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EPIB 619 Systematic Reviews & Meta-Analyses

Exporting search results to EndNote

Note: This procedure helps you keep track of the information that will be needed to report the methods in the article and also to fill in the PRISMA flow diagram.

Have the right EndNote library open in the background before you begin exporting.

Note: We do not generally recommend using Safari as your browser during this process, although it can be used with some tweaking.

For more instructions on using EndNote or other software programs, please see the Citation Guide

The steps below cover Ovid MEDLINE, Embase Classic+Embase on Ovid, PubMed, Web of Science databases, and CINAHL on EBSCO.

If EndNote does not seem to include an export filter for the database you are using (for example, ICTRP) or the available export filter does not seem to be working properly, search the web for [database name] EndNote export filter, or visit https://www.endnote.com/downloads/filters/ to search for an updated or additional filter.

Exporting from Ovid Online

(MEDLINE, Embase, APA PsycInfo, Global Health)

We often start by exporting records from Ovid MEDLINE, if applicable (you may have decided to only use PubMed to search MEDLINE; those instructions are below):

  1. In EndNote, create a new library, with a useful name like SearchConcepts-MEDLINE-yyyymmdd-xRecords.enl, for the records from the database in question (e.g., MEDLINE on Ovid) and have the library ready in the background
  2. From Ovid, export complete reference in groups of <= 6,000 at McGill (e.g., 1-2000, 2001-3000; be careful if exporting in batches of 6,000 as Ovid may time out), do this until all of your records are exported (Export > Export To: EndNote; Select Fields to Display: Complete Reference; Export Citations)

  1. Move batches of exported records to the library you created and check the final number of records in the library against the number of results listed in database
  2. Document the search: From Ovid MEDLINE, use the command ..ps and copy/paste the search into another document, or download the search history for your records using Export (select one record for this) > choose Microsoft Word format, check off Search History, and save the Word document to your documentation folder, with a useful filename in a format like SearchConcepts-yyyymmdd-Search-MEDLINE-xRecords, SearchConcepts-yyyymmdd-Search-Embase-xRecords, etc. You can delete the record from the Word document as that was only needed to permit exporting the search history.
    • The search history can then be copied and pasted into an appendix of the article, to document the search strategy with exactness. Avoids transcription errors
  3. Save the search history to your personal Ovid account (free) and identify the search by database name and date; this greatly facilitates rerunning the search later if an update is needed. Document your Ovid account information as well.
  4. Create a compressed version of the EndNote library for your records

Exporting from PubMed

  1. In EndNote, create a new library, with a useful name like SearchConcepts-PubMed-yyyymmdd-xRecords.enl, for the records from the database in question (PubMed) and have the library open in the background
  2. From PubMed, Click on Send To > Citation manager > Selection: All results > Create file

Click "Send to" button and select "citation manager" from options

Change the "Selection" to "all results"

Depending on the browser you are using and/or your computer setup, this will: (1) export the records directly to EndNote, or (2) prompt you to choose to use EndNote to open the file, or (3) save it as a .txt file which you would then need to import into your library.

Choose to use EndNote to open the file:

In Firefox, select "Open with" and make sure EndNote is the application selected

Import the .txt. file:

If the file was saved to your computer instead of automatically being imported into EndNote, import the file into EndNote (In EndNote menu: File > Import > File and locate the saved PubMed file on your computer) > Select PubMed (NLM) filter (if not visible, click “Other Filters…” to find it)

To import a file into EndNote, choose the file saved on your device, e.g., pubmed_result.txt, use the Import Option PubMed (NLM), and click Import

 

  1. Document the search: Save the search history for your records by clicking Create alert under the search box once you are viewing the results or from the Advanced screen, click Download (upper right corner of History and Search Details) to maintain the line-by-line version (if applicable). The search in Create alert is saved in an agglomerated format but this is useful if you need to rerun the search later for an update and is also valid when including the search strategy in your manuscript
  2. Create a compressed version of the EndNote library for your records

Exporting from Web of Science

  1. In EndNote, create a new library, with a useful name like SearchConcepts-WoS-yyyymmdd-xRecords.enl, for the records from the database in question (Web of Science) and have the library ready in the background
  2. In Web of Science, Click on the arrow for the Save to EndNote online dropdown menu and select Save to EndNote desktop
  3. Export full records in groups of up to 500 (e.g., 1-500, 501-612)
  4. Move batches of exported records to the library you created and check the final number of records in the library against the number of results listed in database
  5. Document the search Copy and paste the search history into a Word document, adjust the formatting
  6. You can save the search history as a file on your computer and this file can later be uploaded to Web of Science to re-execute the search; this is useful later if an update is needed
  7. Document which parts of Web of Science you are searching (Web of Science is composed of multiple databases and access to them is insititution-dependent)
  8. Create a compressed version of the EndNote library for your records

Exporting from CINAHL

  1. In EndNote, create a new library, with a useful name like SearchConcepts-CINAHL-yyyymmdd-xRecords.enl, for the records from the database in question (CINAHL) and have the library ready in the background
  2. In CINAHL, click on View Results for the list of records you will be exporting
  3. For large sets of records: In upper right corner, select Share > Export results: E-mail a link to download exported results (this option is activated at the institutional level, e.g., it's available at McGill but may not be available at other institutions) 
  4. Enter the email address to which to send the records and make sure RIS Format is selected in the right-hand column
  5. You will receive an email (sometimes the delay can be a few hours, and you have 36 hours for the download) with a link to a .zip file: Save the .zip file to your computer and then extract the file
  6. From EndNote, Go to File > Import > File, choose the extracted file, and make sure the Import Option is Reference Manager (RIS) (If it's not an option, click on Other Filters... to find it)
  7. Document the search

Creating a backup, compressed EndNote library for your records

  • Before merging the libraries, create compressed libraries of each of the EndNote libraries from the individual database searches: Keep these compressed libraries for your records (you can also back these up as, e.g., RIS files, to save space)
  • Using the uncompressed versions of those libraries, bring all the records from your separate searches in to one EndNote library if you haven’t done so already: From EndNote menu, File > Import > File > locate individual .enl files; Import: EndNote library. You will perform deduplication in this library.

Creating a new EndNote library for deduplication and backup after deduplicating

See the instructions on deduplicating in EndNote.

Create a compressed library for backup after having removed all duplicates, with a filename like SearchTerms-yyyymmdd-Deduplicated—xRecords.enlx. This will be the library for screening.

Deduplicating in EndNote

Removing duplicates

Systematic review software may offer this functionality, or you can use one of the following methods to remove duplicates from a merged EndNote library.

Before deduplicating, you will need a merged EndNote library containing the records from all your separate EndNote libraries for the individual database searches, if you had previously exported records from each database into separate libraries:

  • Create a new EndNote library that will contain the records from all the databases you searched (I like to put DEDUPING in the EndNote library name)
  • Import the records from each EndNote library you created for the individual database searches:
    • Go to EndNote menu > File > Import > File
    • Next to "Import File", browse to choose the .enl file (NOT the .enlx file) for each library of downloaded records from your searches and select "EndNote Library" as the "Import Option"
    • Once all the records have been added to this new library, check to make sure the final number of records, before removing duplicates, matches the sum of the records found for all the database searches

Using this merged library of records from your individual database searches, you are now ready to remove duplicates. Here are two methods you can use:

1) Earlier version of "Bramer method" for deduplicating, with steps provided in Word document format:

2) Paper describing more advanced configuration options for removing duplicates in EndNote: 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;104(3):240-243. doi:10.3163/1536-5050.104.3.014

After deduplication

Create a compressed library for backup after having removed as many duplicates as possible, with a filename like SearchTerms-yyyymmdd-Deduplicated—xRecords.enlx. This will be the library for screening. You can export the deduplicated library to Rayyan, for example, or other synthesis software, to facilitate the screening process, which usually involves more than one reviewer.

Deduplicating with SRA DeDuplicator

Removing duplicate records with the IEBH SR-Accelerator Deduplicator 

Use the online Deduplicator tool. This is a new version as of August 2021.

Large sets of records

The offline DeDuplicator (old version) may be useful for large sets of records (which used to be considered ≥ 2000). Download the SRA-dedupe-UI application from GitHub. As of October 2020, there were only Linux and Windows versions available.

  • Help using DeDuplicator Offline
  • When exporting your records to an XML file, don't forget to select them all (Help Importing/Exporting EndNote records)
  • If you choose to use the stand alone executable version for Windows, you may get a message that "Windows protected your PC": Click on More info and then a Run anyway button will appear, which you should click if you feel comfortable trusting the software developers

Keep a copy of the RIS or XML file for your records.

See also: Rathbone, J., Carter, M., Hoffmann, T., & Glasziou, P. (2015). Better Duplicate Detection for Systematic Reviewers: Evaluation of Systematic Review Assistant-Deduplication Module. Systematic Reviews, 4(1), 6. doi:10.1186/2046-4053-4-6

Document, document, document

Documenting your searches

Refer to the PRISMA checklist and the published explanation and elaboration document for more information on how to report your systematic review.

See the Search Documentation Template for an example of the types of information you should be tracking and recording:

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Genevieve Gore
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