drzahir@kb.usm.

my

INTENSIVE COURSE ON “ INTERMEDIATE STATISTICS, SCIENTIFIC WRITING &

PRODUCING QUALITY THESIS”
for MMed, MSc and PhD candidates, USM

Introduction, Creating
and Managing:

Dr Wan Mohd Zahiruddin Wan Mohammad

Lecturer (Epidemiology & Biostatistics)
drzahir@kb.usm.my 1
 drzahir@kb.usm.my

Lecture’s contents
“What is Endnote ?”(version X2)
 requirement, compatibilities
 skills in creating and managing Endnote Library

Referencing with Endnote‟s “Cite While You Write”

feature with Microsoft Word for manuscript writing

2
 drzahir@kb.usm.my

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.

3
 drzahir@kb.usm.my

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 punctuations throughout

Consistency is the rule in any system

of referencing….
…...IT’S BEST TO USE A
BIBLIOGRAPHIC SOFTWARE!

4
 drzahir@kb.usm.my

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.

5
 drzahir@kb.usm.my

Introduction to Endnote
 Endnote® is a software developed by ISI Research Soft.
(www.endnote.com)

 This software is useful for

 Creating and managing your own bibliography database
 Online search tool for literature databases
 Retrieving online references (import or export data files)
 Bibliography maker (> 4,000 journal templates formats)
 Helping in writing manuscript and research papers
 cite while you write
 format citations,
 manuscript template etc

6
 drzahir@kb.usm.my

Requirement and compatibility

 Endnote is not a freeware. You are required to purchase it.
 Endnote Version 9 is already good but X2 is much better. Current
version is EndNote X3.
 If your institution has subscription, get the CDROM (PPKT/Library)

System and Hardware requirements:

 Windows® XP (SP 2,3), Vista (32/64 bit)…Windows 7?
 Macintosh: run on OS X (10.4.x, 10.5.x)
 Pentium 450MHz or faster
 180MB hard disk space available
 CD-ROM not required for download installation.
 Internet - access EndNote Web and to search online databases.

7
 drzahir@kb.usm.my

Word Processor compatibility

 EndNote‟ s Cite While You Write (CWYW) is compatible
with following word processing and text formats:
 Microsoft Word® 2003, 2007
 OpenOffice.org Writer 3 (EndNote only)
 WordPerfect and other word processors that can save or export
files in Rich Text Format (RTF).
 Macintosh: compatible with Microsoft Word X, 2004, 2008.

 Microsoft word startup folder should have this file:

EndNote Cwyw

 Go to endnote FAQ website to learn more…

 www.endnote.com/support/faqs/CWYW/faq45.asp#word2003
8
 drzahir@kb.usm.my

Checking your installation:

If EndNote & MS Word are properly installed, the EndNote
X2 menu toolbar will appear; also in “Tools” in Word 2007

MS Word 2007 or (2003)

9
 drzahir@kb.usm.my

Opening an existing Endnote library

 An Endnote library has two files:

*.Data (folder-like file)
*.enl (endnote database)

10
 drzahir@kb.usm.my

Viewing a library, open “Sample_Library.enl” from

Endnote X2 example's folder

Choose the “C:” drive and

click Open; select Program
Files; and then open the
EndNote X2 folder. then the
“Example” folder
11
 drzahir@kb.usm.my

EndNote X2 Windows
Viewing an EndNote library icon toolbar

Reference List pane

displays a multi-column list
of references.

Groups pane lists

various groups of Tab pane displays a Preview
references for easy tab to view formatted references
12
retrieval. and a Search tab for searching
 drzahir@kb.usm.my

Viewing selected reference: abstract

Highlight selected reference to

view the abstract (annotated
view) OR double click a
reference to open it

13
 drzahir@kb.usm.my

Useful EndNote X2 shortcut icons

Insert
Bibliography output
citation
styles
Find full
text…
Online search… Format
bibliography
Import or Export Return to
references MS Word
14
 drzahir@kb.usm.my

General steps in using Endnote

Getting References
(eg. PubMed, online databases, manually)
Import / Export

Cite while you write

Microsoft Word

Selected citation Other citation

styles formatting styles
 drzahir@kb.usm.my

Creating an Endnote library

1. Create a new Endnote library (..name and save it!)
2. Getting references into your EndNote library:
i. Search from Pubmed website and “import” the
saved references
ii. “Export” or “Import” references from subscribed
online databases (e.g Ovid, ProQuest, Science Direct)
iii. Direct online retrieval by EndNote (eg. PubMed)
iv. Manual entry of references

16
 drzahir@kb.usm.my

Creating a new library

 Double click the icon, or
 Open Endnote program
 File  New  Library
Name the file as
“My EndNote Library”
or whatever you
like…….preferably your
research subject

17
 drzahir@kb.usm.my

i. Search and import from PubMed

http://www.ncbi.nlm.nih.gov/pubmed

First, search your references (using keywords, Boolean

methods or your search strategy) from PubMed website.
E.g Search “AIDS” AND “Malaysia” .

Search for references in pubmed 18

Select the selected references and save the
results in a text (*.txt) format

Click “Send to”

Click “File”

Click
“MEDLINE”

Create file

Click “Save file” in text

format (*.txt)
 drzahir@kb.usm.my

Saved the references in a selected folder

(Depending on your browser settings, it may be saved
automatically in the “Download” folder in “My Document”!)

Save it and name the file (e.g

AIDS Malaysia)…and remember
where you save the files.

20
 drzahir@kb.usm.my

Import the saved file

into Endnote

Choose Import option! -

PubMed (NLM)
(if not there yet, search from
“other filters”

Click “Import”!

21
 drzahir@kb.usm.my

Your retrieved references!

The library now has 2 references.

Then, click “Show all references” (from

Reference menu) to show other existing
references in the library

22
 drzahir@kb.usm.my
ii. Getting references from USM-subscribed
Online Databases

Proquest
Ovid
Science Direct

23
 drzahir@kb.usm.my

Search, select references from

PROQUEST….then click “export”

24
 drzahir@kb.usm.my

Export and save the file in your Endnote

25
 drzahir@kb.usm.my

Exporting and saving from Ovid

Check Selected Citations and Fields  Direct Export  Save 

a popup window appear  select a library of “EndNote” to save 26
 drzahir@kb.usm.my

Another example: ScienceDirect

Export citation

27
 drzahir@kb.usm.my

Exporting from Google Scholar

Set the “Scholar Preferences” to
include Endnote.
The scroll down to edit the
“Bibliography Manager”…and save
the preference!

28
 drzahir@kb.usm.my

iii. Online search from EndNote

Use “Search” tab from the

panel..then do you search
accordingly

29
 drzahir@kb.usm.my

Choose the online database (preferably

PubMed NLM) Choose connection file:
Connect to PubMed (NLM), the National
Library of Medicine, public access version
of their MEDLINE database.

• Valid only for selected

databases
• This method is good for
known citations

30
 drzahir@kb.usm.my

Online search menu

Boolean search
Type the appropriate
key words with “AND”,
“OR” or “NOT”
Additional words in
the query can be
added in Any Field.

Retrieved records from 1 through 25.

31
Enter the desired number for XX.
 drzahir@kb.usm.my

Copy selected references to Endnote file

You may want to copy relevant

references to your Endnote file.
Highlight your selected
references only.
Right click the „mouse‟ OR use
“edit – copy” from tool menu to
copy them to your library

32
 drzahir@kb.usm.my

iv. Manual entry of references

Sometime, references are not available through online or databases
e.g unpublished thesis, proceedings, books, annual reports etc.
Now, you may add the references manually into your new or
existing Endnote library.
Cllick “New Reference” in Reference toolbar.

33
 drzahir@kb.usm.my

Manual entry: type of reference?

Select the type of reference

you want to create, e.g
Journal (as default),
proceedings, books, figure
legends etc.

34
 drzahir@kb.usm.my

Manual entry: Write only relevant and

important information
Individual author name must be entered one per line (3 ways to do it).

Last, First Middle First Middle Last Last, 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, you may write the name followed by a coma e.g
“Universiti Sains Malaysia,” ; “World Health Organization,”
35
 drzahir@kb.usm.my

Manual entry: Closing and saving

Choose the reference type,

then type relevant data

Save it from the File menu or Closing the Reference

window by clicking the close button (smaller x).
All information is automatically saved when you
close a window. Your new reference should now
appear in the library window.
36
 drzahir@kb.usm.my

Managing Endnote (demonstration)

 Remove reference duplicates
 Sort ascending, descending
 Copy paste references between libraries
 Compress a Library and Email to Colleague
 Copy output styles into the Endnote folder
 Finding full articles thru Endnote (optional)
 Attach files (pdf, word, jpeg etc)
 Organize references into Groups (or folders)

37
 drzahir@kb.usm.my

Updates output styles versions

into EndNote “Styles” folder

Copy MJMS.ens style file in C:  Program

Files  Endnote  Styles

Copy the Harvard USM Ver3.ens

in the Endnote /styles folder
 drzahir@kb.usm.my

Create a compressed library

Compressed the Endnote Library (“*.enl” and “*.Data” files together)
by renaming it to “*.enlx”
 Open the library in EndNote.
 From the File menu, select Compressed Library and then Create
and save or email.

Create
compressed files
to email it

39
 drzahir@kb.usm.my

Finding full articles to a reference

EndNote X2 can automatically locate and download full text files
by accessing several sources.

The retrieved the full text file is saved and linked as attachment in
library‟s .DATA folder. The file is saved in its native format, which in
most cases is a PDF file.

The full article has been found!

40
 drzahir@kb.usm.my

Go to the reference, click the pdf image or URL to view

the full article OR open the *.Data folder (PDF folder)

41
 drzahir@kb.usm.my

Attach files (pdf, Word or jpeg)

 Store PDF and other files with your EndNote library:

Organize up to 45 files per reference in the "File
Attachment" field. Drag and drop files onto a
reference for auto-linking and storage with the library
references.

42
 drzahir@kb.usm.my

Organize references into Groups

43
 drzahir@kb.usm.my

Referencing with
EndNote® :
(Cite While You Write)

44
 drzahir@kb.usm.my

What is a Reference?

An acknowledgement that you have

referred to (cited) information from
(published) sources in your own work.

In other words, a recognition that you have

borrowed other people‟s work, ideas or
opinions.

45
 drzahir@kb.usm.my

Reference: Why ?
 Published evidence to support your own ideas/
arguments/points of view or give examples
 Avoid plagiarism - using other people‟s work and ideas
as your own without acknowledgement
 Copyright
 Helps others to trace your information sources
 Shows off your research!
 Part of the marking scheme

46
 drzahir@kb.usm.my

Reference: When ?

 When you arrive at a particular theory, argument or

viewpoint
 statistics, examples, case studies
 closely summarising a passage from another writer
(paraphrasing)
 describing using an idea or material (methodology)
which is directly based on the work of another writer
 “direct quotations” - quoting the exact words of another
writer (use sparingly!)

47
 drzahir@kb.usm.my

Reference: How to?

 Various systems but the TWO generic terms:
 Harvard system (Author/Date)
 a generic term for any style which contains author-date references
in the text of the document, such as (Smith,1999) and also be a list
of references at the end of the document, arranged by authors'
names and year of publication.
 the most popular and recommended (in USM)

 Vancouver (numbered)
 a generic term for a style of referencing widely used in the health
sciences, using a numbered reference list.
 references in the text are numbered in parenthesis or superscript
 no official manual of the Vancouver style, but the US NLM's style
guide is now considered the most authoritative manual.

48
 drzahir@kb.usm.my

Citation (in-text reference) & references

list (bibliography)

Citation
(in-text reference)

“Reference list
or Bibliography”
at the end of the
document

49
Eduardo et al. from CMAJ 2002;167(4):349-52
 drzahir@kb.usm.my

Reference: Where to?

 acknowledge others‟ work at the point it appears or is

discussed in your essay
 relies on reader getting the details from your bibliography
or works cited list.

Where to cite in the text (Harvard system)?:

 form part of the sentence: …author’s surname (year)….
 If not part of the sentence, cite it at the end of the
sentence: “……………. (author’s surname, year).

50
 drzahir@kb.usm.my

Bibliography and its syntax

 Reference list or bibliography must:
be in alphabetical order by author‟s surname
have all elements of the reference in the correct order
use consistent punctuation throughout
there is a set pattern to when and how you put
information in a bibliography, even down to the
commas and full stops.
this pattern repeats itself for most forms – journal
articles, books, web pages etc

51
 drzahir@kb.usm.my

Referencing journal articles (MJM style)

1. Author: Anita, S., Zahiruddin, W. M., Sa'iah, A., Rahimah, M. A. and
Sha'ari, B. N
2. Year of publication: 2007
3. Title of article: HIV/AIDS knowledge, attitudes and risk behaviours
among Orang Asli in Peninsular Malaysia
4. Title of journal: Med J Malaysia
5. Volume number : 62
6. Issue number (if present): 3
7. Page number(s): 227 - 233

Anita, S., Zahiruddin, W. M., Sa'iah, A., Rahimah, M. A. &

Sha'ari, B. N. (2007). HIV/AIDS knowledge, attitudes and
risk behaviours among Orang Asli in Peninsular Malaysia.
Med J Malaysia, 62 (3), 227-33.
52
 drzahir@kb.usm.my

Referencing books (MJMS style)

Using the title page note (not the front cover).

1. Author(s): Fletcher R, Fletcher S, Wagner E

2. Title: Clinical epidemiology, the essentials
3. Year of Publication 1998
4. Edition (if not the first) 2nd edition
5. Place of publication Baltimore (USA)
6. Publisher Williams and Wilkins

Fletcher R, Fletcher S, Wagner E. Clinical epidemiology, the

essentials. 2nd ed. Baltimore: Williams and Wilkins, 1998.

53
 drzahir@kb.usm.my

Referencing a website

1. Author/editor/organisation: Loney PL, Chambers LW, Bennett KJ, Roberts

JG, Stratford PW
2. Year written (or last updated): 2004
3. Title: Critical Appraisal of the Health Research Literature Prevalence or
Incidence of a Health Problem
4. URL: http://www.phac-aspc.gc.ca/
5. Date you accessed or retrieved it: 17 March 2009

Loney PL, Chambers LW, Bennett KJ, Roberts JG, Stratford

PW. (2004). Critical Appraisal of the Health Research Literature
Prevalence or Incidence of a Health Problem. Available at:
http://www.phac-aspc.gc.ca/ Accessed on 17 March 2009.
For future reference, print and keep a copy of the website
54
 drzahir@kb.usm.my

Cite While You Write™ (CWYW) in EndNote

 Use CWYW™ to easily and quickly cite references, figures, and

tables, and create a paper with properly formatted citations, a
bibliography, figures, and tables.

 EndNote comes with more than 4,000 predefined bibliographic

styles for the leading journals. Each style can be modified, or you
can create new styles.

 Authors are encouraged to use EndNote built-in Word templates to

guide them through the manuscript requirements of publishers.

 Authors now get more done in less time, and spend less energy on
unformatting or rebuilding bibliographies.
55
 drzahir@kb.usm.my

Cite While You Write (CWYW)

CWYW
Word Endnote

 CWYW gives you access to Endnote references and

formatting commands through a Endnote submenu on
Word‟s Tool menu.
 It helps insert (cite) references into the word document
 It also embeds the references in the word document as
“travelling library”

56
 drzahir@kb.usm.my

Manuscript writing templates

• Beside using plain Word document, you can use a
manuscript template in the Endnote to set up your paper.

• Endnote has hundreds of template files of Journals.

• Open through Endnote program:

Endnote  Tools menu  manuscript templates

• OR through program folders:

 C:  Program Files  Endnote  Templates.
 drzahir@kb.usm.my

Opening Templates for writing

Open “Tools”, then go to
“Manuscript Templates”

Select and double click the

file and start writing up.
 drzahir@kb.usm.my

Manuscript templates in Words doc

 drzahir@kb.usm.my

Basic instructions in CWYW

1. Open the Endnote library files that contain relevant references
you wish to cite.
2. Open the Microsoft Word document .
3. Write up the manuscript text. When you ready to cite a reference,
position the cursor EXACTLY (before the full stop) where you
want to put the citation in the text.

60
 drzahir@kb.usm.my

The reference will be inserted in the

designated place and the citation (and the
rest of other full citations) will appear at the
end of the document (not at footnote).

61
 drzahir@kb.usm.my

Inserting references (in-text citations)

Ref.1: Heath et al, 1999

Ref.2: Skov et al, 1996

62
Ref.3: Guthrie et al, 2000
 drzahir@kb.usm.my
Method 1: Locate the cursor in Word, then select the
reference to be inserted (cited), then click “Insert
Selected Citation” of CWCY tool or “Insert Citation” icon

63
 drzahir@kb.usm.my

Method 2: Insert pre-selected citations from

Endnote library into the Word document

Studies among indigenous communities in many countries have showed that STDs (including
HIV/AIDS) have become public health challenges in the populations. Many evidences have
shown that socio-demographic and economic factors among aborigines may have influenced
sexual risk behaviours and drug abuse among them(1). Among aboriginal population in central
Australia, their mobile lifestyle and also the practice of highly-risked traditional rituals may have
influence the high prevalence of sexually transmitted infections. Furthermore, HIV prevalence
among these aboriginal groups was almost similar to that of the general population of Australia.

REFERENCES

1. Heath KV, Cornelisse PG, Strathdee SA, Palepu A, Miller MLea. HIV-associated risk
factors among young Canadian Aboriginal and non-Aboriginal men who have sex with men. Int
J STD & AIDS. 1999;10:582-7.
64
 drzahir@kb.usm.my

Method 2: Insert pre-selected citations from

Endnote library into the Word document

Studies among indigenous communities in many countries have showed that STDs (including
HIV/AIDS) have become public health challenges in the populations. Many evidences have
shown that socio-demographic and economic factors among aborigines may have influenced
sexual risk behaviours and drug abuse among them(1). Among aboriginal population in central
Australia, their mobile lifestyle and also the practice of highly-risked traditional rituals may have
influence the high prevalence of sexually transmitted infections. Furthermore, HIV prevalence
among these aboriginal groups was almost similar to that of the general population of Australia.

REFERENCES

1. Heath KV, Cornelisse PG, Strathdee SA, Palepu A, Miller MLea. HIV-associated risk
factors among young Canadian Aboriginal and non-Aboriginal men who have sex with men. Int
J STD & AIDS. 1999;10:582-7.
65
 drzahir@kb.usm.my

Method 3: Find the citation using “Find

citation” menu in the Endnote

To insert (Guthrie et al, 2000)

66
 drzahir@kb.usm.my

Continue with other citations in the text

Studies among indigenous communities in many countries have showed that STDs (includ ing
HIV/AIDS) have become public health challenges in the populations. Many evidences have
shown that socio-demographic and economic factors among aborigines may have influenced
sexual risk behaviours and drug abuse among them (1). Among aboriginal population in central
Australia, their mobile lifestyle and also the practice of highly -risked traditional rituals may have
influence the high prevalence of sexually transmitted infections(2). Furthermore, HIV prevalence
among these aboriginal groups was almost similar to that of the general population of
Australia(3).

REFERENCES

1. Heath KV, Cornelisse PG, Strathdee SA, Palepu A, Miller MLea. HIV -associated risk
factors among young Canadian Aboriginal and non -Aboriginal men who have sex with men. Int
J STD & AIDS. 1999;10:582-7.
2. Skov S, Bowden F, McCaul P, Thompson J, Scrimgeour D. Managing HIV. Part 6:
People living with HIV. 6.6 HIV and isolated Aboriginal communities. Med J Aust. 1996 Jul
1;165(1):41-2.
3. Guthrie JA, Dore GJ, McDonald AM, Kaldor JM. HIV and AIDS in aboriginal and
Torres Strait Islander Australians: 1992-1998. The National HIV Surveillance Committee. Med J
Aust. 2000 Mar 20;172(6):266-9.

This is “numbered” or “Vancouver”

referencing format/styles 67
 drzahir@kb.usm.my

Formatting bibliography
 You can change or format your citations and
bibliography as many time as required, based on the
journal default or the output styles manually.

APA 5th is an example of a “Harvard”

referencing format/styles 68
 drzahir@kb.usm.my

The bibliography has been formatted

automatically into another style
(Extracted from Anita et al, 2007)
Studies among indigenous communities in many countries have showed that STDs (includ ing
HIV/AIDS) have become public health challenges in the populations. Many evidences have
shown that socio-demographic and economic factors among aborigines may have influenced
sexual risk behaviours and drug abuse among them (Heath, Cornelisse, Strathdee, Palepu, &
Miller, 1999). Among aboriginal population in central Australia, their mobile lifestyle and also
the practice of highly-risked traditional rituals may have influence the high prevalence of
sexually transmitted infections(Skov, Bowden, McCaul, Thompson, & Scrimgeour, 1996) .
Furthermore, HIV prevalence among these aboriginal groups was almost similar to that of the
general population of Australia(Guthrie, Dore, McDonald, & Kaldor, 2000).

REFERENCES

Guthrie, J. A., Dore, G. J., McDonald, A. M., & Kaldor, J. M. (2000). HIV and AIDS in
aboriginal and Torres Strait Islander Australians: 1992 -1998. The National HIV
Surveillance Committee. Med J Aust, 172(6), 266-269.
Heath, K. V., Cornelisse, P. G., Strathdee, S. A., Palepu, A., & Miller, M. L. e. a. (1999). HIV -
associated risk factors among young Canadian Aboriginal and non -Aboriginal men who
have sex with men. Int J STD & AIDS, 10, 582-587.
Skov, S., Bowden, F., McCaul, P., Thompson, J., & Scrimgeour, D. (1 996). Managing HIV. Part
6: People living with HIV. 6.6 HIV and isolated Aboriginal communities. Med J Aust,
165(1), 41-42.

69
 drzahir@kb.usm.my

Select the output styles as required by

your journal or thesis

70
 drzahir@kb.usm.my

Formatted to USM Harvard-version

(Harvard-USMVer3)

71
 drzahir@kb.usm.my

Editing citations in text documents

• It is not possible to edit citations
or bibliography directly using Word,
as direct edits are lost each time
EndNote reformats the bibliography.

• Edit Citation(s)
Use this command to make
any changes inside a citation,
such as adding page numbers
or removing author names
from author-date citations.

• Edit Library Reference(s)

This command allows you to
quickly access the specific record
for any selected citation.
72
 drzahir@kb.usm.my

Removing field codes

You may be required to remove
your “Endnote‟s field codes"
from your Word document.

Use “Convert to Plain Text”

styles tools in Word document

• This command will create a second copy of the document with all
EndNote field coding removed (generally recognized field codes by their
turning grey when you select them in Word).

• It is used when sending documents to a publisher because the field

coding used for EndNote citations can sometimes cause problems for
publishers‟ page layout programs.
73
 drzahir@kb.usm.my

Summary in CWYW steps

1. Create a reference database (an Endnote library)

which is relevant to the manuscript/paper

2. Insert the citations (selected references from your
Endnote library) into your paper (Word document text)

3. Generate bibliographic formatting as required journal
style into the word document

4. Before sending to journal, remove the “Field codes”.

74
drzahir@kb.usm.my

Thanks

75