Skip all navigation and go to page content
NN/LM Home About PNR | Contact PNR | Feedback |Site Map | Help | Bookmark and Share

FLink: A New Way to Save PubMed Search Results

Flink logo

Those who search PubMed regularly have often wished for a way to import search results into a a program such as Excel. It’s here! A new tool called FLink (Frequency-weighted Links) is now accessible from the NIH National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/Structure/flink/docs/flink_about.html. FLink allows PubMed search results to be saved as a CSV, or comma-separated value, file which can be imported into a program like Excel.

Here are the steps to follow:

  1. Enter the desired query in PubMed.
  2. Open FLink (http://www.ncbi.nlm.nih.gov/Structure/flink/flink.cgi).
  3. Open the “Please choose a database to start” menu and select “PubMed.”
  4. Select “Input from Entrez History” from the dialog box that allows you to select your desired input method.
  5. a) use the pull-down menu on that tab to view a list of your recent PubMed searches;
    b) select the PubMed query for which you’d like to download a CSV formatted search results file;
    c) press “Submit”
  6. FLink will now display your search results in a “PubMed” folder tab.
  7. Select the “Download CSV” option and choose to “open” or “save” the file, as desired. (The browser window will also display the URL at which your results can be retrieved.)
  8. The columns in a CSV file will depend on the database you accessed through FLink. For PubMed, thecolumns will include:
    1. UID (PMID)
    2. Authors
    3. PubDate(Year)
    4. PubDate(Month
    5. Title of article Summary (which includes the following information in a single cell: Authors, title, journal name, year, month (if applicable), volume, issue, pages)

3 Responses to “FLink: A New Way to Save PubMed Search Results”

  1. doris Says:

    This is great!
    Thank so much, you just saved me, I cannot count how many hours of work…will be sharing with my colleagues ASAP
    cheers
    doris

  2. Heidi Sue Adams Says:

    Finally had a chance to try this out! The concept is nifty. However, I can’t get it to work the way I want it to. It only allows me to download the original search – how do I get it to download my Clipboard selections or just a list of my selected citations? Also, are those 5 columns the only information I can retrieve?

  3. Alison Aldrich Says:

    To get it to download from your clipboard, first go to your clipboard, then change the Display setting to PMID list. That gives you just the numbers, and you can ctrl+c copy them. In FLink, after you’ve chosen PubMed as your database, make sure you are on the Input ID List tab and paste in the PMIDs.

    I think those 5 columns are it for now. The article title summary column is a lot of info in a single cell. It would be nice to be able to parse that out a little further and (for example) get journal name in its own cell. If you have enhancement suggestions, you can send them to either the FLink or the PubMed help desk. In both cases, the help desk links are on the bottom right corner of the page.