March is here.
What a great month to add some new AOPs to the AOP-Wiki!
Welcome to the Collaborative Adverse Outcome Pathway Wiki (AOP-Wiki)
This wiki is hosted by the Society for the Advancement of Adverse Outcome Pathways (SAAOP) and serves as one component of a larger OECD-sponsored AOP Knowledgebase (AOP-KB) effort. The AOP-KB represents the central repository for all AOPs developed as part of the OECD AOP Development Effort by the Extended Advisory Group on Molecular Screening and Toxicogenomics. All AOPs from the AOP Knowledgebase are available via the e.AOP.Portal, which is the primary entry point for the AOP-KB. More information about the AOP-KB efforts, the organizations supporting these efforts, and the other modules of the AOP-KB are available on the About page.
The content of this wiki is the sole responsibility of the individual contributors and does not necessarily represent the views of the authors' organizations nor the organizations responsible for development of the AOP-Wiki or the AOP-KB. Mention of trade names or commercial products does not constitute endorsement by any of these organizations.
Before you start
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 have any questions or would like to request author privileges on the training wiki, please contact us at email@example.com.
More detailed help can be found by clicking the Help link at the bottom of the page and by using the context sensitive help throughout the site.
New 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 (humantoxicologyproject.org) and is freely available to any and every one. The course can be downloaded as zip files from https://humantoxicologyproject.org/about-pathways-2/aop-online-course/ or run directly online by clicking on the links below.
For questions or suggestions regarding the course, please contact the course sponsor via the e-mail address available at:
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 firstname.lastname@example.org, and we will work with you to solve the problem.
New version of AOP Developer's Handbook released
The latest version of the OECD AOP Developer's handbook has been released and is available here: https://one.oecd.org/document/ENV/JM/MONO(2016)12/en/pdf. AOP authors are encouraged to follow the best practices outlined in this revised handbook when defining and evaluating their AOPs. As in the past, the AOP-Wiki has been updated to maintain consistency with the handbook. Authors who develop their AOPs in the AOP-Wiki will be able to create snapshots that adhere precisely to the format encouraged by the handbook. While we have updated the help text on the wiki to match the new handbook, we do not provide the same level of detail as the handbook and instead focus specifically on the technical aspects of entering the information into the Wiki. All AOP authors should read the new handbook as several notable changes have been included in this version.
Thanks to the OECD Extended Advisory Group for Molecular Screening and Toxicogenomics and especially the AOP handbook working group for their efforts in revising this document.
Wiki 2.0 Upgrade
User Account Migration
Version 2.0 of the AOP-Wiki was released on December 4, 2016. All users with logins on the previous wiki will need to recreate their passwords. More information is provided on the sign in page. Your previous account including author status was transferred, but it is now tied to your email rather than the previous user name. If you are unsure of the email you had associated with your wiki login or have any problems, please email us at email@example.com.
Confirm AOP Information Following Migration
We encourage all AOP authors to compare the content in the current version of the wiki with the final version contained in this wiki. Great care was taken to maintain the integrity of the information during the migration, but there may be some discrepancies. The original version is permanently available, and we are available to help if you have any problems correcting the issues in the new version. For comparison, you will use the following URLs (replacing 15 with your AOP #):
New wiki version: https://aopwiki.org/aops/15
Old wiki version: https://aopwiki.org/wiki/index.php/Aop:15
Notable Changes for Authors
Author access to individual wiki pages is now restricted. Each AOP from the previous wiki was assigned a point of contact based on the author information provided. This point of contact has permission to add other contributors to the AOP at which point those contributors will have edit permissions. All new AOPs will have the creator listed as point of contact. The point of contact can reassign to another contributor, but there can be only one point of contact. Gardeners will still have edit permission on all AOP pages.
The naming convention for key events has been changed. We no longer require a process/object and a separate action term. This information will soon be captured using the new event components that are based on established biological ontologies. We will be contacting authors of pre-existing AOPs on that topic soon. We encourage all authors to check the names of the key events in their AOPs and adjust those names as needed. We now include both a full title and short name for key events as we've always had for AOPs.