Why Endnote does not find some references in Pubmed


Sometimes I notice that ENdnote does not import a reference, even if it is indexed in Pubmed! 

I thus have to export it from pubmed to text file, and then import in Endnote from the import menu! This is a time consuming compared to the automatic import in Endnote directly!

Is there a reason for this?

There is no way to setup Endnote to import a reference whatever its bibiography or journals’ databases? 

What are “filters”? And why not merge all the filters in one filter only, called “online search”?

As a user, I don’t mind if I will import the reference using the Congress Library, or Pubmed, or web of science or any else!

All what should account, for me at least as a user, is that Endnote should search the desired reference, wherever is it, and propose to download it!

It may be easy to say hard to do, but in a common sense I would be able to set up Endnote working this way!

Because I don’t care if the reference is imported from her or there, via pubmed or web of science!

Morever, when I want to search a reference online, I have to go the "Pubmed (NLM), under "Online Search (left panel), otherwise the remote search wont run!


Why there is not a default option to check, once fo all, the most appropriete database and Endnote will always search in that database without the need to specify it each time?

So far in Endnote main page, there are by default four options available in the left panel of the the program: 

  • Library of congress


  • Pubmed (NLM)

  • Web of Science

I am wondering why there is no option to select/deselect (check/uncheck) one or more of these databases to tell Endnote to search the selected databases as a by-default parameter?

I never used the three other options library of congress, LISTA and web of science)! I mostly and alway use Pubmed!

So, I would like to set this as a default option (with eventually web of science) and ask Endnote to always search my request in these selected databases!

I know, that there are other discipline other than medicale sciences (hence Pubmed), but why not merging all-in-one?

Is it because this will slow donw the search?

Then, how google or other search engines search the huge internet content and give results in a second or so?

Why Endnote does not do a comparable job for the bibliography databases?

Why we cannot set up Endnote in a way that it searches the references in 1, 2, 3, or 4 available databases, without the need to specify each time the database? 

Or at least, offer the possibility to check “by default” a biobliography so when I click on Enter, the search will be done in the selected database!

Or better, offer the possibility to select, or check, more than one databases by default?

For example, I can check NLM, Web of science as my search default and I won’t need each time to specify Pubmed as my online search!

I just want to check it once and let Endnote does the rest!

It is a tricky task that one have to each time click on Pubmed ( as one have to go to Pubmed (NLM)!

Intuitively, I would prefer that Endnote will make the search once I typed the reference and clicked on “Enter” (keyboard) or “search” in the menu!

I don’t know if I explained my idea properly, because I feel a little bit confused! 

So, please tell me if you get my idea or I have to say it differently!

It is very important option, I think!

Thank you

Here is an example of I mentioned above:

“FCA does not bind abscisic acid”, which exists in Pubmed:


but when I search it in Endnote (PubMed NLM filter), it comes with “no matching reference found” !!


So, why Endnote doesn’t found it? 


@endnoter wrote:

Here is an example of I mentioned above:

“FCA does not bind abscisic acid”, which exists in Pubmed:



but when I search it in Endnote (PubMed NLM filter), it comes with “no matching reference found” !!


So, why Endnote doesn’t found it? 



How are you formulating your search parameters? I was able to locate the article by using EndNote’s “PubMed (NLM)” connection file and by searching for the first author (Risk, JM) and part of the title (FCA) – see attached image.

Note that for online database searching EndNote only uses the comparison operator “ Contains ”.  Look up “comparison operators” in the manual which provides the info below (go to the toolbar, click Help > :  Search for Help on… > Index>):

Contains: finds all references where the search field includes the search term. The search term includes both left and right truncation, so a search for “house” would find “house,” “greenhouse,” and “household” anywhere in the field. If you want to limit the search specifically to the word “house,” check the Match Words box on the Search dialog.”

Thank you, CrazyGecko,

I sear by article’s title only! I copy/paste the whole title “FCA does not bind abscisic acid” in Endnote and search it in the title search field! 

But it comes with not found!

Surprisingly, when I use only the first letters (FCA) 57 reference are found including the right one! 

With the full title it is not found but with only the three first letters it is found!

Strange, no?!

The following information from the EndNote Help File may provide some assistance in understanding the search results retrieved by EndNote as compared to a search directly on the database Web interface. The interface used by EndNote to search PubMed is not the same one available through a Web browser:

"When searching an online database, the search menus display a list of available search indexes supported at the remote site. These are not fields in the online database, but rather sets of search terms and synonyms designed to facilitate your searches. It is not uncommon to search for a term in an index and notice that the exact term appears nowhere in the retrieved reference(s).

For example, you might search for “heart attack” in the Title index of a medical database and find references that do not include “heart attack” in the Title field but, instead, they use the term “myocardial infarction.” This apparent discrepancy can be attributed to the search index of the online database, which has mapped the common term “heart attack” to its scientific equivalent “myocardial infarction.”

It is also not uncommon for some of these databases to index personal names that appear in the titles or keywords along with the author names. For example, a search of the Library of Congress for “Charles Dickens” in the Author index displays books about Dickens as well as those written by him. This form of indexing is most commonly seen with library book catalogs and not with the scientific reference databases. Sometimes you can restrict the searches to books by that particular author by setting up a search to find (for example) “Charles Dickens” in Author, NOT “Charles Dickens” in Keywords.

These search indexes are maintained by the providers of the databases and are not controlled by EndNote.

Some of the search options have additional limitations that you wouldn’t encounter when searching an EndNote library. For example, some databases prohibit searching for a year alone. The year can be specified only to limit a search (these are called “limit fields”). In such a case, a search for 1997 as the year would be denied, but searching for Smith as an author AND 1997 as the year (thereby limiting the results of the author search), would be allowed.

If you have set up a search that is not accepted by the online database, an error message will describe the source of the problem as specifically as possible. Keep in mind that these restrictions are set by the information provider, not EndNote. Documentation from the information provider may help to clarify what search options are available."

Apologies if this gets posted more than once - I certainly intent to post this only once…  When trying to post, I’m getting a funny error message claiming “invalid HTML” (yes, it’s been copied and pasted from an existing PubMed ref)  – I had to change . to [dot]

Unfortunately, Jason’s suggestion still doesn’t resolve the problem with PubMed.  Go to PubMed: “www[dot]ncbi[dot]nlm[dot]nih[dot]gov/pubmed/15006833”  When I try to find this article by copying and pasting its title into the Online Search/PubMed(ML), the Title field, I get the frustrating “No matches found” message.  BUT when I enter the lead author’s last name and the year, I get 6 articles one of which is the article in question.

Jason,  I would appreciate you trying this and giving your feedback.


Dudes sometimes even If you do your search properly nothing is going to be found no matter what!

The only resort is to go on the paper website and export the reference by clicking export to RIS than open the file in endnote,