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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