export PubMed cites in EN to Excel

Good afternoon.  I’m the EndNote person at my library.  I’m an intermediate level user, I believe.  I don’t use Excel at all, really.  Someone just emailed me the following question. 

“I’m trying to export PubMed citations in EndNote to an Excel file and it always adds in a bunch of blank lines then some weird affiliation info, with everything else in the same row. If you have any thoughts that might help troubleshoot, they would be appreciated.”

Can anyone here help me?  Thanks! 


How are you exporting the EndNote PubMed cites?  If you’re using the Tab Delimited output style it will generate a file that may be imported into Excel.

Thanks for responding, CrazyGecko!

My colleague answered the following: 

“That’s the way I export. Then when I open it in Excel, there is a row of fields for the citations, but then there are a bunch of blank rows for each citation and then after those blank rows, the affiliation information in its own row with a few other things.”

Just some thoughts:

  1. Did your colleague customize or modify any of the original  reference type fields (which may no longer be corresponding the fields in EndNote’s Tab Delimited output style)? Were the fields in the Tab Delimited output style re-checked to confirm that there are no missing fields?

  2. Are there any “blank” or invalid references appearing in the EndNote library that should be deleted?

3. Has your colleague taken a look at the problematic EndNote references (actually “open” the reference) by cross-checking them against the .txt delimited file and see whether any of the fields might accidently contain any extra “return” or other unwanted coding that should be removed?

  1. When your colleague opens the EndNote tab-limited .txt file within Excel, does Excel’s Text Import Wizard (Step 1) use the default “Delimited” setting for “Choose the file type that best describes your data”? And for Step 2, is the “Tab” option selected as the delimiter?

Could a sample tab delimited export file with a few references (particularly the problematic ones) be attached so folks on the forum may take a look?

her reply:

“The really weird thing is that we’re not having problems with the columns…the tab delimited style should export each reference into its own row. What’s happening is that it’s exporting all the information into its own row, then each citation also gets a corresponding and variable number of blank rows (not columns) and then there is a row that has part of the affiliation field and something else.   I’ve looked at the export style for tab delimited and it just doesn’t make any sense, there is nothing extra there that should be causing all these problems”

Should I instruct her to call EN tech support?  I’ve never used EN with Excel at all, so I have absolutely no idea if they’ll be able to help her or not.

Thanks again for the help!

Yes, might be time for tech support.  But one last thing she could try is going to the EndNote website (via the  boolbar’s Help “Web Styles Finder” ) to download a “fresh” Tab Delimited output style and use that instead of the current file. (To help rule-out that the problem lies with the output style itself.)

And make sure that they are using the tab delimited style in the “export” dialog and not assuming it is the one being used as it is selected in the endnote program. 

Thank you all for your assistance.  I wanted to let you know that the person found a different solution, in case it’s ever useful for any of you.  Here is what she emailed me:

"So, it turns out that a workaround has dropped into my lap due to serendipity!  I can export directly from PubMed in a comma delimited file that opens very nicely in Excel.  

The Send to File option now includes a CSV selection to generate an abbreviated summary citation in a comma separated file."

So maybe this will help someone else someday!  Again, we both really appreciate all the time and effort you guys took to answer us and suggest potential fixes.  This forum rocks!