Writing a Research Paper

Report
Journal Searching and Citation
Management with EndnoteWeb
Nancy B. Clark, M.Ed.
Director of Medical Informatics Education
FSU College of Medicine
Summer 2011
All recourses are available online in Medical
Informatics site under Topics: Research
1
My Goal
All faculty and students will correctly cite all
copyrighted resources (images, articles,
videos, etc.) in their:
Presentations
Posters
Papers –Annotated Bibliography, Health Topic
Brief, and Surgery Research Paper
2
Session Objectives
Attendees will be able to
Use Pubmed to search the medical journals
Find full text peer-reviewed journal articles
Find online health stats
Cite appropriately in a specified style
Use Endnote Web to manage citations and
references for papers, posters and presentations
3
Tutorials Available
Tutorials at Pubmed
Searching PubMed
Using Mesh Terms
Using My NCBI
Tutorials at EndnoteWeb.com
4
Supportive Materials
Policy Brief Instructions
Examples of AMA style citations
5
Essential Software
MSWord 2010
Endnote Web Cite While you Write plugin
http://www.endnoteweb.com
Stedman’s Medical Spellchecker
6
Find the Journals
7
Levels of References
 Primary:
Peer Reviewed
journal articles
 Secondary:
Primary
Not peer reviewed
Secondary
8
Levels of Peer Reviewed Information
Primary: original
research
Primary
Secondary
Secondary: review
articles
Tertiary: textbooks,
summaries
Tertiary
9
Clarification for Assignment
Primary means original research on topic
Secondary means everything else
Annotated Bibliography 8 references requires
10
Periodical Databases
 See FSU Libraries > Databases A-Z or
Databases By Subject
 ERIC (education journals)
 Lexis-Nexis Academic Universe (business,
government, medical, legal...)
 Access World News (major newspapers)
 PsychINFO (social sciences)
 Web of Knowledge/Science (science, social
science, arts and literature citations)
 MEDLINE (medicine)
11
What is MEDLINE?
produced by the National Library of Medicine
electronic version of Index Medicus, International
Nursing Index, International Dental Literature
1966 – present
4,000+ international biomedical journals
includes journal articles, reviews, letters, editorials,
comments, some conference proceedings and books
12
MEDLINE Fields
Author
Title
Date
Type of publication
Journal, Volume, Issue
Page numbers
Abstract
Institution
MeSH Headings
A lot of cataloging
numbers
13
Where is MEDLINE?
Pubmed (NLM)
Google Scholar
MDConsult
Medscape
Links to
Full text journal
articles
Books
EBM databases
14
Getting To PubMed From Library
1. Use Search Engines PubMed Box or
2. Use MedResources List or Map
3. Type PubMed into Online Resources search
ID is built into links
15
PubMed MEDLINE
Entering PubMed
Type search terms
Tutorials
Save searches
in NCBI
16
Why get NCBI Account?
Save searches
Save citations in My Bibliography
Automatically update and e-mail search results
from your saved searches
Filter search results
Highlighting search terms
17
18
PubMed MEDLINE
Preliminary Results
Large number of hits.
Scroll down to ‘Details’ to show how PubMed
translated the search. (You can modify the search by
typing in the text box.)
19
Boolean Operators
AND
OR
NOT
Parenthesis
*
quotes
“medication errors” AND
“quality improvement” NOT
(ambulatory OR “nursing
home”)
20
PubMed MEDLINE
Limit Results
Click on ‘Limits’
Limit by
• Pub Date
• Subjects
• Type journal
• Type research
• Language
• …
Warning: Limits
all searches until
removed
21
Types of Articles
Editorials
Letters
Review Articles
Meta-Analysis
 Systematic reviews
Clinical Guidelines
Original Research
 Case Studies
 Case Control
 Time Series
 Cross sectional
 Cohort
 Control trials
 Randomized Control
Trials
22
PubMed MEDLINE
Refined Results
Number of hits is still
quite large. (384 from
previous 22,441)
Add ‘cancer
ethics’ to the
search terms.
23
PubMed MEDLINE
Combining Searches
Multiple Terms:
Use Advanced
Search
History
#2 AND #3
Click on number
of hits to see
results
24
Getting the articles
Display Settings:
Select ‘Abstract’
view and click on
‘Apply’
Click on FSU icon
to link to full text.
25
Click on Article Title: Abstract View
Link to full text FSU subscriptions
Related Citations
26
MeSH Terms
Use MeSH terms to find
search terms.
27
28
When there is no FSU Button…
29
Identify the Full Journal Title
30
Finding Full Text Articles
Pubmed Linked to full text? No…
1. Medical E-Journals list from library
webpage? Not listed…
2. FSU E-Journals from library webpage.
In electronic format? No...
3. Interlibrary loans for titles not owned
by FSU: [email protected]
31
Medical E-Journals
In electronic less
than 12~ years
Each journal
different
Digitizing old
issues slowly
32
PubMed MEDLINE
Getting the articles when there is no FSU icon
If there is no FSU icon, there are
other options:
1. Search E-Journal Titles for the
journal name
33
All FSU E-Journals
Under Resources
Expand E-Journals
Click on
All FSU E-Journals
34
FSU Libraries E-Journals
35
FSU E-Journals
Consultant Pharmacist only up to 2000
36
Interlibrary Loan
Interlibrary Loan:
1. Sign into EZProxy
2. Fill out form
3. Copy and Paste info from
PubMed Citation into Section 2
4. Get PMID #
37
Finding Journal Articles at FSU
DOOR 1
Direct Link to
full-text
article.
JOURNAL ARTICLES
DOOR 2
Locate the
e-journal
with Medical Library
E-Journals list.
DOOR 3
Locate the e-journal
with Serials Solutions
Interlibrary
INTER-LIBRARY
LOAN
[email protected]
.edu
Loan
38
Interesting New Tool: knalij.com
Use Chrome Browser (FireFox second choice)
Open Library site and open Pubmed
In another tab, open knalij.com
Additional Types of Searches
Journal Cluster Map
Co-author Map
Impact of funding Map
39
Finding Health Statistics
40
Informatics Resources
Topic Areas > Research
Health Statistics
41
Types of Health Statistics Questions
Fact lookups [population, demographics]
Research
Presentations
Social and Policy indicators
42
Strategies for Finding Health Stats
Google Search
Use Portal
Start at Internet site
Start with book or article
43
Internet Portals of Health Stats
Lists of links that provide starting points for
browsing or searching
Keyword search in portal vs Google
General idea what you want
The National Center for Health Statistics portal:
http://www.cdc.gov/nchs/
Health Services Research Information Central (NLM)
44
Lexis-Nexis Statistical Universe
Subscription resource
Searches stat data
Subject List
Limit search
Reports or tables
http://web.lexisnexis.com/statuniv?B1=Connect+to+Statistical
+Universe
45
MMWR
Morbidity – illness
Mortality – death
http://www.cdc.gov/mmwr/
Disease Trends
Tables - searchable
46
Health Care Data
Healthcare Cost and Utilization Project
HCUPnet
Hospital discharges
Ambulatory service
Costs
Amount of care
By diagnosis and procedure
Surveys of hosp, physicians, nursing homes
47
Health Consequences
Costs to society, individuals
Cost from care
Costs of illness
Impact on infrastructure
HCFACMS Health Accounts
http://cms.hhs.gov/
48
State and International Data
Floridahealthstat.com - Where Florida Health
Data Resides
KFF State Health Facts Online
United Nations Statistics Division
World Health Organization Research Tools
49
Citations and References
Note: Endnote Web Camtasia
Tutorials on Library Tutorials Page
50
Style Guides
Format of citation on referenced items
AMA Style Guide*
Examples of AMA Citations
Other Style Guides
What do I mean by Style Guides?
Format required for submitting articles to journal
Informatics Resources|Topics|Research|Style Guides
51
APA Style
Now is the time for all good men to come to the aid of their
country.(Alpay & Russell, 2002) Four score and seven years ago
our forefathers brought forth a new nation conceived in liberty and
dedicated to the proposition that all men are created equal.(Balen
& Jewesson, 2004)
References
Alpay, L., & Russell, A. (2002). Information technology training
in primary care: the nurses' voice. Comput Inform Nurs, 20(4),
136-142.
Balen, R. M., & Jewesson, P. J. (2004). Pharmacist computer
skills and needs assessment survey. J Med Internet Res, 6(1),
e11.
52
JAMA Style
Now is the time for all good men to come to the aid of their
country.1 Four score and seven years ago our forefathers
brought forth a new nation conceived in liberty and dedicated
to the proposition that all men are created equal.2
References
1. Alpay L, Russell A. Information technology training in
primary care: the nurses' voice. Comput Inform Nurs. Jul-Aug
2002;20(4):136-142.
2. Balen RM, Jewesson PJ. Pharmacist computer skills and needs
assessment survey. J Med Internet Res. Mar 29 2004;6(1):e11.
53
EndnoteWeb
Stores your reference citations on the web
Assign to topic groups
Word add-in
Manages Citations
Inserts References in Word
Automatically formats in selected style
Does not store PDF articles. Endnote desktop
54
does.
Research Paper
Endnote Library
of References
Now is the time for all
good men to come to
the aid of their country.
(citation)
Stack of
References:
Journal articles
Book chapters
Web sites
Monographs
References
- Bibliographic citation
-
Word Document
55
First Time You Start Endnote Web
1.
2.
3.
4.
www.myendnoteweb.com
Set up Account
UserID: email
Password (8 character minimum, must have
at least 1 letter, 1 number, 1 symbol)
56
Start Endnote Web in Word
2010
X
Endnote Web Tool Bar on Ribbon
Will ask you to sign in
57
Use Endnote Web in Word
1. Create an Endnote Library online
2. Add all cited articles, books, websites, etc. to
library
3. Set the Format to JAMA
4. As you type, Find and insert citation
•
Pick reference from library
5. Endnote creates the bibliography
58
Organize Your References
Create New Group for a project
59
How to Populate the Library - Options
Endnote Web References
 Manually enter references
 Connect to Pubmed or other
database and capture
 Search Pubmed or other DB
and save results then import
(see tutorials on Library
website)
 In Google Scholar, WOS or
OVID, search and export
directly to Endnote
60
Add Citations to Library
Type them in
Book chapters
Images
Newspaper articles
Statistical Reports
Websites
Let Endnote Web grab from PubMed,
PsychLit, OVID, etc.
Journal articles
61
How to Type in Citation
In Endnote Web
 Collect Tab
 Select New Reference
Pick reference type
Type in fields
Pick Group to save to
Click SAVE
62
What Fields Do You Need to fill in?
Look at or print our
Examples AMA Citations
Under Style Guides in Research
63
Citing Images
 Use Audiovisual Material: should contain the following
information about the image:
 Photographer's or artist's name (often not given)
 Title of picture or Name of subject
 Date of picture (often not given)
 Title of website
 URL of page in which image found (not of image itself)
 Date you accessed the picture.
 SAMPLE:
Kawasaki, Satoko. Bobby Valentine. October 14, 2005. The Japan Times.
www.japantimes.co.jp/ sports/2004bbpreview.htm October 27, 2005.
64
How to Capture References
Collect Tab
Online Search
Pick a source
Pubmed [NLM]
Connect
Select Favorites to
limit scrolling
65
Perform Search
If article known
Use Author and Title word
Search
66
Perform Search
Retrieve Articles found
Pick article(s)
Add to Group
Pick group
67
Export References from Pubmed
 Collect articles in Clipboard [Check articles
as found and Send to Clipboard.]
Open Clipboard and check all articles to
export
Send to >> File
Format >> MEDLINE
Save on desktop
68
Import file into Endnote Web
Collect Tab >>
Import References
Browse to file
Import Options:
Pubmed (NLM)
To: >> pick a group
Import button
69
Cite While You Write
In Word
1. Put Cursor on spot
2. Endnote Web
Ribbon
•
Find Citation
3. Type author or
distinctive word in
title
4. Click Find
5. Click citation of
choice
6. Click Insert
Insert
70
Citation and Reference Appear in Word Document
71
Set AMA Style
Need to load 1 time
In Endnote Web Ribbon
Style: dropdown
Find JAMA
If not there…
Open Bibliography
dialog box
Pick JAMA under
output style
72
Export References
Citations for posters or
presentations
Pick Style
Format >>
Bibliography
Save as RTF
Open in Word
Copy and paste in
PowerPoint/Publisher
73
Hands on practice
Do a few on your own.
If you are missing Endnote Web or
Stedmans, go by IT office or tell Help
Desk and get them installed.
74
In Summary
Use Pubmed to Search for Articles, My NCBI
to manage
Use red FSU button to find articles
If no button: Med eJournals list > FSU
eJournals > Interlibrary loan
Any journal article you need, we will get
Use Endnote to manage your citations in your
papers, presentations and posters
75
Using NCBI
Register and get a Username and
Password
76
Why get NCBI Account?
Save searches
Save citations in My Bibliography
Automatically update and e-mail search results
from your saved searches
Filter search results
Highlighting search terms
77
78
My NCBI
79
Customize My NCBI
Tutorials: http://www.nlm.nih.gov/bsd/disted/myncbi.html
Saving Searches
Saving References
Customizing the Tabs
Highlighting Search Terms
80 80
My NCBI – Saving a Search
Develop a search.
Click on ‘Save Search’.
April 29, 2008
Medical Informatics Seminar Session 6
81 81
My NCBI – Saving a Search
Give name and
Save
Complete form for
email notification
‘My NCBI’ puts
the search in your
list.
82
My NCBI – Saving References (1)
Develop a search.
Check the references you want to save.
Click on ‘Send To’ and select ‘Clipboard’.
April 29, 2008
Medical Informatics Seminar Session 6
83 83
My NCBI – Saving References (2)
Go to the ‘Clipboard’
Click on ‘Send To’ and select Collections.
84
My NCBI – Saving References (3)
Tell My NCBI what to
call the collection
Or Append to an existing
collection
April 29, 2008
Medical Informatics Seminar Session 6
85 85
My NCBI – Saving References (4)
To see the collection or
saved search, click on
‘My NCBI’ >
Collections
Can download
collections into a
reference manager
such as EndNote or
RefWorks.
86 86
My NCBI – Customizing the Filters
1. Click on ‘My NCBI’
2. ‘Manage Filters’
87
My NCBI – Customizing the Filters
 Try “Browse Filters” to see different types
88
My NCBI – Highlighting Search Terms
Click on ‘NCBI Site
Preferences’.
Click on ‘Highlighting’
Pick colors
89
Have Journal Contents Sent (1)
1. Search ‘Journals Database’
2. Enter a general subject term, e.g. “Pediatrics”, then
‘Go’.
3. Click on a journal title to get information about that
journal.
4. Continue with another search for a Journal, find and
select
5. Click on ‘Send to’ and select ‘Search Box with OR’.
90
91
Have Journal Contents Sent (2)
4. Click on ‘Search PubMed’.
5. Click on ‘Save Search’, name it, and set up
email as earlier.
6. You will be notified when new articles are
published in these journals.
92
Links to Other NCBI Databases
NCBI has other databases
that link to PubMed.
(examples: CoreNucleotide,
Gene, HomoloGene,
Protein, Protein)
93 93

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