A Short Introduction to Reference Management Software...EndNote Web •Cloud storage •Browser...
Transcript of A Short Introduction to Reference Management Software...EndNote Web •Cloud storage •Browser...
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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
www.ceb‐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
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Bibliographic Software
•Database maintaining records of bibliography
Example:• EndNote• Zotero•Mendeley•Microsoft Word 2007+• Papers for Mac OSX/iOS• Reference Manager• ProCite• Etc…
Frequently Used Software Comparison
Current Version
Platforms Available
License Price Cloudbackup
WordProcessor Integration
EndNote X7.7(2016)
Windows, Mac OSX,
Web, iOSProprietary $299.95 Yes MS Word
OpenOffice
Zotero 4.0.29Windows,Mac
OSX,Linux
AGPL Free Yes MS WordOpenOffice
Mendeley 1.16.1 Windows,Mac OSX,Linux, iOS
Proprietary Free Yes MS WordOpenOffice
Microsoft Word
2016 Windows,Mac OSX
Proprietary$99
(University version)
No N/A
Papers 3.2.3 Mac OSX, iOS, Windows, Web
Proprietary $ 79 Yes Maconly
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Software usage among 78 systematic reviewers
Lorenzetti and Ghali BMC Medical Research Methodology 2013 13:141
Frequency Percent Mean functionality rating
EndNote 41 52.6% 7.5 (range 3 to 10)
Reference Manager 14 17.9% 7.0 (range 6 to 9)
RefWorks 6 7.7% 7.8 (range 6 to 10)
Excel 1 1.3% 8.0None 16 20.5% NA
Total 78 100%
EndNote
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EndNote X7.7
•Available for MU students and staffs via Mahidol Intranet Software Download (http://myinternet.mahidol/software/)
• 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
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EndNote Program
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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
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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)”
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Import from SCOPUS
•Select items and choose Export
•Export format: RIS format
•Endnote• File – Import• Import Option: “Reference Manager (RIS)”
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Manually Input Data
•Menu References » New Reference• Ctrl+N• Toolbar Icon
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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
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Group
Smart Group
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Group Set
•Set of groups•For multiple projects
Duplication Management
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PDF File attachments
PDF File attachments
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Find Full Text
• Works within Mahidol University network
• Settings: Edit >> Preference
• Check all boxes
• Open URL path: http://www.google.com
• Authenticate with URL: http://onlinelibrary.wiley.com/ http://www.sciencedirect.com
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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
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EndNote Web
EndNote Desktop
EndNote iPad
EndNote for iPad app
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EndNote for iPad app
EndNote for iPad app
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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
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Sharing an EndNote library
• Instead, use “Compressed Library” in File menu.
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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
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EndNote LibraryEndNote Library
Tab‐separated Text file
Tab‐separated Text file
Excel or AccessExcel or Access
1. create a new style
•Choose Edit → Output Styles → New Style
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2. select Bibliography Template from the Left side
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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>
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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
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•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
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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
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•Set find in to: Any field•Find the Carriage return•Replace with anything you want, I suggest “;”.
Select OK
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Now author field will contain only one line
Now, export
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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
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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
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Mendeley
•Free•Mendeley Ltd
•August 2008•2GB web storage space•Social features
• “Share” documents online with group
• “Comment”• “Like”
www.mendeley.com
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Mendeley Desktop
Social features
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Import Files
•NBIB•RIS•PubMed
Microsoft Word Plugin
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Mendeley Lite app
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Thank You!
Any question can be asked at our section’s facebook page
Facebook.com/ramaclinicalepi
Or you can visit www.ceb‐rama.org