ResMethod - Literature Search and Personal Reference Databases - Y2019

Research Methodology in Biomedical Engineering:
LITERATURE SEARCH and PERSONAL REFERENCE DATABASES
Instructor: Nguyen Thi Lan Phuong

Email: ntlphuong@medvnu.edu.vn
Jul 13, 2021, HCMC, Viet Nam 1

LITERATURE SEARCH and
PERSONAL REFERENCE DATABASES
Contents
1 How to formulate a query? Develop a search strategy
2 Search technique - Exploring search engines -Principle

bibliographic databases
3 Medical and scientific internet search engine
4 References and bibliography

2
Sources to search
 Databases: general health sciences vs subject-specific

General health sciences databases: Subject-specific databases:
-Medline, -CINAHL (nursing and allied health)
-Embase, -PsycInfo (mental health)
-Central, -etc.
-etc.
 Check reference lists: in relevant studies and previous relevant systematic

reviews
 Grey literature: unpublished data such as theses, conference proceeding,

official document Sources:
-Google Scholar
-Scopus,
-Web of Sciences,
-etc.
 Personal contact with experts in fields 3

Sources to search
 Use multiple sources and start with the sources that return the most studies
 At least 2 databases will be used to conduct searching
 Database selection will depend on the research topic

• (Bramer et al., 2017. Systematic Reviews.;6:1-2.)
• regardless of the topic, searches for biomedical systematic reviews

should combine Embase, MEDLINE, Web of Science (Core Collection),
and Google Scholar (the 200 first relevant references) at minimum
• Consider adding special topics databases such as CINAHL and

PsycINFO if the topic of the review focuses on a specialized subject
database
• (The Cochrane handbook v6.2)
• For reviews focus on experimental trials (RCTs), Cochrane CENTRAL, 4
MEDLINE and Embase are recommended

Types of scientific publications
Primary or original Secondary or Tertiary

Special articles Gray literature
research articles review articles literature
- Randomized
controlled trial - Letters/ - Textbooks,
- Narrative
correspondence handbooks,
- Clinical trial review
manuals - Conference
- Before-and-after - Systematic - Short proceedings, posters,
communications - Trade or
study review abstracts
professional
- Cohort study - Meta-analysis - Editorials/opinion - Government reports
publication
- Case-control study - Commentaries articles - For-profit and
- Cross-sectional - Pictorial essay - Encyclopedias nonprofit organization
survey - Other special reports online forums
- Diagnostic test categories - Blogs, microblogs,
assessment and other social
media
- Case report/case
series
- Technical note
5
Impact factors (IF)
(1961) - the ISI Science Citation Index provides a basis for the impact factor (IF)
• Is a measure of the citation frequency of the average article in a particular journal

for a given year
• Is calculated as the ratio of citations over a specific year generated by articles
published in that journal in the previous two year.
• IF should be used with care
6
DEVELOP A SEARCH STRATEGY
Choose the elements in PICOS framework that would be

Choose
most helpful in planning a search; commonly use P, I, S
Finding search terms for each elements and build a search

Finding terms library including key concept, synonyms, alternative
words, control vocabulary
Process search: search text words (Title/abstract or All

Process
fields) and index terms (MeSH terms)
Refine search strategy: Consider the balance of the sensitivity and

specificity
Refine If there are too many, or too few results → revise the search strategy
If the search result is accepted → refine search terms: check and exclude
overlap search terms
7
Define research question: PICOS framework
Population / Patients (demographic factors, disease status, etc. )

P
Who are you interested in studying in your review?
Interventions/Exposures (drugs, procedure, etc.)

I What is the intervention or group of interventions you want to test?
Comparison (alternative interventions, placebo, etc.)

C
What will the interventions be compared to?
Outcomes (improvement, effect, measure, etc.)

O
What outcomes will tell you which intervention is the most effective?
Study designs (RCTs, economic evaluations, etc.)

S Which study designs are fit your outcomes of interests?
8
EXAMPLES OF HOW TO DEVELOP A SEARCH STRATEGY
Research question: Evidence on economic evaluation of

atezolizumab in the treatment of non-small cell lung cancer
patients with high PD-L1 expression?
1 Choose the elements in PICOS framework
P: non-small cell lung cancer

I: atezolizumab
S: economic evaluation
9
Research question: Evidence on economic evaluation of
atezolizumab in the treatment of non-small cell lung cancer
patients with high PD-L1 expression?
2 Finding search terms and build a search terms library
Element P I S
Key concept non-small cell lung cancer atezolizumab economic evaluation
Synonyms, non small cell lung carcinoma Tecentriq economic analysis

nonsmall-cell lung cancer RO5541267 cost-minimization
alternative
NSCLC cost-effectiveness
words
non small cell pulmonary cancer cost-utility
non small cell pulmonary carcinoma cost-benefit
non small cell lung tumour cost-efficacy
large cell lung carcinoma pharmacoeconomic
large cell lung cancer pharmaceutical analysis
lung adenocarcinoma
Controlled carcinoma, non-small-cell lung - analyses, cost benefit
vocabulary
10
Title
Abstract
11
Keywords
Controlled vocabulary/index term
12
No. Query Results
P #1 “non-small cell lung cancer”[All Fields] 66,327
#2 “non small cell lung carcinoma”[All Fields] 5,015
#3 “non small cell lung carcinomas”[All Fields] 1,052
3 #4 “nonsmall-cell lung cancer”[All Fields] 2,612
#5 “NSCLC”[All Fields] 51,486
Process #6 “non small cell pulmonary cancer”[All Fields] 4
search #7 “non small cell pulmonary carcinoma”[All Fields] 11

#8 “non small cell lung tumour”[All Fields] 10
with text #9 “large cell lung carcinoma”[All Fields] 186
#10 “large cell lung cancer”[All Fields] 218
words and
#11 “lung adenocarcinoma”[All Fields] 18,714
index term #12 “carcinoma, non small cell lung”[MeSH Terms] 61,138
I #13 Tecentriq[All Fields] 2008
#14 Atezolizumab[All Fields] 2003
S #15 “economic evaluation”[All Fields] 11,855
#16 “economic analysis”[All Fields] 6,560
#17 “cost-minimization”[All Fields] 1,153
#18 “cost-effectiveness”[All Fields] 67,766
#19 “cost-utility”[All Fields] 5,581
#20 “cost-benefit”[All Fields] 94,801
#21 “cost-efficacy”[All Fields] 759
#22 “pharmacoeconomic”[All Fields] 3,794
#23 “pharmaceutical analysis”[All Fields] 5,774
13
#24 “cost-benefit analysis”[MeSH Terms] 87,801
3 Process search with text words and index term
No. Query Results

P #25 #1 OR #2 OR #3 OR #4 OR #5 OR #6 102,652
OR #7 OR #8 OR #9 OR #10 OR #11
OR #12
I #26 #13 OR #14 2008
S #27 #15 OR #16 OR #17 OR #18 OR #19 143,449
OR #20 OR #21 OR #22 OR #23 OR
#24
P AND I AND S #28 #25 AND #26 AND #27 19
14
4 Refine search strategy Check and exclude overlap search terms
A
A
B
B
(A) OR (B) = (A) → exclude term (B) (B) NOT (A) = 0 → exclude term (B)
→ Remove the term Atezolizumab

15
No. Query Results
#1 “non-small cell lung cancer”[All Fields] 66,327
#2 “non small cell lung carcinoma”[All Fields] 5,015
#3 “non small cell lung carcinomas”[All Fields] 1,052
#4 “nonsmall-cell lung cancer”[All Fields] 2,612 Present final search strategy:
#5 “NSCLC”[All Fields] 51,486 see item 7 in PRISMA
#6 “non small cell pulmonary cancer”[All Fields] 4
P
#7 “non small cell pulmonary carcinoma”[All Fields] 11
#8 “non small cell lung tumour”[All Fields] 10
#9 “large cell lung carcinoma”[All Fields] 186
#10 “large cell lung cancer”[All Fields] 218
No. Query Results
#11 “lung adenocarcinoma”[All Fields] 18,714
#12 “carcinoma, non small cell lung”[MeSH Terms] 61,138 #24 #1 OR #2 OR #3 OR #4 102,652
I #13 Tecentriq[All Fields] 2008 OR #5 OR #6 OR #7

P
#14 “economic evaluation”[All Fields] 11,855 OR #8 OR #9 OR #10
#15 “economic analysis”[All Fields] 6,560 OR #11 OR #12

I #25 #13 2008
#16 “cost-minimization”[All Fields] 1,153
#17 “cost-effectiveness”[All Fields] 67,766 #26 #14 OR #15 OR #16 143,449
OR #17 OR #18 OR
#18 “cost-utility”[All Fields] 5,581 S
S #19 OR #20 OR #21
#19 “cost-benefit”[All Fields] 94,801
OR #22 OR #23
#20 “cost-efficacy”[All Fields] 759
P AND I #27 #24 AND #25 AND #26 19
#21 “pharmacoeconomic”[All Fields] 3,794
AND S
#22 “pharmaceutical analysis”[All Fields] 5,774
#23 “cost-benefit analysis”[MeSH Terms] 87,801 Searched on 26 Dec, 2021 16
Contents
2 Search technique - Exploring search engines -

Principle bibliographic databases

17
2 Exploring search engines Pubmed
Access link: https://pubmed.ncbi.nlm.nih.gov/
18
Pubmed: Overview
 Available to the public online since

1996
 Free resource developed and

maintained by the National Center for
Biotechnology Information (NCBI), at
the U.S. National Library of Medicine
(NLM)
 Comprise > 30 million citations and

abstracts of biomedicine and health
fields, and related disciplines such as
life sciences, behavioral sciences,
chemical sciences, and bioengineering
19
Pubmed: Searching
Basic
search
Advanced
Search
20
Pubmed: Advanced search
Advantages of “advanced search” function
▪ Search for terms in a specific field
▪ Combine searches and build complex search strings
▪ See how each query was translated by PubMed
▪ Compare number of results for different queries
1 2 3
5
4
21
1 Exploring Pubmed and Cochrane library
Pubmed: Advanced search Text words
Title/Abstract [TIAB]
Words and numbers included in a citation's title, collection title,
abstract, and keywords
All Fields [ALL]

•Untagged terms and terms tagged with [all fields] are processed
using Automatic Term Mapping (ATM) if possible
•Terms that do not map are searched in all search fields except for
Place of Publication, Transliterated Title, Create Date, Completion
Date, Entrez Date, MeSH Date, and Modification Date
• PubMed ignores stopwords (a, about, because, been, can, could,

etc.) 22
Automatic Term Mapping (ATM) feature:

▪ Automatically matching your word with MeSH terms, journal and authors
and investigators, as well as doing an ‘All Fields’ search
▪ ATM feature will be off if search terms are enclosed in double quotes (“ ”),
or terms are truncated (*), or search terms not enclosed in (“ ”) but with a
search field other than [All fields] such as: [Title], [Text word], etc.
We have lung cancer in the search bar

This is how Pubmed translated the term using
ATM to search for the MeSH lung neoplasms OR
the words lung and neoplasms together in any
field OR the phrase lung neoplasms in any field
OR the words lung and cancer in any field OR the
phrase lung cancer in any field
23
Automatic Term Mapping (ATM) feature:

▪ Automatically matching your word with MeSH terms, journal and authors
and investigators, as well as doing an ‘All Fields’ search
▪ ATM feature will be off if search terms are enclosed in double quotes (“ ”),
or terms are truncated (*), or search terms not enclosed in (“ ”) but with a
search field other than [All fields] such as: [Title], [Text word], etc.
ATM feature automatically

turned off
24
Index terms
MeSH [MH]
•The Medical Subject headings is the is the National Library of

Medicine's (NLM) controlled vocabulary of biomedical terms
described the subject of each journal article in MEDLINE
•Updated annually by skilled subject analysts
•Arranged in a tree structure by subject categories with more

specific terms arranged beneath broader terms
25
Pubmed: MeSH database
Access MeSH
database
26
MeSH database interface
27
Pubmed: MeSH database overview
28
Definition of terms
Subheadings: allow
to restrict the search
to a subtopic of
interest
29
Entry terms are

synonyms, alternate forms,
or alternate spellings of the
MeSH terms Tree structure:
Automatic explosion
Entry terms of “lung neoplasms”
30
31
Why should use MeSH?

▪ Contains all synonyms, alternate form of a MeSH term, and any
specific terms intended under that term in the MeSH hierarchy
→Search for medical concepts using the Medical Subject Headings

(MeSH) thesaurus
→Allows users to search complex medical concepts using a single term

without the need to type long list of synonyms
▪ MeSH ensures that articles are uniformly indexed by subject,

whatever the author's words → effective for searching and retrieving
articles related to a concept, even though those words described
that concept did not appear in the text of the articles
32
Boolean operators
• Combine or exclude search terms

•AND: Retrieves results that include all the search terms:
•Example: insulin AND diabetes
•OR: Retrieves results that include at least one of the search terms
•Example: heart OR cardiac
•NOT: Excludes the retrieval of terms from your search

•Example: aids NOT hearing
33
AND OR NOT
Pubmed: Advanced search Search syntax
❑ Phrase searching- using double quotes “ ”: keep words together and in order
Example: “lung cancer”, “chronic kidney disease”
❑ Using Wildcards (truncation): search for all terms that begin with a word root
• Asterisk *: find for one or more characters
At least 4 characters must be provided in the word root. The wildcard must be
added to the end of the term
Example: gene*: search for gene, genes, genetics
***Search for phrase including a truncated term: The truncated term must be the
last word in the phrase, use the following formats:
o Enclose the phrase in double quotes: “lung cancer*"
o Use a search tag other than [All fields]: lung cancer*[tiab]
o Use a hyphen: lung-cancer*
34
Pubmed: Advanced search Save search
Save Search
•Register on PubMed and log in to your account (FREE)
•Click "Create alert“ under the search bar to receive an automatic email update for searches
35
Pubmed: Advanced search Save search
Save Search
•Register on PubMed and log in to your account (FREE)
•Click "Create alert“ under the search bar to receive an automatic email update for searches
36
Pubmed: More to explore
37
Pubmed: More to explore
38
Cochrane library
Access link: https://www.cochranelibrary.com/
39
Cochrane library: Overview
• A collection of databases that contain

different types of high-quality, independent
evidence to inform healthcare decision-
making
• Produced by the Cochrane Collaboration
Databases includes:
✓ The Cochrane Database of Systematic Reviews (CDSR),
✓ The Cochrane Central Register of Controlled Trials (CENTRAL),
Cochrane Clinical Answers,
✓ Other external databases
The Cochrane Database of Systematic Reviews (CDSR) is the

leading resource for systematic reviews in health care
40
Cochrane library: Basic search
41
Cochrane library: Basic search
42
Cochrane library: Advanced search
43
•perform quick searches using just a few terms
•pull down menus to search using field labels
Search tab •auto-suggest feature
•support up to five search rows
•Enter search term(s) in box (by default common variants of the word
are searched)
44
Search tab
Word variations will be

searched by default in
the ‘Search’ tab but
can be turned off by
unchecking the box
45
• Create complex multi-line search strategies

Search • Enter search term(s) in box. (By default, common
manager variants of the word are NOT searched)
• Can perform a MeSH search directly
46
Search manager
The search
slideout to
choose search
fields (abstract,
keyword, etc. via
menu selections
The MeSH
slideout to
perform a MeSH
search directly
within the
Search manager
The filter button

to open the
search limite
47
Automatic stemming feature
• Searching all common variants of a term

Linguistic variants: clear finds clear, clears, cleared, clearing, clearer, clearest
Common British vs. American spelling variants: tumor also finds tumour
Non-standard plural variants: mouse also finds mice
Common irregular verbs: run also finds ran, runs, running
• Can be turned on and off using the limits selection box
• By default, Automatic stemming will be turned on in the “Search” tab and
turned off in the “Search Manager” tab
• Automatic stemming will be disabled if search terms include truncation (*)
48
Cohrane library: Advanced search
MeSH searching
49
MeSH searching
Enter your search terms here. Auto-complete

presents common search terms as you type
Use MeSH
subheadings to limit
your search
50
MeSH searching
Use this area to add a

MeSH search to your
Search manager, view
your results, or save an
individual MeSH search
51
MeSH searching in Search Manager
Add a MeSH Search

Use the "MeSH"
button to add a
MeSH term to the
Search manager
Enter a MeSH Search directly in Search Manager

▪ [mh] is used to indicate the search term/string contains a MeSH heading
▪ Phrases must be placed in double quotation marks
▪ ^ can be placed before the MeSH heading to turn explosion off
Example: [mh cancer]; [mh “breast cancer"]; [mh ^”breast cancer”]
52
Boolean operators
• Combine or exclude search terms
•AND: Retrieves results that include all the search terms:
•Example: insulin AND diabetes
•OR: Retrieves results that include at least one of the search terms
•Example: heart OR cardiac
•NOT: Excludes the retrieval of terms from your search

•Example: aids NOT hearing
53
AND OR NOT
Proximity operators
NEAR
•Finds the terms when they are within 6 words of each other. Terms can
appear in either order
•Example: cancer near lung (finds lung cancer as well as cancer of the lung)
NEAR/X
•Finds the terms when they are within X words of each other
•X = the maximum number of words between search terms. Terms can
appear in either order
•Example: cancer near/3 lung (finds lung cancer, as well as, cancer of the lung)
NEXT
•Finds the terms when they appear next to each other. Terms must
appear in the order specified. Use for phrase searching with wildcards
•Example: lung next cancer (finds lung cancer but not cancer of the lung)
•Example: hearing NEXT aid* (finds hearing aid and hearing aids)
54
Search syntax
❑ Phrase searching: using double quotes “ ”:
Example: “lung cancer”, “chronic kidney disease”
❑ Using Wildcards (truncation) – search for all terms containing a word root
• Asterisk *: search for zero or more characters
• Question mark ?: search for zero or one characters
A wildcard can be added to the end of term, beginning of term or within a term
At least 3 characters must be provided in the word root
Example: *glycemia: finds hyperglycemia or hypoglycemia

Leuk*mia: finds both leukemia and leukaemia
Wom?n finds women or woman; system?
❑ ***Search for phrase including a wildcard: use “NEXT”

Example: hearing NEXT aid* (finds hearing aid and hearing aids)
55
Save search
•Save Search
•Register with the Cochrane Library and log in to your account (FREE)
56
View saved searchs
•“Load” button: run a saved search
•“Email alert” button: receive an email every time new articles indexed with their
search terms are published in the Cochrane Library
•“Append” button: to add your saved search strategy to an existing strategy in

Search Manager
•“Share” button: to send a link to another user to let them run and view results of
your shared strategy on The Cochrane Library
57
Cochrane library: More to explore
58
Other search engines
59
Principle bibliographic databases
Database MEDLINE EMBASE COCHRANE LIBRARY

Time span 1966- 1974- Aims at comprehensiveness
>4900 journals from 70 >4400 systematic reviews;
Extent >5000 journals from 70 countries
countries >478000 controlled trials
Cochrane Reviews; other
General medical database. Biomedical and pharmacological
reviews (DARE); clinical trials;
Covers medicine, nursing, database. Human medicine, clinical and
Scope methods studies; technology
dentistry, veterinary medicine, experimental. Broad coverage of
assessments; economic
public health, allied health pharmacology, toxicology, drug therapy
evaluations
Clinical medicine; evidence-
Focus Biomedicine Medicine; pharmacology; drug research
based medicine
Varies according to vendor;: Weekly. New entries indexed earlier than
Updating Quarterly
daily, weekly, quarterly in Medline
Medical Subject Headings EMTREE: >52000 subject terms, of
Controlled
(MeSH): 24000 subject which >25000 cover drugs and MeSH
vocabulary
headings chemicals
Free access in PubMed Best databases for pharmacological
Updated systematic reviews in
interface. topics; strong on European research;
Benefits full text; best database for
General database for all more subject terms assigned than in
controlled trials
healthcare workers Medline
60% overlapping at journal 60% overlapping at journal level vs All control trials form Medline
level vs EMBASE; cover South Medline; 10-75% overlapping depending included, likewise from other
Overlapping
America and Japan better than on topic searched; covers Africa and sources; systematic reviews
EMBASE Asia better than Medline indexed in Medline 60
Contents


61
Google Scholar
62
What is Google Scholar?
- A free accessible web search engine that indexes the full text or
metadata of scholarly literature across an array of publishing
formats and disciplines
- Search all scholarly literature from one convenient place
- Explore related works, citations, authors, and publications
- Locate the complete document through your library or on the web
- Keep up with recent developments in any area of research
- Check who's citing your publications, create a public author profile
- Allow to search grey literature
63
How to search on Google Scholar?
Searching box
64
Advanced search: Search more precisely
- Find with all the words – OR

- Find with the exact phrase – “”
- Find with at least one of the words – AND
- Find without the words – NOT
- See resources by a specific author
- Specific journals
- Limit to specific years
65
Save article
66
Quick citation
67
Access PDF file
68
Search by time
69
E-mail alert
70
Contents


71
References versus Bibliography
72
References management using Endnote
Introduce to Endnote
•Create, store and manage your references/citations
•Insert references/citations from your EndNote into your

Microsoft Word document, and automatically create a
bibliography
•Bibliographies are created in your chosen referencing

style (e.g. APA, Harvard, Vancouver, etc.)
•Create, store, insert references/citations

73
References management using Endnote software
Import references from electronic databases into EndNote
1 Create a reference file

PubMed
Select “Send to” → “Citation Manager” → “Selection: All results” → “Create File”
74
Cochrane Library:
75
Cochrane Library:
76
2 Import into Endnote: File → Import → File
Import Option
▪ Pubmed → “Pubmed (NLM)”
▪ Cochrane → “Reference
Manager (RIS)”
77
3 Group references
•Create Group
•Create Group Set
•Create From Groups …
78
3 Group references
•Group references
•Create Group
•Create Group Set
•Create From Groups …
Create Group Set
Create Group
Create From Groups

79
Remove duplicates: a simple way
•Find duplicated articles

•References -> Find Duplicates
80
Remove duplicates: a systematic way
81
Remove duplicates: a systematic way
1. Show “page numbers” column
1. Go to Edit >
2 Preferences
> Display
Fields
2. Under Field,
select
Pages for
one of the
larger
numbered
columns
3 3. Click OK
82
Remove duplicates 2. Customize an Endnote style to create
export files in which abbreviated page
numbers are expanded
1. Choose
“_Correct
Pages.ens
1
(the file will
open in
Endnote)
2. In Endnote,
click File →
Save As
3. Remove the
text “copy”
from the file
name and 3
click save 2
83
Remove duplicates 2. Customize an Endnote style to create
export files in which abbreviated page
numbers are expanded
1. Choose
“_Import 1
Corrected
Pages.enf
(the file will
open in
Endnote)
2. In Endnote,
click File →
Save As
3. Remove the
text “copy”
from the file 3
name and 2
click save
84
Remove duplicates 3. Importing references
85
1. Select all references from

“combine” group
2. Go to file → Export
3. Select the output style: 2
1
_Correct Pages and save
the resulting file with the
extension “.txt”
4. Create a new group
Endnote
5. Import as usual and use
the import filter “_Import
Corrected Pages
4
86
1. Select all references from 5

“combine” group
2. Go to file → Export
3. Select the output style:
_Correct Pages and save
the resulting file with the
extension “.txt”
4. Create a new group
Endnote
5. Import as usual and use
the import filter “_Import
Corrected Pages”
87
Remove duplicates 4. De-duplication
Follow these steps for row

A and B
Set field preferences Steps to remove duplicates
1. Go to Edit > Preferences A. Author | Year | Title | Press <Delete> to remove all selected
> Duplicates, and select Secondary title (Journal) duplicates without manual assessment
the fields to match the
ones mentioned in row A B. Author | Year | Title | Pages Press <Delete> to remove all selected
under “Set field duplicates without manual assessment
preferences” and click
[OK]
C. Title | Volume | Pages Manually assess and delete duplicates
2. Select a reference group
that we are working on
removing duplicates → D. Author | Volume | Pages Manually assess and delete duplicates
select one references in
that group at random E. Year | Volume | Issue | Pages Manually assess and delete duplicates
3. Go to References > Find
Duplicates F. Title Manually assess and delete duplicates
4. Click on [Cancel]
5. Follow the steps as
G. Author | Year Manually assess and delete duplicates
described in row A under
“Steps to remove
duplicate
6. Repeat the process
again from step 1
88
onward for row A and B
Follow these steps for row

C to G Set field preferences Steps to remove duplicates
A. Author | Year | Title | Press <Delete> to remove all selected
1. Go to Edit > Preferences Secondary title (Journal) duplicates without manual assessment
> Duplicates, and select
the fields to match the B. Author | Year | Title | Pages Press <Delete> to remove all selected
ones mentioned in row C duplicates without manual assessment
under “Set field
preferences” and click
C. Title | Volume | Pages Manually assess and delete duplicates
[OK]
2. Select a reference group
that we are working on D. Author | Volume | Pages Manually assess and delete duplicates
removing duplicates →
select one references in E. Year | Volume | Issue | Pages Manually assess and delete duplicates
that group at random
3. Go to References > Find F. Title Manually assess and delete duplicates
Duplicates
4. Manually assess and
G. Author | Year Manually assess and delete duplicates
delete duplicates
5. Repeat the process
again from step 1
onward for row C to G
89
Manually assess and delete duplicates

Tip: keep records that have more information
90
Other references management
•Zotero (Free)
91
Other references management
•Mendeley (Free)
•etc.
92
Literature screening using Rayyan tool
Introduction to Rayyan tool
• Access link: rayyan.qcri.org

• A free, online application to assist
researchers with systematic review projects
• Developed by Qatar Computing Research
Institute (QCRI)
• Allows users to upload citations and full-text
articles
• You can navigate, filter, label, export,
collaborate with others
93
Sign in
94
1. Creating a new review
95
2. Import records into Rayyan
▪ Export all citations

from each database 2
into EndNote
▪ Deduplicate your
reference library
▪ Export citations from

Endnote 1
96
▪ Export
citations
from
Endnote
4
3
97

▪ Import the endnote file to Rayyan: Select files → Continue
6 98
3. Collaboration: invite
4
99
3. Collaboration: blind mode
100
4. Screening title/abstract
Screening
Title/abstract
101
Resolve conflicts after screening title/abstract
102
5. Screening Full text:

Upload full-text articles (PDF) to Rayyan
Download full-text articles
103
Download full-text articles
104
Upload full-text of all articles (PDF) that were eligible after screening
title/abstract to Rayyan
1
2
105
Upload full-text of all articles (PDF) that were eligible after screening
title/abstract to Rayyan
6
106
Screening full-text
107
Resolve conflicts→ change to “Blind on” →Document results
Check the
numbers
Documenting exclusion reasons

and numbers of included articles in
the full-text screening step
Documenting exclusion reasons and

numbers of included articles in the
ti/ab screening step 108
Advantages Disadvantages
• Free access • Not support 2 screening stages
• Save time on the same project
• Collaboration • Can not edit, delete individual

articles
• Label, highlight keywords
109
Using Rayyan tool in SR More to explore
110
REFERENCES
1. Higgins JPT, et al. Cochrane Handbook for Systematic Reviews of

Interventions version 6.2 (updated February 2021). Cochrane, 2021. Available from
www.training.cochrane.org/handbook.
2. How to Perform a Systematic Literature Review. DOI:

https://doi.org/10.1007/978-3-030-49672-2
3. Bramer et al. Syst Rev 6, 245 (2017). https://doi.org/10.1186/s13643-017-0644-y
4. Laake P, Benestad HB, Olsen BR, editors. Research methodology in the medical
and biological sciences. Academic Press; 2007 Nov 5.
111

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Research Methodology in Biomedical Engineering:

LITERATURE SEARCH and PERSONAL REFERENCE DATABASES

Instructor: Nguyen Thi Lan Phuong

Jul 13, 2021, HCMC, Viet Nam 1

1 How to formulate a query? Develop a search strategy

2 Search technique - Exploring search engines -Principle

3 Medical and scientific internet search engine

4 References and bibliography

 Databases: general health sciences vs subject-specific

 Check reference lists: in relevant studies and previous relevant systematic

 Grey literature: unpublished data such as theses, conference proceeding,

 Personal contact with experts in fields 3

 At least 2 databases will be used to conduct searching

 Database selection will depend on the research topic

• regardless of the topic, searches for biomedical systematic reviews

• Consider adding special topics databases such as CINAHL and

• (The Cochrane handbook v6.2)

• For reviews focus on experimental trials (RCTs), Cochrane CENTRAL, 4

MEDLINE and Embase are recommended

Primary or original Secondary or Tertiary

• Is a measure of the citation frequency of the average article in a particular journal

• IF should be used with care

Choose the elements in PICOS framework that would be

Finding search terms for each elements and build a search

Process search: search text words (Title/abstract or All

Refine search strategy: Consider the balance of the sensitivity and

Population / Patients (demographic factors, disease status, etc. )

Interventions/Exposures (drugs, procedure, etc.)

Comparison (alternative interventions, placebo, etc.)

Outcomes (improvement, effect, measure, etc.)

Study designs (RCTs, economic evaluations, etc.)

Research question: Evidence on economic evaluation of

1 Choose the elements in PICOS framework

P: non-small cell lung cancer

2 Finding search terms and build a search terms library

Synonyms, non small cell lung carcinoma Tecentriq economic analysis

Controlled vocabulary/index term

search #7 “non small cell pulmonary carcinoma”[All Fields] 11

No. Query Results

→ Remove the term Atezolizumab

I #13 Tecentriq[All Fields] 2008 OR #5 OR #6 OR #7

#15 “economic analysis”[All Fields] 6,560 OR #11 OR #12

1 How to formulate a query? Develop a search strategy

2 Search technique - Exploring search engines -

3 Medical and scientific internet search engine

4 References and bibliography

Access link: https://pubmed.ncbi.nlm.nih.gov/

 Available to the public online since

 Free resource developed and

 Comprise > 30 million citations and

Pubmed: Advanced search Text words

All Fields [ALL]

• PubMed ignores stopwords (a, about, because, been, can, could,

Automatic Term Mapping (ATM) feature:

We have lung cancer in the search bar

Automatic Term Mapping (ATM) feature:

ATM feature automatically

•The Medical Subject headings is the is the National Library of

•Updated annually by skilled subject analysts

•Arranged in a tree structure by subject categories with more

Entry terms are

Why should use MeSH?