A About the 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 Partner organizations. Mention of trade names or commercial products does not constitute endorsement by any of the Partner organizations.
The Adverse Outcome Pathway (AOP) Wiki serves as the primary repository of qualitative information for the international AOP development effort coordinated by the Organisation for Economic Co-operation and Development (OECD). It describes an AOP in terms of key events (KEs), which represent measurable steps along a pathway from a molecular perturbation to an adverse outcome for an organism or population. KEs are connected via relationships (KERs), which capture the evidence supporting the AOP in a structured way. Connections among different AOPs are automatically made when two or more AOPs share a common KE. The AOP-Wiki provides access to the AOP information via a web interface that supports browsing and searching for AOPs, KEs, KERs, and stressors known to perturb the AOPs. The AOP-Wiki also provides programmatic access to all information via web services as well as downloadable files containing all content in XML format. In addition, the AOP-Wiki provides a user the ability to create snapshots of each AOP in html and pdf formats, which can be used for offline access. The snapshots also represent a static version of the AOP and are currently used for the OECD review of AOPs that are part of the OECD AOP workplan. The AOP Wiki represents one module of a larger AOP knowledgebase, and content from all modules is available via a central e.AOP.Portal (https://aopkb.oecd.org/).
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. The OECD AOP Users' Handbook to this Guidance 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. 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 Programe on Chemical Safety (IPCS) Mode of Action Steering Group.
Society for the Advancement of Adverse Outcome Pathways (SAAOP)
The Society for the Advancement of Adverse Outcome Pathways (SAAOP) was formed in 2013 to host the AOP-Wiki and promote the development of AOPs. More information on the SAAOP is available on the society website. Anyone may apply to be a member of the SAAOP. There are two levels of membership, Associate and Full. Any person who has an interest and some familiarity with AOPs may apply to be an Associate Member. Associate Members, after a minimum period of one year, are eligible to apply for Full Membership. Full membership requires scientific contributions to development and use of AOPs, and a record of published research in this area or general recognition as expert. Full membership also requires approval by the Executive Council and payment of annual dues.
From its inception, the SAAOP has coordinated activities with the OECD Extended Advisory Group on Molecular Screening and Toxicogenomics (EAGMST). The EAGMST and SAAOP issued a statement in June of 2016 describing the relationship between the SAAOP and the OECD EAGMST, which clarifies development, maintenance and oversight of AOP Wiki. Briefly, the SAAOP allows a less formal process for gaining access to the AOP Wiki; AOP developers who are not yet ready to submit formal projects to the OECD may apply for access through the SAAOP.
B Release Notes
Release 2.6 (4/29/2023)
This release provides a number of new features and bug fixes as outlined below:
- Ruby upgrade to 2.6, Rails upgrade to 6.1
- Updated license for wiki content. Default license is now Creative Commons BY SA for all content. Authors can choose an All Rights Reserved license for a limited time while the AOP is being developed.
- Removed author and SAAOP status fields.
- Assign a handbook version to all AOPs. The default assignment is the version of the handbook available with the AOP was created. Authors are able to choose a newer version of the handbook, but they cannot choose an older version.
- Add Coaches to the AOP page. These individuals can be assigned using the same process as for contributors.
- Added ability to search for Prototypical Stressor by PubChem ID.
- Updated the AOP table.
- Added Recaptcha for new account registration.
XML exports do not yet include the new fields that were added in releases 2.5 and 2.6. This is a known issue that will be fixed with the 2.7 release in fall 2023.
Patch 1 (9/11/2023)
Fixed error with author contact link in the AOP table on the KER page.
Release 2.5 (7/16/2022)
This release provides a number of new features and bug fixes as outlined below.
- An integrated electronic version of the AOP Developer's Handbook provides direct access to the latest version of the OECD handbook from within the AOP-Wiki. The wiki help pages now provide links to the corresponding section of the handbook to allow easy reference for specific sections. Previous versions of the handbook are available via a handbook archive accessible from the top right corner of the current handbook. This link also provides access to release notes and a PDF download for all versions of the handbook.
- The AOP table has been enhanced to provide more filtering options and to keep the information in the table up to date.
- In addition to sorting by columns, filters can now be applied to each column in the table to further refine search results or simply browse the content.
- The MIE and AO columns are now automatically synced with the entries on the AOP page itself to eliminate inconsistencies between the two views.
- The language within the AOP-Wiki has been adjusted to emphasize that the stressors noted are prototypical stressors used to establish the AOP and are not intended to be an exhaustive list of potential stressors that act through the AOP. Information regarding the latter is available from a number of other sources such as the EPA's CompTox Chemicals Dashboard, which provides links to AOPs in the wiki.
- The AOP and KER pages now include sections outlining the strategies used for collecting and evaluating evidence. This increases trust and transparency and represents an intial step towards incorporating systematic approaches into the AOP development process.
- KER pages now include a section allowing developers to define the modulating factors that impact whether the upstream key event will trigger the downstream key event.
- This release also introduces a tigher integration between the AOP-Wiki and third party tools. There is now a Third Party Tools page that lists the third party tools currently utilizing AOP-Wiki information. The visualization options for AOPs in the wiki have been expanded by providing direct links to the Wiki-Kaptis tool. This represents the first of many new AOP-Wiki features that will directly incorporate mature third party tools into the wiki itself.
- A new AOP Training page provides a summary of the available training options with links to the appropriate materials.
- The Key Events table on the AOP page now allows authors to change the MIE type. Previously, this could only be specified when adding a new KE to the table.
Patch 1 (7/23/2022)
- Fixed issue with PDF downloads of the Developer's handbook.
- Fixed heading on edit form for the Context section.
- Addition instructions available for adding chemicals to a Stressor.
Patch 2 (10/15/2022)
- Fixed error where the modulating factor table on the AOP page is lost when saving.
- Added favicon for more desktop browsers.
Patch 3 (3/24/2023)
- Backend changes to prepare for licensing shift with Release 2.6.
Release 2.4 (4/24/2021)
Added a check for existing key events before allowing the user to create a new key event. The user is now presented with a list of existing key events matching the terms in the title entered by the user that includes information about the AOPs containing those key events and an indication of how complete the key events are. The user can select from one of the existing key events or confirm that they wish to create a new one.
This release also fixes some formatting errors introduced with the 2.3 release.
Patch 1 (5/7/2022)
This patch fixes the following errors:
- The API button on the key event and key event relationship pages now points to the correct URL.
- Biological organization information is now displayed on key event pages.
- JSON feeds for key event relationships now include the name and identifier of the key events.
- Fixed errors with XML exports.
- Removed description field from stressors for both key events and AOPs.
- Moved the listing of intermediate key events in an AOP to the correct order between molecular initiating events and adverse outcomes.
- Taxonomic applicability is now included for AOPs.
- Renamed the taxonomic-applicability section for key event relationships to applicability to match the convention for key events and AOPs.
- Fixed instances where the XML exports did not conform to the XML schema.
Release 2.3 (12/5/2020)
This release includes a complete UI redesign to make the AOP-Wiki mobile friendly. It also includes a new forum capability to provide help and a place for the AOP community to interact. The wiki now includes default license designations on each page. Key Event and Key Event Relationship pages now provide contact options when AOPs include those pages.
Release 2.2 (1/28/2018)
This release introduced download files to allow users to get all AOP-Wiki content in an easily usable form. This includes XML downloads with both static quarterly releases and a non-permanent file updatedly nightly. Information for a single AOP can be obtained in XML format can be obtained dynamically any time. Users can now request new terms for fields where input is restricted. These requests will be reviewed by wiki gardeners and approved unless an equivalent term can be found in the existing vocabulary. Users can now request author access via forms in the wiki itself rather than emailing forms outside of the wiki. The AOP pages have been redesigned based on user feedback to provide information in a more useful order. The network view has been updated to allow users to save node locations as well as to toggle aop and relationship nodes on and off. Event components now provide a more detailed description of each term to aid authors in the selection of the correct term. Emails will now be sent to wiki gardeners when new authors create AOPs, so that the gardening team can reach out to the new authors and provide advice on the AOP development process. The AOP snapshot format has been updated to match newest version of the OECD AOP Development Handbook. Finally, the new release includes new navigational tips to improve the usability as well as several bug fixes identified during the development process.
Patch 1 (2/24/18)
Updates to author requests, added key events to the AOP XML output, additional error checking for text fields.
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)
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 (12/11/2016)
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"
- 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
- 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
- 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.
- 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
#Internal release for AOP wiki working group members only. #Used for demo at May, 2013 OECD EAG meeting.