Mendeley Workshop Handout


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A guide to using Mendeley, used as a handout at the Mendeley Workshop at the University of Warwick.

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Mendeley Workshop Handout

  1. 1. Managing your References and PDFs with MendeleyMendeley has some great features that can really help to improve your productivity and savetime. As this tutorial will show, it contains many features that are not available in otherreference managers, like Refworks and Endnote. The downside to this is that most of thesefeatures require installed software, which makes it more difficult to use the system on publiccomputers. What I love about it personally is that it offers a whole-workflow solution todoing your literature research. You use it when you first find PDFs, to organize them anddecide which ones to read first. You use it for reading those PDFs, and making notes. You useit again for producing references in your reports, papers or dissertation. Finally, if your workis published, you may even use it for promoting your work to other researchers.Is Mendeley the right tool for you? Pros Cons Quick and easy to use Mendeley Web is quite limited. Desktop software combines PDF This is not very convenient if you reader and reference manager need to work on your paper Make notes on PDFs and share from a library computer them with colleagues Free version limited to 1GB of Keep PDFs organized across online storage. (~800 PDFs) multiple computers Currently need Admin to install Automatically rename 3621a.pdf and update on Staff Desktop. to Title – Year – Author.pdf Mendeley updates frequently. OpenOffice and Word plugins for making bibliographiesSession Outline 1. Getting Started 2. Getting Data In 3. Folders and Groups 4. Changing the Settings 5. Finding your References Again 6. Creating a Bibliography 7. Annotating Files 8. Exporting and Backing-Up
  2. 2. Exercise 1 – Getting Started:  Go to  Click “sign up” for free  Create a new account. Use a personal e-mail address as this will be available to you after you leave the university  Download and install Mendeley Desktop for your operating system  Start Mendeley Desktop and sign in with your email and passwordExercise 2 – Getting Data InDrag-and-drop method  Search for some papers in your subject area in Google Scholar, ScienceDirect etc.  Save the PDFs on your desktop temporarily  Click on “All Documents” in Mendeley and Drag and drop multiple PDFs into Mendeley  Bibliographic details will be automatically extracted from the PDFs  Check the details for accuracy and completeness  If there are missing details (page numbers, issue number) check the title is correct, and click “Search by Title”. Mendeley will attempt fetch missing details from Google Scholar
  3. 3. Add Files / Add Folder  Useful if you have a USB stick or folder on your laptop with 300 PDFs in it, and you don’t want to drag-and-drop them all  In Mendeley, go to File menu, and click ‘Add Files’ or ‘Add Folder’ and browse to the right location. If adding a folder, you can choose whether to include subfolders or not.Add Entry Manually  Useful if you want to add a reference that you have no electronic file for e.g. a book, thesis, magazine article, web page etc.  In Mendeley, go to the File menu and select “Add entry manually”, then select the type and fill out as many fields as you wishAdd Entry via Mendeley Web  Useful when you are on a computer where you don’t have Mendeley Desktop installed. Unfortunately, you can’t add PDFs or other files this way, only references  Go to and sign in with your email and password  Click on “My Library”  Click “Add Document”  Select the type and fill in as many details as you wishAdd Entry via Web Importer  From Mendeley Desktop go to Tools > Install Web Importer; or On Mendeley Web go to My Library > Web Importer  Right Click the “Import to Mendeley” button, and add it to your bookmarks, or drag it to your browser’s bookmarks toolbar. You may need to enable the bookmark toolbar in your browser options  Go to a database you’ve used before, or try a new one out. Find a paper. Click “Import to Mendeley” in your bookmarks toolbar.  If the popup is blocked, click on the warning message and select to alow popups from the site. Also ensure you are allowing popups from  In the popup, you can choose to save a webpage screenshot or add notes  If this worked, you will see the reference in Mendeley Web, and also in Mendeley Desktop. If you had the access rights, you may also now have the PDF in your library, though sometimes you will need to add this manuallyExercise 3 – Folders and Groups
  4. 4. You have the option to create new Folders or Groups to keep organized. This is useful if you areworking on several projects or subjects that have little or no crossover in terms of references, or if youwish to use Mendeley to collaborate with people. Folders are for your own organization, while Groupsallow you to share references and papers with a small group of other Mendeley users. If there is anypossibility that you will want to do this, use Groups rather than Folders.By default you already have the folders “All Documents”, “Recently Added”, “Favourites”, “NeedsReview”, “My Publications” and “Unsorted”.  “All Documents” contains everything in your library  “Recently Added” speaks for itself  You add documents to “Favourites” by clicking the star next to a reference  “Needs Review” is the documents you haven’t read yet. You can mark a document as read/unread by clicking on the green dot next to a reference (green = unread)  Add documents to “My Publications” by dragging a reference into it, or add it in any of the ways shown in Exercise 2. You will be asked to confirm that you authored the document. Documents in “My Publications” will appear on your Mendeley Web profile, with a download link, unless you select the setting “Unpublished Work – exclude from Mendeley web catalog”. Be aware of copyright restrictions, but most journals allow authors to self-archive in this way.There are a few different options for Groups:  Private Groups are visible to members only, and are invite-only. These allow sharing of references and files among a small group of people  Public Groups are visible to everyone, and can either allow anyone to join, or require them to be confirmed by the group owner. Great for creating a reading list for a module  Group ownership can later be changedExercise 4 – Changing the Settings
  5. 5. Mendeley Desktop settings are native to the computer and profile you are using it on. So you mayhave different settings on different computersTo Synchronise or Not To Synchronise?  Select “All Documents” or your own Group/Folder and click “Edit Settings”  You can choose whether to “Synchronise Attached Files” for your entire Library or for individual Folders/Groups. What this means is that Mendeley Desktop will automatically download new files that have appeared in your online storage – either because: o You added them through Mendeley Web o You added them using Mendeley Desktop from another computer o Another member added documents to a group that you belong to  If you prefer, you can download each file as you need it, by double clicking a reference  For example: on my office computer, I synchronise attached files, because I refer to them often. On my laptop, which is old and has a small hard drive, I don’t synchronise attached filesFile Organiser  Mendeley is also a File Organiser – you can choose a location to store your PDFs, and let Mendeley do the tedious organizing for you  To do this, go to Tools > Options and select the File Organizer tab  If you wish, it can also organize them into subfolders by Year, Title, Author and Journal in any order. I don’t bother doing this, because now I only look for my PDFs from Mendeley  It can rename your files automatically using any combination of Title, year, Author and Journal with different separation options. This is nice when you come to email some files to somebody  By the way, did I mention that you can email files to people without leaving Mendeley? Simply select multiple references using shift+click or ctrl+click; right click on one of the references and click “Send by email”. Select some of your Mendeley contacts or enter email addresses, to send a download link for each file, which will stay active for a couple of weeks.
  6. 6. Other Settings From Tools > Options, you can also add “Watched Folders” if you wish. This will import any documents that are saved to a particular directory on your computer. For example, you could add a Dropbox folder, or a folder where you always save new journal PDFs Also in Tools > Options, you can customise the Document Detail fields for each type of document. The default settings are usually fine If you use LaTeX, you can synchronise a Folder/Group or each document with a BibTeX file
  7. 7. Exercise 5 – Finding your References AgainIf you already have your own large collection of PDFs, that you’ve been keeping on USB sticks, foldersand subfolders; with enigmatic filenames, you can breathe a sigh of relief. You can churn this lotthrough Mendeley in minutes. The resulting metadata isn’t going to be perfect, but you are going tobe instantly a lot more organized. You can help yourself by adding important references to Favourites.If you have a large collection, there are some features in Mendeley to help you narrow down yoursearch.FilteringIn the bottom left panel, you have the option to Filter by: Author, Publication, My Tags, AuthorsKeywords. Of course, if you want to use “My Tags” you have to add Tags to your references.For example, if you select a particular author, you will only see documents that have that personlisted as an author. You can actually use this to improve the metadata of your collection while you arelooking for a paper. If you see multiple names that are clearly the same person (e.g. Runyan, R B;Runyan, Raymond; and Runyan, Raymond B) you can drag the less specific names onto the morespecific one, to rename all instances of the less specific name. This is useful because some citationstyles use full names, while others only use initials for first names, so it’s always better to have morecomplete information. You can also do the same thing for publications.Remember, if you want to switch the filter off, you need to go to the top of the list, and select “All”, orclick “Clear”.
  8. 8. OrderingThere are categories listed across the top of the References panel, and you can use these to orderreferences in ascending or descending order by clicking on the category title. For example, you can seethe files in the order they were added by clicking on “Added”.SearchingBy clicking on the search icon in the search field, you can choose to search only particular fields. Youcould also type for example, Author:Hunter OR NickersonYou can combine Filtering, Ordering and Searching in any order that you wish, to drill down to exactlythe documents you want to find. It can also help you to re-discover related documents that you neverknew you had.One quirk of Mendeley is that you use the same search field to search within a file when you have itopen. This will just search through the text of that PDF you are looking at, and highlight the words youare searching.
  9. 9. Exercise 6 – Creating a BibliographyThe Copy-and-Paste Way  The trick here is that you can change citation style from within Mendeley desktop. It will allow you to copy and paste them as text, and they will be in the style you have chosen.  Go to View > Citation Style and choose a popular style. You can also select More Styles to add more options. If you still can’t find what you want, you could even find a CSL file for the style online, and copy it into your Mendeley Desktop citation styles directory  Select one reference, or multiple references using ctrl+click or shift+click. Right click and “Copy Citation”. Then paste it in your word processor, and edit as needed.  This is a good method if you are editing a template, so can’t use the plugin.The Plugin Way  There are plugins for Microsoft Word, Mac Word and OpenOffice. Here the process is illustrated for Microsoft Word.  From Mendeley Desktop go to Tools > Install MS Word Plugin, and install the plugin.  Open MS Word and go to the References Tab; you should see the Mendeley plugin  You can select a style from the dropdown menu  Click on “Insert Citation” in the Mendeley plugin  You can search your collection from within Word, or you can go back to Mendeley to find the reference you want and then send it to Word  When you have inserted some citations, click “Insert Bibliography” in the Mendeley plugin, at the bottom of your document. You can also export as an OpenOffice compatible file, or as a Word File with the Mendeley fields changed to normal text.
  10. 10. Exercise 7 – Annotating Files  Mendeley offers tabbed browsing for reading several PDF files at once. It will also remember what page you were on the last time you closed a file, and open it up in the same place.  There are some straightforward options for Annotating files, such as adding “Sticky Notes” or highlighting text. There is a highlight rectangle option for files where the text hasn’t been properly recognized.  In the righthand panel, you can select between reference Details and Notes, and sticky notes will also appear in order here. You can also write some notes for the whole document.  If you use a Private Group to share files with your colleagues, you will be able to see each other’s annotations, which will appear in a different colour. Exercise 8 – Exporting and Backing-Up  There are a range of options to ensure that the effort you put into creating a Mendeley Library will be available to you if you want to switch to a different tool or way of working  Under Help you can create a Backup ZIP file of your whole collection  Under File you can export a particular PDF with its annotations on it  You can also export a range of formats used by other tools, such as RIS used by Refworks, or Endnote XML, and also BibTeX  Export the whole collection, or just select a few references