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How to export references from PubMed to EndNote

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Overview:

This guide explains exactly how to export references from PubMed and import them into EndNote using the NBIB or RIS file format. It works for both single citations and bulk exports. The process ensures full metadata retention (authors, journal title, DOI, abstract, MeSH terms).

Step-by-Step instructions

1. Open PubMed and select references

  1. Go to https://pubmed.ncbi.nlm.nih.gov/
  2. Run your search
  3. Select citations:
    • Single reference: Open the record → Click Cite.
    • Multiple references: Use the checkboxes next to each article in the results list.

2. Export using the citation manager

  1. Click Send to (located above the search results).
  2. Select Citation Manager from the dropdown.
  3. Click Create file.

PubMed will download a .nbib file (default for PubMed). Save to an easy-to-find location (e.g., Desktop or Downloads).

4. Import file into EndNote

  1. Open EndNote.
  2. Navigate to File → Import → File.
  3. Select the .nbib file you downloaded.
  4. Under Import Option, select:
    • PubMed (NLM) for .nbib
    • Reference Manager (RIS) for .ris (if you exported RIS instead)
  5. Click Import.

You may also double-click the .nbib file you downloaded and tell your computer always to open these files with EndNote.

Verify imported references

  • Check the Imported References group in EndNote.
  • Confirm authors, titles, journal names, and DOIs are correct.
  • Move to the appropriate group in your EndNote library.

Best practices

  • Always use NBIB for maximum metadata from PubMed.
  • Update your EndNote import filters regularly.
  • For large exports, consider saving searches in My NCBI first.

Common problems and solutions

Problem Cause Fix
References appear incomplete Wrong import filter selected Use PubMed (NLM)
File doesn’t open Double-clicking skips EndNote Use File → Import inside EndNote
DOI missing PubMed record lacks a DOI Manually add from the publisher site, or run “Reference Update”

 

FAQ

Q1: How do I export citations from PubMed to EndNote?
A: Use Send to → Citation Manager → Create file, then import the .nbib file into EndNote using the PubMed (NLM) filter.

Q2: What file format should I use to export from PubMed to EndNote?
A: Use NBIB for full metadata. Use RIS if working cross-platform with other citation managers.

Q3: Why aren’t my references importing correctly into EndNote?
A: Most often, the wrong import filter is used. Select PubMed (NLM) for .nbib files.

Q4: Can I export multiple references from PubMed at once?
A: Yes — check the boxes next to the desired results, then export via Send to → Citation Manager.

Q5: How do I fix missing DOIs after importing from PubMed?
A: If PubMed doesn’t list a DOI, retrieve it from the publisher’s site and add it manually in EndNote. Additionally, you can run the EndNote “Update Reference” function.

 

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