De-duplicating EndNote results against a previous search

Well hello my friends! It’s been a long time since I’ve posted. Forgive me, as much has happened in the last year, including: moving across an ocean, subsequently moving across a city, starting a busy freelance information specialist business, and many mundane crises, trips, and side-projects in between.

I was tasked recently with updating a systematic review search with a new and improved search strategy completely unlike the previous one. There were new search terms added to this search, but also several irrelevant search terms that had been deleted. I’d done systematic review updates before, but I’d always simply used date filters in the databases to capture results from the date of previous search.

But this time, the researchers wanted any articles that would be captured by the new search, in any date period, and wanted to ensure they weren’t screening any citations that had already been previously screened with the old search.

I’d heard other information specialists talk about using EndNote to de-duplicate against a previous search, but never tried it myself. It just seemed unduly complicated. Date filters seemed to be working perfectly fine.

It was around this same time that I found out that date filters were not perfectly fine.

One day, I went to date limit an Embase search using the advice from a LibGuide at a high-ranking university…. and was horrified to find out that a not insignificant number of citations that ought to have been picked up had not.

Cue a minor panic as I tried to figure out whether I had royally screwed up any of my previous projects.

Friends, I have learned the error of my ways, and will henceforth de-duplicate my systematic review update searches in EndNote when possible. Cross my heart, etc, etc.

As usual when picking up a new skill, I went to Twitter to see what all the experts were doing.

Here follows the method that I ended up using. I’ve documented it for my own purposes and hope that it can come in handy for others as well.

1. De-duplicate your total search results in EndNote, as normal.

You can use whatever process works best for you. I tend to use a modified version of Bramer et al, 2016 in which I progressively choose different field combinations in EndNote to test for duplicates, and manually go through the results. The field combinations suggested in the article include (in this order):

  • Author | Year | Title | Secondary Title (Journal)
  • Author | Year | Title | Pages
  • Title | Volume | Pages
  • Author | Volume | Pages
  • Year | Volume | Issue | Pages
  • Title
  • Author | Year

But if you want to get fancy about it, the article supplies a more complicated process than this.

2. Label your citations by search date.

At this point, you’ll want to load up your citations from the previously conducted search into a separate EndNote Library. Then, use one of the custom fields to mark these citations.

  1. Select one of your citations from the “All Refs” group, then click cmd + A or ctrl + A to select all in the entire library.
  2. Then, go to tools, then Change/move/copy fields
  3. Select “Custom 1” (or another field of your choosing), then “replace whole field with”
  4. Choose text that is meaningful for you for remembering which citations these are. Something as simple as “OLD” may suffice (this is what I did, based on a Twitter tip).
  5. Next, do the same for your “new” search results.

Note that this is an important step if your search strategy has changed such that some results that were previously returned will not be returned in the new search. Otherwise, you will end up re-screening those articles!

3. Combine your “old” and “new” EndNote Libraries together

To combine your two libraries together, navigate to your “old” library and select all the citations by clicking ctrl + A or cmd + A.

Then click “references”, then “copy references to”, and choose your “new” library. Easy peasy!

4. Remove duplicates

Use your EndNote Library which contains both your “old” and “new” records (both of which have previously had duplicates removed!), and remove your duplicates as you normally do, or following the process in Step 1.

But this time, there’s one big difference – every time you find a duplicate, instead of removing the duplicate record, you’ll remove BOTH records, since they represent a previously screened record that you won’t need to screen again.

5. Remove any remaining previously screened citations

This step won’t be necessary if no search terms have been removed since the original search was conducted.

In my case, the search had changed drastically since its creation by someone else, and I needed to remove any citations that were picked up by the original search, but not by the new one. Removing these records is easy if you have followed Step 2, above!

Simply create a smart group by right-hand clicking over “my groups” in EndNote. Then, set the parameters to find your old citations (e.g. “custom 1”, “is”, “OLD”). Then, navigate to your smart group and delete all the citations in this group. These have already been previously screened and weren’t retrieved by the new search.

And that’s basically it! I was able to tackle this new skill that originally seemed kind of hard, and you can too!

For more information, the following papers may also be useful:

Bramer WM, Bain P. Updating search strategies for systematic reviews using EndNote. Journal of the Medical Library Association: JMLA. 2017 Jul;105(3):285.

Bramer WM, Giustini D, de Jonge GB, Holland L, Bekhuis T. De-duplication of database search results for systematic reviews in EndNote. Journal of the Medical Library Association: JMLA. 2016 Jul;104(3):240.

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Workbook for systematic review consultations

I’m often approached by masters and PhD students and researchers in my institution to advise on systematic review projects in the early stages. I’ve found that the skill levels to complete a systematic or scoping review are variable, and that many researchers need a primer to get up to speed about the process of conducting a review, what skills are required, and in particular, how to go about the planning process.

I support many projects in depth from start to finish, but for many projects at my institution, I only have the time to provide advice and consultations. Unfortunately, I quickly learned that throwing a lot of information at people in a short period of time was not useful, and I would sometimes see the same researchers at a later consultation who hadn’t gotten very far with their projects and needed a lot of the same information again.

notebookPhoto by Glenn Carstens-Peters on Unsplash

There are many, many resources online for conducting review projects, including some enviable LibGuides (I personally like the Queens University knowledge synthesis guide and University of Toronto learning to search guide). However, I wanted a resource that I could use when physically sitting with someone in a meeting room, where we could plan out their review project together. And I was getting pretty tired of drawing the same venn diagrams of how “AND” and “OR” boolean operators work on whatever scratch paper I had handy.

I recently developed a guide that fits these purposes, and after a few iterations and some testing and feedback, I’ve put it online for others to use and edit as they wish with a CC-NC-SA 4.0 License. The goal of this guide is to provide a resource that:

  • Can be printed and used as a workbook to guide a systematic reviews consultation
  • Also contains enough information to be a stand-alone self-learning resource for after the consultation (e.g. the information on boolean operators)
  • Is not too long to be intimidating or overwhelming for someone just getting started

Without a doubt, there will be further refinements and additions to the guide over time, but for now, please feel free to download, use, and edit for your own purposes. Any feedback or comments are also gratefully accepted. 🙂

You can find the guide here at Open Science Framework.

screenshot of OSF

Building a Twitter bot!

I have long admired – and, I’ll admit – been a bit fearful of cool technology projects that make use of APIs. To be honest, I’m still not *entirely* sure how an API works. It feels a bit like magic. You need keys and secret keys and bits of code and all those things need to be in the right place at the right time and I might even have to use scary things like the command line!

So you can imagine, I’ve been looking at all the cool Twitter bots launched over the past few years with much wistfulness… some examples of my favourites:

When I recently saw Andrew Booth’s tweet about his “Random Review Label Generator”, I knew it was time for me to get in on the action.

As it turns out, a lovely fellow has made the process of creating Twitter bots super easy by coding all the hard stuff and launching a user-friendly template with step-by-step instructions, freely available for anyone to use. Special thanks to Zach Whalen for creating and putting this online!

So: without further ado, I present to you a Twitter bot that randomly generates a new healthcare review project every hour. You’re welcome!

The beauty of this bot is that some of the project names are so ridiculous… any yet you wouldn’t be surprised to see many of them actually published. I am endlessly entertained by the combinations that it comes up with, and I hope you are too!