Help:Edit AOP

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To add text to any section except "Summary of the AOP", click the Edit link to the right of the Heading for that section. Type your notes in the resulting text box and click the save page button at the bottom. Don't delete the ==Heading== line at the top. For more details on editing free text sections see the main help page.

You shouldn't manually edit the " Summary of the AOP" section. Please make those changes via the automated process described below.

  1. On the main Wiki page, under "Summary of the AOP", follow the link to the widget page.
  2. Click the "Add Item" button.
  3. Fill out the appropriate boxes in the pop up box. Details for each are given below.
  4. Click the Submit button.

Return to Help:Contents

Molecular Initiating Event, Key Event, Adverse Outcome Tables

KE Popup.png

The popup box for these tables contains two to three fields: The first field captures the action component of the key event. Users are encouraged to use one of the existing options from the autocomplete dropdown if it accurately describes the action. Otherwise, the user can enter a new one that will then be available to future users. The second field describes the biological object or process that is perturbed. The autocomplete dropdown will list existing key events/adverse outcomes (KE/AOs) matching the text entered; existing KE/AOs can be viewed by clicking the arrow to the right of the text box or by typing an entry. If an action has been previously specified in the first box, only KE/AOs matching the specified action will be shown. If an existing item matches the desired KE/AO, select it from the list. If not, type a short description of the biological object/process in the box. If you wish to make an assertion regarding the support for essentiality of the KE, choose an option from the "Evidence Supporting Essentiality" list. Please refer to OECD guidance for definitions of these rankings. The popup box for AO will not include this third field.

After clicking submit, a new row will be added to the event table on the Wiki event page. The KE/AO name will have the following format: Biological object/process, Action. This name will be linked to the AOP page. The support for essentiality evaluation will be stored in a second column. This value will link to the Essentiality of the Key Events section of the Wiki event page.

If you create a new KE/AO, a stub page will be created and you will be redirected to that page to fill in any information you have. A new row will be added in the AOP table contained in the Overview section of this page. Following the AOP Name link will return to the AOP page. If you want to edit information about an existing KE/AO, click the name of the KE/AO in the table, which will take you to the KE/AO page. Make your edits on the KE/AO page, and return to the AOP page via the AOP link in the Overview section.


Relationships Table

RelationshipPopup.png

The popup box for this table "Relationships among Key Events and the Adverse Outcome" contains five fields. The first field, "Event," is for entering the upstream key event in the pair. The options in this box automatically compile based on the events and adverse outcomes entered earlier on the page. If you wish to add new events, they should be added in their appropriate table above the relationship table. Afterwards, the new event will then appear as an option in the dropdown menu in the relationship popup box. The second field, "Description," describes the relationship between the two key events. The user must choose among the options listed. If addition options are needed, please add this to our list of feature requests. The third field, "Triggers," is for entering the downstream key event or adverse outcome of the pair. This field works similarly to the first. The fourth field, "Weight of Evidence," allows you to make an assertion regarding the strength of evidence for the linkage between the two events. The final field, "Quantitative Understanding," allows you to make an assertion regarding the quantitative understanding of the linkage between the two events. Please refer to the OECD guidance for definitions of these rankings.

Clicking submit will add a row to the "Relationships" table. The key event names will link to corresponding "Key Event Overview" pages as for the tables above. The description term will now link to a new "Key Event Relationship Overview" page with sections for including the weight of evidence supporting the relationship between these two entities. The evidence term will link to the same page as the description term but will focus the screen on the Biological Plausibility section. That page will have links back to the AOP Wiki page as well as the individual key events, which are automatically generated. The quantitative understanding term will link to the Quantitative Considerations section further down on the Relationship Overview page. As for the KE/AOs, if a new relationship page is created, the user will be redirected to that page. If an existing relationship is used, the user will remain on the AOP page.


Life Stage and Sex Tables

SexLSPopup.png

In the widget, under "Life Stage Applicability" and "Sex Applicability," clicking the "Add" button will create a popup box contain two fields. The first field allows for the entry of an affected life stage or sex term accordingly. Users are encouraged to use one of the existing options from the autocomplete if it accurately describes their entry. Otherwise, the user can enter a new one that will then be available to future users. The final box allows you to make an assertion regarding the strength of evidence for the inclusion of the life stage or sex in this AOP, choose an option from the list. Please refer to the OECD guidance for definitions of these rankings.

Clicking "Submit" will add a row to the appropriate table on the AOP Wiki page. A link to a new page will be produced along with the user's entry and the specified evidence.


Taxonomic Applicability

SpeciesPopup1.png
SpeciesPopup2.png

This popup box contains three fields. The first field allows for the entry of a species. Users are encouraged to use one of the existing options from the autocomplete if it accurately describes their species. Otherwise, the user can enter a new one that will then be available to future users. This autocomplete provides a controlled vocabulary of taxonomy terms based on the NCBI taxonomy. The second field is disabled until the user enters a species into the first field and clicks the "Search" button. The final box allows you to make an assertion regarding the strength of evidence for the inclusion of the species in this AOP, choose an option from the list.

Clicking search will cause the widget to attempt to compile scientific names for the species entered by the user. As the list attempts to compile, a dialog box will appear informing the user that this process is being run. After the process is completed, if no scientific names were found the second field will remain disabled, the search button will disappear, and a submit button will appear. However, if scientific names are retrieved, the second field will become enabled and will be populated with a list of scientific names related to the genus of the entered species. The user can then either select a scientific name from the list or leave the field blank. Altering the first field after clicking search will cause the second field to once again become disabled, the search button to reappear, and the submit button to disappear again.

Clicking submit will add a row to the appropriate table. An external link to the appropriate NCBI taxonomy page will also be added to the table if the user selected one of the compiled scientific names from the second field.


Adding a Graphical Representation

Uploading an Existing Graphic

If you already have a graphical representation of the AOP, the last subsection under the "Summary of the AOP" heading provides an easy mechanism to upload this image. If you have saved your image using the jpeg (.jpg) format, you simply click the "Click to upload graphical representation" link from the AOP Wiki page. This will bring up a page for uploading your file. Under "Source File," click the "Choose File" button to select your file. Use the "File Description" and "Upload Options" to choose a filename and upload options for the file. Click the "Upload file" button at the bottom of the page. Do not change the destination file name or it will break the link between the image and the AOP page. If you want to upload a format other than jpeg, you will need to change the file extension on the destination file name. In this case, you will need to return to the AOP Wiki page, click on the "[Edit]" link beside the "Graphical Representation" subheading. Find the original file name and change the extension to match that of the uploaded file.

Downloading the Template to Create a New Graphic

If you do not have a graphical representation of the AOP, clicking on the "Click to download template for graphical representation" link will download a PowerPoint file with a template for creating an AOP graphic. The template contains detailed instructions for saving the resulting graphic in the jpeg format required for import. Once you have created your jpeg image, follow the instructions above to import the file into the wiki.

Size Restrictions for the Graphic File

When uploading the image file, the image size must be less that 4000x3050 for the image to display correctly on the AOP page. If you get an error when uploading the file that says "Error creating thumbnail: Invalid thumbnail parameters", this is likely the cause. If you use the PowerPoint template and save according to the instructions provided, you should get a resolution that falls within this range. If you are using a different program to create your image, consult the instructions for that program on changing the resolution of the image.

For Windows users, you can reduce the size of your image using the Paint program. Open the jpeg image in Paint. In the Image dropdown menu, select "Stretch/Skew...". Change the "Horizontal" and "Vertical" percent values in the "Stretch" box to get the image size under the 4000x3050 limit and save the file. You must put the same value in each box or the image will be stretched! Click OK and save the file. It is safest to click "Save as" and pick a different file name as your original image will be unchanged. If you don't know the resolution of your original image, you can select the "Attributes..." option in the "Image" dropdown menu before opening the "Stretch/Skew..." dialog box. The width and height boxes will give you the current dimensions of your image. Don't change your image size using the "Attributes..." dialog box. That will crop the image to the selected dimensions rather than resizing the image.

Paint menu:
PaintImageMenu.png

Size before modification:
PaintAttribBefore.png

Reduce size (this example reduced the file size by half):
PaintStretch.png

Size after modification:
PaintAttribAfter.png