1. Managing References : Mendeley

2. Table of Contents Why use a reference management software and what is reference management software? Mendeley features and functionality: Accessing Web and downloading Earth version (free) Creating your Mendeley library Managing documents and references Citing references

3. Typical researcher writing a paper… Source: flickr/toennessen

4. Problem statement… Your paper reference list/bibliography Lots of typing Lost references Mistakes article book conference paper Your topic: citations

5. Use a reference management tool! Your article article book conference paper EndNoteWeb Mendeley Etc. citations reference list/bibliography

6. Reference management softwares Tools that help scholars to create and manage their lists of references for research projects. Most tools are designed to organize citations into specific formats for the preparation of manuscripts and bibliographies. Many search tools provide ways to download references into reference management tools.

7. What is Mendeley? Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

8. Syncs Desktop & Web applications Desktop – a free academic software to manage, share, read, annotate and cite your research papers Web - a research network to manage your papers online, discover research trends and statistics, and to connect to like- minded researchers

9. This is the Web version of Mendeley which is used to manage your papers online. My Library/ Collections References Tabbed menu or Resources Main menu or Function menu

10. This is the Desktop version of Mendeley which is used to manage, annotate and cite your research papers. Collections Filters References Reference details

11. The basic or Earth version of Mendeley is free. On top of the free version, you can also upgrade to their premium plans with additional features for a fee.

12. To register and use Mendeley, go to the following address: http://www.mendeley.com From the Mendeley homepage, you will see the Sign up for free and Sign in box. Click on Sign up for free to Register. You can also use your Facebook account to Sign in.

13. Once you click on Sign up for free, the short Registration page will display. Please provide all the required information and click on Finish.

14. Once youre signed in, you have the option to Download Mendeley Desktop. You can choose to download it right away or later.

15. If you choose to download Mendeley, click Save so that you can use the file again - if you decide to install it in other computers or laptops.

16. To be able to share your profile and make it searchable to other users of Mendeley, you must verify your account. Open the email address that you use during the sign up/registration.

17. Click on the URL or the link provided in the email to verify your Mendeley account.

18. After clicking on the URL or link, you will be sent to this page that verifies your account.

19. Exercise 1 1. Open your preferred web browser (IE, Firefox, Chrome, etc.) 2. Go to the website: www.mendeley.comwww.mendeley.com 3. Sign up for an account and download the Mendeley Desktop.

20. Creating your Mendeley Library There are several ways: Search references within the Mendeley website Add a PDF Add a folder of PDFs Drag and drop PDFs in Mendeley Desktop Import/export to and from other reference management software Add reference manually Watch folders to automatically add PDFs to Mendeley Desktop One-click Web Importer

21. You can also search references within the Mendeley website. In Mendeley Web click the Papers tab and perform a search. Within the search results, just click either Save PDF to library or Save reference to library.

22. If you want to have access to your PDFs from anywhere, activate the Sync Library feature from Mendeley Desktop. By enabling this feature you are able to access your PDF files in your Mendeley Web library. Note: Always use the Sync Library in Mendeley Desktop every time you use the Mendeley Web to add references to your library.

23. In Mendeley Desktop, click Add Documents, browse to the location of the pdf and click the Open button.

24. This slide shows that the pdf has been added to your library. Mendeley will attempt to automatically detect the document details (bibliographic data). Any documents whose details Mendeley is uncertain about will be added to the Needs Review section for manual verification.

25. Click Add Folder, browse to the location of the folder. Then click the OK button.

26. This slide shows that all PDFs have been added to your library. Two were added. Mendeley will attempt to automatically detect the document details (bibliographic data). Any documents whose details Mendeley is uncertain about will be added to the Needs Review section for manual verification.

27. Drag & drop PDFs here to add them to your library.

28. Export and Import to and from other reference management software

29. Add Entry manually lets you add references to Mendeley Desktop by completing a form.

30. Exercise 2 1. Log in to your Mendeley Web account then click the Papers tab. 2. In the search box, search for the article: The scientific foundation for tobacco harm reduction, 2006-2011 by Brad Rodu 3. Save it to your library. 4. Open your Mendeley Desktop and click Sync Library. The article should be displayed.

31. Exercise 3 1. In Mendeley Desktop, click File - Add Entry Manually. 2. Select Book and enter the following: Title: Tuberculosis Control in the Western Pacific Region - 2010 Report Author: World Health Organization. Regional Office for the Western Pacific Publisher and publication date: WHO Regional Office for the Western Pacific, 2011. 3. Click Save.

32. Exercise 4 1.Download the following article and save to your desktop: Multidrug-resistant tuberculosis today by A Matteelli et al. Click to get full text pdf 2. Drag and drop the pdf file in the Reference section of your Mendeley Desktop. 3. Review the details of the article before clicking the button - Details are Collect.

33. Exercise 5 1.In EndNoteWeb, export any of your references. Click Format – Export references. Choose RefMan (RIS) Export as the export style then click Save. 2.In Mendeley Desktop, click Add Documents, locate the file you exported from EndNoteWeb then click Open. Note: you will need an account in EndNoteWeb which is available via HINARIs Reference Sources drop down menu.

34. Use Watch folders to automatically add PDFs to Mendeley Desktop. When you place a document in a watched folder, it will be automatically added to Mendeley.

35. Web Importer lets you import references and documents from a wide range of academic databases with a single click. In addition to this, it lets you save a snapshot of any webpage you are viewing. To install it, click Tools – Install Web Importer.

36. Follow the instructions from the Mendeley website. The Web Importer can import documents from different sites including PubMed.

37. In this example, we will use the Web Importer to import references from PubMed. We will do a search in PubMed, then go to Favorites (IE) or Bookmarks (Firefox & Chrome) and click on Import to Mendeley.

38. Click Import to import the references and their pdf (if available) to your Mendeley Library.

39. The green check marks indicates that the references (and their pdf if available) are imported to your Mendeley Library. To view them, click View in your Mendeley Library.

40. Review the details of the reference and, when finished, click Save.

41. Exercise 6 1.Install the Web Importer in your Mendeley Desktop by clicking Tools – Install Web Importer and then follow the succeeding instructions. 2.Go to PubMed and type: tobacco control 2012 in the search box. 3.Click Favorites (IE) or Bookmarks (Firefox & Chrome) and click Import to Mendeley. 4.Import the first 3 articles by clicking Import. 5.Click Sync Library to display the exported articles to your Mendeley Desktop.

42. Managing your documents and references Check duplicates and merge duplicate author names, tags, or publications Documents can be marked read/unread Search as you type Annotate PDFs File Organizer

43. Occasionally when you are importing references into Mendeley Desktop, they can become duplicated. This often happens when importing from completely different sources, such as a paper using the web importer bookmarklet, and then dragging a PDF of that same reference into Mendeley. You can find duplicates by selecting the Tools menu, and clicking the Check for Duplicates option.

44. Sets of duplicates will then be shown. Select a set and review the metadata in the right hand details pane. Any field which has a tick to the left of it has no conflicts while un-checked fields means 2 or more duplicates in the set have conflicting data. Click the Confirm Merge button to merge the set.

45. Documents can be marked read/unread. When you add documents to Mendeley Desktop, they are marked unread by a small green dot. If you open them within the Mendeley PDF viewer, they will be marked read. Or simply click on the green dot to toggle read/unread. Read Unread

46. You can mark your favorite documents (or documents you keep want to track of) with the star icon. Simply click to star, and click again to un-star. All favorite documents will appear in the Favorites Folder, which you can refer back to them with one click. Favorites

47. All favorite documents will appear in the Favorites Folder, so you can refer back to them with one click.

48. Search as you type. Smart search in documents highlights the search term as you type, so you can find what you're looking for quickly. Just type into the search box and Mendeley will find the matching terms in the document. We have searched for the term lessons.

49. Annotate PDFs. You can add highlights and notes to documents within Mendeley Desktop. Open a PDF in Mendeley's PDF viewer by clicking on the pdf icon. Add highlights and notes by clicking on the Highlight Text or Add Note buttons on the menu.

50. Exercise 7 1.In your Mendeley Desktop, open the pdf of the article: The scientific foundation for tobacco harm reduction, 2006-2011. 2.Highlight the title of the article. 3.Add a Note in the article.

51. Mendeley Desktops File Organizer can automatically rename your PDFs and file them in a clear folder structure, making it easier to find your files outside of Mendeley. You can find it here: Tools - Options - File Organizer tab 1 2 3

52. Citing references Word and OpenOffice plug-in How to cite references How to insert bibliography

53. To be able to cite a document, generate a bibliography, or manually edit any entry, you should install the Word and OpenOffice plug-in in Mendeley Desktop. Go to Tools – Install MS Word Plugin.

54. The Mendeley Word & OpenOffice plug-ins integrate Mendeley into these word processors. Once installed you will have tool bar buttons that will allow you to cite a document, generate a bibliography, or manually edit any entry. This will save you time and effort when you write. The default citation style is the American Psychological Association 6 th Edition. You can select other citation style in the drop down menu in your word processor.

55. To insert citation, put the cursor where you want the citation inserted. Click Insert Citation button then click Go to Mendeley.

56. Select the citation, then click Send Citation to Word Processor.

57. Another option is to type keywords (i.e., author, title or year) in the search box after clicking Insert Citation (instead of clicking Go to Mendeley). Then, click the corresponding article to insert the citation.

58. The citation has been inserted. Continue adding all the citations in your paper.

59. To insert the bibliography, put the cursor where you want the bibliography inserted. Then click Insert Bibliography and all the cited references will be added to your paper.

60. Exercise 8 1.Install the MS Word Plugin in your Mendeley Desktop by clicking Tools – Install MS Word Plugin. Once installed you will have a Mendeley tool bar. 2.Open an article (or a sample article) in MS Word and insert citation to it. 3.Add 3-5 citations to the article. 4.Insert the bibliography at the end of the article.

61. Sharing Documents and References (cont.) How to create a group Adding members and documents Using groups

62. Groups are a simple way for you to collaborate with your colleagues and share a collection of documents. Any member of a group may upload documents to it. In Mendeley Desktop, you can create a group by clicking on Create Group in the left column.

63. Once you have clicked Create Group, a dialog asking you to enter details of your group will appear.

64. Sharing Documents and References (cont.) Three types of groups: Private Groups – These are invite-only groups whose content will only be visible to members of the group. Public Invite-only Groups – These are groups which are visible to anyone, but only members can contribute to them. Public Open Groups – These are groups anyone may join and contribute to.

65. In this example, we will create a group named Dengue with group description - Dengue references and click Create Group.

66. Once you have created your group, you can add members and documents to it. To Invite Members to the group, go to the Members tab. You can either add people that are already Mendeley users by clicking on Find or you can invite people to join you on Mendeley by clicking on Invite. You can view the documents of a group by going to the Documents tab. To Add Documents, go to the group and click on Add documents in the top bar. Alternatively, you can simply drag and drop documents to the group (either from your Mendeley folders, or from anywhere else on your computer).

67. The Overview tab shows a summary of what has happened in your Group. You can see updates on who has joined, who said what, and which papers have been added by whom. You can also post status updates by entering your update into the box at the top of the overview section. This is the end of Module 5.2

68. References Getting started with Mendeley. Available at: http://www.mendeley.com/getting- started/ Zotero Reference Management Software. Available at: http://www.who.int/entity/hinari/training/ Module_5_2_Zotero_Reference_Mana gement_Software_2011_08.ppt

69. This module was developed by: Mark Gil Bendo, MLIS Assistant/Library World Health Organization Regional Office for the Western Pacific Updated 2012 02