EndNote X4 PDF Import

Has anyone been able to use the new PDF import feature to auto-magically add a reference to the library? I’ve tried with a couple PDFs (supposedly with DOI info), but with no success. All that happens is that X4 adds a reference with the file name as a title.

If anyone knows a PDF that works with the new feature, would you reply with the bibliographic info? I’m teaching a class on EndNote in my department, and I’d like to show people how this new feature works in practice.


In my experience it is a bit hit or miss, at best.  I did note this in the help file:

“Note: When performing the import function, if the are two DOIs found in the first two pages of a PDF document, EndNote will put both DOIs in the DOI field. The PDF is then attached and the file name is put in the Title field.”

I DID NOT  get the PDFs downloading from these refs (and noticed that some of the PDFs I had downloaded were NIH Public Access versions and not from the journals website):

Bachmann, M.P., Bartsch, H., Gross, J.K., Maier, S.M., Gross, T.F., Workman, J.L., James, J.A., Farris, A.D., Jung, B., Franke, C., et al. (2006). Autoimmunity as a result of escape from RNA surveillance. J Immunol 177, 1698-1707.

Florens, L., Carozza, M.J., Swanson, S.K., Fournier, M., Coleman, M.K., Workman, J.L., and Washburn, M.P. (2006). Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40, 303-311.

John, S., Howe, L., Tafrov, S.T., Grant, P.A., Sternglanz, R., and Workman, J.L. (2000). The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev 14, 1196-1208.

And I DID get the PDFs downloaded from these two references to import correctly:

Mosley, A.L., Pattenden, S.G., Carey, M., Venkatesh, S., Gilmore, J.M., Florens, L., Workman, J.L., and Washburn, M.P. (2009). Rtr1 Is a CTD Phosphatase that Regulates RNA Polymerase II during the Transition from Serine 5 to Serine 2 Phosphorylation. Molecular Cell 34, 168-178.

Workman, J.L. (2004). Histone H3 variants and modifications on transcribed genes. Proceedings of the National Academy of Sciences 101, 1429-1430.

The last two worked for me. Hopefully more and more publishers will suport this feature.


and I’ve posted my theory here:


I have had success with the importing. I did some testing with acrobat pro and added some meta data to some pdfs. EndNote is much simpler. It detects the DOI in the text, ignoring the pdf metadata. Most importantly, the computer needs to be connected to the internet for this to work. Also, the source must be in crossref.org.

I have tried to import the two articles, but to no avail.  So, not sure if it is related to the subscription source. 

Our institution subscribes to Molecular Cell via ScienceDirect.   As for Proceedings of the National Academy of Sciences, we have subscription via PNAS and JSTOR.

Many of my PDFs don’t have DOIs, or the DOI import didn’t work - so now I’ve got a bunch of refs in the database that are listed as <filename.pdf>

I can easily open the PDF, look the ref up on Google Scholar, etc., and import the ref list into Endnote

NOW I have 2 “duplicate” references, the ref from online, and <filename.pdf>.  Is there a way to merge them?  How about a better workflow?  I don’t want to have to attach each pdf, because I have thousands.