About

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


Background

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.

Disclaimer

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.

B Release Notes


Release 2.1 (3/9/2017)

This release includes full support for creating snapshots of AOPs.  Users are now able to create a static version of their AOP and download a PDF of that static version for offline use.  These snapshots will be used in the future for the OECD review process.

Patch 1 (6/7/2017)

Bug fixes and usability enhancements.

Patch 2 (9/9/2017)

Usability enhancements.

Release 2.0 (12/4/2016)

This was a major shift from the previous wiki.  All text fields are now captured as separate entities.  This makes reorganizing content on the site easier, allows more automated validations to be performed on AOP entries, and allows us to provide all AOP information in a downloadable form in the future.

Patch 1 (12/11/2106)

Fixes minor bugs with the 2.0 release.

Patch 2 (1/24/2017)

Fixed additional bugs with the 2.0 release.

Release 1.5 (1/17/2016)

  • Fixed performance issues when loading AOP pages.
  • Added snapshot function to create static versions of AOPs.
  • Provided programmatic access to AOPs & Key Events.
  • Updated network view:  removed Adobe Flash requirement, node size driven by Essentiality, associated AOPs are shown.
  • Moved back to the aopwiki.org domain.
Patch 1 (2/13/2016)
  • Fixed bug in snapshot code that resulted in missing text
  • Fixed bug in snapshot code that resulting in missing sections
  • Added an automatically updating AOP list
  • Added an AOP table view that allows sorting by MIE, AO, or Category/Status
  • Added a searchable Key Event list for authors

Release 1.0 (9/28/2014)

  • Updated templates to match the revised OECD handbook.
  • Merge the KE & AO templates and allow use of one event in both scenarios to allow for context dependency (i.e. individual level AO considered a regular key event for some population-related AOPs).
    • there is a duplication problem with the table of contents (key events overviews is listed twice).  This glitch likely occurred in the process of changing the name of the main page from "Ahr" to "AHR1 activation leading to developmental abnormalities and embryolethality (in birds)".
  • no entries in Key relationship table > "add record">event
    • We have traced this to a parsing error involving the Greek characters in the MIE name.  We are looking at a short term fix for the broken page and a long term fix to be released in September.> MIE name changed, problem not solved the problem as the Greek characters are also in the AOP name, would it be possible to change the name for "PPAR alpha activation leading to reproductive toxicity" ? instead of "750732 PPARα&γ activation leading to decreased fertility"
Patch (10/19/2014)
  • I can't get the widget to add in my MIE or anything else. The page just times out. -- Fixed
  • Fixed bugs in widgets on non-AOP pages
  • Migrated chemical initiator pages and fixed bugs with chemical initiator widgets
  • Added new anti-spam features
Patch (11/8/2014)
  • Items from bug reports that have been fixed
    • Sync tables icon on widget page is not working. Rows in the tables can be reordered, but the ordering is not saved currently.
    • The widgets for adding chemicals to the chemical initiator pages are having intermittent problems. The tables on the widget pages themselves don't always reflect the current chemical list either. The wiki pages seem to update correctly, however.
  • Network view is now operational again
  • A revision table in the Status section will now report changes to linked pages in addition to the changes on the AOP page itself
  • the link to AOP 42 is not working - you get this message...Aop:42 (Redirected from TPO Inhibition and Altered Neurodevelopment)
    • Aop:42 > TPO Inhibition and Altered Neurodevelopment > Special:RecentChanges > Special:WhatLinksHere/Main Page > Relationship:295
Patch (1/11/2015)
  • The Chemical Initiators on the MIE page do not update. See for example <Thyroperoxidase, Inhibition>.
  • Fixed errors where duplicate entries are inserted into wiki tables.
  • Fixed sync issues between the wiki page and the structured event and relationship information in the widget database.
  • Added code for periodically validating wiki pages against the wiki database to identify any synchronization issues.
Patch (1/31/2015)
  • Fixed error when entering an unrecognized common name for species in Taxonomic Applicability widget
  • Fixed duplicate entries on Chemical Initiator pages.

 

Beta Release 4 (6/28/2014)

  • From Kevin:  Suggest adding drop down box for the "Level of Biological Organization" section of the MIE and Key Events.
  • Tables created before the beta3 release will not update due to a formatting difference.  This will be resolved soon.
  • Edit buttons not working correctly in any of the tables.
  • Autocomplete boxes have duplicate entries.

Beta Release 3 (4/8/2014)

  • Updated templates to match new AOP development handbook.
  • The new release contains the [http://en.wikipedia.org/wiki/Help:Referencing_for_beginners#Using_the_refToolbar refToolbar].
    • To activate it, you need to turn on the enhanced editing toolbar as described [[Help:Setting_preferences#Turn on enhanced editing toolbar |here]].
  • Resolved the following outstanding bugs:
    • Chemical drop down list will give slightly different chemical lists when the same prefix is typed.
    • Key Event and KE Relationship pages that existed before the 7/20/2013 release do not have the new Taxonomy widget. These pages will be updated to include the widget soon.
    • Add chemical button on Chemical Initiator page isn't working on Apple computers.
    •  I routinely have to enter my login and password information twice in order to get logged in.  The first time simply brings me back to the login page.
    • When a scientific name is entered for the species in the initial box, no NCBI link is created.
    • When a change is made to a name in an upstream section in the AOP pathway page, the changes aren't carried forward in all subsequent sections that refer/link to it. An example is where changes are made in a key event description or MIE after creation of the relationship table: the updates are not reflected in the relationship table.

Beta Release 2 (7/20/2013)

  • Added widgets for Life Stage, Taxonomy, Sex, and Target Organ.
  • Fixed issues with the Chemical widgets.
  • Don't allow entry of new key events/adverse outcomes in relationship input boxes.
  • Alert box when deleting table rows so user knows when the operation completes.
Patch (7/25/2013) Fixes
  •  Fixed: The adverse outcome widget is not behaving correctly following the latest upgrade.  
  •  Fixed problem allowing the user to accidentally submit a record twice.
Patch (8/8/2013) Fixes
  • When deleting a link that points to a redirect page, the wiki will now follow the redirect and delete the link from the new page.

Beta Release (6/30/2013)

  • First external release
  • Converted Key Event and Adverse Outcome lists to tables with evidence.
  • Added separate Molecular Initiating Event heading.
  • Added table to describe relationships among key events.
  • Added Chemical Initiator and Chemical widgets.
Patch (7/2/2013) Fixes
  • Hitting enter while using the pop up boxes prevents the page links from being created.
  • Code for adding Chemical sections to a pre-existing key event doesn't seem to be working.
  • Selection of a known chemical on the MIE page should prepopulate the first row in the chemical table of the Chemical Initiator page, but it doesn't.
  • The ACToR links aren't being created in the Chemical table.
  • Fix gap in Key Event template where Chemical section would be for an MIE.
  •  Edit and Delete buttons in tables not working in Firefox on multiple platforms. These both test OK in Chrome and Internet Explorer 8 & 10.  The delete has a lag where it looks like it didn't work.  We probably want to pop up an alert box and then close it once the delete completes.
  • Adverse outcomes not created when using Internet Explorer 8.
  •  Edit and Delete buttons in Adverse Outcome and Relationship tables not working correctly. 
  •  If you attempt to edit records too fast in Firefox it will delete the record but will display an error and refuse to add the record back in.
Patch (7/3/2013) Fixes
  • Auto-numbering for relationship table stops at 10.
  • The Chemical Initiator has disappeared from the MIE page (Clemens, 2013-07-03 14:55 CEST)
  • Added code to trim spaces surrounding biological processes/objects and actions before assembling key event names

Alpha Release

#Internal release for AOP wiki working group members only.
#Used for demo at May, 2013 OECD EAG meeting.