• In fo rm e d de ci si on mak in g throu gh out Ph arm ac euti cal

d e v e l o pme nt

Building smart and effective

biomedical literature search
strategies
Jean-Dominique Pierret, PhD
Customer consultant drug safety, Elsevier
j.pierret@elsevier.com
Caroline Muller, PhD
Head of Strategic Analysis, Bioledge
caroline.muller@bioledgepartners.com
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Poll 1: What biomedical literature use case is
most relevant for you?

• Competitive intelligence
• Clinical research
• Medical communication
• Regulatory affairs
• Pharmacovigilance
Our speakers of today

Jean-dominique Pierret, PhD Caroline Muller, PhD

• Customer consultant drug safety • Head of Strategic Analysis
• Elsevier • Bioledge
• j.pierret@elsevier.com • caroline.muller@bioledgepartners.com
• LinkedIn • LinkedIn
Agenda
• The age of information overload
• The need for comprehensive search strategies in biomedical research
• Optimizing your search: an iterative process
• How to create/write a search string: defining the purpose of the search
• Tips & Tricks to optimize you search strategy (Booleans, proximity, etc…)
• How to fine tune a search string (silence and noise, depending on the
context), that’s, once we know the tips, how to use and articulates together
to get the expected result
• Q&A
Information overload, knowledge fragmentation
Information overload, knowledge fragmentation
4.000.000

= 39,8M citations

= 33,1M citations
3.000.000
= 79,2 M citations
Embase PubMed Scopus

2.000.000

1.000.000

0
1940 1950 1960 1970 1980 1990 2000 2010 2020
Information overload, knowledge fragmentation
4.000.000

3.000.000

Embase Medline Scopus

2.000.000

1.000.000

0
1940 1950 1960 1970 1980 1990 2000 2010 2020
Information overload, knowledge fragmentation
Comprehensive search strategies are critical
throughout pharmaceutical & MedTech development
• Target validation
• Safety risk
assessment
• Regulatory approval
• Supportive evidence
collection

Project Non clinical

Clinical R&D Approval Post market
identification R&D

• White space analysis • Trial design • Medical

• Competitive analysis • Clinical evaluation communication
• Meta data analysis
 What if you need to closely assess this risk?

aspirin AND angioedema 465 hits

Is this query smart enough for a comprehensive search?

Sure to get as much as really available?
 Aspirin and angioedema

aspirin AND angioedema 465 hits

('acetylsalicylic acid' OR acetylsalicylate OR aspirin)

AND ('quincke edema' OR 'quincke oedema' OR
1768 hits
'angioneurotic edema' OR 'angioneurotic oedema' OR
angioedema OR angiooedema)
Poll 2: What are you struggling with when
designing your biomedical literature search

1. Identifying the right database for my search

2. Building a comprehensive search strategy
3. Getting the right signal-to-noise ratio
4. Evaluating if my results contain all relevant
articles
Structuring a smart search strategy
Design, search, evaluate, repeat
Step #1 Step #2 Step #3

?
Write down Group concepts Draw circles,
relevant terms and rank
Question

1. Silence
2. High noise

Step #6 Step #5 Step #4

Evaluate results Translate and Select right
execute search database

!
The right
answer with
good signal-to-
noise
How We Write a Search Strategy

• Step #1 - We write everything we are looking for

• Step #2 – We gather same concepts together and rank them
according to their importance
• Step #3 – We draw circles, just to be sure
• Step #4 – We select the database
• Step #5 – We write the first draft of the search string, and, if needed,
apply limits or discard the less important concepts
• Step #6 – We evaluate the results and refine the search if required
(back to step #1)
How We Write a Search Strategy, an Example

Step Step
#1 #2

Step Step
#6 #3
Steps
#4 &
#5
Specificity of PCR for Coronavirus

Query Results

(specific*[TI] OR sensitiv*[TI] OR accura*[TI] OR ((true[TI] OR false[TI]) AND (positive[TI] OR negative[TI])))

47
AND (pcr[TI] OR "polymerase chain reaction"[TI]) AND ("2019 ncov"[TI] OR "sars cov 2"[TI] OR "covid 19
virus"[TI] OR "severe acute respiratory syndrome coronavirus 2"[TI])

(specific*[TIAB] OR sensitiv*[TIAB] OR accura*[TIAB] OR ((true[TIAB] OR false[TIAB]) AND (positive[TIAB]

OR negative[TIAB]))) AND (pcr[TI] OR "polymerase chain reaction"[TI]) AND ("2019 ncov"[TI] OR "sars cov 172
2"[TI] OR "covid 19 virus"[TI] OR "severe acute respiratory syndrome coronavirus 2"[TI])

(specific*[TIAB] OR sensitiv*[TIAB] OR accura*[TIAB] OR ((true[TIAB] OR false[TIAB]) AND (positive[TIAB]

OR negative[TIAB]))) AND (pcr[TIAB] OR "polymerase chain reaction"[TIAB]) AND ("2019 ncov"[TIAB] OR 1,379
"sars cov 2"[TIAB] OR "covid 19 virus"[TIAB] OR "severe acute respiratory syndrome coronavirus 2"[TIAB])
Specificity of PCR for Coronavirus
False Positive Results With SARS-CoV-2 RT-PCR Tests and How to Evaluate a RT-PCR-Positive Test for the Possibility of a False Positive Result.
Braunstein GD, Schwartz L, Hymel P et al.
J Occup Environ Med. 2021 Jan 6

Sensitivity and specificity of 14 SARS-CoV-2 serological assays and their diagnostic potential in RT-PCR negative COVID-19 infections.
Van Honacker E, Coorevits L, Boelens J et al.
Acta Clin Belg. 2020 Dec 22:1-6.

Sensitivity evaluation of 2019 novel coronavirus (SARS-CoV-2) RT-PCR detection kits and strategy to reduce false negative.
Zhou Y, Pei F, Ji M et al.
PLoS One. 2020 Nov 18;15(11):e0241469.

Frequency of serological non-responders and false-negative RT-PCR results in SARS-CoV-2 testing: a population-based study.
Baron RC, Risch L, Weber M et al.
Clin Chem Lab Med. 2020 Aug 31;58(12):2131-2140.

Estimation of the diagnostic accuracy of real-time reverse transcription quantitative polymerase chain reaction for SARS-CoV-2 using re-analysis of
published data.
Lorentzen HF, Schmidt SA, Sandholdt H et al.
Dan Med J. 2020 Aug 7;67(9):A04200237.
Booleans

Scopus/Embase/PubMed Scopus/Embase/PubMed Embase/PubMed: A NOT

B
A AND B A OR B Scopus: A AND NOT B

aspirin AND clopidogrel aspirin OR clopidogrel aspirin NOT clopidogrel

7,933 results in PubMed 75,431 results in PubMed 60,540 results in PubMed

Example: tamsulosin and IFIS
Goal: to monitor iris adverse effects induced by tamsulosin, esp.
intraoperative floppy iris syndrome. Having the highest recall = not missing
any relevant citation

(tamsulosin OR alna OR flomax OR harnal OR josir OR monic OR secotex)

AND (iris OR ifis)

PubMed = 159 citations

Embase = 308 citations
 Bibliographic databases
• i.e. abstracts databases
• provide short descriptions (abstracts) of
articles
• frequently provide links to the full texts
• the full text material is not included
• an abstract helps you to decide whether
to read the full text
• the producer can add specific keywords
(from specialized ontologies or
thesaurus), codes (genes, EC#,
substance ids), or
tradenames/manufacturers
How to critically appraise the clinical literature
Cronin P.; Rawson J.V.; Heilbrun M.E.; Lee J.M.; Kelly A.M.; Sanelli
P.C.; Bresnahan B.W.; Paladin A.M.
Academic Radiology (2014) 21:9 (1117-1128)
Recent efforts have been made to standardize the critical appraisal of clinical
health care research. In this article, critical appraisal of diagnostic test accuracy
studies, screening studies, therapeutic studies, systematic reviews and meta-
analyses, cost-effectiveness studies, recommendations and/or guidelines, and
medical education studies is discussed as are the available instruments to
appraise the literature […]
EMTREE INDEX TERMS
medical literature; article; cost effectiveness analysis; diagnostic test
accuracy study; human; medical education; medical research; medical
school; meta analysis; patient care;
practice guideline; priority journal;
student; systematic review
http://dx.doi.org/10.1016/j.acra.2014.05.004
PubMed, Embase and Scopus
National Library of Medicine
Focused on biomedical information and life science
Full text indexing
+27M citations
Freely accessible using PubMed

Elsevier
Focused on biomedical information and pharmacology
Full text indexing
+39M citations
Paid access through Embase.com

Elsevier Covers life sciences, social sciences, physical sciences,

Abstract and citation database health sciences
Paid access +79M citations
Text Operators: truncations, wildcards
Unlimited # of characters: * (Scopus/PubMed/Embase)
tox* = toxic, toxicity, toxin, toxA, toxicology, toxoid, …

Exactly one character: ?

sulf?nyl = sulfanyl, sulfonyl (Embase, Scopus)
anali?e = analise, analize

Zero or one character: $

hea$t = heat, heart
Behavio$r = behaviour, behaviour
cat$= cat, cats (plurals maybe automatically retrieved: Scopus)
Text Operators: proximity
Proximity = distance between words
When order doesn’t matter W/n (Scopus) or NEAR/n (Embase) where n is
the distance between the words:
cardiac W/2 therapy = cardiac gene therapy, therapy ameliorates cardiac,
cardiac therapy…

When order matters PRE/n (Scopus) or NEXT/n (Embase):

drug NEXT/2 reaction = drug reaction, drug hypersensitivity reaction, but not
reaction to a drug
Text Operators: finding phrases
PubMed
“breast feed*” works. If not result, PubMed will search for breast AND feed*.
breast-feed* works also, yet if no results, PubMed won’t search for breast AND
feed*

Embase
‘breast feed*’ or breast-feed*

Scopus
Exact phrase {breast feeding} ≠ {breast-feeding}
Loose, plurals and spelling variants are included: “heart attack” includes heart
attacks, “anesthesia” includes anaesthesia. “heart* attack*” works
Example: stents for heart infarction (literature review)

Goal: to assess the medical unmet needs of coronary stents

Query: (PubMed)
6,195
754

(myocard* OR heart OR cardi*) AND (infarct* OR attack)

140
AND (“drug eluting stent*” OR “drug coated stent*”)
+ filter: (review OR systematic review)
+ filter: publication date ≥ 2018 After selection on title / controlled
terms / abstracts:
~30 relevant papers
for literature review writing
Example: stents for heart infarction (scientific landscape)

Goal: to establish a coronary stents landscape from the last 10 years

(bibliometric analysis of major trends / academic innovators / product types)

Affiliations
Query: (Scopus)
Authors

TITLE-ABS-KEY ((myocard* OR heart OR cardi*) W/3

(infarct* OR attack)) AND ((drug W/3 (eluting OR coated) W/3 Product 2 Product 3
stent*) OR "drug eluting stent*" OR "drug coated stent*" OR
des) Product
4
+ filter: publication date ≥ 2011
8604 citations
Product 1
Our own rules of grammar
As far as it’s possible…

Booleans and operators: UPPERCASE and Search terms: lowercase

Split the search string in meaningful parts using brackets:

Example: stents for heart infarction

((myocard* OR heart OR cardi*) W/3 (infarct* OR attack)) AND ((drug W/3 (eluting OR
coated) W/3 stent*) OR "drug eluting stent*" OR "drug coated stent*" OR des)

This rule will make the query easier to understand

Search history: splitting the search into simple steps
The Sound of Silence
• Managing obesity/overload, focusing the search:
− use AND
− limits
− define more precisely the scope of some criteria

• Going beyond a limited set of results

− use OR
− expanding concepts (synonyms)
− discarding the less important concepts
 Synonyms: Push the Limits
• Biomedical terminology: MeSH, Emtree, NCI Emtree

• Diseases: OMIM

• Drugs, Chemicals: WHO ATC, DrugBank,

ChEMBL, PubChem Compound

• Proteins, Genes: UniProt, Entrez Protein,

Entrez Gene, GeneCards, EBI,
Drug Target Ontology

• Ontologies Search: OLS (EMBL-EBI)

Take home messages

• Have a clear goal

• Step back and write
• Know the database you are using
• An iterative process
• Try to think out of the box
Let us know!
1. If there’s a follow-up webinar, what subject would you to hear
more about?

2. If you have interest in Embase, Scopus or other Elsevier or

Bioledge services?
You can type this in the chat (“ask a
question”) and we get back to you
 Questions?
Elsevier for life sciences
Elsevier Scopus

Elsevier Pharma R&D today

Elsevier Scopus for R&D
Elsevier Embase
Thank you
Caroline Muller, PhD
Head of Strategic Analysis, Bioledge
caroline.muller@bioledgepartners.com

Jean-Dominique Pierret, PhD

Customer consultant drug safety, Elsevier
j.pierret@elsevier.com