LITERATURE SEARCHING SKILLS: SEARCHING
ELECTRONIC DATABASES
January 2014
Why is it useful to know how to search
electronic databases?
• There are approximately 25 000 journals in science,
technology, and medicine, and their number is increasing
by 3.5% a year; in 2009, they published 1.5 million
articles. PubMed now includes more than 20 million
papers.
2
Where are my articles?
“I have tried a couple of searches just selecting
Mesh terms and tend to get only a few papers,
often without the papers I knew were relevant.
However, if I just type in the search to Pubmed it
gives me thousands of papers.”
3
Can I just search Google Scholar?
• Google Scholar (GS) lacks a controlled vocabulary
• GS cannot store search histories, and it is not possible to
combine searches or evaluate changes made to search
queries.
• Wildcards and limits (for instance study types) cannot be
used precisely.
• Only the first 1,000 citations of any search in GS are
viewable and search strings must be kept under 256
characters.
• GS does not allow to download results in bulk to
reference management software.
4
Search plan
Select
search terms
Select
databases to
search
Run
searches
Export and
assess the
results
Report the
searching
process
5
Summary
1. Select search terms and sources of
information
2. Run searches and manage search
results
3. Report your search
4. Prepare a bibliography for your
article/thesis
6
Where to search: which information
sources shall I use?
• Journal articles
• Textbooks
• Conference
proceedings
• Newspapers
• Dissertations
• Websites
• All of these
sources are
available to search
through
specialized
electronic
databases
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Choice of electronic databases
• According to your subject area (Life sciences,
social sciences, humanities, agriculture, etc…)
• According to availability:
Open access (Pubmed)
University login: OVID, EbscoHost,
Web of Science
Other : Professional associations
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UNIVERSITY of GLASGOW LIBRARY PAGE
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Main life sciences databases
• Medline (available through OVID, EbscoHost, Web of
Science, or as Pubmed ) – biomedical and life sciences
• Embase (OVID) – biomedical and life sciences
• Web of Science (it includes Science Citation Index, Index
to Conference Proceedings and Journal Citation Reports) –
biomedical and life sciences
• Cinahl (EbscoHost) –nursing, biomedicine,
alternative/complementary medicine, consumer health and
other allied health disciplines.
• PsychInfo (EbscoHost) - behavioural sciences and mental
health.
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Main life sciences databases –
cont’d
• Biosis (Web of science)- biological abstracts
• Scopus – covers scientific, technical, medical, and social sciences
(including arts and humanities)
• CAB Abstracts – covers agriculture, environment, veterinary
sciences, applied economics, food science and nutrition
• Google Scholar (freely available) - includes most peer-reviewed
online journals, scholarly books and other non-peer reviewed
journals
• The Cochrane Library (freely available in the UK and in many
countries) - includes Cochrane systematic reviews, CENTRAL
register of randomized trials, other evidence-based databases.
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Which one should I use - MEDLINE or Pubmed?
MEDLINE® is the National
Library of Medicine® (NLM®)
journal citation database. As
of January 2013, it provided
over 20 million references to
biomedical and life sciences
journal articles back to
1946, from approximately
5,600 journals. MEDLINE is
available from Ovid,
EbscoHost, Web of
Knowledge, ProQuest, and
other database search
interfaces.
Pubmed is a free database
also maintained by NLM at
the National of Health.
Pubmed mainly contains
the same references as
MEDLINE, + citations for
very recent articles, not yet
indexed; citations to some
additional life sciences
journals; citations for books
available on the NCBI
Bookshelf
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Use PubMed:
• if you want user-friendly search features
that you can access (free of charge)
anywhere.
• when you are looking for extremely recent
citations
• When you are looking for a quick,
comprehensive search (however, Pubmed
can be also used for quite complex searches)
13
Use MEDLINE:
• to be able to run a more controlled search.
• to build a search strategy in well-defined
steps and by trying multiple combinations.
• To be able to use adjacent (proximity)
operators in your searches: “higher adj3
education”
14
Something to remember…
• The search page and the way to query different
databases can vary considerably
• However, searching skills and terminology are
common to most databases and once you learn
the basics, they can be applied efficiently to
different databases.
15
Select search terms (Prepare your
search strategy)
Identify topic scope – words and concepts
• Patients’
adherence to TB
treatment in low
and middle
income countries
• TB; tuberculosis;
• Treatment; regimen;
medication; medicine
• Patient; client; case;
subject
• Adherence;
compliance
17
Identify topic scope – words and concepts
• Rapid diagnostic
tests for visceral
leishmaniasis
• Rapid diagnostic tests,
RDTs
• LIST of RDTs
• Visceral
leishmaniasis, kalaazar
• Leishmania donovani,
Leishmania infantum
18
A well-designed search strategy consists of a
combination of keywords and controlled
vocabulary search terms.
Keywords are “natural
language” words
describing your topic.
The search engine
looks for keywords
anywhere in the record
(title, author name,
abstract, journal name..)
often returns many
irrelevant results.
A controlled vocabulary
is a standardized set of
terms used by a
database to categorize
articles based on the
content. Using terms
from a database’s
controlled vocabulary
retrieves more relevant
articles.
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Medline controlled vocabulary: MeSH
• MeSH (medical subjects headings) is the controlled
vocabulary thesaurus used for indexing articles for
Medline.
• MEDLINE citations are manually indexed at the U.S.
National Library of Medicine (NLM) using the MeSH
controlled vocabulary. The human indexers read the full
text of the article and assign MeSH descriptors that
represent the concepts that are reported in the article. It
takes a while for an article to get indexed.
• Other bibliographic databases either use MeSH (i.e., the
Cochrane Library) or have their own thesaurus (Emtree for
Embase).Other names used are: Subject Terms;
Thesaurus; Descriptors.
20
Using MESH: “Patient adherence”
21
Using MeSH: finding the right term: “jiggers”
22
Other Mesh examples
Search for…
Mesh definition
• Field worker?
• Health personnel
• Paramedic?
• “Emergency Medical
Technicians” OR
“Allied Health
Personnel”
• Teaching hospital
• "hospitals, teaching“
OR "academic medical
centers"
23
MeSh Subheadings
24
Mesh tree and “exploding” it to retrieve all
of its narrower, more specific terms
25
How to combine Mesh terms and keyword: use
the logical operators (AND, OR, NOT)
Logical operators: the easy one - AND
‘and’ looks for articles containing both terms
and it narrows the search
27
Logical operators: OR
Adherence
Compliance
“or” broadens the search
Looks for articles containing
either search term or both
28
Logical operators: the difficult one - NOT
• Excludes terms from the search
• Looks for articles containing “Africa”, excludes those
containing “Asia”
• Watch out because you will eliminate records which
include both terms
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How to combine MeSH terms and free text
Patients’
adherence to TB
treatment in low
and middle income
countries
“Tuberculosis"[Mesh] OR tuberculosis
[Title/Abstract]
AND
patient* OR client* OR subject*
[Title/Abstract] OR “Patients"[Mesh]
AND
adherence OR compliance [Title/Abstract]
OR “patient compliance” [MeSH]
AND
low-resource countries OR resource poor
countries [Title/Abstract ] OR "Developing
Countries"[Mesh] OR developing countr*
[Title/Abstract ] OR LMIC
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How this search looks in Pubmed
31
How to combine MeSH terms and free text (2)
Rapid diagnostic
tests for visceral
leishmaniasis
Leishmaniasis, visceral [MeSH] OR
Leishmania donovani [MeSH] OR
Leishmania infantum [MeSH] OR “Kala
azar OR kala-azar” ti, ab OR “Visceral
leishmania*” ti, ab
AND
“Rapid diagnos*” OR RDT* OR “Antigen*
detect*” ti, ab OR “Antibod* detect*” ti ab
OR Latex Fixation Tests [MeSH]
Lateral flow test ti, ab OR Enzyme-Linked
Immunosorbent Assay [MeSH] OR “ELISA”
ti, ab OR “Dipstick*” ti, ab OR K39 antigen,
Leishmania [Substance Name] OR K26
antigen, Leishmania [Substance Name]
OR “K39 Or rK39” ti, ab OR “Strip test*” ti,
ab OR Reagent kits, diagnostic [MeSH]
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Other searching techniques : truncation
• Truncation (usually * or $) allows you to retrieve records
with all possible word’s endings (saving you some
typing!).
• “pharma*” - retrieves pharmacy, pharmacist, pharmacies,
pharmacology…
• “Child*” will retrieve child, children, childhood,
childbirth…
• Be careful - apply only when appropriate or you may
retrieve too much irrelevant information.
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Other searching techniques : limits (or filters)
• Many databases allow you to “limit” your
search in different ways, thus refining the
search and reducing the number of results.
• Limits are usually available on advanced
search screens, or you can apply them
after doing your keyword search.
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Search filters (Pubmed/Medline)
35
Use your search “history” (or “Search
builder”) to check results and combine them
• All electronic databases maintain a “history”
of your searches, until you log out (or for 8 hrs
for Pubmed)
• This search history allows you to check the
searches you have run, access the results
again, and combine the results of different
searches.
36
After you have run the search: What to do
with your search results
3) What to do with your search results
• Assess your results and refine the
search if necessary
• “Snowballing “
• Export results
38
Assessing results: what to expect
• You may get too many (irrelevant) results or too
few results.
• Use your knowledge of the topic (including
previously identified studies) to decide whether
the search results are enough and relevant to
the topic.
• It is perfectly normal to obtain a number of totally
irrelevant results, especially if you have
searched without using limits.
39
Refining your searches
• If you get too many
results:
• If you get too few
results:
• you may need to narrow
the focus and increase
the specificity/precision of
the search:
• add additional/more
specific keywords with
‘AND’;
• Use appropriate limits
• you need to increase the
sensitivity of the search to
include all possible
keywords/thesaurus
terms:
• check your spelling;
• use truncation;
• use all possible
synonyms, alternative
terminology/spelling and
combine these using
‘OR’.
40
Snowballing…
• Once you have identified some relevant
references (even one!), these can be used to
help you identify other similar references.
• From the full text article, check the list of
references cited
• Check the thesaurus terms used to describe the
subject content, and use them to rerun the
search.
41
Snowballing: In Pubmed, use the “Related
citations” function
42
Exporting search results
• Once you have looked at your results, you
have to decide whether to keep them all or
only select the relevant ones.
• You can email records to yourself, or
export them into a bibliographic
management software database (e.g.
Endnote, Reference Manager, RefWorks,
and many others).
43
Exporting results to Endnote/Reference
Manager/other software
• In Pubmed you can use the “Clipboard” to
temporarily save results (up to 8 hrs) –
useful if you want to re-run some
searches.
• Export results as text file, select “Medline”
• style, save with an appropriate name
• Often databases have a “direct export”
function
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Import into Endnote
45
Import into Reference Manager
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Reporting the searching process
4) Reporting your search: use the search history
Recent queries
Search
Add to
builder
Query
#5
Add
Search (((malaria) AND child*) AND amodiaquine)
#4
Add
Search child* Field: Title/Abstract
#3
Add
Search amodiaquine "[Mesh]
#2
Add
Search malaria Field: Title/Abstract
Items
found
Time
526 12:43:17
2009629 12:39:06
1433 12:38:59
67669 12:38:52
48
Example of a search report for your article, review,
dissertation…
Electronic searches
We searched the following databases up to March 2013 using the
search terms and strategy described in Table 1: Cochrane Infectious
Disease Group Specialized Register; Cochrane Central Register of
Controlled Trials (CENTRAL); MEDLINE; EMBASE; and LILACS. We
also searched the metaRegister of Controlled Trials (mRCT) using
’tuberculosis’ and ’supplementation’ as search terms. In addition we
searched the Indian Journal of Tuberculosis using the keywords given
in the search strategy (Appendix 1).
Searching other resources
We also checked the reference lists of all studies identified.
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Example of a search table
Search set MEDLINE2
1
Tuberculosis [MeSH]
2
Tuberculosis ti, ab
3
1 or 2
4
Drug Therapy, Combination [Mesh]
5
Fixed dose ti, ab
6
Combination* ti, ab
7
Fixed multidose ti, ab
8
Blister pack ti, ab
9
4-8/OR
10
3 AND 9
11
Limit 10 to Humans
50
Prepare the reference list : reference styles
Harvard
‘author and date’ in text referencing
alphabetical order in reference list
Vancouver
consecutive numbering in text
numerical order in reference list
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Prepare your reference list in
Endnote: File/export/
52
Prepare your reference list in Reference
manager: Bibliography/generate from list…
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If you have further questions about
searching
Contact me at: vlutje@liv.ac.uk
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