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Intensive Course for MMed/Msc/PhD USM
December 2014
Assoc. Prof. Dr WM ZAHIRUDDIN WAN MOHAMMAD M.D, M.Comm. Med. (Epid. & Biostats) USM [email protected]
Referencing with
Referencing in scientific writing
Time consuming Writing proposal and publishing research require gathering
references and creating properly formatted bibliographic citations.
Keeping track of your bibliography as your research into a subject becomes deeper, and the literature
base expands to thousands of articles.
Standard formatting almost every journal requires a different format for citations
(numbered or alphabetized)……and you can find yourself reformatting (and retyping) your citations time and time again.
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Using bibliography softwares
Reference list or bibliography must: be in alphabetical order by author’s surname (Harvard system)
or by ordered numbers (Vancouver) have all elements of the reference in the correct order with
consistent syntax and punctuations throughout
Consistency is the rule in any system of referencing…. …...IT’S BEST TO USE A BIBLIOGRAPHIC SOFTWARE!
There are many software's that can be used for writing manuscripts and research papers.
Endnote is one of the most popular software among students and researchers.
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In today’s session
Part 1 - how to create an Endnote library, enter new references, download references from online databases and sort your library.
Part 2 - how to create bibliographies and to insert citations into your thesis/documents using different referencing styles by Endnote.
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Introduction to Endnote Endnote® is a software developed by ISI Research Soft.
(www.endnote.com) Endnote is not a freeware, need to purchase. Current version (licensed) is EndNote X7. If your institution subscribes it, get the CDROM
This software is useful for
Creating and managing your own personal bibliography Managing pdf files Online search tool for articles (import or export files) Bibliography maker (> 4,000 journal templates formats)
Cite while you write (CWYW) Writing manuscript /thesis/research papers formatting citations and manuscript template
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Words compatibility and Tutorials EndNote’ s Cite While You Write (CWYW) is compatible
with following word processing and text formats: Microsoft Word® OpenOffice.org Writer 3 (EndNote only) WordPerfect/word processors with Rich Text Format (RTF). Macintosh: compatible with Microsoft Word X, 2004, 2008.
Go to Endnote’s FAQ website to learn more.
One of the best Endnote X7 website tutorial/handout: http://une.au.libguides.com/
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Checking your installation: If EndNote & MS Word are properly installed, both will be accessible via the menu toolbars
Accessing MS Word through “Tools” from Endnote X7 program
Accessing Endnote X7 through “menu toolbar” in MS Word
Opening an existing Endnote library
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An Endnote library has two files: *.Data (folder-like file) *.enl (endnote database)
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How to view a sample Endnote library
Go to “C:” drive and click Open. Select Program Files; looks for EndNote X7 folder, then click the “Example’s shortcut”
Viewing an Endnote library
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EndNote X7 Windows icon toolbar
Reference List pane displays a multi-column list of references.
This window displays a Preview tab to view formatted references (Abstracts or Output styles) , manage PDF file and insert attachments
Groups pane lists various groups of references for easy retrieval.
How to view an abstract
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Highlight selected reference to view the abstract (use Annotated view & click Preview)
How to view the “Output styles”
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Highlight selected reference and click the “output styles” (e.g APA 6th format)
Getting References (eg. PubMed, online databases, manually)
Microsoft Word
Import / Export
Cite while you write
Selected citation styles
Other citation styles formatting
General steps in using Endnote
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Creating an Endnote library
1. Open Endnote program 2. Create a new Endnote library (..name and save it!) 3. Getting references into your EndNote library: Search from Pubmed website and “import” it “Export” references from subscribed online
databases (e.g Ovid, ProQuest, Science Direct etc)
Export from Google Scholar Direct “pdf files” import or download Online retrieval through EndNote Manual entry of references
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i. Search and import from PubMed
Search for references in pubmed
First, search your references (using keywords, Boolean methods or your search strategy) from PubMed website. E.g Search “AIDS” “Malaysia” “Knowledge” as keywords
www.ncbi.nlm.nih.gov/pubmed
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Use “Citation manager” to send selected (ticked boxes) Pubmed file(s) to your Endote library
Note: the selected files will be created automatically to your open Endnote program
Importing to Endnote
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Note: You may be asked to “Save file” as “citations.nbib” in a folder, then import into an open Endnote thru PubMed(NLM) option.
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ii. Getting references from USM-subscribed Online Databases (use Ez-proxy if off-campus login)
Examples: Proquest, Ovid, Science Direct, ISI Web of Knowledge etc
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From PROQUEST, tick/select the retrieved references, then click “Export/Save” to “Endnote” (follow the instructions)
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Proquest database: Export and save the file in your Endnote
Scroll down, then click “Continue”….
Save the file (or open through RIS files), and it will automatically be imported to an active Endnote library
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Choose Endnote. Citation + Abstract. Export citation(s) Then save the file (ovidweb.cgi), then double click it to import it to your active Endnote library
Exporting and saving from Ovid database Click “Export” after selecting the references
Other subscribed databases
You may retrieve references from many other subscribed databases, and look for “Export” to Endnote menu ISI Web of Knowledge Scopus Science Direct Specific journal database
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iii. Exporting from Google Scholar directly (customize the setting preferences for EndNote)
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Set the “Scholar Preferences” . Select “Show links to import
citations into”, select EndNote from the drop-down.
Click Save Preferences.
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Exporting from Google Scholar directly via “Import into EndNote”
Use “Open” to import the selected references into the Endnote (for IE and Firefox). For Google chrome, save as “scholar.enw” files then click it to import. Note: - Can only import one citation at a time into EndNote. - Imported references may not follow proper bibliographic formatting!
iv. Importing PDF articles You can import publisher-created PDFs into EndNote
and, in many cases, EndNote will create a reference in your EndNote library at the same time.
EndNote can extract the reference information using its Digital Object Identifier (DOI). If the DOI is not present the PDF will be imported, but you will need to do extensive editing in required fields of the reference.
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Importing and attached a pdf file (or folder) to selected reference
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Choose to import the selected file using Import Option “PDF”, then click Import
Importing PDF file with DOI
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Using “Import” procedure in EndNote, it can extract the reference information using its Digital Object Identifier (DOI).
Need to edit information in selected fields of the imported pdf file without “DOI”
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Need to edit in reference preview
Finding full-text pdf articles
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EndNote X7 can automatically locate and download full text files by accessing several sources. But with conditions…. 1. If the articles are FREELY AVAILABLE online, they will
most likely be found and attached. 2. You are connected to your library website’s subscribed
databases The retrieved the full text file is saved as pdf files in the library’s “DATA” folder and linked as attachment.
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v. Online search directly from EndNote (make sure online for remote searching)
Type the appropriate key words based on your search strategy (e.g Bolean seacrh techniques) in Any Field.
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Choose the online database (preferably PubMed NLM)
Choose connection file:
Connect to PubMed (NLM), public access version of MEDLINE.
• Valid only for selected databases
• This method is good for known citations
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vi. Manual entry of references Some references are not available through online or databases e.g unpublished thesis, proceedings, books, annual reports etc.
Need to add the references manually into existing Endnote library.
Click on the New Reference button or on the toolbar.
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Choose type of reference, then fill in required fields
Select the type of reference you want to create, e.g Journal (as default), proceedings, books, reports etc.
Fill in the required information based on the reference types
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Manual entry: Write only relevant information in the fields
Individual author name must be entered one per line (3 ways to do it).
Last, First Middle First Middle Last Last, (abbr) Middle.Last.
As you type, Endnote will suggest names similar name as entering. If the name appears in RED, it indicates a new name for authors in your library.
For institution or corporate authors, you may write the name followed by a coma e.g “Universiti Sains Malaysia,” , “World Health Organization,”
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Manual entry: Closing and saving
Save it from the File menu or Closing the Reference window by clicking the close button (smaller x).
All information is automatically saved into your active library when you close a window.
Important points to remember when entering data manually! The output styles can only format data correctly if the data is
entered correctly. Just add the basic data, in the default EndNote font. The output style
will change this to bold or italics and add extra text such as "vol." or "Ed." (if required by the style)
Fields such as Abstract, Notes, Research Notes are for your use Use the URL field to link to an electronic version of the document Use the File Attachments field to add a PDF version of the
document to your library If you use abbreviated journal titles in your publications, you can set
up a Journal Term list to store the abbreviations
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Managing Endnote (demonstration)
Copy output styles into the Endnote folder Remove reference duplicates Sort ascending, descending Copy paste references between libraries Compress a Library and Email to colleague Attach files (pdf, word, jpeg etc) Organize references into Groups (or folders)
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Create a compressed library to email Compressed the Endnote Library (“*.enl” and “*.Data” files
together) as “*.enlx”.
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Save or send compressed files to email it (with/without attachments)
Attach files (pdf, Word or jpeg) Store PDF and other files with your EndNote library: In Endnote X7, there is unlimited size for external files
attachments per reference. You may copy-paste or Drag and drop files in "File Attachment" field onto a reference for auto-linking and storage.
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Find duplicates
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It is important to try to avoid duplicates of references in your EndNote Library. To check, go to References and select Find Duplicates.
You may sort references by title to ensure no duplicate records have been missed. To delete duplicate records, select duplicate records, right click, then select Move References to Trash. In addition, when importing in PDF files EndNote gives you the option to Import into Duplicates Library
Organize references into Groups
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Adding a Group to your Group Set You can create several groups under a group set. Adding References to a group Drag and drop the references to a group. Smart Groups When new references are added to the library, they are searched by each of the smart groups. If the references fit the search criteria they are automatically added to that group.
