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A unique method for fast, high-quality systematic searching Wichor M. Bramer Erasmus MC Rotterdam the Netherlands MLA - Austin TX –May 18th 2015 handouts: bit.ly/mlabramer1
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A unique method for fast, high-quality systematic searching
Wichor M. BramerErasmus MC
Rotterdam the NetherlandsMLA - Austin TX –May 18th 2015
handouts: bit.ly/mlabramer1
Research Question
Is exercise therapy an effective treatment for hip osteoarthritis
Simple search strategy:exercise therapy effectiveness hip osteoarthritis
PubMed 69 hits
Embase.com 1916
('hip osteoarthritis'/exp OR ((arthritis/de OR osteoarthritis/de) AND (hip/de OR 'hip pain'/exp)) OR (coxarth* OR ((hip OR cox) NEAR/6 (arthrit* OR arthrosis* OR arthroses* OR osteoarth* OR oa)) OR 'malum coxae senilis'):ab,ti) AND ('kinesiotherapy'/exp OR exercise/exp OR physiotherapy/exp OR 'conservative treatment'/de OR (kinesiotherap* OR kinesitherap* OR exercis* OR physiotherap* OR gymnastic* OR ((movement* OR motion OR manual OR phys* OR conservative* OR nonoperat* OR nonsurg* OR non-operative OR non-surgical OR paramedic* OR para-medical) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water OR management* )) OR ((muscle* OR muscul*) NEAR/3 (train*))):ab,ti)
Research question exhaustive search
Systematic searching
1. Examining the research question2. Identifying key terms
a. Thesaurus termsb. Free text terms
3. Creating a basic search strategy 4. Optimizing the basic strategy5. Translating the strategy between databases
The Research Question
Clear and focused
7
Clear and focused research questionHow can gist knowledge of patients be measured
Is scopic stabilisation better than Bristow Latarjet for treating an Anterior glenohumeral luxation with labrum injury (no ossale disorder) in a 20 YO rugby player for recurrent luxation or other Patient Related Outcome Measures
Dietary intake and cardiovascular disease
TOO VAGUE
TOO SPECIFIC
TOO BROAD
The Research Question
Clear and focusedWhich articles can answer the question?
Which articles can answer the question?
Facilitators and barriers in preconception care
evaluation studies of preconception care
Predictive factors for oronasal fistulas in children treated for clef lip
follow up studies of children treated for clef lip
The Research Question
Clear and focusedWhich articles can answer the question?Elements (Key Concepts):
- Watch our for Bias and Duplicates- Which elements to use in search?
Elements : Bias
Very specific characteristicsDuration of breastfeeding and intelligence
JudgementsPoor family functioning, harsh parenting and bullying behavior
Elements : Duplicates
Pre-eclampsia AND pregnant AND women
Lichtenstein therapy AND inguinal hernias
Which elements to use:Exercise therapy effective for hip osteoarthritis??
generalspecific
important
unimportant
Exercise therapy
Hip osteoarthritis
Treatment effectiveness
Exercise therapy
Hip osteoarthritis
Treatment effectiveness
Identifying thesaurus terms
One element One emtree term
Identifying thesaurus terms
One element One emtree termexercise therapy kinesiotherapy
One element More thesaurus terms (OR)
Identifying thesaurus terms
One element One emtree termOne element Multiple MeSH terms (OR)
prevention and control (Subheading) OR Preventive Medicine OR Preventive Health Services
Multiple elements One emtree term
Identifying thesaurus terms
One element One emtree termOne element Multiple MeSH terms (OR)
Multiple elements One emtree term('cancer mortality' OR (neoplasm AND mortality))(neoplasm OR 'cancer mortality') AND (mortality OR 'cancer mortality')
One element Multiple MeSH terms (AND)Bennett Fracture: (Fracture, Bone AND metacarpal bones AND thumb)Alcohol metabolites: alcohols/metabolism
Identifying free text words
Optimal sensitivity only by additionally searching in title / abstract:• Relevant, non-inverted terms from synonyms/
entry terms
Identifying free text words
Optimal sensitivity only by additionally searching in title / abstract:• Relevant, non-inverted terms from synonyms /
entry termsShoulder: glenohumeral joint- humeroscapular joint- scapulo humeral joint- scapulohumeral joint- articulatio humeri
• Relevant words / phrases from narrower terms
Identifying free text words
Optimal sensitivity only by additionally searching in title / abstract:• Relevant, non-inverted terms from synonyms /
entry termsShoulder: glenohumeral joint- humeroscapular joint- scapulo humeral joint- scapulohumeral joint- articulatio humeri
• Relevant words / phrases from narrower termsColorectal Neoplasms: Colonic cancer- Cancer of Sigmoid- Rectum tumor- Anal Neoplasms…etc…
Creating a basic search strategy
Build your query in WordCopy the query to the database to test itMake changes and translations in Word
The word document is simultaneously:- Supplementary file or the resulting article- Storage of search strategies for customers
Embase.com OvidSP PubMedBoolean AND, OR, NOTThesaurus /exp exp …/ [mh]---- Unexploded /de …/ [mh:noexp]Title / abstract ():ab,ti ().ab,ti. [tiab]Phrases ‘single quotes’ No quotes
needed“Double quotes” or *
Proximity NEAR/n ADJn Not possible: use AND or phrases
Standard syntaxExtended version (20 syntaxes in 7 databases) available upon request
Example
Research Question:Is exercise therapy an effective treatment for hip osteoarthritis
Elements:1. Hip osteoarthritis2. Exercise therapy3. (Treatment effectiveness)
DEMO
Example
Research Question:Is exercise therapy an effective treatment for hip osteoarthritis
Elements:1. Hip osteoarthritis2. Exercise therapy3. (Treatment effectiveness)
Hip osteoarthritis
()
Hip osteoarthritis
(''/exp)
('hip osteoarthritis'/exp)
Hip osteoarthritis
('hip osteoarthritis'/exp OR ():ab,ti)
('hip osteoarthritis'/exp OR (coxarth*):ab,ti)
('hip osteoarthritis'/exp OR (coxarth* OR (() NEAR/3 ())):ab,ti)
Hip osteoarthritis
('hip osteoarthritis'/exp OR (coxarth* OR ((hip OR cox) NEAR/3 (arth* OR osteoarth*))):ab,ti)
('hip osteoarthritis'/exp OR (coxarth* OR ((hip OR cox) NEAR/3 (arth* OR osteoarth*)) OR 'malum coxae senilis'):ab,ti)
Exercise therapy
Exercise therapy
('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR ((exercis*) NEAR/3 (technique* OR therap* OR treat*))):ab,ti)
Exercise therapy
('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR ((exercis* OR movement*) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet*)) OR ((muscle*) NEAR/3 (train*))):ab,ti)
Treatment effectiveness
Treatment effectiveness
('clinical effectiveness'/exp OR 'comparative effectiveness'/exp OR 'cost effectiveness analysis '/exp OR 'program cost effectiveness'/exp OR 'program effectiveness'/exp)
Treatment effectiveness
('clinical effectiveness'/exp OR 'comparative effectiveness'/exp OR 'cost effectiveness analysis '/exp OR 'program cost effectiveness'/exp OR 'program effectiveness'/exp OR ():ab,ti)
Treatment effectiveness
('clinical effectiveness'/exp OR 'comparative effectiveness'/exp OR 'cost effectiveness analysis '/exp OR 'program cost effectiveness'/exp OR 'program effectiveness'/exp OR (effectiv*):ab,ti)
Concept query('hip osteoarthritis'/exp OR (coxarth* OR ((hip OR cox) NEAR/3 (arth* OR osteoarth*)) OR 'malum coxae senilis'):ab,ti) AND ('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR ((exercis* OR movement*) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet*)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp OR 'comparative effectiveness'/exp OR 'cost effectiveness analysis '/exp OR 'program cost effectiveness'/exp OR 'program effectiveness'/exp OR (effectiv*):ab,ti)
152 hits
Creating a basic search strategy (summary)
• Type code in Word• Open an element with ()• For emtree terms type ''/exp and paste term• After pasting all emtree terms, type OR ():ab,ti within
that element once for free text words• Type single word synonyms first• Type (() NEAR/3 ()) somewhere in the document to
reuse• Copy (() NEAR/3 ()) into the ():ab,ti part search for
phrase variants, and add the words
Optimizing your strategy
Sort by relevance and check title / abstract and thesaurusAdd new relevant words to the search in Word
Temporarily change the syntax and check words:Per element, keeping the rest unchanged• (emtree) NOT (free text)• (free text) NOT (emtree)
DEMO
Step 3: optimizing your strategy
1. Check retrieved articles for relevant words
('hip osteoarthritis'/exp OR (coxarth* OR ((hip OR cox) NEAR/3 (arth* OR osteoarth*)) OR 'malum coxae senilis'):ab,ti) AND ('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR ((exercis* OR movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp OR 'comparative effectiveness'/exp OR 'cost effectiveness analysis '/exp OR 'program cost effectiveness'/exp OR 'program effectiveness'/exp OR (effectiv*):ab,ti)
160 hits
Step 3: optimizing your strategy
1. Check retrieved articles for relevant words2. Temporarily change the syntax for one of the
elements into (emtree) NOT (free text)while keeping the rest unchanged
('hip osteoarthritis'/exp …) AND ('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR ((exercis* OR movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp …)
('hip osteoarthritis'/exp …) AND ('kinesiotherapy'/exp NOT (kinesiotherap* OR kinesitherap* OR ((exercis* OR movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp …)
('hip osteoarthritis'/exp …) AND ('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR exercis* OR physiotherap* OR ((movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp …)
267 hits
Step 3: optimizing your strategy
1. Check retrieved articles for relevant words2. Temporarily change the syntax for one of the
elements into (emtree) NOT (free text)3. Temporarily change the syntax for one of the
elements into (free text) NOT (emtree)while keeping the rest unchanged
('hip osteoarthritis'/exp …) AND ('kinesiotherapy'/exp OR (kinesiotherap* OR kinesitherap* OR exercis* OR physiotherap* OR ((movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp …)
('hip osteoarthritis'/exp …) AND ((kinesiotherap* OR kinesitherap* OR exercis* OR physiotherap* OR ((movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp …) NOT 'kinesiotherapy'/exp
('hip osteoarthritis'/exp …) AND ('kinesiotherapy'/exp OR exercise/exp OR physiotherapy/exp OR (kinesiotherap* OR kinesitherap* OR exercis* OR physiotherap* OR ((movement* OR motion OR manual) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water)) OR ((muscle*) NEAR/3 (train*))):ab,ti) AND ('clinical effectiveness'/exp …)
355 hits
End Result – Systematic Review
('hip osteoarthritis'/exp OR ((arthritis/de OR osteoarthritis/de) AND (hip/de OR 'hip pain'/exp)) OR (coxarth* OR ((hip OR cox) NEAR/6 (arthrit* OR arthrosis* OR arthroses* OR osteoarth* OR oa)) OR 'malum coxae senilis'):ab,ti) AND ('kinesiotherapy'/exp OR exercise/exp OR physiotherapy/exp OR 'conservative treatment'/de OR (kinesiotherap* OR kinesitherap* OR exercis* OR physiotherap* OR gymnastic* OR ((movement* OR motion OR manual OR phys* OR conservative* OR nonoperat* OR nonsurg* OR non-operative OR non-surgical OR paramedic* OR para-medical) NEAR/3 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR water OR management* )) OR ((muscle* OR muscul*) NEAR/3 (train*))):ab,ti)
1916 hits
Considerations
Explode a broad term or not?Start exploded, when many irrelevant results
appear, be more specificTruncate a term or not?
Truncate as much as possible, hardly noisePhrases or proximity?
Always proximity, easier and more sensitiveHow broad should proximity be?
Start with 3, increase with 3 andevaluate newly retrieved articles
Step 5: Translating the strategy between databases
Embase.com (Embase and Medline)Thorough optimization of thesaurus terms and title / abstract terms in search strategy
Macro and edit thesaurus
Medline (OvidSP)MeSH terms in PubMed / Optimization
Add extra terms Remove thesaurus
Cochrane library
Macro
Web-of-science
Macro
Scopus
Macro
PubMed publisher
[sb]
Macro and edit
thesaurus
CINAHL (EBSCO)
edit thesaurus
PsycINFO (OvidSP)
Macro and edit
Google Scholar
Macro and edit
Lilacs / Scielo / Eric / Clinical trials etc etc
DEMO
Success factors
• Optimization techniques • Macros for database translation• Single-line search strategies• Database choice and order• Direct feedback by researcher• Creating queries in Word• Computer literaracy• Experience (be pro active)
Contact details
E-mail: [email protected]: @wichorLinkedIn: nl.linkedin.com/in/wichorSlideshare: www.slideshare.net/wichor
Upcoming international workshops:June 2015 Edinburgh (UK) – EAHIL Workshop September 2015 Basel (CH) – AGMB Workshop
Further reading:• Bramer WM, Giustini D, Kramer BM, Anderson PF.
The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews. Syst Rev. 2013 Dec 23;2:115.
• Bramer WM, Holland L, Mollema J, Hannon T, Bekhuis T. Removing duplicates in retrieval sets from electronic databases: comparing the efficiency and accuracy of the Bramer-method with other methods and software packages (Eahil conference, Rome)
• Embase webinar : Systematic searching with Wichor Bramer (25 feb 2015)• Bramer WM, Pols DHJ, Bindels PJE, Bohnen AM. A fast, reliable and
objective method for creating thematic search filters in bibliographic databases [in process]
• Work in progress on coverage, retrieval and relevance ranking of the major databases for systematic reviews (>450 review searches; >100 finished; >4500 included references)
• Two articles in progress about this methodology (how to, and how well)
Single line approach or set numbers?Well structured?#1 brassica/exp#2 brassica*:ab,ti#3 broccoli:ab,ti#4 #1 OR #2 OR #3#5 neoplasm/exp#6 neoplas*:ab,ti#7 cancer*:ab,ti#8 tumor*:ab,ti#9 #5 OR #6 OR #7 OR #8#10 #4 AND #9#11 [animals]/lim#12 [humans]/lim#13 #11 AND #12#14 #11 NOT #13#15 #10 NOT #14
Unstructured?
(brassica/exp OR (brassica* OR broccoli):ab,ti) AND (neoplasm/exp OR (neoplas* OR cancer* OR tumor*):ab,ti) NOT ([animals]/lim NOT [humans]/lim)
What to do with subheadingsSeparate element(broccoli/de OR (broccoli* OR bassica*):ab,ti) AND (neoplasm/exp OR (cancer* OR neoplas*):ab,ti) AND (prevention:lnk OR prevention/exp OR (prevent*):ab,ti)
Combined element(broccoli/de OR (broccoli* OR bassica*):ab,ti) AND (neoplasms/exp/dm_pc OR ‘cancer prevention’/de OR ((cancer OR neoplasm) NEAR/3 (prevent*)):ab,ti)
Sensitive More hits : 345 (101 unique) Less chance of missing relevant articles Recommended for start For SRs highly recommended
Specific Less hits : 257 (13 unique) Higher chance of missing relevant
articles To reduce the number of hits Use proximity in free text
Why start in embase?Source: Unpublished research Bramer (5048 included references from 111 reviews)
Relevance ranking
Interface choiceEmbase.comPros- Very good relevance ranking
Cons- Translating between embase
and medline more complicated
- No wildcard (?) in truncation- Special characters not
normalized ( VO2max )
OvidSPPros- Equal syntax to medline
(OvidSP)
Cons- No relevance ranking on
complicated queries- Complex thesaurus interface
My advice: relevance ranking is very helpful during optimization. Problems are only minor. Start in embase.com and translate with macros
The databases I use:Database Used in % of SR
Embase.com 100%
Medline (OvidSP) 99%
(PubMed the other 1%)
Cochrane central 98%
Web-of-Science 95%
Google Scholar 92%
PubMed (publisher) 91%
Scopus 36%
Cinahl 25%
PsycINFO 19%
Others (proquest, sportdiscus, lilacs, scielo, eric, amed etc)
7%
Do you need to fully understand the research question?
What is the Cell contribution to chondroid / endochondreal / intramembranous bone formation
((('bone development'/de OR 'bone mineralization'/de OR 'bone maturation'/de OR ossification/de OR 'bone conduction'/de OR 'bone transplantation'/exp OR 'bone matrix'/exp OR 'bone growth'/exp OR 'bone remodeling'/de OR ((bone NEAR/6 (minerali* OR develop* OR format* OR synthesis* OR growth* OR graft* OR transplant* OR engineer* OR defect* OR matri* OR remodel* OR conduct* OR maturat*)) OR osteogen* OR ossificat*):ab,ti) AND (chondroid* OR transchondroid* OR enchondr* OR endochondr* OR intermembran* OR cartilagin* OR (inter NEXT/1 membran*)):ab,ti) OR 'enchondral ossification'/de) AND ('cell death'/de OR 'cell survival'/de OR apoptosis/de OR 'cell differentiation'/de OR 'cell fate'/de OR 'host cell'/de OR 'cell lineage'/de OR (((cell* OR msc OR osteoblast* OR osteocyte* OR osteoclast* OR preosteoblast*) NEAR/3 (death OR senescen* OR contribut* OR differentiat* OR fate OR plasticit* OR reprogram* OR donor* OR host* OR recruit* OR surviv* OR viabilit* OR lineage*)) OR apoptosis):ab,ti)
PICO?P 67 73%I 51 55%C 2 2%O 37 40%S 24 26%? 29 32%
PI 14PO 8PIS 7IO 6P? 6PIO 4P 4I? 4PS? 4PI? 3IOS 3I 3? 2PO? 2IO? 2
Embase.com syntax
()
(''/exp)
('hip osteoarthritis'/exp)
('hip osteoarthritis'/exp OR ():ab,ti)
('hip osteoarthritis'/exp OR (coxarth*):ab,ti)
('hip osteoarthritis'/exp OR (coxarth* OR (() NEAR/3 ())):ab,ti)
('hip osteoarthritis'/exp OR (coxarth* OR ((hip OR cox) NEAR/3 (arthrit* OR arthros* OR osteoarth*))):ab,ti)
Ovid (Medline) syntax
()
(exp ""/)
(exp "osteoarthritis, hip"/)
(exp "osteoarthritis, hip"/ OR ().ab,ti.)
(exp "osteoarthritis, hip"/ OR (coxarth*).ab,ti.)
(exp "osteoarthritis, hip"/ OR (coxarth* OR (() ADJ3 ())).ab,ti.)
(exp "osteoarthritis, hip"/ OR (coxarth* OR ((hip OR cox) ADJ3 (arthrit* OR arthros* OR osteoarth*))).ab,ti.)
PubMed syntax (not optimal)
()
(""[mh])
("osteoarthritis, hip"[mh])
(exp "osteoarthritis, hip"/ OR coxarth*[tiab])
(exp "osteoarthritis, hip"/ OR coxarth*[tiab] OR ((hip[tiab] OR cox[tiab]) AND (arthrit*[tiab] OR arthros*[tiab] OR …)))
(exp "osteoarthritis, hip"/ OR coxarth*[tiab] OR hip arthrit*[tiab] OR cox arthrit*[tiab] OR hip arthros*[tiab] OR cox arthros*[tiab] OR hip osteoarthrit*[tiab] OR …)
How well do the searches perform?
Benchmark This study# terms 46 54# databases 3 7# hits 1399 2224# includes 19 25precision 1.2% 2.0%
Benckmark: 93 systematic reviews from 2014 with an acknowledgement or co-authorship of a medical information specialist from another Dutch academic hospital.
Hausner, 2015 (13); Saleh, 2014 (17); Allen, 1999 (19); Gann, 2013 (47); Lyon, 2014 (9) [1-5] and unpublished data from London Health Sciences Centre in Canada (43)
0 5 10 15 20 25 30 35 40 45 500%
25%
50%
75%
100%
Meta-analysis (N=148)
Hours needed to create search strategy
Perc
enta
ge o
f Sys
tem
atic
Revi
ews
And the speed?
0 5 10 15 20 25 30 35 40 45 500%
25%
50%
75%
100%
Meta-analysis (N=148)
Bramer (N=258)
Hours needed to create search strategy
Perc
enta
ge o
f Sys
tem
atic
Revi
ews
Hausner, 2015 (13); Saleh, 2014 (17); Allen, 1999 (19); Gann, 2013 (47); Lyon, 2014 (9) [1-5] and unpublished data from London Health Sciences Centre in Canada (43)
And the speed?
