A Short Introduction to Reference Management Software

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1 A Short Introduction to Reference Management Software Pawin Numthavaj M.D. Section for Clinical Epidemiology and Biostatistics Faculty of Medicine, Ramathibodi Hospital, Mahidol University Bangkok, Thailand rama.org Problem with Manual Maintenance of Search Results Re type from electronic search Duplicated item management Re writing text and changing of reference numbers Different style systems Reuse of same reference in another paper 1

2 Bibliographic Software Database maintaining records of bibliography Example: EndNote Zotero Mendeley Microsoft Word Papers for Mac OSX/iOS Reference Manager ProCite Etc Frequently Used Software Comparison Current Version Platforms Available License Price Cloud backup Word Processor Integration EndNote X7.7 (2016) Windows, Mac OSX, Web, ios Proprietary $ Yes MS Word OpenOffice Zotero Windows, Mac OSX, Linux AGPL Free Yes MS Word OpenOffice Mendeley Windows, Mac OSX, Linux, ios Proprietary Free Yes MS Word OpenOffice Microsoft Word 2016 Windows, Mac OSX Proprietary $99 (University version) No N/A Papers Mac OSX, ios, Windows, Web Proprietary $ 79 Yes Mac only 2

3 Software usage among 78 systematic reviewers Frequency Percent Mean functionality rating EndNote % 7.5 (range 3 to 10) Reference Manager % 7.0 (range 6 to 9) RefWorks 6 7.7% 7.8 (range 6 to 10) Excel 1 1.3% 8.0 None % NA Total % Lorenzetti and Ghali BMC Medical Research Methodology :141 EndNote 3

4 EndNote X7.7 Available for MU students and staffs via Mahidol Intranet Software Download ( Integration with Microsoft Word, OpenOffice.org Find Full Text feature Cloud backup (Free EndNote Web 2 year subscription) Also provided manuscript templates for several journals (but do check with author guidelines!) EndNote X7.7 Smart and combined group syncs across desktops PDF annotation tools support underline and strikethrough Highlighted quick search results 4

5 EndNote Program 5

6 EndNote Reference Input 1. Importing (Preferred way) 2. Searching online 3. Manually typing in Importing EndNote support importing from Online searches from search engines: PubMed SCOPUS Ovid Online book catalogues: Google Books, Amazon Text/PDF Files EndNote Web Capture 6

7 Let s try to find something on PubMed "Acyclovir"[Mesh] AND "Bell Palsy"[Mesh] Import from PubMed Option 1 Select destination as File Choose format as MEDLINE.txt file will be downloaded In EndNote: File > Import, select import option: PubMed (NLM) If there is no PubMed (NLM) choose Other Filters and then choose PubMed (NLM) Option 2 PubMed s Send To Command Select destination as Citation Manager (Limit 200).nbib file will be downloaded In EndNote: File > Import, select import option: PubMed (NLM) 7

8 8

9 Import from SCOPUS Select items and choose Export Export format: RIS format Endnote File Import Import Option: Reference Manager (RIS) 9

10 Manually Input Data Menu References» New Reference Ctrl+N Toolbar Icon 10

11 Reference Management Inside EndNote Library Grouping Group: Folder Smart Group: Automatic folder by specified criteria Group set: Groups of folder Duplication management PDF file attachments Find Full Text 11

12 Group Smart Group 12

13 Group Set Set of groups For multiple projects Duplication Management 13

14 PDF File attachments PDF File attachments 14

15 Find Full Text Works within Mahidol University network Settings: Edit >> Preference Check all boxes Open URL path: Authenticate with URL:

16 EndNote Web Cloud storage Browser front end without the need for installation of EndNote desktop program Can sync with EndNote X6 desktop library Handy for backup your library Recommended PDF Workflow for Tablet Users 1. Use EndNote for ipad app $ 3.99 Free App for ios Will sync automatically with EndNote web 2. Manually over cloud services Sync the content of <filename>.data\pdf with cloud services (such as DropBox) Use PDF readers that support the cloud service (such as GoodReader) on ipad 16

17 EndNote Desktop EndNote Web EndNote ipad EndNote for ipad app 17

18 EndNote for ipad app EndNote for ipad app 18

19 EndNote for ipad app Sharing an EndNote library Sometimes you need to share an EndNote library (ex: when doing a systematic review) EndNote saves a library into.enl file and other files in <document.data> folder It is usually not wise to copy all of these files and send to others 19

20 Sharing an EndNote library Instead, use Compressed Library in File menu. 20

21 Note You may also use this technique to backup your library as.enlx files Special Use of Style: Export to Excel In some situation, e.g. doing a systematic review, you may need to export EndNote library into a spreadsheet or database program like Excel/Access EndNote has no direct support to export database We need to produce a text file that is separated each items with <tab> A separation with commas will interfere with many of the field such as Author name so it would not be practical 21

22 EndNote Library Tab separated Text file Excel or Access 1. create a new style Choose Edit Output Styles New Style 22

23 2. select Bibliography Template from the Left side 23

24 3. Click Reference Types and choose Journal Article template 4. Insert fields that you want with button on the right side and separate fields with Tab Example: Record Number <tab> Author <tab> Year <tab> 24

25 Recommended fields to export First author name Title of paper Year of publication Journal name E mail address/contact information of author (Optional: Abstract) You may set the format of author name with Surname first in the Bibliography > Author Names section if you like 25

26 Save the style with the name you want (File Save As) Next, open the library you want to export Please note that Endnote separated Author field with a carriage return (a new line) This is important as Excel will also treat carriage return as the start of new cell We need to get rid of these carriage returns 26

27 NOTE: Before we further remove these carriage returns, we need to save a copy of our library first! (There is no way to reinsert back automatically) Select Edit >> Find and Replace 27

28 Set find in to: Any field Find the Carriage return Replace with anything you want, I suggest ;. Select OK 28

29 Now author field will contain only one line Now, export 29

30 Select style that you have just created earlier and then save In Excel Choose File Open in Excel Choose the text file you just exported Use the Import Text wizard as follow 30

31 31

32 32

33 Remember! You MUST backup your library or make an edit on a copy of your library There is no way to undo from removing carriage returns Mendeley 33

34 Mendeley Free Mendeley Ltd August GB web storage space Social features Share documents online with group Comment Like 34

35 35

36 Mendeley Desktop Social features 36

37 Import Files NBIB RIS PubMed Microsoft Word Plugin 37

38 Mendeley Lite app 38

39 Thank You! Any question can be asked at our section s facebook page Facebook.com/ramaclinicalepi Or you can visit rama.org 39

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