A bibliographical reference or citation manager is a tool that allows you to create and organize bibliographical references obtained from different sources. It makes it easier to create, maintain, organize, and give shape to bibliographical references according to different citation styles. It also incorporates a series of functions that allows you to share them with other users or export them to automatically create a bibliography. Multiple reference managers exist: Zotero, Refworks, Mendeley, EndNote.



Mendeley is a bibliographical reference manager that combines an online version with a local, desktop version. In addition, it incorporates 2.0 network features that help researchers organize their work, collaborate with other online users, navigate contents uploaded by others and discover publications on a specific subject.



In order to use Mendeley, visit their website, http://www.mendeley.com, and create an account by clicking on Create a free account. It is essential that you use your institutional email, the one ending in @htsi.url.edu.

Mendeley allows you to configure your account by adding other professional or academic details to your profile. This information can be modified at any time by accessing your profile from the Settings section.


The next step is to download the local Mendeley Desktop application, which allows you to work without having to use a browser, or even an Internet connection. After you download the application, the Mendeley icon will automatically appear on your desktop, and the program will open automatically. You can access it using the same password you used to register.

From here on, you can decide either to access your account from http://www.mendeley.com or using the local version of Mendeley (access via the desktop icon). Mendeley 2

Mendeley allows you to install the local version (Mendeley Desktop) on any of the devices you normally use (tablets, laptops, mobiles, etc.) so you can manage your documents from any of them.

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The first time you access the program from the local version installed on your computer, a window allowing you to directly add references will appear.



You can add PDF files saved to one of your devices without having to worry about the file name. Mendeley recognizes the metadata within the file and will import the full reference.


If you select the Next option, Mendeley will automatically show a series of references that can be recognized as of your own authorship, since the name of the author is similar to the name used in the program profile. In this case, you can either recognize these articles as your own (in other words, the article is written by the registered user) or reject them. You should only select articles that are truly yours.


If you select the Next option, Mendeley will show a series of articles related to the field of investigation selected in the initial registration (when your account was created). These articles may be of interest in this area of study, and as a result it is worthwhile to take a few minutes to go over the list. When you select the references, Mendeley will automatically add them to your desktop.


 If you select the Next option, Mendeley will automatically update the added references.

Screen layout in the local version (Mendeley Desktop)

Mendeley Desktop 1

1.- My Library. Content organized as an index (all of Mendeley, my library organized into folders, Group contents, labels, etc.). From here, you can configure and manage your different collections of documents. You can apply filters by author, keyword, etc.

2.- Viewing references in their short form.

3.- Viewing the details of the selected document (metadata). From here, you can add labels and notes.



When you select any of the references (by double-clicking), you will see the document on your screen, as well as the associated metadata which will automatically appear in the right-hand panel. This metadata can be modified or filled out at any time by selecting any of it so that, once completed, it will be visible for all Mendeley users (the research community).


The left-hand panel will allow you to recover all of your documents, but recently-read or recently-added documents can also be filtered out using the Recently read and Recently added options.

When you add a reference to Mendeley, it is marked as unread with a green circle. Once it is opened (even if you don’t read it) the green circle disappears and the references are marked as read. Mendeley allows you to mark them and unmark them as unread as many times as you want.

You can select the documents that seem most relevant by marking them with a star that appears to the left of each reference. They can be marked by simply clicking on them, and by clicking again they can be unmarked. All documents marked as favourites will appear in the Favourites folder in the left-hand panel. This way, you can also filter out new documents by only selecting the most relevant ones, choosing the Favourites option in the left-hand panel.


Often, when Mendeley compares added data to data from its database, inconsistencies appear. In this case, a warning will appear on the left-hand panel under the option Needs review. Documents are placed under this option when their metadata needs to be reviewed. When one of the references is selected, Mendeley will present you with two options in the right-hand panel: you can either find the source of the article with the Search option or indicate that the data describing the article is correct with the Details are correct option.


It is a good idea to review metadata, and not fully trust the default data offered by Mendeley, as it may not be entirely correct. In addition, it is important to remember that this metadata is later used to put together a bibliography.

Any documents that need to be reviewed will be automatically added to a folder called Needs Review (right-hand panel).

You can filter documents by type using the Type option (right-hand panel), selecting the type of document you are interested in in the drop-down menu.

The metadata in the right-hand panel can be hidden, so that the reading area is larger and articles can be more comfortably read.

Your institutional HTSI account will allow you to store 2 GB of documents. By clicking on the Edit settings option, you can see how much memory you are using.



From the local version of Mendeley, you can easily and quickly add any references stored on your computer, USB drive, etc. (PDF files of articles).

From the main menu, click on File in the toolbar and choose the option Add files. You can also drag and drop PDFs directly in the content panel. The Add folder option allows you to import all the PDFs you have stored in a certain folder at once.

Mendeley automatically recovers metadata from documents: author, title, etc. However, this data is often incorrect. It can be completed or corrected directly in the right-hand panel. It is a good idea to also review the type of document: journal article, book, thesis, etc. Mendeley recognizes multiple types of documents. Depending on the type of document chosen, the fields to fill out will vary. It is important to pay close attention to the type of document selected, as this will affect how your reference appears (a book is not cited in the same way as a chapter in a book, etc.).

When you introduce the data from each document, you must remember that:

  • authors’ names must be added in the format Last Name, First Name.
  • tags must be separated using semicolons.




Mendeley allows you to manage documents and to group them in folders on a certain subject or a specific segment of the research (theoretical framework, methodology, etc.), etc.

In order to create a folder, you simply need to select the Create Folder option in the left-hand panel. Mendeley also allows you to create subfolders. To do so, select the Create Folder option, assign a name to the new folder, and drag it to the folder you would like it to depend on. When you select the superior folder, you will be able to see all the articles within, both those included in this folder and those in the subordinate folders.



We often import references without realizing that they have already been imported. Mendeley allows us to manage duplicates from the Tools option by selecting Check for duplicates. The reference with the most complete metadata will be kept, and the other references can be eliminated.

If you find two documents that Mendeley has marked as duplicates even though they really are not, simply select the document erroneously marked as a duplicate and select Not a Duplicate (right-hand panel). This generally happens with references without a title. Not a Duplicate status is temporary. If you use the Check for duplicates tool once again, these documents will once again be marked as duplicates.



When you open a document to see the full text of the article in PDF form, you can highlight interesting text using the Highlight option in the menu above. If you would like to annotate this text segment, select the Note option and click on the paragraph once again. Mendeley will introduce a note with the current time and date. If this article is later shared with the members of a previously-created research group using Mendeley, they will be able to see who wrote the note and when.




You can see and manage all of your notes from the Notes window in the right-hand panel. If you click on any of them, Mendeley will go directly to the place in the paragraph where the note was applied.

The menu also offers other interesting options such as Share, although you must first create a group with contacts to use it.

Mendeley allows you to view the document in fullscreen mode by selecting the Fullscreen option.



In order to configure options in Mendeley, access the Tools option by selecting Options.

The first General tab provides information on available personal space, but also on space shared with other groups. In this window, the option to automatically mark the documents we have read will be selected by default.


The second tab, Document details, will allow us to configure our metadata options for each type of document. Any fields you would like to show can be added, or you can eliminate any that are shown by default but are not of interest.


The File Organizer tab allows you to change the location of the folder where Mendeley keeps all of your information.

The Watched Folders option shows different updates to folders as you work on them.

The next options, BibTex and Zotero, are directly related to the reference managers LaTeX and Zotero, and they allow you to add Mendeley references to these other managers, so that if you work with both applications you can import changes made in Zotero and vice versa.



In order to generate citations and bibliographies, you must first install the plug-ins available for Word. This tool generally appears directly when you install the local version of Mendeley (Mendeley Desktop), and is added to the Word toolbar in the References option (or in the Complements option in earlier versions of Word, such as 2007).


If this option does not appear, it can be added manually. Make sure you have closed Word, and select the Tools, Install MS Word Plugin option in Mendeley. If you have already installed it, the option that will appear will be Uninstall MS Word Plugin.


You may find that the option still does not appear in Word. Should this happen, search for the option File, Options in Word, and in the dialog box select the Complements section. When the list appears, select the Mendeley option, and finally click OK.

Once the installation is complete, it will be added to the Word toolbar in the References option (or in the Complements option if you work with an older version of Word, such as 2007).



Mendeley allows you to easily add citations and format a bibliography. To do so, you must have installed the plug-ins available for Word and OpenOffice. To cite a reference in a text, you must open the Word document you would like to work in, and place the cursor where you would like to add the citation.

It is important to pay attention to the citation style you have configured. At HTSI we use the Harvard system, but you can change your citation style from Word using the option References < Insert citation.




En el recuadro es posible buscar la referencia por autor, título, etc. Pero también se puede seleccionar la opción Go To Mendeley que abrirá la aplicación. Una vez en Mendeley, se marca la referencia que interesa, y se selecciona Cite. Automáticamente se puede ver que Mendeley ha incorporado la cita en el texto con el formato (Autor, año de publicación). Esta cita se podría modificar directamente, añadiendo las páginas etc. sin que la referencia original guardada en Mendeley se vea afectada.



Mendeley also gives you the option to insert bibliographical references. You can leave this process for the very end, so that it will insert all references cited in the text. In order to insert references, you must open the Word document you would like to work in and place the cursor where you would like to add the references (normally, at the end of the piece). Select the References option from the upper menu. Then, select Insert Bibliography and Mendeley will automatically insert the references.

It is important to pay attention to the citation style you have configured. At HTSI we work with the Harvard system, but this citation style can be changed. If the style you are looking for does not appear, select the option More styles. From the dialog box, you can select the style you are interested in and even update it. It is also worth taking into account that although Mendeley is a manager that operates in English, it allows you to change your citation language. If, for example, you select Spanish, you will note some changes in the citations and references; for example, the separation between two authors will become Y instead of &.



Another interesting feature of Mendeley is that it allows you to work collaboratively. You can create a group of collaborators either from the web application or from the local version (Mendeley Desktop). From the local version, you can create groups the same way you create folders, by going to the left-hand panel and selecting the option Create Groups or using the Edit < New Group option in the main menu.



You can also open a group from the online version of Mendeley by selecting Create group (in the upper, right-hand corner of the window).


In either case, a window will appear that will allow you to name the group and decide what type of group it will be (private, by invitation or open).

  • Private groups. You can only be a part of these groups by invitation. Their contents are only visible for group members. These groups are for private research projects or to share documents and annotations.
  • Invite-only groups. These groups are visible to anyone, but only group members can contribute.
  • Open groups. Anyone can join these groups and contribute. They are designed to be open discussion groups on a certain subject.


In order to create the group, you must then select the Create group button. Mendeley will then give you the option to invite other members. It is important to remember that in order to join a group, you must be registered in Mendeley.

Group criteria can be changed at any time (adding new members, etc.) by selecting the group and then the option Edit settings.

Once the group has been created, you can begin to share documents with all members (using the Documents tab). Mendeley distinguishes the different notes added to a document by colours. Each member has an assigned colour. If you would like to download an article with all of its annotations, bring it on screen and select the option File < Export PDF with annotations.

You can add new members at any time using the Members tab, where you will see that the creator of the group is labelled as the administrator.



The local version of Mendeley (Mendeley Desktop) contains a search engine found in the upper right-hand corner of the window. It will allow you to search for documents containing a certain term. Keywords can be written directly, but Mendeley also gives you the option to search by fields: author, title of publication, etc.

Mendeley allows you to apply other filters for a more precise search using the data that appears in the description in the right-hand panel. To do so, write the name of the descriptor followed by a colon Mendeley27 and the word you would like to search (no blank spaces).




For example:

tag: tag name.



abstract: keyword. It is important to remember that abstracts are not always present in English, so the keyword may not appear.


Mendeley does not only allow you to search for information within added documents, but also gives you the opportunity to search other publications related to a certain area of interest. These are publications added to other Mendeley users’ accounts, which can be added directly to your own collection. To do so, you must open the online version of Mendeley, and search using the Search option. By entering the search term, it is possible that Mendeley may recover a large number of results with different articles. If you click on any of the results obtained, Mendeley will show a series of information on the reference: abstract, tags, related articles, etc. In some cases, you can even save the reference in the local version of Mendeley (Mendeley Desktop).

Using this option, we can also find groups of users similar to ours, follow them and even contact them by email.




Mendeley offers another simple means of importing documents, capturing information directly from your browser using the Web Importer function (be it Firefox, Chrome, Opera, Explorer…). This can be done in two ways:

  • From the local version of Mendeley (desktop version), clicking on Tools, Install Web Importer.

The instructions offered by Mendeley will be followed according to the browser you are currently using (Chrome, Firefox, etc.).

Once installed, you can look for the article of interest and click on the Mendeley button within the browser. A window with different references will automatically appear. Click on the first, which generally includes the article in PDF form (the rest are references). Then, select Save.


It is important to remember that you will not be able to see it in the local version of Mendeley until you synchronize it by clicking on the Sync (Synchronize Library) button. You must always synchronize the local version of Mendeley to not lose updated information.


Most databases include the option that allows you to directly export searches to Mendeley (Export option, or a separate button with the Mendeley identifier).




When this option does not appear, you can still export the reference and the PDF. For example, in the case of ISI Web of Knowledge:

  • Select the option Save in other file formats
  • In the File format option, select BibTex to create a file that will be saved to your computer (normally to Downloads)
  • From the local version of Mendeley, select File, Import, BibTex








Although I have the local version of Mendeley installed on my desktop, the option to insert citations in Word does not appear.

First, it is a good idea to see if the COMPLEMENTS option appears instead of the REFERENCES option (this happens if you work with older versions of Office, such as Word 2007).

If not, you can click on the option (Word) file < Word Options < Trust Centre and select the Trust Centre configuration. Then, in macro configuration activate the Enable all macros option. Close Word and search for the option My computer < Local C drive < Program files, where you can open the Mendeley Desktop folder and click on WordPlugin. Then, open Word. The plug-in should automatically activate so you can insert citations.


If it still does not work, it is probably because your version of Word is not compatible.



It is important to remember that before you close Mendeley Desktop, you must always synchronize your library with the Sync function. That way, the references on your desktop account will be updated, but in addition the Mendeley web version and your mobile devices will be updated.



But also the .PDF files from All Documents, Edit Setting.