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MS Word and AOPWiki
Forum: AOP-Wiki Technical Assistance
Last Post: DanV-AOP
09 Mar 2021, 14:30
» Replies: 1
» Views: 198
Forum: AOP FAQ
Last Post: Travis Karschnik
02 Mar 2021, 15:59
» Replies: 0
» Views: 105
Page History
Forum: AOP FAQ
Last Post: Travis Karschnik
02 Mar 2021, 15:57
» Replies: 0
» Views: 95
Login Problems
Forum: AOP FAQ
Last Post: Travis Karschnik
02 Mar 2021, 15:50
» Replies: 0
» Views: 84
Finding Pages
Forum: AOP FAQ
Last Post: Travis Karschnik
02 Mar 2021, 15:48
» Replies: 0
» Views: 91
Editing and Formatting
Forum: AOP FAQ
Last Post: Travis Karschnik
02 Mar 2021, 15:46
» Replies: 0
» Views: 99
Citing the AOP-Wiki
Forum: AOP FAQ
Last Post: Travis Karschnik
02 Mar 2021, 15:34
» Replies: 0
» Views: 93
Do you want to join the c...
Forum: AOP Training
Last Post: Brigitte Landesmann
16 Feb 2021, 16:05
» Replies: 2
» Views: 285
Merging KEs
Forum: AOP-Wiki Technical Assistance
Last Post: DanV-AOP
16 Feb 2021, 15:47
» Replies: 0
» Views: 128
Stressor fields
Forum: AOP Guidance
Last Post: DanV-AOP
16 Feb 2021, 15:37
» Replies: 0
» Views: 115

  MS Word and AOPWiki
Posted by: Moderator KC - 03 Mar 2021, 16:45 - Forum: AOP-Wiki Technical Assistance - Replies (1)

Is anyone interested in a Word template for AOP development. Something that would allow easier tracking of changes when working on teams, use of reference managers etc.

It would mean you will need to cut and paste in to the Wiki to start or update an AOP.


Posted by: Travis Karschnik - 02 Mar 2021, 15:59 - Forum: AOP FAQ - No Replies

Resolution of figures
Why is the resolution of the figures in my snapshot lower than the resolution on the AOP page itself?
This is an inherent limitation of the available PDF conversion tools. There is an html version of the snapshot that will have the high resolution figures (see below).  For offline use, the user would need to use the html snapshot to create an acceptable version using their own publishing tools. If you have Adobe Acrobat software, there are some instructions for increasing the image resolution here:  https://forums.adobe.com/thread/1300445. Once you have adjusted the settings, you can create the PDF directly from the html snapshot by selecting the "Create from web page" option.  If users have instructions for other software tools, please pass them along and we will update this entry.

[Image: 2cbxpb0yen_snapshot.png]

  Page History
Posted by: Travis Karschnik - 02 Mar 2021, 15:57 - Forum: AOP FAQ - No Replies

Reverting to a previous version of a page
Someone has modified my information on a KE, KER, or Stressor page.  How do I revert their changes?
The KE, KER, or Stressor pages are considered shared information, so no one should modify the content of one of these pages such that the original meaning is lost. If you are unable to modify the page to match your AOP without losing the original content, you should create a new KE, KER, Stressor and add your information to that.  As the Event Components come online, we'll be able to identify KEs and eventually KERs that are similar even if they are separate. If someone has modified your page, you should work together to revert the content to the original state and then add the new content in such a way that the original content is retained.  To revert to a previous version of any wiki page, you need to click on the "View history" button in the top right of the page to view the changes that have been made on that page. The full change log is shown at the bottom of the page, and the versions of the page highlighting the text changes are shown at the top.  To revert changes that involved the adding or deleting of controlled terms or linked pages, you simply need to add/delete the objects as needed to revert the changes. 

To revert the text on the page to an earlier version, you will find a column of radio buttons on the right side of the top table.  You should select the right button for the most recent change, then select the left button for the last version of the page before the unwanted changes. Then click the compare button at the top or bottom of the table. The resulting view will show the comparison of the text between the two versions selected. Note that the text includes the html formatting tags rather than the formatted view you get when editing the text. Scroll to the bottom of that page and confirm along the way that the changes shown are indeed the changes you want to revert. In the bottom left corner of the page, click the blue "Revert" button to return the text to the earlier version.  This will show as a new change in the version history and the previous versions will still show the modifications as well as the change required to revert those modifications.

Note that you are able to compare any two versions of the page not just earlier versions with the latest version.  Because reverting the changes will always revert all changes made since the version selected by the lefthand radio button, the revert button will only show at the bottom of the comparison page if the most recent version of the page is selected for the righthand radio button. This ensures that you see all the changes that will be reverted by that action.

Notifications for changes
How do I get notifications when changes are made to my AOP or the associated KE or KER pages?
To get notified for an AOP and all associated pages, you simply click the "Watch" button in the top right corner of the page.  This is a toggle button, so you are watching a page if the icon shows a checkmark in the box and not watching if the box is empty.  If you want to watch an AOP page but not all of the associated pages (or only certain associated pages), you can select individual pages by clicking on your name in the top corner of the wiki when you're logged in and selecting "My Profile" in the dropdown list.  All pages on your watch list are shown in the bottom right corner of your profile page with individual checkboxes for each page.  Unchecking the box will remove your watch for that page. 

To receive notifications, you must also make sure you are subscribed for email notifications.  This check box is in the top right corner of the profile page.  By default users are subscribed for email notifications, so this should be checked unless you have previously changed it.

  Login Problems
Posted by: Travis Karschnik - 02 Mar 2021, 15:50 - Forum: AOP FAQ - No Replies

Original wiki login no longer active
I'm trying to login to the wiki with my email and password, but I am getting a login error.
The most likely possibility is that you are using the login page from the original wiki.  The new “wiki” doesn’t use any of the original wiki features including the login page.  You want to use the “Login” link at the top of the new pages (at the far right of the black navigation bar at the top).

[Image: 7s3jd2qd3d_login.PNG]

If you are trying to access this link (https://aopwiki.org). and do not see a black bar at the top of the page, it is likely that your browser has stored an old cache of the original wiki. If this is the case for you, please check the instructions in the Finding Pages section above.

Once you see a black navigation bar at the top of your main page, click the sign-in button to the right of that bar.  After you reach the sign-in page, follow the instructions at the bottom of the page to reset your password.  Your original password will not work with the new version of the wiki.

  Finding Pages
Posted by: Travis Karschnik - 02 Mar 2021, 15:48 - Forum: AOP FAQ - No Replies

Redirects to the old wiki
Why do I see the old wiki (https://aopwiki.org/wiki/index.php/Main_Page) when I try to access the main page of the new wiki (https://aopwiki.org)?
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...efox-cache

  Editing and Formatting
Posted by: Travis Karschnik - 02 Mar 2021, 15:46 - Forum: AOP FAQ - No Replies

Reordering Tables
My Key Events, Relationships, etc. are out of order in my summary table.  How do I reorder the table rows to match the order in my AOP?
When logged in with author privileges, this can be done on the viewing page without the need to click the edit button.  Simply click and drag the row to the desired location within the table then release the click to place the row in the new location.  You will see the other rows shift as you move the selected row up and down in the table and a flash of yellow as the row settles into the new location.

Editing Tables From Original Wiki
How do I edit tables that were created in the original wiki?
In this case, you have two options.  If you would like to keep the original wiki table and format, you can simply cut the table out of the text field (Ctrl-X or Scissors icon in the formatting bar) and paste the whole table into Microsoft Word or another HTML compatible word processor. Note that if the table is the only text in the text field, the easiest way to select the table is by pressing Ctrl-A to select the whole text field.  You can do this even if other text exists in the field, you will just need to remember to include the extra text when you put the revised table back into the wiki in the next step.  You can then edit the table as desired in the word processing program. After you complete your edits, you cut the whole table and paste (Ctrl-V or the first clipboard option in the formatting bar) the table back into the text field on the wiki.

MySQL Error
What does the following error message mean when trying to enter text?
MySQL Error: Make sure that '[column name here]' doesn't have any special characters.
This occurs sometimes when trying to paste special characters from Word documents. The problem is caused by the character encoding not being recognized by the database that holds the wiki information. The most common examples we've found have been greek letters.  Often, you can find another option in Word to get the same greek letter that will be compatible. Alternatively, you can delete the character in Word and insert the symbol using the text editor in the wiki itself. We apologize for the inconvenience.

Changing the Author Status
How do I change the author status for my AOP?
The author status is actually changed on the same page where you edit the text boxes, so you first have to click the blue Edit in the set of buttons in the top right. 
[Image: h5kwdwr83_edit.png]

Once you’re on the edit page, the dropdown for the status is just below the author text box. 
[Image: 69ik7n1xox_dropdown.png]

We understand that this may be confusing because both the contributor list and the point of contact are modified directly on the main page for the AOP.  The author status will likely move to that page as well in the near future.

Page Display Too Small When Viewing Snapshots
When viewing my PDF snapshot, the text is too small to see. How do I fix it?
Some users may experience an issue when viewing the pdf version of a snapshot, where the pdf downloads but the text is too small to view. This is being caused by an error with preformatted text. To avoid this issue, the author should remove any preformatted text (viewable in the snapshot as a line of text going all the way across the page) from their AOP.

Internet Explorer
Why do some of the buttons in the wiki not work when I click them?
The implementation of the tools for adding key events, key event relationships, stressors, etc. to AOP pages requires modern web browsers to function properly.  Unfortunately, these are not compatible with the Internet Explorer, which is no longer under active development and is being replaced by the new Edge browser developed by Microsoft. We apologize for the incovenience, but the added capabilities were deemed substantial enough to break the backward compatibility with this browser.  Each AOP-Wiki release is tested using the Chrome, Firefox, and Edge browsers, and we have had no reports of issues using the Safari browser on MacOS.  Please try one of these browsers if you are having trouble with Internet Explorer.  Note that the issues are specific to certain author functions.  The ability to view content and comment on the information in the AOP-Wiki should work in Internet Explorer.

  Citing the AOP-Wiki
Posted by: Travis Karschnik - 02 Mar 2021, 15:34 - Forum: AOP FAQ - No Replies

Entire AOP-Wiki

  •     Reference:  Society for Advancement of AOPs. [year]. AOP-Wiki. [Cited date]. Available from http://aopwiki.org.
  •     Text citation:  (Society for Advancement of AOPs, [year])
  •     URL citation.  (aopwiki.org)
Specific AOP, Event, or Relationship Pages
Cite the page-specific URL * Note - before citing a specific AOP page, please check the "author status" field to determine whether it is open for citation. If the status reads "under development, not open for comment, do not cite", the page should not be cited without permission from the contact author. 

Citing a Snapshot
  •     Because the content on AOP-Wiki pages may evolve over time, to cite the content as it was observed on a given date, please create and cite a snapshot.
  •     After creating the snapshot, cite the URL associated with that snapshot; e.g., https://aopwiki.org/aopwiki/snapshot/htm...00:00.html 
  •     Note, you must be logged in as an AOP author to create a snapshot.  If you do not have author access to the AOP-Wiki, please contact aopwiki@googlegroups.com to request a snapshot.  Please specify the AOP page you would like a snapshot of (all linked Event and Relationship pages will be included) and a short title for your snapshot and request that the URL for the snapshot be sent to you.

  Merging KEs
Posted by: DanV-AOP - 16 Feb 2021, 15:47 - Forum: AOP-Wiki Technical Assistance - No Replies

As part of an AOP I am working on, I have identified some potentially synonymous KEs (1521 and 1467).  Can these KEs be harmonized and merged?  How would I go about that?

  Stressor fields
Posted by: DanV-AOP - 16 Feb 2021, 15:37 - Forum: AOP Guidance - No Replies

I'm not sure what kinds of stressors I should identify on my AOP page.

A couple things to keep in mind about "stressors" identified in relation to an AOP:

  • AOPs are chemical agnostics
  • The "stressor" field is not intended to provide a comprehensive list of stressors that can activate an AOP.
  • The AOP pages are intended moreso to identify "prototypical stressors" as those upon which a lot of the weight of evidence for the AOP is based.  This will generally be just one or a handful.

  KER - Estrogen receptor agonism leading to reproductive dysfunction
Posted by: DanV-AOP - 16 Feb 2021, 15:36 - Forum: General Questions about AOPs - No Replies

Hello AOP forum - my research team is starting to work on a (non-adjacent) KER linking estrogen receptor agonism to reproductive dysfunction.  If you have interest in collaborating /contributing to this KER development, feel free to reach out.