Is it possible to import all my search results from PubMed into Zotero?

bellademo

I have only been able to import to Zotero the results of my search by page using the plug-in. However, some of my searches are coming up with 10,000+ results, is there a way to import all the results of my searches rather than importing by page?

adamsmith

In a PubMed search at the top about in the middle:
Send to ---> Citation Manager --> All results --> Create file

The downloaded (.nbib) file will import into Zotero. Note that importing 10k+ items into Zotero will take some time and it'll likely freeze. Just let it run.

DWL-SDCA

With the (no longer especially) new PubMed interface with a selected summary of each record, you may want to pre-screen the items you import to Zotero. I run a daily search that results in between 500 and 1500 items (depending upon the number of results from MDPI and Frontiers journals). My search is quite sensitive and only 20% to 25% of the results are relevant to my needs. I do article screening / tick-box selection on PubMed before I download them to Zotero. many PubMed records are obviously not relevant to my needs and for questionable ones; I like the ability to view the full abstract and, if necessary, link to the full text from PubMed rather than doing this from within Zotero.

You can also limit the number of PubMed articles by specifying a range of dates wherein the record was added to the PubMed database. I use a single-day time-range but this range could easily be changed to week, month, year. I use the record creation date in preference to the publication date.

I preface my daily search string with:

(("2022/03/15 00:00:01"[CRDT] : "2022/03/15 23:59:59"[CRDT]) AND (....

where
'....' is a 4800+ character Boolean search string.

danieljheller

I have exported a reference to my mac desktop from PubMed. I can see it there, in .nbib format.
In Zotero, I click File > Import > From a File....and it doesn't recognize the .nbib on my desktop.

What am I missing?
Adam Smith's reply above doesn't even bother to mention the steps, only says "the file will import". Unfortunately, it doesn't do it itself, at least not in the way I'm trying to do it.

Followup: I found a workaround. I have to open my whole drive, search for .nbib, and then it finds it. It would be more convenient if Zotero automatically found the .nbib file that is there on my desktop.

DWL-SDCA

An easier way would be to download to directory/folder sorted by recently added (if on a Mac, use the Downloads folder). In Zotero, File / Import and move to the folder where you saved the nbib file. (It should be at or near the top of the list.) Next time, save to the same folder when you give the Zotero import command it will remember where you put the file and all you need to do is click the recent nbib file. Once you have saved one nbib file to your download folder (on a Mac) all subsequent nbib saves should also go there by default.

If you have many items on the Desktop files can get "lost"
Edit see my detailed instructions in my post below

DWL-SDCA

To be more detailed:

From PubMed item list
- select the item(s) you want to import
- At the top of the page click Send to
- from the drop-down list select Citation manager
- Click on Create file
- a green notice should appear stating that the file is being saved
- Be sure that you have set your browser to save files to your Downloads folder*

In Zotero go to File / Import
Where do you want to import from?
- select the A file( ...) radio button
- Continue
A Finder window will open
- if the downloads folder isn't showing move to the downloads folder
- select the nbib file and click Open
- The PubMed nbib file items will be added to a new collection
Click Done

*Browser settings

If you are using Safari
- Preferences / General / File download location

If you are using Firefox
- Click the hamburger button to the far right at the very top of your screen
- Settings
- Scroll down to Files and Applications
- Save files to Downloads

If you are using Chrome
- Under the Chrome menu select Preferences
- Settings Advanced
- Downloads
- set the preferred location
- /Users/YourUserName/Downloads

toni_baum

Does anybody has an idea why this doesn't work in my zotero? I did it exactely as you described but it always comes an error that says that something was wrong with my dataset. It is nbib from pubmed.
Thanks for your help!

adamsmith

Can you try with a single item from PubMed exported that way and see if that works? If it doesn't, open the file in a text editor and paste its content here.