Cochrane and Data Language have devloped a tool kit to annotate Cochrane reviews.

For immediate access click on the buttons above.

How to access the tools

Tool	URL	Login
Annotator	https://data.cochrane.org/pico-annotator/?#ajax/home.html	your Cochrane login
QA Dashboard	https://data.cochrane.org/qa-dashboard/	your Cochrane login

Annotator

Interface

Section	Description	Image
Left pane	Once a review is loaded this column can be expanded to show the various sections provided in the review. Review Navigator: requires a review to be loaded so as to show the sections, that can be navigated, in the review
	Review Search: this permits loading a list of all reviews by review group, from which you can select which one to annotate.
Centre pane	The review sections needed for annotation will be displayed here when the review is loaded. Search box: to load a review using this box it is necessary to use the CD number of the review
	Login: click on the green arrow to enter your Cochrane account details

<a href="#com-atlassian-confluence">Back to Top</a>

Loading a review

Two options	Description	Image
Search Box	you will need to know the CD number of your review. This can be found in the DOI number of the published review e.g. http://onlinelibrary.wiley.com/doi/10.1002/14651858.CD011660.pub2/full on the History and Advanced tabs of the review information in Archie
Review Search	this is not ideal as reviews cannot be sorted or filtered. It is necessary to click on the page numbers at the bottom to move through the list
	Once loaded you can navigate to the sections to be annotated by scrolling down through the text or using the navigation menu in the lefthand pane by clicking on the section of interest.

																															<a href="#com-atlassian-confluence">Back to Top</a>

Annotation widget

The annotation widget is placed beside the methods section, included studies and the analyses in each review.

Description of icons found on the widget

Function	Description	Image
Notes	Annotator can insert quick notes which can also be seen in the QAdashboard
Docking icon	Allows the user to detach the annotator from its associated content so you can scroll further down the document to further relevant informations without the annotator scrolling off the screen - it should toggle between broken and unbroken chain
Cascade effect	This element turns on and off the cascade effect. This effect pre populates the PICOs for studies based on the annotations from the review.
Discard changes	To cancel the edits/changes made over a PICO just click on this element and it closes the widget and the edit icon replaces it.
Edit	When the widget has been populated this icon is appears on the menu bar to permit edits.
Save	When in edit mode, you can save your work in the annotator and choose to cancel or to close the widget (No or Yes). Also see "How to save an annotation with a specific status" below.
Close	This closes the widget without saving any new or edited work.
Navigation	This element makes it possible to move through PICO.
Operators	Options so use Boolean operators as required
Reset	Clears the annotation for the component or group (outcomes, different arms) that you are viewing. It does NOT clear the entire PICO.
Delete	This option is only available for the the extra, groups/arms and outcomes that may be added to the annotation
New Group/Arm	I or C: Use this to add multiple arms O: use to add multiple outcomes

																															<a href="#com-atlassian-confluence">Back to Top</a>

Saving an annotation

Using the Navigation arrows (), click on the right-hand arrow until it takes you to the end of the annotation. You can then select from the following options: Cancel, In Progress, Ready for QA, In QA, Discussion Queue, In Discussion, Blocked, Ready for Re-annotation, or Complete.

Status icons

Annotation Knowledge Base > Annotation tools > image2018-3-6_12-13-46.png

Status (seen on dashboard)	Icon (seen at sections to be annotated in annotator)	Description
Not annotated		This highlights those reviews or studies that are waiting to be annotated
In Progress		Annotation of the PICO is in progress
Ready For QA		This status acts as a queue for PICO's where the annotation has been completed by the annotator, but now must be checked by an QA person
In QA		The PICO is being checked by the QA person
Discussion Queue		This status acts as a queue for PICO's where an issue has been identified and the PICO must be discussed between the annotator and the QA person
In Discussion		The PICO is being actively discussed between the annotator and the QA person to resolve any identified issues
Blocked		The annotation process for this PICO cannot continue, as an issue that cannot be resolved by either the annotator or the QA person has been identified
Ready for Re-Annotation		This status acts as a queue for PICOs where any identified annotation issues have been resolved, and the annotator may now update the annotation
Complete		The annotation process for this PICO has been completed and the PICO has been approved by the QA person
Superceded	None

<a href="#com-atlassian-confluence">Back to Top</a>

Overview of data type to insert in the different fields

Participants/Condition

Annotation Knowledge Base > Annotation tools > image2019-2-20_12-13-4.png

Interventions/Comparators

Annotation Knowledge Base > Annotation tools > image2019-2-20_12-14-59.png

Outcomes

Annotation Knowledge Base > Annotation tools > image2019-2-20_13-19-26.png

QA Dashboard updated

Once an annotation has been saved it can be viewed in the QA dashboard. On the table pane you can view which reviews or studies have been annotated, by whom, the CRG and the status (state) of the annotation.

Features	Description	Image
Filtering data	Type, Group, By and State can be filtered by clicking on the arrow in the field at the top of each column To clear any filters click on the x beside the data selected
Filtering data
Sorting data	Clicking on the arrows beside the column headings will reorder the columns, either alphabetically or numerically
Print & export	Prints the data table as seen on the screen CSV allows a data sheet to be imported into Excel
Viewing options	The default view is 25 rows Click on the button if you wish to show more annotations on a page

PICO annotation

Text in Pink is taken from the reviews
Text in Green is the annotation
Terms in blue are those chosen from the vocabularies - hover over them to see which vocabulary they originate from.

Notes

Notes can be added to an annotation in the annotator or on the dashboard
They are ordered by author, date and time
It is NOT possible to delete notes

<a href="#com-atlassian-confluence">Back to Top</a>

How to change an annotation state (status)

	Step	Image
1	Select the required annotation
2	Click on State in the right-hand side panel (NOT in the table) - this opens a drop-down list of states.
3	Click the green Save Annotation button

Image

<a href="#com-atlassian-confluence">Back to Top</a>

Search

Before entering your term in the search box you may need to select a tab first as each one will retrieve different results.

Tabs	Description	Image
All	when you insert a term it will search all sections of the dashboard (notes, annotation, names of groups and annotators)
Table	use this when you want to search for a status, a Cochrane group, or name of annotator
Notes	this is for searching within the notes that have been added to each of the annotations

Vocabulary terms

You can also search for a vocab term to see the annotations that have been tagged with that term. A drop-down list will show relevant options retrieved from the Cochrane vocabulary. Click on the preferred term to view the annotations using that term:

Annotation Knowledge Base > Annotation tools > image2018-3-6_12-42-38.png

<a href="#com-atlassian-confluence">Back to Top</a>

<script type="text/javascript">
AJS.toInit(function(){
AJS.$('#comments-section').hide();
});
 for (var i=0; i<nr_li; i++) {
    // if the element has the class fom 'clasa' parameter
    if(tags_li[i].getAttribute('class') == 'innerCell'){
         tags_li[i].style.overflow = 'visible';
            //tags_li[i].style.overflow-y= 'visible';
    }   
  }
</script>