to confirm.

Subscribe/Unsubscribe to Email Notifications

To subscribe/unsubscribe to email notifications, navigate to the User Profile page as before, and under the Email Notifications section, where it says 'Suscribed?' check the box and click 'Update.' The email listed on your profile will be subscribed to email notifications.

To unsubscribe, where it says 'Suscribed?' uncheck the box and click 'Update.' The email listed on your profile will be unsubscribed from email notifications.

Roles

On the user profile page, the Roles section lists what user roles an individual user has. A user may have either admin, author, or gardener roles.

Update watch list

The Watch List provides a list of individual AOP, KE, KER, or Stressor that a user is currently watching, similar to Bookmarks on an internet browser.

To remove a page from the Watch List, on the User Profiles page, uncheck the AOP, KE, KER, or Stressor that you wish to remove. Click 'Update Watch List' and then 'OK.' The item should no longer be listed under the Watch List.

Viewing and Commenting on AOPs

Create or Edit a Comment

Each AOP, Key Event, Key Event Relationship, and Stressor page has a comment button located in the top right corner of the page.  All registered users are welcome to comment on any of these pages.  AOP authors are encouraged to respond to comments on their AOP pages as well as associated pages where the comments are relevant to their AOP.

To create a new comment on an AOP, KE, KER, or Stressor page, in the upper right hand panel menu, click 'Comment.' This will direct you to a new page entitled, "New Comment." You can enter text in the Comment text window, as well as upload a picture. To upload an image, click 'Browse' and then select the desired image from your computer. Click 'Create comment' to save your changes. You will be directed to a page entitled, "Comments for [AOP/KE/KER/Stressor: #]."

On AOP pages, an attachment or image may be added to a comment. To add an attachment, under the Comment text box click 'Browse..' Select a file from your computer. You should see the file name next to the Browse... button when it is uploaded. Click 'Create comment to save your changes. On the "Comments for [AOP: #]" page you should see the "Uploaded file:[Your filename]" below your comment. Clicking on your filename should open your attachment in a new browser window.

To edit a comment on an AOP, KE, KER, or Stressor page, in the upper right hand panel menu, click 'Discussion.' This will bring you to the page entitled, "Comments for [AOP/KE/KER/Stressor: #]." Click 'Edit' to make changes to the Comment text or file attachment, and 'Update comment' to save your changes. You may only edit a comment which you have made.

Reply to a Comment

To reply to a comment on an AOP, KE, KER, or Stressor page, in the upper right hand panel menu, click 'Discussion.' This will bring you to the page entitled, "Comments for [AOP/KE/KER/Stressor: #]." Click 'Reply' under an individual comment to bring up an empty text dialog window. Type in your desired response and click 'Reply.' The reply should be listed under the original comment. 

To edit a reply, under the reply you wish to edit, click 'Edit.' You will be redirected to the "Edit Comment" page where you can edit your comment and click 'Update comment' to save. You may only edit your own replies.