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Managing your References and PDFs with Mendeley

Mendeley has some great features that can really help to improve your productivity and save time. As this tutorial will show, it contains many features that are not available in other reference managers, like Refworks and Endnote. The downside to this is that most of these features require installed software, which makes it more difficult to use the system on public computers. What I love about it personally is that it offers a whole-workflow solution to doing your literature research. You use it when you first find PDFs, to organize them and decide which ones to read first. You use it for reading those PDFs, and making notes. You use it again for producing references in your reports, papers or dissertation. Finally, if your work is published, you may even use it for promoting your work to other researchers.

Is Mendeley the right tool for you? Pros Quick and easy to use Desktop software combines PDF reader and reference manager Make notes on PDFs and share them with colleagues Keep PDFs organized across multiple computers Automatically rename 3621a.pdf to Title – Year – Author.pdf OpenOffice and Word plugins for making bibliographies Session Outline
1. 2. 3. 4. 5. 6. 7. 8. Getting Started Getting Data In Folders and Groups Changing the Settings Finding your References Again Creating a Bibliography Annotating Files Exporting and Backing-Up

Cons Mendeley Web is quite limited. This is not very convenient if you need to work on your paper from a library computer Free version limited to 1GB of online storage. (~800 PDFs) Currently need Admin to install and update on Staff Desktop. Mendeley updates frequently.

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

Exercise 1 – Getting Started:
     Go to www.mendeley.com 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 Select Mendeley from your desktop Start Mendeley Desktop and sign in with your email and password

Exercise 2 – Getting Data In
Drag-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

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

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 wish

Add 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 www.mendeley.com 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 wish

Add 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 www.mendeley.com 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 manually

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Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

Exercise 3 – Folders and Groups
You have the option to create new Folders or Groups to keep organized. This is useful if you are working on several projects or subjects that have little or no crossover in terms of references, or if you wish to use Mendeley to collaborate with people. Folders are for your own organization, while Groups allow you to share references and papers with a small group of other Mendeley users. If there is any possibility that you will want to do this, use Groups rather than Folders. By default you already have the folders “All Documents”, “Recently Added”, “Favourites”, “Needs Review”, “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 changed

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

Exercise 4 – Changing the Settings
Mendeley Desktop settings are native to the computer and profile you are using it on. So you may have different settings on different computers To 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 files

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File 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.

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

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

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Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

Exercise 5 – Finding your References Again
If you already have your own large collection of PDFs, that you’ve been keeping on USB sticks, folders and subfolders; with enigmatic filenames, you can breathe a sigh of relief. You can churn this lot through Mendeley in minutes. The resulting metadata isn’t going to be perfect, but you are going to be 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 your search. Filtering In the bottom left panel, you have the option to Filter by: Author, Publication, My Tags, Authors Keywords. 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 person listed as an author. You can actually use this to improve the metadata of your collection while you are looking 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 more specific one, to rename all instances of the less specific name. This is useful because some citation styles use full names, while others only use initials for first names, so it’s always better to have more complete 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”, or click “Clear”.
Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

Ordering There are categories listed across the top of the References panel, and you can use these to order references in ascending or descending order by clicking on the category title. For example, you can see the files in the order they were added by clicking on “Added”.

Searching By clicking on the search icon in the search field, you can choose to search only particular fields. You could also type for example, Author:Hunter OR Nickerson

You can combine Filtering, Ordering and Searching in any order that you wish, to drill down to exactly the documents you want to find. It can also help you to re-discover related documents that you never knew you had. One quirk of Mendeley is that you use the same search field to search within a file when you have it open. This will just search through the text of that PDF you are looking at, and highlight the words you are searching.

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

Exercise 6 – Creating a Bibliography
The 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.

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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.

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)

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

Workshop: Organising references using Mendeley, 16 Feb 2012, run by Salma Patel (salma.patel@warwick.ac.uk, Twitter: @salma_patel)