1. Managing references : Mendeley

2. Table of Contents Why use a reference management software?
What is reference management software?
Mendeley features and functionality
*Trainer Notes
Introduce yourself and welcome everyone to course. Ask participants to introduce themselves and give some information on what they expect to gain from the workshop. Distribute the manuals and discuss briefly each item on the list.
The topics to be covered in this review are:
Basic definition of Internet terms and concepts that are routinely used in discussions on using the Internet.
A brief history of the Internet will be provided.
The structure of the Internet and the tools that drive the use of the resources will be covered including the World Wide Web and its components.
Types of Information resources and guidelines for their evaluation will be addressed.
Search tools and techniques for accessing information will be covered.
Researching Health and Biomedical Information on the WWW. 2

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

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

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

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. This is a comparison of selected Reference management softwares.

8. 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

9. 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

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

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

12. The basic version of Mendeley Web is free with 2 GB Personal Web Space and 500 MB Shared Web Space
You can also upgrade to their premium plans with additional storage and features for a fee.

13. To register and use Mendeley, go to the following address:
From the Mendeley homepage, you will see the Sign up & Download and Sign in box. Click on Sign up & Download to Register.
You can also use your Facebook account to Sign in.

15. Mendeley will automatically detect the operating system that you are using.
Click Save so you can use the file again if you decide to install it in your other computers or laptops.

16. If you decide to use your Facebook account to Sign in, you have to provide your email and password.

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

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

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

20. Creating your Mendeley Library
There are several ways:
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
Search references within the Mendeley website 20

21. Click Add Files, browse to the location of the pdf then, click the Open button.

22. 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 Reference details section for manual verification.

23. Click Add Folder, browse to the location of the folder then, click the Ok button.

24. Any documents whose details Mendeley is
All pdfs inside the folder
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.

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

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

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

28. 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.

29. 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.

30. Then follow the succeeding instructions.
The Web Importer can import documents from different sites including PubMed.

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

32. Click the “+” icon to choose individual articles or click Save all to save the entire list and the pdf (if available) to your Mendeley Library.

33. The green check marks indicates that the references are saved in your Mendeley Library.
To view it, click View in Mendeley Desktop.

34. 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.

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

36. 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 36

37. Occasionally when you are importing references into Mendeley, 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.

38. Sets of duplicates will then be shown
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.

39. Documents can be marked read/unread.
When you add documents to Mendeley, 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

40. 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, so you can refer back to them with one click.
Favorites

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

42. 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 bar and watch Mendeley find matching terms in the document.

43. 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.

44. Mendeley's 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

45. Citing references Word and OpenOffice plug-in How to cite references
How to insert bibliography 45

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

47. 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, saving you time and effort when you write.
The default citation style is the American Psychological Association 6th Edition. You can select other citation style in the drop down menu in your word processor.
This screenshot was taken using Word 2003.

48. This screenshot was taken using Word 2010.
Mendeley tool bar is located under the References tab.
Add-in for Word is not appearing
c:\Program Files\Mendeley Desktop\wordPlugin

49. To insert citation, put the cursor where you want the citation inserted and then press Alt+M or click the Insert Citation button.
Lastly, click Go To Mendeley button.

50. Select the citation, then click Cite.

51. Or you could just type keywords (i. e
Or you could just type keywords (i.e., author, title or year) in the search box instead of clicking Go to Mendeley after clicking Insert Citation.
Then, click the corresponding article to insert the citation.

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

53. 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.

54. Sharing Documents and References (cont.)
How to create a group
Adding members and documents
Using groups 54

55. 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. You can create a group by clicking on Create Group in the left hand pane.

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

57. Sharing Documents and References (cont.)
Three types of groups:
Private – Share references and full-text files. Only group members can see the group, good for sharing in private.
Invite-only – Share references only. Public can follow the group only, good for sharing references or reading lists.
Open – Share references only. Public can become a member or follow the group, good for crowd sourcing reading lists. 57

58. In this example, we will create a private group named Diabetes with group description - Diabetes references and click Create Group.

59. Then, we will invite people by supplying their email address
Then, we will invite people by supplying their address. This step can also be skipped and done in another time.
A custom message is optional. Then click Send Invites.

60. You will be brought to this page which confirms that the Invites were sent and that the group was created.
Click Continue to group.

61. 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).
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.

62. The Overview tab shows a summary of what has happened in your Group
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

63. References
Getting started with Mendeley. Available at: started/
Zotero Reference Management Software. Available at: Module_5_2_Zotero_Reference_Mana gement_Software_2011_08.ppt 63

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

65. 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, by Brad Rodu
3. Save it to your library.
4. Open your Mendeley Desktop and click Sync. The article should be displayed.

66. 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 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.

67. Exercise 4 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.

68. Exercise 5
Try to export any of your references from the reference management software which you are currently using (i.e., BibTeX, EndNote, RIS and Zotero). Then Save it in your desktop.
In Mendeley Desktop, click File – Import – [Choose the format of the exported file] and then locate the file you exported then click Open.

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

70. Exercise 7
In your Mendeley Desktop, open the pdf of the article: The scientific foundation for tobacco harm reduction,
Highlight the title of the article.
Add a Note in the article.

71. Exercise 8
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.
Open an article (or a sample article) in MS Word and insert citation to it.
Add 3-5 citations to the article.
Insert the bibliography at the end of the article.