Wiki 2.1 Release
The next feature release of the wiki will be during the weekend of March 4-5. There may be short interruptions in service during the weekend, but no extended downtime is expected. The major change in this release is the snapshot functionality. The snapshots will conform to the current format described in the OECD User Handbook and will include information previously not included such as the graphical representation of the AOP. The formatting of the snapshots is improved as well.
This release will also include several smaller user features that have been requested since the 2.0 launch and will allow a user to find AOPs, Key Events, and Relationships by the numeric identifier when known in addition to the current search capabilty.
Event Components Coming Soon
With the new release of the wiki, we introduced the concept of an event component, which will be a structured representation of the key event. You can have one or more event components per key event, and each event component will be described using terms from a pre-defined biological ontology. Several authors have noticed that you can't yet select terms. We are working behind to scenes to annotate all the existing AOPs using a minimal set of existing biological ontologies. Once this process has been completed, we will be uploading both the list of terms from these ontologies and the pre-defined event components for the existing AOPs. This process should begin soon starting with the AOPs that are currently endorsed or under review by the OECD. We are reaching out to authors to verify the event component assignments prior to uploading any information to the wiki. If you have not been contacted about this, you will be soon.
This also impacts the cellular and organ context terms for all key events in the wiki. We expect to have the full term lists for those fields at the same time we release the initial set of event components.
Welcome to the Collaborative Adverse Outcome Pathway Wiki (AOP-Wiki)
If you are interested in contributing AOP-related knowledge to the AOP-KB, please follow the instructions laid out at the OECD Adverse Outcome Pathways, Molecular Screeing and Toxicogenomics page. The Guidance on Developing and Assessing AOPs document is the basis for all work related to contributing and sharing AOP-related knowledge. A Users' Handbook Supplement to this Gudance has been written to aid systematic development and transparent assessment of Adverse Outcome Pathways (AOPs). That handbook contains a template to guide AOP description and provides focused and practical instructions for develpers and assessors indended to assist in identifying, organizing, and evaluating critical information on key events and linkages (i.e., key event relationships (KER)) with the AOP, as well as guidance on how to assess the weight of evidence supporting the overall AOP.
This wiki represents a joint effort between the European Commision - DG Joint Research Centre (JRC) and U.S Environmental Protection Agency (EPA). This serves as one component of a larger OECD-sponsored AOP Knowledgebase effort and 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. The other major components of this knowledgebase are Effectopedia, produced by the Organisation for Economic Co-operation and Development (OECD), the AOP Xplorer, produced by the US Army Corps of Engineers - Engineering Research and Development Center, and the Intermediate Effects DB produced by the JRC.
This wiki is based upon the Chemical Mode of Action wiki developed by the EPA under the auspices of the WHO International Programe on Chemical Safety (IPCS) Mode of Action Steering Group.
The content of this wiki is the sole responsibility of the individual contributors and does not necessarily represent the views of the Partner organizations. Mention of trade names or commercial products does not constitute endorsement by any of the Partner 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.
More detailed help can be found by clicking the Help link at the bottom of the page.
Additional information will be provided in the upcoming weeks. 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 firstname.lastname@example.org.
Requesting Access to Create and Edit AOPs
Read-access to all contents 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): Author access to the AOP-Wiki can be obtained by submitting a brief author access application to the SAAOP. Navigate to http://www.saaop.org/AccessPage.html. Click on the “Download Access Application” link. The requestor must confirm that they have read the “rights and responsibilities” defined for contributors to the AOP-Wiki and should provide a brief description of their intended contribution along with AOP-Wiki Usernames and affiliation information for all project team members requesting access. Author access applications submitted to the SAAOP are typically reviewed within 2 working days of submission.
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:
Firefox Users Redirecting to Old Wiki
We've had reports that users are being redirected into the old wiki when attempting to access the main page (this page) of the new wiki. If you are using the Firefox web browser, this is due to the browser saving a cache of the location for the old web site locally on your computer. To fix it, follow the instructions under the “Clear the cache” section in this link:
Please notify us at email@example.com if you experience this problem with a browser other than Firefox, and we will post the solution for those browsers too.
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.
Thank you for your patience as we work through the migration issues associated with this major upgrade.
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.