Blog

Blog

December update

We have arrived at the end of 2021 when most of us are ready to take a break!

NB: Cochrane will be closed from the 25th December until the 3rd January incl. and many staff are on leave from the 20th December therefore queries may not be dealt with until January. (CALENDAR)

As I have already communicated I am leaving Cochrane this month so from today please direct all your PICO annotation queries to Anna Last in the Slack annotation channel and continue to make vocabulary reqeusts via the usual request form.

If you are having any tech issues with the tools remember to post them to the Slack annotation channel.

Enjoy your time off and happy new year (smile) 


November update

Staff change

Just to note that from the end of December I (Deirdre) will no longer be working with Cochrane but PICO annotation will continue as usual.

I would just like to thank you all for your support and annotations during the last five years. Working with you all is always great and I have enjoyed the chats.

I do hope we keep in contact and that maybe we get to work together again in the future. 😊

Holidays

The CET will be closed from the 25th December until the 3rd January.

Training/catchups

Previously I had asked if you would have liked to have a group call for questions or just to discuss how PICO annotation is going and some of you responded to say yes. However, since then due to forthcoming changes in Cochrane I have put off arranging anything but please contact me if you wish to have a call and we can talk through any issues you may have.

Not for annotation!

Many of you have been emailing about this status in the dashboard. I use this for records that will probably not be annotated however you can change this if you wish. In many instances I have marked protocols as Not for annotation only because most of you are not annotating them. I do this so I can understand what is needs to be annotated.

Guidance

Reminder that our guidance is available HERE.

September udpate

Annotation Progress

Over 6700 completed annotations to date! 

Status

A reminder of how we are using some of the status.

Unannotated

Q: Why is a review marked as Not for Annotation when in fact the authors have just published the full review? 

A: I (Deirdre) have marked many older reviews and protocols that are not being annotated with this status.If you find any reviews that have this status but there is a published review, new or updated, please change the status and annotate.

Note: I continue to screen through the Unannotated in the QA dashboard:

    • reviews that we are not annotating I have marked them Not for Annotation
    • most protocols I have marked them Not for Annotation

Blocked

Please mark annotations as Blocked when you request a term to be added to vocabulary for

  • Population/Condition
  • Intervention

For outcomes request the term and mark the annotation as complete.

Please continue to submit your term requests via the form in Confluence.

Email update 25/03/2021

Updates

Blogs

In our Annotation Knowledge Base in Confluence we can create blogs. I will create short blogs

  • For quick reminders, or updates to guidance or
  • Or where I will copy the contents of these emails

Email & CIS newsletter

I will continue to email when necessary and add some information to the CIS newsletter (we have some annotators who are not CIS so the latter is not ideal for everyone).

Reviews

Annotation status

  • By now the pre 2020 reviews should be annotated. If you have not annotated all the post 2015 publications for your Group myself and Carol Friesen will go through them. Email me 😊.
  • We aim to annotate new and updated reviews as soon as published. It would be helpful for me to know if you 
    • Are going on long holidays
    • Any kind of long term leave e.g. maternity
    • Even just swamped with work (!)

and you think that your CRG will publish reviews during your absence and we can do them

Flexible format

We can now annotate reviews that are published using this format.

  • Annotate if you have intervention reviews in this format – if you are unclear about this please email me
  • Most seem to be rapid reviews (am not sure how widely it is being used)

Vocabulary

Requesting vocabulary terms

The vocabulary request form is found on the main Annotation Knowledge Base page. On the same page under Vocabulary there is guidance on how to check your open requests.

    • ONLY use Block for annotations that are waiting for terms for P or I/C
    • If  P and I/C are completed but you need to wait for terms for outcomes mark the annotation Complete

Blocked annotations

Remember to check

Outcomes

Annotate each outcome as a new group

Core outcome sets (COS)

I am creating a list of COS for CRGs if there are any. If your CRG has a specific list or is working to create one please let me know. They are helpful for vocabulary development.

CRG name changes & merges

Those of you who belong to CRGs that have merged with others or had a name change may notice that when you load a review into the annotator you still see your old name or in the case of merged Groups ‘undefined’.

  • Most of these are reviews that were registered before the name change
  • The annotation is saved with the correct review for the correct Group so do not worry!
  • This also applies to the term request form that you use – this I will check and update

Issues with tools/annotations

  • Some annotations may not appear with the review on the CDSR but the developers are aware of this and the issue should be resolved soon (versioning issue)
  • When you have saved the annotation to a new version of a review please make sure that the older version(s) are marked Superceded – this is automatic for most reviews but not for some (versioning issue)
  • In recent months we had an issue which prevented some CDs from loading – this has been resolved. If you have not annotated since last year I would recommend that you clear you browser cache before you return to annotating
  • If you receive the message in the image below when you try to load a CD into the annotator it does not necessarily mean what it says!
    • Withdrawn reviews published before 2015 may give you this message if you try to load them. (Reviews withdrawn that were published from 2014 will have a message stating that they are withdrawn)
    • If Archie is down you may also receive this message
    • Anyway, email me if you are having issues with the tools

Confluence

You can see the status of your requests either in your CRG space or on the home page of the Annotation Knowledge Base Please see Video demos.

Jira

When you submit a request it is automatically logged in JIRA(login is same as for Confluence). Here you can filter by requester, date and CRG.

For more information on using JIRA see HERE.

This has been resolved.

Some of us have been seeing this message intermittently even when logged in. The team is working to resolve it. 

In the meantime I suggest you try the following:

  • clear your navigation history
  • try another browser
  • try a few times to load the review even a couple of minutes/hours later if possible

If you continue to have a problem please post in this channel with the following information:

  • browser you were using
  • if you are working on a vpn
  • CD number you were trying to load

Sorry for the inconvenience but hopefully this will be resolved soon.

This state can be applied to any reviews that you are not going to annotate such as

  1. Prognostic
  2. Diagnostic
  3. Withdrawn (see table below)
  4. Anything else we are not annotating

The state can always be changed if we ever decide to annotate any of the above.

Please note the following:

Withdrawn Reviews
 pre 2014from 2014
are not found so you cannot change the state change state to Not for Annotation


If the population or group is not specified this field should be left empty.

Some examples:

CD numberReview titlePopulation descibred in the inclusion criteria 
CD008077

Slow versus fast subcutaneous heparin injections for prevention of bruising and site pain intensity

We included studies in which participants were males and females 18 years of age or older who were admitted to hospitals or clinics and treated with subcutaneous injections of heparin including LMWH and UFH.
CD011047

Colchicine for prevention of cardiovascular events

We included trials in adults (aged 18 years and over) with any condition or disease.
CD012805

Aluminium adjuvants used in vaccines versus placebo or no intervention

We will include all trial participants regardless of sex, age, ethnicity, diagnosis, comorbidity, and country of residence.

Annotate the intervention part of the mix (if there is one).  

Example:

Interventions to support the resilience and mental health of frontline health and social care professionals during and after a disease outbreak, epidemic or pandemic: a mixed methods systematic review (CD013779)


ObjectivesDescription
1Objective 1to assess the effects of interventions aimed at supporting the resilience and mental health of frontline health and social care professionals during and after a disease outbreak, epidemic or pandemic.
2Objective 2Ignore

Outcomes
1SoFT1Annotate
2SoFT2Ignore


Annotating Death

Category heading:

Mortality

Term:

Death (clicking on the term takes you to the concept browser where you can view broader and narrower terms)





This was posted to the annotation channel in Slack on the 22 July 2020.

Issue

We've had a few issues of late, where periodically lots of review annotations have been marked incorrectly as "superceded".

We're in investigating why this is happening in earnest, however while we fix this issue, we're removing the automated process that marks a review annotation as being "superceded" when the latest review has an annotation marked as "complete"

Annotating a review that has no previous PICO annotations:

If you are annotating a review that has never been PICO annotated before, then there is no change to your process

Annotating a review that has been updated AND has already been PICO annotated:

If you are annotating a new review version, where a previous review version has been PICO annotated then on completing your PICO annotation (of the new review) you will need to follow the steps below:

  • Mark the status of the new review version as complete
  • Go to the QA dashboard: https://data.cochrane.org/qa-dashboard/
  • Login (top right hand corner)
  • Find the older review version with a status of "Complete" and Change the status to "Superceded"

This is a temporary change, and if you have any questions please do reach out to a member of the linked-data team directly.

When checking vocabulary terms in the concept browser you will now see COVID19 studies listed.

  • COVID-19 studies are listed under Studies
  • Included studies in reviews are listed under Studies included in reviews

A number of your CRG reviews are included in the COVID-19 Special Collections.

If you are aware of your reviews (intervention only) being added to any Special Collection please make sure they are annotated regardless of what year they were published.

Earlier this year Deirdre started annotating them (if not already done) however it would be helpful if you could check them as you may wish to make changes.

To find any of your reviews annotated by Deirdre use the filtering on the QA dashboard:

We have been using 'No Active Treatment' category for Usual or Standard Care however a decision has been made recently to change this to 'Other'.


  • Viral Load is usually an outcome
  • Category: Physiological or clinical