Reference management: Mendeley

Mendeley Reference Manager 

• 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-students:
• Download and install Mendeley Reference Manager
• Install the Mendeley Web Importer (see above)) and, if you want to, also the Citation plugin for Word (Mendeley Cite)
• Next open Reference Manager here: mendeley.com/reference-manager
   
• UU-staff:
  See above, Mendeley is no longer available via the sofwarecenter
   
• 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.
   
• 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).

Get going:
In Mendeley Reference Manager choose under 'Collections' for 'New collection'.
Useful start page for MRM: https://www.mendeley.com/guides/mendeley-reference-manager/01.-your-mendeley-library

Tips & tricks

• If you still use Mendeley Desktop you can (for the time being) use it 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 Reference Manager
Options:
1. importing from another already existing collection (for instance from another reference tool);
. add files from your computer (drag & drop);
3. add manually)
https://www.mendeley.com/guides/mendeley-reference-manager/02.-adding-references

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

• 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 Reference Manager
(manage existing collections and creating and searching new collections)
https://www.mendeley.com/guides/mendeley-reference-manager/03.-searching-and-organizing-references 
(selecting, adding notes, highlighting, adding sticky notes, zooming in)
https://www.mendeley.com/guides/mendeley-reference-manager/04.-reading-and-annotating-documents

Please note:  If you want to modify the data of the reference, click on the title in question and next on the field to be modified under 'Info'.

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

• 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 Mendeley Desktop you open PDFs by clicking on the PDF icon.
  
  
  
  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 Reference Manager: to see all sticky notes in the PDF,  select the 'Info' button and choose the 'Annotations' tab
    • In Desktop: All notes can be viewed in the 'Notes' tab (next to the 'Details' tab in the right column)..
    • 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 Reference Manager
Mendeley Reference Manager automatically deduplicates references on import. MRM looks at references that are already or have been in your library (previously removed references also count). You cannot stop or influence this process.
Since Mendeley Reference Manager does not have a reliable, transparent way to deduplicate, we therefore advise against using Mendeley in research, such as for systematic reviews and meta-analyses. In that case, choose another reference manager

If you still have Mendeley Desktop you can deduplicate following the steps below:

• 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:  Also Mendeley Desktop 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 supporting 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 Reference Manager: Mendeley Cite

Install Mendeley Cite for Word (and Libre Office).
For more information about Mendeley Cite see the help guide, for instance about:

• how to open your Mendeley Cite
• inserting a citation in your text
• manually modifying a reference, for instance to add a page number
• creating a bibliography
• choosing or changing citation styles
• Mendeley Citation Hub

NB. You can also use Mendeley Cite with Mendeley Desktop as long as you use a supported version of Microsoft Word and your Mendeley library is synchronised in the cloud.

For Mendeley Desktop: the Mendeley Citation Plugin
(need a citation tool: use Mendeley Cite)

It is no longer possible to install Desktop or Desktop applications.
If you still use Mendeley Citation Plugin, here is some information:

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 Mendeley Reference Manager
https://www.mendeley.com/guides/private-groups/mendeley-reference-manager/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 Reference Manager. Synchronising.

Mendeley Reference Manager saves all your references in the cloud (so not locally on your computer). If you are online, synchronisation is automatic and all modifications you made are saved. Hover with your mouse cursor over the sync icon to see when the most recent synchronisation took place and click on the icon to synchronise manually.

See also: https://www.mendeley.com/guides/mendeley-reference-manager/07.-syncing

Please note! It is possible to add references manually off line in MRM. But make sure you regularly work online to synchronise with the cloud.

The offline use of Mendeley Reference Manager has some well-known problems. If you have problems, have a look here: https://service.elsevier.com/app/answers/detail/a_id/29758/supporthub/mendeley/p/16075/

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.