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EPIB-629: Knowledge Synthesis - Library Guide

Exporting search results to EndNote - Steps

Exporting search results into 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, and Web of Science.

Exporting to EndNote from Ovid Online

Ovid MEDLINE

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 for the records from the database in question (MEDLINE on Ovid) and have the library ready in the background
  2. From Ovid, export complete reference in groups of <= 1000 (e.g., 1-1000, 1001-2000), 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. From Ovid MEDLINE: Download the search history for your records: Export (1, 1-10) > 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 SearchTerms-yyyymmdd-MEDLINESearch-xRecords
    • Not including the records themselves, 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
  4. Create a compressed version of the EndNote library for your records

Embase Classic+Embase

  1. In EndNote, create a new library for the records from the database in question (Embase Classic+Embase) and have the library ready in the background
  2. From Ovid, export complete reference in groups of <= 1000 (e.g., 1-1000, 1001-2000), 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. From Ovid Embase: Download the search history for your records: Export (1, 1-10) > 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 SearchTerms-yyyymmdd-EmbaseSearch-xRecords
    • Not including the records themselves, 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 and date; this greatly facilitates rerunning the search later if an update is needed
  4. Create a compressed version of the EndNote library for your records

Exporting to EndNote from PubMed

PubMed

  1. In EndNote, create a new library for the records from the database in question (PubMed) and have the library ready in the background
  2. From PubMed, Click on Send To > Choose Destination: File > Format: MEDLINE > Create File

  1. In Firefox: Open with EndNote

  1. 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)

 

  1. Save the search history for your records: From PubMed: Click Create alert under the search box or from the Advanced screen, click Download history to maintain the line-by-line version (if applicable). The search is saved in an agglomerated format but this is useful if you need to rerun the search later for an update
  2. Create a compressed version of the EndNote library for your records

Exporting to EndNote from Web of Science

Web of Science

  1. In EndNote, create a new library 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. From Web of Science: 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. Create a compressed version of the EndNote library for your records

Create a backup, compressed EndNote library for your records

Create 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
  • 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.

Create a new EndNote library for deduplication and backup after deduplicating

Create a new EndNote library for deduplication and backup after deduplicating

Removing duplicates

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.

Document, document, document

Document, document, document

Record the information (names of databases/platforms searched, database time coverage, date searched, number of records from each database before deduplicating, number of records after deduplicating, etc.) in separate sheet.

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