EPIB 619 Systematic Reviews & Meta-Analyses

McGill University Library has a subscription to Covidence, a useful tool for importing database records, removing duplicate records, screening, documenting critical appraisal/risk of bias and data extraction, and exporting data. Covidence also allows members of the McGill community to invite external reviewers to join their review team.

For access and support for Covidence, please consult: https://support.covidence.org/help/mcgill-university-library

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.

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

• More information available (Cochrane Library, ProQuest databases, Scopus, Web of Science databases) via the University of Alberta Scott Health Sciences Library

We recommend exporting RIS files that can be imported into Covidence for deduplication and screening.

You can use EndNote or other citation software as an intermediary step, although it is not required. EndNote is useful for managing references and full text.

If EndNote does not seem to include an export filter for the database you are using 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 records from databases on Ovid (MEDLINE, Embase, Global Health, APA PsycInfo, et al.)

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. From Ovid, just above your search results, either check the box "All" or enter ranges of records up to 6000 (this is the maximum set at McGill), e.g., 1-6000, then click Export, then select Format: RIS; Fields: Complete Reference; then click Export; be careful if exporting in batches of 6,000 as Ovid may time out; do this until all of your records are exported
2. Use a standardized filename for your .ris files such as SearchConcepts_DatabaseName_Export_yyyymmdd.ris, e.g., LiverTransplantPrehabilitation_MEDLINE_Export_20230322.ris (if exporting in batches, identify ris files accordingly, e.g., LiverTransplantPrehabilitation_MEDLINE_Export_20230322_1-6000.ris);
3. Import the ris file(s) into Covidence and label them by database name; check that the # of records matches up

Documenting your Ovid MEDLINE, Embase, Global Health, and/or APA PsycInfo et al. searches

1. Document the search: Use the Copy Search History Details button below the search history to copy/paste the search into your documentation or records. If you would like to upload a search to DataVerse, save the file in .rtf format with a standardized filename along with your other searches; we recommend SearchConcepts_Search_SearcherLastName_yyyymmdd.rtf as the search filename, e.g., LiverTransplantPrehabilitation_Search_Boruff_20230322.rtf 
   • Copying and pasting the search history details in their exact version will avoid transcription errors 
2. Use the Copy Search History Link button below the search history to create a reusable URL for your search strategy, and/or
3. Save the search history to your personal Ovid account (create an account for free) and identify the search by database name and date; this facilitates rerunning the search later if an update is needed (the search history link suggested in the step above is also useful for this). Document your Ovid account information as well.

Exporting records from PubMed

• From PubMed, there are two options:
  • Click on Save > Selection: all results and Format: Pubmed; the file will be saved as .txt, which can be imported into Covidence or EndNote
  • Click on Send to > Citation manager > Selection: All results > Create file, File as Type: All Files and File name: SearchConcepts_PubMed_Export_yyyymmdd.ris -- changed from .nbib (be sure to choose an appropriate location for the file); Covidence will not allow you to import the file with the .nbib extension, but you can change the extension manually to .ris

Documenting your PubMed search

There are a couple of options for documenting your PubMed search:

• To save a version that can later be rerun fairly easily, but which is saved in a hard-to-read format: Log into your PubMed account and save the search for your records and for future updates by clicking Create alert under the search box. 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; or 
• From the Advanced screen, click Download (upper right corner of History and Search Details) to maintain the original structure of your search. The search will be saved by default as a .csv file. If you need to rerun this search at a later date, multiple-line searches will need to be copied and pasted into the PubMed Advanced Search Builder to reproduce the search.

Exporting records from Web of Science Core Collection databases

1. In Web of Science, Click on the arrow for the Export dropdown menu and select RIS (other reference software)
2. Export full records in groups of up to 1000 (e.g., 1-1000, 1001-1243)
3. Use naming convention for your files, e.g., SearchConcepts_WoS_Export_yyyymmdd.ris (be sure to save it in an appropriate location)
4. This RIS file can be imported into EndNote or Covidence, as needed

Documenting your Web of Science search

1. Document the search by clicking on the clock icon in the left-hand column (copy the query link as well) and select Export: Plain text file

Exporting records from CINAHL

1. In CINAHL, click on View Results for the list of records you will be exporting
2. 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) 
3. Enter the email address to which to send the records and make sure RIS Format is selected in the right-hand column
4. 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
5. Rename the extracted RIS file with standardized naming such as SearchConcepts_CINAHL_Export_yyyymmdd.ris, (be sure to save it in an appropriate location); this file can now be imported into Covidence

Documenting your CINAHL search

• Document the search: Click on Print Search History to view the search, then copy and paste it into your search documentation, reformatting the table as needed

Removing duplicate records with Covidence

McGill University Library has an institutional license for Covidence. For access and support for Covidence, please consult: https://support.covidence.org/help/mcgill-university-library

Covidence removes duplicate records automatically. The Covidence support pages explain the process in detail.

Please note: It has been reported that exporting records from Ovid databases in RIS format results in better removal of duplicates than exporting records from Ovid databases in EndNote format.

Study supporting the use of Covidence: McKeown S, Mir ZM. Considerations for Conducting Systematic Reviews: Evaluating the Performance of Different Methods for De-Duplicating References. Syst Rev. 2021;10(1):38. doi:10.1186/s13643-021-01583-y

Removing duplicate records with EndNote

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 (if applicable) 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 -- you may need to open that beforehand to "create" the .enl 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 then export this deduplicated record set from EndNote to Covidence:

• In EndNote, select all the records for screening (Ctrl-A on a PC or Cmd-A on a Mac)
• From the EndNote menu, click on File > Export > Save as type: Text File (*.txt) and Output Style: RefMan (RIS Export), note/change the location to which you are saving the file if needed, then save the file
• Import the text file into Covidence.

Removing duplicate records with the IEBH SR-Accelerator Deduplicator 

Use the online Deduplicator tool.

• Help using Deduplicator

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

Documenting your searches

Refer to the PRISMA 2020 checklists (including an expanded version with additional guidance) for more information on how to report your systematic review.

Refer to the PRISMA searching (PDF, Word, or Excel) guidance for more information on how to report your searches

Complete the PRISMA flow diagram

See also: Rethlefsen ML, Page MJ. PRISMA 2020 and PRISMA-S: common questions on tracking records and the flow diagram. J Med Libr Assoc. 2022;110(2):253-257. doi:10.5195/jmla.2022.1449

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