Mendeley handout IEC 22-01-2013

By R. Deurenberg and E. Matlou

This handout helps students get started with Mendeley reference management system. 1

Contents 1. Introduction, create an account ..................................................................................................... 4 Film: Mendeley youtube, june 2012 (4min) ; slides by Oregon (see attached powerpoint presentation or the website) .......................................................................................................... 4 2. a. Wat is mendeley?.................................................................................................................... 4 Create an account: sign up, download the desktop application, install the webimporter. ... 5 Download the Desktop application......................................................................................... 5 Install Web importer and check the Pop-up Blocker for collecting citations. ........................ 6

Mendeley desktop .......................................................................................................................... 6 Adding references to Mendeley Desktop ................................................................................... 6 Importing pdfs to Mendeley ( journal articles, newspaper articles, etc) and getting bibliographic data. .......................................................................................................................... 6 b. Manually add citation ............................................................................................................. 7 Search electronic databases ................................................................................................... 7 Organizing and using the library in Mendeley Desktop .............................................................. 7 Folders/Collections of documents. ......................................................................................... 7 Tagging of documents. ............................................................................................................ 7 Use the ability to quickly mark documents as Favorites or Read/Unread. ............................ 8 Reading of PDFs from within a Mendeley PDF viewer. .......................................................... 8

Use of Plug-ins to connect to Microsoft Word (PC and Mac), OpenOffice (Mac), and NeoOffice (Mac). ............................................................................................................................. 8 c. 3. a. b. c. Citing Items in Word with the MS Word Plugin. ......................................................................... 8 Install the Word plugin............................................................................................................ 8 Open Word and click on the "References" tab. ...................................................................... 9 Mendeley Cite-O-Matic........................................................................................................... 9 Search Google Scholar for additions or corrections to the citation. .................................... 11 Sync your Library with your Mendeley web account. .......................................................... 11 File Management .................................................................................................................. 11

Mendeley Web .............................................................................................................................. 12 Importing to Mendeley Web .................................................................................................... 12 Getting the "Import to Mendeley" Bookmarklet ...................................................................... 12 Import citations using the Web Importer tool.......................................................................... 14 On a search results page: ...................................................................................................... 14 On the page of a single item: ................................................................................................ 15 2

 d. e. 4. a. 5. a. b. 6.

Import some PDFs using the Web Importer tool .................................................................. 16 Similarities between desktop and web app .............................................................................. 16 Syncing ...................................................................................................................................... 16

Groups ........................................................................................................................................... 17 Collaborating through Mendeley .............................................................................................. 17 Private groups ....................................................................................................................... 18 Public groups that are invite-only ......................................................................................... 18 Public groups that are open .................................................................................................. 18 Creating groups ..................................................................................................................... 18

Papers ........................................................................................................................................... 18 Taking Advantage of Mendeley's Papers feature ..................................................................... 18 How does it work? ................................................................................................................ 19 Saving PDFs and citations directly ........................................................................................ 20 Hints .......................................................................................................................................... 20 Hint 1 web importer per browser ...................................................................................... 20 Hint 2 Search ...................................................................................................................... 21 Hint 3 Review references and edit metadata .................................................................... 21 Hint 4 Document/citation management ............................................................................ 22

Contact .......................................................................................................................................... 23

Mendeley handout
last update: 04-01-2013 http://www.mendeley.com/features/backup-sync-mobile/

1. Introduction, create an account

Film: Mendeley youtube, june 2012 (4min) ; slides by Oregon (see attached powerpoint presentation or the website)

http://www.youtube.com/watch?v=0XQdu5PT2X8

Mendeley presentatie oregon.ppt

Wat is mendeley?

At its most basic level, Mendeley is a citation management tool, but it can also help with other aspects of research, such as: Organizing PDFs of research papers, including annotations and highlights. Inserting bibliographies and citations into a word processor. Sharing research. Discovering articles in your field. Interface of Mendeley desktop, an example

The basic Mendeley account is free. To get the most out of Mendeley, its best to use both the web (browser based) application and the desktop application (which is available for Mac, Windows and Linux). To use Mendeley you will sign up for a free account on Mendeley.com. And from there, you can also download the desktop application.

Create an account: sign up, download the desktop application, install the webimporter.

Go to https://www.mendeley.com/join/ and click the Sign up for free link in the upper right corner.

The free account gives you 1 GB of space (500 MB for personal documents and 500 MB of shared space to use with groups), the ability to create a private group with a maximum of 10 users per group. Paid options allow you to increase those limits. Once you have your account set up, you can edit your profile to share additional details about yourself with colleagues you connect to through Mendeley. In your profile, you can also mark publications in your library for which you are the author, and Mendeley will track page view, reader and download statistics on those articles for you.

Download the Desktop application

Go to http://www.mendeley.com/download-mendeley-desktop/ and download the appropriate version for your operating system. Windows, Mac and Linux versions are available.

Note: You can use Mendeley Desktop without creating an account in Mendeley Web but the program is much more useful if you have an account. The instructions here assume you are using both the desktop version (referred to as Mendeley Desktop) and the browser-based version (referred to as Mendeley Web) in tandem.

Install Web importer and check the Pop-up Blocker for collecting citations.

Go to http://www.mendeley.com/import/ and follow the instructions for adding the Import to Mendeley button in your browser. It is an application in your browser's bookmark bar; you will click the bookmark when you want to save a citation from an online source. If you use more than one browser regularly, do this to all of them. Do run the Pop-up Blocker Test and turn off blocking for Mendeley or you will not be able to automatically collect citations. See 5b of this handout Hint 1 web importer per browser. Although Mendeley Desktop and Mendeley Web look similar, there are some feature differences that dictate how you will use each one. -Use Mendeley Desktop for storing PDFs and automatically creating citation data from the information in the PDF. Mendeley desktop also offers excellent features for managing your PDFs on your computer and searching and viewing them. -Mendeley Web allows you to access your saved research on the go (depending on how much of your data you decide to sync) and collect citations while browsing online databases. Mendeley Web will also ingest PDFs from a very small selection of journals, but this is neither widely supported nor very reliable. Mendeley Web also provides access to "largest crowd-sourced research catalog" via its Papers collection.

2. Mendeley desktop
a. Adding references to Mendeley Desktop
Importing pdfs to Mendeley ( journal articles, newspaper articles, etc) and getting bibliographic data.

While importing a PDF, Mendeley will attempt to extract metadata from the PDF to create a citation author, title, year, volume, etc. You can do this by: Add Documents button.

File menu Add Files (or Control/Command + O) Drag-and-drop from your computer to the Document Pane (the middle part of the window).

(An extra option is by creating a Watched Folder. When a PDF (or multiple PDFs) are dropped into this Watched Folder, Mendeley will automatically ingest them. Set up the Watched folder in the Options (PC) or Preferences (Mac) menu item., option under File in Mendeley desktop) Manually add citation (=add entry manually, option under File). This is useful if you dont have a PDF to ingest. If you manually add a citation and later, if you have the PDF, this PDF can be added to the citation.

Search electronic databases f.e. Google Scholar or other compatible databases (see the list

databases). Use google scholar to search new documents: you can lookup document details with Google Scholar on the Mendeley desktop interface if data is missing. (Note: The lookup works only for imported PDF files and not for manually added entries.) References from other databases: See chapter 3C Import citation using web importer tool

b. Organizing and using the library in Mendeley Desktop

Folders/Collections of documents.
You can create collections to organize your documents in whatever groupings make sense to you. Documents can be in more than one collection. By default, Mendeley has these collections: All Documents Recently Added Favorites News Review My Publications Unsorted Documents can be added from one folder to the other by drag and drop . See Hint 2 Searching within mendeley, if you want to search for specific details in all folders. Tagging of documents. This is in addition to the keywords, which could be pulled from journal databases. Tags can be more informal words that help you arrange your documents around concepts that make the most sense to you. Tags are a more granular way to classify your documents than collections are.

Use the ability to quickly mark documents as Favorites or Read/Unread.

Reading of PDFs from within a Mendeley PDF viewer.

In the viewer, you can highlight text, create notes, and select text.

Use of Plug-ins to connect to Microsoft Word (PC and Mac), OpenOffice (Mac), and NeoOffice (Mac).

The plug-ins allow access to your Mendeley Library from Word to create citations and bibliographies in your Word document.

c. Citing Items in Word with the MS Word Plugin.

Install the Word plugin.

Make sure Word is not open on your computer. Open Mendeley Desktop and select "Tools"->"Install MS Word plugin". If the Word plugin is already installed, this option will be changed to "Uninstall MS Word Plugin". If that's the case, you can skip this step.

Open Word and click on the "References" tab. Mendeley Cite-O-Matic

In the Menu, you should see a box titled "Mendeley Cite-O-Matic." This is the MS Word Plugin. To insert one or more citation you click Insert citation button within this box (see below), a window pops up with 2 options to search the Mendeley Library or "Go To Mendeley".

Option 1: Searching citation within mendeley box in word : If you search for an item directly from this box, you'll see a list of results appears below the search bar. Select the one you want, click "Ok" and you'll see the citation appear in your paper.

Option 2: Go to Mendeley: If you choose "Go To Mendeley," Mendeley Desktop will pop up, allowing you to select an item from your library. Note: Mendeley Desktop has a couple of buttons it doesn't usually have . If you click the one shaped like an "X" you'll be sent back to Word with no changes. If you click the one shaped like a page, the citation for the item you have selected will appear in Word.

Insert bibliography: In Word, you can automatically generate a bibliography or Works Cited page, by clicking "Insert Bibliography." This tool will create a bibliography entry for every Mendeley item that you have cited in your paper. Check the layout of the bibliography. You can change the style and in the layout, DOI is preferred above URL.

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 Search Google Scholar for additions or corrections to the citation. Upon import of a PDF as much metadata is extracted as possible, but due to limitations of some PDFs, metadata will be missing. The citations for all imported PDFs are marked with a Red Question Mark, (in the folder needs review) indicating that you should review the information. You have the ability to edit the information by hand, click a button called Details are Correct to remove the Red Question Mark or click Search by Title to search Google Scholar for additional metadata. See hint 3 for more tips on how to review the reference.

See Hint 3 Review references and add corrections Sync your Library with your Mendeley web account. This will allow you to access to your data on your Mendeley Web account. If you want to have the desktop application installed on more than one computer, syncing through the Mendeley Web account will keep the information up-to-date on all of your computers. File Management Important! By default, when you import a PDF, Mendeley does not move that file; it just creates a reference so it knows where to find that file on your computer. If you later move or delete that file, Mendeley will not be able to access it. There are two ways to address this: a. PC folder system: If you already have a folder system on your computer that you use for research documents (and you're happy with it), just move the PDF into the correct folder before importing it to Mendeley. Then, leave the PDF there. b. Automatic file organization: Turn on automatic file organization. If turned on in Tools, under Options/(preferences) File Organizer, this feature will move files from wherever they are imported to a designated Mendeley directory on your hard drive. You can choose if the files are automatically

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placed in subfolders (based on such characteristics as author name) or even whether the PDFs are renamed. If you do not already have a good file organization system on your computer, this may be helpful. c. See hint 4 about document and citation management.

3. Mendeley Web
a. Importing to Mendeley Web
Mendeley Web allows you to access your saved research (search results from a database search) on the go (depending on how much of your data you decide to sync) and collect citations while browsing online databases. The Web application also excels at creating citations while you are actively doing research by allowing you to use the Web Importer (the "Import To Mendeley" button installed in your browsers bookmarks bar) to capture the citation of the article currently displayed in your browser.

b. Getting the "Import to Mendeley" Bookmarklet

Go to http://www.mendeley.com/import/ Drag the button that says "Import to Mendeley" to the bookmarks menu or toolbar.

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Importing Citation Info from a Database:With the "Web Importer" bookmarklet, you can pull citation information directly from some academic article databases like Academic Search Premier or JSTOR, the university catalog, Google Scholar, or even commercial sites like Amazon.

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Before you use the bookmarklet you may need to change the settings of your popup blocker. See also Hint 1 web importer per browser Once a page or set of search results has been selected, click the "Import to Mendeley" bookmark and the citation information will be gathered and displayed in a pop-up window (as shown in the next section), so you can mark it for import into your Mendeley library. Some databases or websites may have multiple ways of displaying information, Mendeley is usually only interactive with one of those (e.g. it interacts with the library's default catalog but not the older "Classic Catalog"). Or, on a computer with the desktop app, you can download the fulltext and merge the citation info from the database with the record for the file by selecting "File?Merge."

c. Import citations using the Web Importer tool

After you install the Web Importer in your browser's bookmark, it will remain there. You can use it while when you are on a page with multiple search results or on a page describing a single item. On a search results page: Click Import to Mendeley If you are not already logged in, you will be prompted to do so. A new window will appear, displaying on the search results and you can click the plus next to the ones you want to grab.

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After doing, so you can also click Edit Tags and Notes to immediately add information to the imported citation including assigning it to a Folder/Collection. On the page of a single item: Click Import to Mendeley If you are not already logged in, you will be prompted to do so. A window will appear that confirms the item was imported and giving you the option of adding tags and notes and/or assigning to a Folder/Collection.

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Import some PDFs using the Web Importer tool

While the Web Importer tends to grab most citations well, it can also go wrong ingesting pdf. If you have incomplete record the see hint 3 for solutions on reviewing the reference.

d. Similarities between mendeley desktop and mendeley web

Manually add citation (This is labeled Add Document but you are just adding information not a PDF). Make Folders/Collections of citations and documents. Edit citation. Add tags to a citation. Ability to quickly mark documents as Favorites or Read/Unread.

e. Syncing
A free Mendeley account provides you with 500MB of space for your personal library documents and 500 MB for documents you share with other people. (You can purchase more space.) Because of this limitation, you may choose not to sync all the documents from your Mendeley Desktop to your Mendeley Web account.

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These settings are controlled in the Mendeley Desktop application. There is a Sync Library button in the Mendeley Desktop that will collect changes made in Mendeley Web and send changes to Mendeley Web.

Turning Syncing on and off can be done at the level of All Documents or per Folder/Collection. An Edit Settings button is visible when either All Documents or a Folder/Collection is selected; this allows you to toggle synchronization on and off. See hint 4 about Personal and shared spaces

4. Groups
a. Collaborating through Mendeley
Mendeley's Groups feature is available via both Mendeley Desktop and Mendeley Web. There are three types of groups to facilitate different levels of openness and kinds of sharing.

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Private groups

Share documents and citations with others by inviting them to participate in the group. With the basic Mendeley plan, private groups can only have 10 members. With the basic plan, you have 500 MB of space for all your private groups.

Public groups that are invite-only

Publicly visible. These have restricted membership list, which is controlled by the group's owners. You can upload PDFs, but they will only be available to others if they have access through their own institutions (or if they are Open Access articles).

Public groups that are open

Publicly visible, everyone can contribute; great for open discussion groups around any subject. Citations only.

Creating groups

You can create groups and access group content from both Mendeley Desktop and Mendeley Web.

5. Papers
a. Taking Advantage of Mendeley's Papers feature
The Papers tab appears at the top of the Mendeley window. Clicking on the Papers tab reveals statistics about the more than millions of papers in Mendeley. The idea is that you can use Mendeley to monitor articles that popular or newly added to a particular discipline.

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How does it work?

When you create your Mendeley account, you are required to choose an academic discipline. (You can change this by editing your profile.) When you upload PDFs and save citations to your Mendeley account, Mendeley anonymously connects the academic discipline with this particular paper/citation. When more people (hundreds and evens thousands of people), in your discipline also save the same paper/citation, it gives the connection even more weight. Another feature that allows you take full advantage of the Papers collection is the ability indicate to Mendeley that you are affiliated with the Technical University of Eindhoven (or any other institutional library youre

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affiliated with). Then, Mendeley will attempt to link to a full text version among the materials purchased by this University. For this to work, you will have to indicate your affiliation to the University of Eindhoven in your profile. Saving PDFs and citations directly At the very least, when browsing articles in Papers, you will have the option to Save a Reference to your library. If there is a PDF attached that is from an Open Acces journal or a publicly accessible repository, such as PubMed Central, you will have the option to Save PDF to your library.

b. Hints
The support webpage on mendeley website can guide you in solving problems you might encounter. Hint 1 web importer per browser The instructions for installing the web importer vary slightly according to which browser you use. Please see below for details for each of the browsers mendeley support: Internet Explorer Go to www.mendeley.com/import. Right click the red "Import to Mendeley" button on the page and click Add to Favorites. You can then import pages to Mendeley by clicking the Import to Mendeley link in your Favorites. To allow automatic pop-ups from www.mendeley.com in Internet Explorer 1. 2. 3. 4. 5. Open mendeley.com/import on Internet Explorer Click the Tools button on the far top right of the window or press Alt + X, Choose Internet options which leads you to settings. Click tab Privacy and Turn on Pop-up Blocker by checking the box. The click OK.

Google Chrome Go to www.mendeley.com/import and press Ctrl + Shift + B to show the Bookmarks bar under the address bar, and then drag and drop the red Import to Mendeley button into the Bookmarks bar. You can then import page to Mendeley by clicking this link. In Chrome, popups are treated as coming from the website you are importing from, and not from Mendeley. To manually allow pop-ups from a site, follow the steps below: 1. 2. 3. Click the Chrome menu on the browser toolbar. Select Settings. Click Show advanced settings.

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4. 5.

in the "Privacy" section, click the Content settings button. In the "Pop-ups" section, click Manage exceptions.

Firefox Go to www.mendeley.com/import Press Ctrl + Shift + B on your keyboard to show the Bookmarks bar under the address bar in Firefox, and then drag and drop the red Import to Mendeley button into the Bookmarks bar. You can then import page to Mendeley by clicking this link. To allow automatic pop-ups from www.mendeley.com in Firefox 1. 2. 3. 4. At the top of the Firefox window, click on the Firefox button (Tools menu in Windows XP) and then click Options Select the Content panel. Click Exceptions Add www.mendeley.com and click Allow

Hint 2 Search Searching within your own library in mendeley desktop . Enter search term in search box top right of the desktop window. You can narrow down which fields Mendeley Desktop should search for your specific keyword by using the following syntax, field:search term. Just replace the field with one of the values from the list below, for which fields you want to search. author, by, contributor, name: You can use any one of these keywords to specify that your term should only be searched for within a reference's authors, editors or translators. For example, author:Smith andname:Smith are both the same, and will search for references that have Smith in their authors, editors or translators. keyword: This will limit your search term to matching just the author's keywords for a document. publication: You can search amongst your references' journal titles or publications by using this keyword. tag: Using 'tag' will allow for you to search amongst documents that have a tag that contain your term. title: If you wish to search amongst just your reference titles, you can do so by using 'title'. Hint 3 Review references and edit metadata See if bibliographic details needs reviewing and add metadata if necessary 1. Review references If you have imported a PDF file, and find that it is wrongly labelled, or that no metadata has been entered for the article at all, please try the following steps: 1. Copy and paste the correct article title from the PDF into the title field in the Details tab 2. Right-click (Cmd + click for Macs) on the document in the central library list and select Mark As > Needs Review 3. In the Details tab, click Search by Title which will look for a match in Google Scholar. 2. Adding title manually and filling up the rest of reference details via DOI.

Mendeley internet search is supported by Google scholar. Might you not find the reference details via de Document details look-up window provided by mendeley, you can choose to automatically fill up the details using the DOI you found in another database. Search reference in one of the database supporting Mendeley (see list of databases).If found then copy and paste the DOI in the DOI detail field in mendeley desktop. Click the search glass and the rest of the details fills up automatically. 3. Adding authors names

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Different authors with same name and / or initials: This issue may be caused by your having more than one author with the same surname, or multiple cases of the same author being parsed as different authors by the program (for example, Smith, J, Smith, J., and Smith, John are all read as different authors by Mendeley at the current time). This will lead to the program attempting to disambiguate between the authors by adding initials or the first name. This problem can be avoided by ensuring all authors are added in the same format. Hint 4 Document/citation management Always empty the trash to create more space. Syncing annotations If you have a Mendeley Web account, Mendeley will sync your references with the web if you click on sync button. The annotations you sync can only be shared within the group and will not appear on web. The simplest way to migrate to another computer is to install the software on your new PC and then enter your account details when prompted after starting the program for the first time. Your documents and annotations will then be fetched from the web and changes made on any PC will be synced to the others. Note that only files which are synced with Mendeley Web will be copied across. To change which files are synced, click the 'Edit Settings' button above the central documents list in Mendeley Desktop. Personal web space Free web space limited. Be careful with sync. Use sync only for important folders. Otherwise you will need to either pay to upgrade your account, or delete documents with attached files until you are within your usage capacity. You will never lose access to documents already on Mendeley Web. Shared webspace full When you run out of Shared Web Space, you and the other members of your collections will not be able to add or edit documents in your private or invite-only groups, and you cannot create any new private or inviteonly groups. You will need to either upgrade your account, delete documents (or rather: attached PDF-files) until you are within your group usage capacity, or transfer the ownership of one or more of your private or invite-only groups to someone else in the group. Checking for duplicates 1. 2. 3. 4. Select any folder or group you would like to check for duplicates (eg: All Documents). Select the "Tools" menu, and select the "Check for Duplicates" option. Sets of duplicates will then be shown. Think of a set as what the result of your merge will look like when you confirm it. You can double click a set to expand it and view each duplicate document individually. Delete the least complete reference from the duplicated set by simply right clicking the reference and choosing delete.

Manually merging duplicates If you notice that you have duplicates that the tool isn't finding for some reason, no matter! You can merge any documents you like manually. Simply select 2 or more documents while holding down the CTRL key (or CMD key for Mac users) and you'll see that a "Merge Documents" button appears on the right hand pane. Click this and then follow the regular steps above.

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6. Contact
Rikie Deurenberg h.w.j.deurenberg@tue.nl Eunice Matlou e.m.matlou@tue.nl

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