Transferring Your Library from Mendeley

Mendeley Transfer Blog Image

A while back we started a series on how to transfer your library from different tools. In this week’s post, we have some tips and tricks on how to migrate your library over from Mendeley that will ensure your references, PDF files, notes, and more are all accessible in ReadCube Papers.

Exporting your Metadata

First, if you don’t already have it installed, you’re going to want to download the Papers desktop app to your computer (Mac/Windows). There are two parts to getting your information out of Mendeley and into ReadCube Papers. We’ll start by exporting your metadata first.

Select all your references from My Documents. Don’t worry about grabbing the PDFs we will get them a bit later. Once your references are selected right-click to pull up the menu and choose Export. A dialogue box will appear where you can name the collection and save it to your computer. We recommend keeping the file name simple as My Collection and saving it to your desktop.

mendeley library export

You can also choose what type of file to save your library. Our recommendation is to save the file as a .bib or .ris file. The .ris file is more commonly used for transferring information and includes more fields that aren’t necessarily for writing a paper. You can use .ris if most of your library consists of references without any PDFs attached. Both will transfer traditional metadata (like the DOI, title, authors, etc.) but the .bib file type may not transfer custom fields that you may have created in Mendeley.

Download Your PDFs

Now that you have all the metadata ready to import we need to do one more step which is grabbing your PDFs. Neither .bib or .ris files can download the full-text so we have to manually extract those PDFs out of Mendeley.

File Organizer Options

If you set up File Organizer for your Mendeley library then all of your PDFs are already downloaded to your computer. To find where Mendeley is storing those PDFs you can head to Mendeley Desktop > File Organizer and you will be able to see the file folder path.

The advantages of having the File Organizer set up allow you easily transfer your folders. You will want to create the same folders in ReadCube Papers – so if you have a folder called Elephant Shark in Mendeley you’ll want to create an Elephant Shark in Papers. Then you can simply drag the folders from your Mendeley Desktop folder (or whenever the folders live on your computer) to the new folder in Papers. This makes it easier to keep your folders instead of moving references one by one.

While this is the easier method since your PDFs are already out of Mendeley if you have a large folder structure you can be dealing with multiple folders that will take up storage on your computer.

Manual Download

If you don’t have the file organizer set up you will have to manually transfer your PDFs from Mendeley into ReadCube Papers. The easiest way to grab all the PDFs in your library is to arrange and sort your library so your references are files first.

Mendeley file sort

Once sorted you will then highlight all the references with files attached. Right-click and choose to Export PDF(s) with Annotations.

Mendeley export pdf with annotations

Choose a place to save the PDFs – we recommend creating a folder on your desktop and save them there.

mendeley file save

Now you’re ready for the transfer.

Transferring Your Data

Although it took a few steps to get here, the good news is that moving all your data in Papers is the easy part! We’ll start with moving over you .ris/.bib file. Simply drag and drop that file into Papers and your reference metadata will begin to populate. Next, open the folder that holds all the PDFs you export and drag those into Papers.

During the PDF transfer, the files will import first. Then Papers will begin resolving each PDF individually so if the metadata does not immediately appear please allow time to sync. Papers is going through each article’s metadata and matching it against the information from the .bib/.ris file to find and match any duplicates. Once it has deduplicated any files it will then begin looking for the metadata on the remaining articles and auto-resolve the metadata.

Common Transfer FAQ’s

Do I need to do both steps – first export a .bib file and then import PDFs into Papers?

Yes, a .bib or .ris file will not grab the PDFs from your library. Using the .bib will guarantee all your metadata for any manual references or references without PDFs is transferred over.

Will transferring a .bib/.ris and PDFs create two items for each entry?

If the reference metadata in the .bib/.ris files contains DOI’s then it will automatically merge itself to any PDFs that Papers can identify with a DOI.

If the references do not have DOI’s duplicate entries may occur because Papers will think that it’s a different reference. You will then have to manually merge the duplicates.

Will my notes, highlights, and annotations transfer?

Yes, any markings made on your PDFs will transfer into ReadCube Papers. The highlighting colors, sticky notes, etc. may be different though. This is because Papers uses different colors than Mendeley, but it will try to match the colors as closely as possible.

Mendeley to ReadCube Papers PDF annotation transfer

Will my Tags transfer?

Tags will transfer in the .bib or .ris file.

Will my file structure remain?

No. Unfortunately, Mendeley is a different application than Papers so we do not share the same developing construction. This means we can’t match the file structure in place in Mendeley so you will have to manually create the folderse.

Do I need to keep the Mendeley desktop app?

If you are satisfied with the transfer and you no longer need to use Mendeley you can delete the app from your computer.

If you do get stuck with any part of the transfer please reach out to us for help!

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Val Podbelski