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Wiki Down Time

The AOP-Wiki had an unexpected outage this weekend.  The server is back up and seems to be operating normally.  We apologize for any inconvenience. Please report any problems to aopwiki@googlegroups.com.

Help Pages Under Revision

In preparation for the release of a revised AOP Users' Handbook supplement to the OECD Guidance for AOP development, we are revising the help pages in the AOP-Wiki.  We apologize for any confusion as the instructions are changed to match the new handbook recommendations.  The changes to the wiki itself will be released along with the handbook. Until that time, some help information may not exactly match the current behavior of the wiki.

Event Components Are Here!

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 set of pre-defined biological ontologies.  All AOPs created before December 4, 2016 have been annotated and are now available on the AOP-Wiki.  All authors are encouraged to check the annotations for their AOPs and report any issues to aopwiki@googlegroups.com.

The schedule for the remaining AOPs is as follows:

  1. All AOPs created after December 4, 2016 (having an AOP identifier greater than 201) will be annotated by the authors with assistance from our annotators.  We will be reaching out to these authors beginning in September.  Authors who are comfortable annotating their own AOPs (i.e. have already worked with us on annotating an existing AOP) are welcome to annotate their AOPs now that the ontology terms are loaded. If you would like assistance before we contact you, please email aopwiki@googlegroups.com.
  2. We are continuing to update the documentation on how to annotate Key Events using Event Components such that we maintain a consistency in annotations across different AOPs.  We will be posting this information on the wiki soon, and will be updating frequently based on feedback from authors.  We hope to have the documentation refined to the point where new authors can accurately annotate their AOPs without assistance by the end of 2017.

AOP Welcome


Welcome to the Collaborative Adverse Outcome Pathway Wiki (AOP-Wiki)

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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 (AOP-KB) 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.  All AOPs from the AOP Knowledgebase are available via the e.AOP.Portal, which is the primary entry point for the AOP-KB.

This wiki is based upon the Chemical Mode of Action wiki developed by the EPA under the auspices of the WHO International Programme on Chemical Safety (IPCS) Mode of Action Steering Group.

Disclaimer

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.

Help


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 aopwiki@googlegroups.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 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 at: 
https://humantoxicologyproject.org/about-pathways-2/aop-online-course/

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 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:
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.

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 aopwiki@googlegroups.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 #):

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.

Wiki 2.1 Release

The latest version of the AOP-Wiki (2.1) was released on March 7, 2017. The major change in this release is the snapshot functionality. The snapshots conform to the current format described in the OECD User Handbook and include information previously not included such as the graphical representation of the AOP.  This release  also includes several smaller user features that have been requested since the 2.0 launch and allows a user to find AOPs, Key Events, and Relationships by the numeric identifier when known in addition to now including full text search results. Title matches still appear at the top of the search results, but the sidebar provides links to full text search results farther down the page.

Please email aopwiki@googlegroups.com if you notice any problems with the new release or would like to request new features for a future release.  Please also note the FAQ link at the bottom of each page. We are posting common questions that users have on this page, so you may learn new features or get the answer to your specific queston there.

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:

https://support.mozilla.org/en-US/kb/how-clear-firefox-cache.  

Please notify us at aopwiki@googlegroups.com if you experience this problem with a browser other than Firefox, and we will post the solution for those browsers too.