Import a Plain Text Bibliography into Endnote with this Tool

There are a number of useful alternatives to PubMed that incorporate external functionality to augment the database’s already-impressive capabilities. For a comprehensive list (and descriptions) of these tools, check out MSK Library’s LibGuide on PubMed Alternative Interfaces.

One such alternative, HubMed, has a particularly remarkable ability that makes it enormously useful:

It can search for an entire plain text bibliography (ie. a reference list with multiple citations that does not include PMID or DOI numbers) and find the equivalent PubMed records (if available) within minutes. It then gives you the option to download the citations in either RIS or BibTeX formats.

A few things to keep in mind when using the HubMed Citation Finder:

Fig 1. Pasting citations into HubMed from your list

-When you paste in a bibliography, there does appear to be a limit to how many citations can be searched at one. (I easily did just over 60 without any issues.)

-Each citation needs to be on a separate line. (My double-spaced test bibliography worked fine.)

Fig 2. Reviewing HubMed’s citation matches (Note: It default “selects” the first/best match in the list of options in yellow.)

-The search did not work for me in the IE browser but worked fine using Google Chrome.

-This works for reference lists of articles from journals indexed in PubMed. (Note: You may not get an 100% for all your citations so you do want to check them to be sure HubMed found a true match.)

Fig 3. You can download the yellow highlighted (ie. “selected”) citations as an RIS (or BibTeX) file

Fig 4. You can then double-click on this RIS file and directly export it into your open Endnote library

For more information on using HubMed, you can see the online HubMed Documentation or read this description of the product by its creator published in Nucleic Acids Research:

Eaton AD. HubMed: a web-based biomedical literature search interface. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W745-7. PubMed PMID: 16845111; PubMed Central PMCID: PMC1538859.

For more tips (or trouble-shooting help) when dealing with reference lists and citation managers, be sure to contact us at the MSK Library.