Reference management: Mendeley

Mendeley Desktop

• If you have not done so already, create a free account (NB: UU has no institutional account. To avoid problems when logging in with Mendeley Desktop or Mendeley Reference Manager we advise you to create your account by using a private e-mail address and NOT your UU mail address.). If you have forgotten your password, click on 'Forgot password?' to reset.
• UU-staff:
  Follow the explanation on UU intranet (under Reference Management).
• UMCU staff:
  Via the UMCU IT helpdesk you can request permission to use EndNote. See UMCU intranet. Please note that the Mendeley Web Importer can not be downloaded within your browser on a UMCU desktop.
• UU-students:
  Mendeley Desktop is available via MyWorkplace.
• Installing on your own computer?
  Download the software to install Mendeley Desktop.
   
• Install, if you want to, the Mendeley Web Importer (for Chrome, Microsoft Edge and Firefox) in your browser and drag/find the button in your bookmarks/favourites. This browser extension scans your current browser screen for references to articles and picks up possible metadata and full-text PDFs to add them to your library.
• If you want to, also install the Citation plugin for Word (Mendeley Cite).

Mendeley Web does not need installing. Go to www.mendeley.com and log in at Mendeley by clicking on the 'Sign in' button in the top right hand corner

Create one or more folders in Mendeley Desktop. Under 'My Library' select 'Create Folder'.
Useful start page for Desktop: https://www.mendeley.com/guides/desktop/01-desktop-interface 

For further information, see:
https://www.mendeley.com/download-desktop-new/
https://www.mendeley.com/guides/web
https://www.mendeley.com/guides/download-mendeley-desktop/windows/instructions
https://www.mendeley.com/guides/download-mendeley-desktop/mac/instructions
https://www.mendeley.com/guides/download-mendeley-desktop/linux/instructions
https://www.mendeley.com/guides/download-mendeley-desktop/ubuntu/instructions

Tips & tricks

• For the time being Mendeley Desktop has a few more options than Mendeley Reference Manager. Use Desktop for managing your library and Reference Manager for working online and synchronization in the cloud
• This means that you can use Mendeley Desktop at the same time with Mendeley Reference Manager. If you synchronise manually in Mendeley Desktop, all changes you have made will be automatically updated in Mendeley Reference Manager. And vice versa: all changes you have made in Mendeley Reference Manager will be automatically synchronised in the cloud and will show in Mendeley Desktop after you have carried out a manual synchronisation there.
• On your telephone: download the free app for iOS or Android from your app store

Mendeley offers a number of options to collect references.

Mendeley Desktop
You can add documents to your Mendeley library by dragging and dropping a PDF into the Mendeley Desktop window. 
You can also use the File menu to Add files or manually create an entry.
https://www.mendeley.com/guides/desktop/02-adding-documents

Extra option: the Mendeley Web Importer
Save references from the web directly to your Mendeley library with the Mendeley Web Importer. This browser extension scans your current browser window for references to articles and retrieves metadata and full-text PDFs where possible to add to your library.
https://www.mendeley.com/guides/web-importer

Elsevier option: from a search system with Direct Export
From other Elsevier products, such as Scopus and ScienceDirect, you can import references in Mendeley via the Direct Export option 

1. Log in at Mendeley before you start your search
2. Select the title(s) from the list of results and click on Export. Next you choose the option Mendeley.

NB. Mendeley will not always find and add all data correctly, so always check your references. Improve and supplement them  with more data where necessary.
 

Tips & tricks

• Give the Mendeley Web Catalogue a try. Use the search field on  Mendeley.com and click on 'Add to library' to add the references you found. This tool supplements missing data, but works less well in the case of relatively unknown sources and may then add incorrect information or overwrite data! Always keep checking yourself! 
• In Desktop you could use a DOI, PMID or ArXiv ID to collect data. Paste the identifier in the appropriate field and click on the magnifying glass icon.. The item will be searched for in the Mendeley Catalogue and will collect reference details available from other Mendeley users. If the reference is new, data will be collected from the owner of the identifier.
  Also in Reference Manager you can have data collected automatically in this way. Go to 'Add new', 'Add Manual Entry' and copy/paste the DOI in the field DOI field.
  
  Please note! The data can be incomplete or incorrect so always check the data yourself!

In Mendeley, you can organise your sources in several ways and add information to them. For instance, you can give your references a star so they are added to your 'Favorites' folder or mark them as (un)read. Or create folders yourself.
When you add a reference to a newly created folder/collection, you do not move it, but you give the reference a label. All your references are kept in the folder 'All References'. If you delete a folder/collection, the reference will remain available in 'All References'.

Mendeley Desktop
(use of filters, creating folders and subfolders, searching and adding tags)
https://www.mendeley.com/guides/desktop/03-organizing-documents
(the PDF reader including the options: adding notes, highlighting texts, zooming in, synchronising)
https://www.mendeley.com/guides/desktop/04-read-highlight-annotate
 

In the PDF reader you can read documents (PDFs) and add notes to them:

• In Mendeley Desktop you open PDFs by clicking on the PDF icon, in Reference Manager you click on the green tick under File. Or double-click on the title which both systems allow. The document opens in a separate tab.
  
  
  
  In the PDF reader you can
  • Search in the text (use the search box on the right in the taskbar) The used search terms are highlighted in the text 
  • Highlight sections of the text
  • In Desktop: You can add notes about the entire document in the field 'General notes'
  • You can add 'Sticky notes' to specific sections in the text. In the text sticky notes are indicated by an icon. Click on the icon to read the note
    • In Desktop: All notes can be viewed in the 'Notes' tab (next to the 'Details' tab in the right column).
    • In Reference Manager: to see all sticky notes in the PDF,  select the 'Info' button and choose the 'Annotations' tab.
    • For more information about  'share, export, or print annotations', read this blog post.

Tips & tricks

• In Reference Manager: use Mendeley Notebook to save highlights and notes from several PDFs in one place. You can open the notebook with the Notebook button above the PDF.

Mendeley Desktop

• Select in the left column the folder you want to deduplicate, this may be the folder 'All Documents', but also a folder you created yourself
• Go to the Tools menu and select 'Check for Duplicates'
• Now you see a list of duplicates
• Click on the title you want to deduplicate to have a look at the underlying double references (select 'Details' in the right column)
• Mendeley indicates which fields of the original titles have been chosen. You may adjust this by ticking or unticking the check box next to each field
• Next click on 'Merge documents' to merge the references
• You can also select 'Not a duplicate' to keep both the references
• Repeat these steps for all your duplicates

Please note: Mendeley can automatically deduplicate titles when importing them without your knowing. You cannot switch off this function. This means you might lose references without you wanting to. That is why Mendeley is not suitable for creating systematic reviews.

For more information on deduplicating in Desktop see:
https://blog.mendeley.com/tag/deduplication/ 
or watch these videos:

Source: https://www.youtube.com/watch?v=BzREf4RJ25w

Source: https://www.youtube.com/watch?v=0-p2XHRm-UE

For Mendeley Desktop: the Mendeley Citation Plugin
(see also Mendeley Cite below)

You can install it from your Mendeley library:

1. Make sure you have not opened Word
2. Go to your Mendeley library and open the Tools menu. Mendeley will now indicate which word processor programmes you have, so the given options may vary. Choose the most suitable option.
3. Installation is quick and you get a message when it is finished
4. Now open Word and click on the button References: there you will see a set of tools for Mendeley:

NB. At Libre Office of Microsoft Word for Mac it looks slightly different.

For more information about the Mendeley Citation Plugin see the help guide, for instance about:

• inserting citations in a text
• making a bibliography
• how to change citation styles
•  how to merge and modify citations
• and how you can export the document
   

Sharing documents and collaborating with others can be done in 'private groups'.  There is no limit to the number of private group members, but as a free user you may only create a maximum of five groups with a maximum of 25 participants.

You can add the full text of your PDF to the group so that everybody works in the same document. Everyone can highlight the text or add notes.

Private groups for Desktop
https://www.mendeley.com/guides/private-groups/mendeley-desktop/01-adding-documents-private-group

N.B.: Some manuals still give information about Public Groups and invite-only groups. However, they have been cancelled as of April 2020.

Mendeley Desktop

If you work online Mendeley Desktop is fully synchronised with Mendeley Web. Your refererences are saved in the cloud. You can also synchronise manually by clicking on the Sync icon in Mendeley Desktop. Notes and annotations made in a group will then be available for other participants as well.
Please note! Your locally saved data may be of a  larger size than your free storage options in the cloud!

See also: https://www.mendeley.com/guides/desktop/07-how-sync-works

If you also regularly work off line or if you want to make sure that your library is safe in the case of an unexpected event, we recommend you to make regular backups of your Mendeley library. Also if you change accounts you must first make a backup. Go to the Help menu and click on Create Backup. Now you make a .zip file which you can save in a safe place on your computer.

To restore your backup, select Restore backup in the Help menu and next Other. Browse to your (most recent) saved zip file.

See also: https://service.elsevier.com/app/answers/detail/a_id/18153/p/16075/supporthub/mendeley/related/1/

NB: You can use Mendeley Desktop at the same time with Mendeley Reference Manager. If you synchronise manually in Mendeley Desktop, all changes you have made will be automatically updated in Mendeley Reference Manager. And vice versa: all changes you have made in Mendeley Reference Manager will be automatically synchronised in the cloud and will show in Mendeley Desktop after you have carried out a manual synchronisation there.

Exporting

You can also export your references to a file. This file can be imported later (or in another programme).
Go to: Mendeley Desktop of: Mendeley Reference manager for instructions.