Systematic Literature Retrieval in PubMed

Workshop
Systematic Literature
Retrieval in PubMed
Tuesday 11 December 2012

Wichor Bramer | Gerdien de Jonge
Information specialists Medical Library (Cf-232)
info.mb@erasmusmc.nl | www.erasmusmc.nl/medbib
phone: 010-70 43785
@wichor | slideshare.net/wichor | nl.linkedin.com/in/wichor

Today’s scope
What will you be learning today?
How to search systematically
Finding the right keywords
Optimizing your search in PubMed to be sure you didn’t miss important
articles
How to avoid the frequent (but unknown to many) pitfalls

What will you not be learning today?
The basics of PubMed
We assume you already know how to use it, you’re all experienced searchers,
but we want to change the way you search.

Today’s rules:
- Feel free to ask any question that comes up
- If you see text in red you are asked to participate in the demonstration
- In your handouts important lessons are marked in a gray box
Medische Bibliotheek Erasmus MC 2

Warning
Don´t think you know what you´re about to see
You al are experienced users, but have adapted methods that are
counter effective.

Pay close attention
We teach you subtle changes in the way you search PubMed that will
have great impact on your search results.

And change PubMed into a more valuable tool
We want to change the way you use PubMed to make it more
effective!


What databases do we use?
PubMed (Medline) SLR in PubMed (today)

Embase SLR in other databases (next week)
Medline (OvidSP)
Cochrane Central
Systematic Literature Retrieval
Scopus or Web-of-Science uses at least these databases
PsycInfo
Cinahl
PEDro (etc etc)

Not one of them is the absolute best, to capture all articles you need to
search multiple databases (and even more)


Discussion:
Do we really need all these databases, couldn’t publishers
just put their data in one spot?
What is the added value of that many databases?


Practicum (discussion): Base level (homework)
1. How did the process go?
2. Was it hard to find relevant articles?
3. Was it hard to find a small set of articles that still contain
enough relevant articles?


Homework : results & feedback
Not using truncation ALL (5)
Using automatic term mapping (let pubmed do the thinking) 4
No or incorrect use of parentheses 4
Using automatic query builder 2
No or incorrect use of Boolean operators (AND, OR, NOT) 1
Using MeSH terms only 1
Using standard PubMed filters (RCT, humans) -
Building a search from record numbers -
Using time limits -

We’d like to teach you better ways to get to better results
 Systematic Literature Retrieval


Homework : best practice
Myrthe Tielemans

("Pregnancy"[Mesh] OR pregnancy OR preconceptional)
AND ("Depression, Postpartum"[Mesh] OR "postpartum
depression" OR depression OR "postnatal depression")
AND (dietary patterns OR diet OR nutrition OR
micronutrients OR macronutrients OR omega-3 OR
folate OR thiamine OR "vitamine B-12" OR
"polyunsaturated fatty acids" OR zinc OR iron)

Pay special attention.
For people with the most knowledge about PubMed
it is harder to change the way you’ve always
searched!

Homework : effect of optimization
You Me Only I found Only you Relevant
found
Eva M 524 42 36 (86%) 518 (99%) 0/1
Eva B 363 952 912 (96%) 322 (89%)
Geriolda 2431
Karen / 1709 296 257 (87%) 1670 (98%) 0/2
Yannan
Mateus 1413 2930 1658 (57%) 141 (10%) 6/6
Myrte 535 344 269 (78%) 460 (86%) 14/21
Rianne 4019


Homework : problems addressed
 Where do you start?
 How do you translate your question into the right search
words
 What do you do when no proper MeSH terms are found for
(parts of) your search
 How can you reduce the number of hits without losing
important articles
 How can you improve the relevance of your results
 Using AND, OR and parentheses


What is Systematic Literature Retrieval ?
 To tell databases exactly the conditions an article has to meet
to be found
 Without reservation or bias
 Long proces of optimisation and evaluation
 Combining results from multiple databases

Why?
 Verifiable and accountable
 Repeatable to others, but also to yourself at a later moment.
 To prevent missing important articles


What is Systematic Literature Retrieval ?

Sensitive search Specific search
Goal Finding as much relevant Most of the found
articles as posible articles are relevant
# of hits High Much lower

# of relevant Low Much higher
articles missed

Think about this: What do you think you would be
likely to focus on in a database that lacks relevance
ranking (like PubMed). And to what consequences?

Medische Bibliotheek Erasmus MC

How to search systematically?
1. What is your research question?


What is your research question?
PICO(ST)
Patient / Intervention / Comparison / Outcome (Setting / Timing)
can be useful, but don’t focus too much on this

Domain
Therapy & Prevention / Diagnosis / Etiology & Risk / Prognosis

Background question
Diseases etc in general (handbooks, narrative reviews, etc)

Foreground question
Specific and relevant for a specific concrete problem


2. What elements (key concepts) does the question contain?
- are they specific or general and important or less important?


Elements in your research question
Why use elements? To determine where to start your search!
Elements are distinguishable concepts in your research question:
 Substances
 Actions
 Diseases/ symptoms
 Persons
 Features/ characterizations
 Locations/ settings
 Domains
Keep in mind:
Elements cannot always be translated to search terms one on one:
• Sometimes a search term combines two elements
• Sometimes an element has to be searched with a combination of two (or more)
search terms
• Broccoli Cancer Prevention
Very frequently an element can be found in multiple mesh terms
What are not elements?
 General terms, describing relations: effect, relation, significant etc etc.


Elements : be careful!
Bias in your elements
Including outcomes in your query means bias!
Including very specific characteristics mean bias!
WHY?
Articles that find a relevant result for a certain outcome or specific
characteristic will mention that in the abstract.

Accidental duplication in your elements
Sometimes an element overlaps almost completely with another
 Choose only the most specific
Pre-ecclampsia AND pregnant AND women
Broccoli Cancer
meconium AND neonates Prevention
But sometimes less evident: a certain therapy only used in a specific disease:
Lichtenstein therapy AND inguinal hernias

Elements : on a gliding scale

specific general
important
broccoli cancer

prevention

broccoli cancer prevention
unimportant

Practicum: elements
4. Open a word document and describe your research question in one
phrase
5. Split your research question into elements, and plot them on the scale
a. Are the elements very specific or more general?
Are you the first using this element or do you think many more
people could have used it before? Will the element result in a small
set of results, or will the number be very high?
b. Are they important to your question or less?
Could you think of relevant articles without this element? Are
elements related to each other? If there’s much overlap the most
specific is the most important


Rianne : Relationship between falls and functional status in hospitalized
adults

specific general
important falls Functional
status

hospitalization

adults

unimportant

Eva v B : The burden of informal care of (hospitalized) elderly

specific general
important burden elderly
Informal
care

hospitalization

unimportant

Karen / Yannan : methodologies used in studies evaluating the effect of a
population-level policy of intervention on health inequalities

specific general
important Population- Health
level policy inequalities

Evaluation
studies

Intervention Methodologies

unimportant

3. Translate these elements (synonyms, alternatives, abbreviations)
- Determine the elements to start with
- List these elements in a Word file (one element per line)
- Translate each element in as much relevant synonyms as possible


Elements : where to start
Start with the Important specific elements
If a combination all important specific elements already results in a relatively
small selection of relevant articles, stop there

Add important general elements
If the important specific elements generate too much hits, add extra filters for
the general elements

Add less important elements
If after adding all important elements still too much results appear, only then
add the less important elements.
But beware: translate them thoroughly, and allways check if the articles you
Broccoli Cancer
dropped by adding it can indeed be missed. Prevention

 If you add the less important elements you lose systematicity

How do you find the right search words?
 Use google or wikipedia to find alternative descriptions of your topic
 If you don't have a clue: try typing in something and see what PubMed
comes up with in search details (and use those word in you queries)
 Search the MeSH database
 Pay attention to entry terms (but don’t use them all without reviewing),
hierarchical tree, description etc..
 Read the description to see if this fits your research question
 Truncate every word when searching the MeSH database!
 Think of spelling differences (UK/USA)
 Tumor / tumour; Organisation / organization; non cardiac or noncardiac;
pediatrics/ paediatrics
 Inversions: Quality of life / Life quality
 Abbreviations
 Pay attention to abbreviations with multiple meanings. Then combine
abbreviation with words from the complete form
(clock AND draw AND test) OR (CDT AND (clock OR draw OR test))
 Partially abbreviations: "sentinel LN"

How do you find the right search words?
 Unfamiliar with English terms? Search for articles in you native
languague using [tt] and scan the translated title
 No usefull MeSH terms available?
 search for some very relevant articles and see what MeSH terms
they use. Or use related articles for that.
 Think of the opposite. Sometimes that can be a MeSH term

But, the most important source is: Scan
resulting articles for relevant terms you
haven't yet included in you search
strategy (optimization)

How to find useful filters?
In the database itself
PubMed has some good standard filters (and some bad ones too)

Preferred standard filters to use Rather do not use
Subsets (aids, bioethics, cancer) Limits in the left side of the PubMed
Sensitive Clinical Queries (therapy, result screen (humans, children, RCTs)
diagnosis, etiology etc) Specific clinical queries

In other (good) systematic reviews
Other (possibly cochrane) reviews have used the same element before.
Check the appendices of that for the strategy they used
But never take that search strategy for granted:
 always check if they didn’t make mistakes
 Translating that filter to other interfaces can be difficult

Practicum : synonyms
--- continue with the elements provided by the workshop leader ---
--- Start to search for synonyms in the MeSH database, do not search
for articles yet ---
6. Translate each of these elements into synonyms
a. Start with the important unique elements
b. What words/ phrases are used in the controlled vocabulary (MeSH)
and what type are they? Do you spot: MeSH terms, subheadings,
pharmacological actions, supplementary concepts (explained later)?
c. What other words can you find (synonyms / narrower terms)
d. For many general elements filters exist that you can find in the
database as a subset or standard seach query (for instance cancer
subset or diagnosis clinical query) or evaluated and published filters
(Cochrane filter for children).


Practicum : feedback
Geriolda and Mateus:
Cardiovascular diseases / risk

Cardiovascular Diseases[mh]
Cardiovascular
Cardiac
Heart[mh]
Vascular
Blood Vessels[mh]


4. Combine accoring to set theory (Boolean logic)
- combine terms within an element with OR
- combine elements with AND
- use parentheses for priority
- use truncation to search different word (or phrase) endings


Boolean operators

broccoli broccoli #2
OR AND NOT
brassica cancer #1

ALWAYS USE CAPITALS FOR BOOLEAN OPERATORS
priority with parentheses: (broccoli OR brassica) AND (cancer OR neoplasm)
Be careful: Automatic parentheses from query builder will result in errors
((((broccoli) OR brassica) AND cancer) OR neoplasm)


Truncation
Word truncation
prevent* = prevent OR prevention OR preventing OR …etc
limitations: maximum of 600 variations (mind the warning)
Solution: elongate the word stem (maybe use multiple variants)
Phrase truncation
When an asterisk is used PubMed tries to do phrase truncation
Except with priority parentheses of Boolean operators, or when a
searched phrase is not known!

When to use Quotes and truncation
For free text words ([tiab]) never use quotes and truncate when relevant
 Truncation will be ignored in quotes
With mesh terms ([mesh]) always use quotes, and never truncate
 Mesh term may be mapped to another term


5. Use the syntax of the chosen database
[tw] [tiab] [mesh]

Interactive Demo :
Red Blood Cells

Practically Concurrent!


Automatic Term Mapping Field Names
 Based on Entry Terms query is  Manually describe fields in which
translated to [MeSH] words should be present between
 Combined with mesh term and quare brackets
exact search words in [All Fields]

 Translation to MeSH sometime incorrect  Exact translation to the desired MeSH term

 Use of [All Fields] undesirable  Combined with exact phrasing in title and abstract
 Specific MeSH terms exploded or ignored
 No truncation
 Truncation possible
 Query details much longer than necessary
 Query as short as possible


Don't use Automatic Term Mapping!

Conclusion: Automatic Term Mapping is never optimal
For systematic searches always use field names to tell a database exactly
what you are looking for

How to prevent Automatic Term Mapping?
 Always use field names
 Use (phrase) truncation as much as possible
 After each synonym
(PubMed will only execute ATM when inexperienced users don't use
field codes and/or truncation)
Keep in mind this automatically reduces the need of quotes, because in
this way phrases will be kept together when possible

Field names
Keywords:
[mesh] exact mesh term (with all subbranches)
[mesh:noexp] exact mesh term (without all subbranches)

Free text:
[tiab] the exact word or phrase in title or abstract

Less frequently used:
[sh] subheading (with explode) see furter
[pa] pharmacological action (with explode) see furter
[nm] Supplementary concepts see furter
[pt] Publication type see furter
Don't use:
[majr] en [ti] Due to the lack of relevance sorting you want need to reduce
your results to the most relevant ones, with major mesh terms, or free text in the
title. Don't use this in systematic literature retrieval

Keyword Free text
 Seach for a specific concept  All records contain text, but not all contain
 Independent of the autor's choice of MeSH terms (recent ones)
words  Are the additions correct?
 Search for related terms using the  Concepts not covered by mesh terms, or
explode function only recently

Both varieties have their pro's and con's so when seaching systematically
combine both

The safest Method:

Look for corresponding MeSH term(s) [mesh]
Determine whether to explode these or not [mesh:noexp]
Combine in an OR relation with free text words
(at least those in entry terms) [tiab]


Subheadings [sh]
If subheadings are about a certain general concept: treat them as a
separate element
Don't combine MeSH terms and subheadings into one element. You will
lose important articles. Add the subheading as an distinct element, with
keywords and free text word search.
(psoriasis[mesh] OR psoria*[tiab]) AND (etiology[sh] OR etiology[tiab])

If an element can only be translated by a combination of MeSH term
and specific subheading : treat them as one element
In this element search for the combination of MeSH and subheading or
free text phrases.
For instance: alcohol metabolites:
(ethanol/metabolism[mh] OR alcohol metabolit*[tiab])

Pharmacological actions [pa] (drug types)

PAY ATTENTION when looking for drug types
Drug[mesh] added to articles about a drug, drug[pa] added to articles about
research that have used this drug
The field Pharmacological actions is not retrieved with [tiab] or [mesh]. Use
[pa] additionally

anticoagulants 185322
anticoagulant* 194100
anticoagulant*[tiab] 38754
anticoagulants[mesh] 51966
anticoagulants[pa] 179174
anticoagulants[mesh] OR anticoagulants[pa] 180671
anticoagulants[mesh] OR anticoagulants[pa] OR anticoagulant*[tiab] 195372

(OR circulating anticoagulants[nm] 195380)


Supplementary concept [nm] (Substance Name)

Additional to the MeSH terms (25000), extra 140000 supplementary
concepts.
 Not part of the thesaurus tree
 Contain usually links to the best matching MeSH term(s)
 Mainly chemical substances (hence the abbreviation nm, substance
name), or rare diseases
 When searching [pa] (pharmacological action) both relevant MeSH
terms and supplementary concepts will be searched.


Publication type [pt]
 Case Reports
 Clinical Trial
 Comparative Study
 Evaluation Studies
 Meta-Analysis
 Validation Studies

Can be used to limit your results to a certain type of publication, but
never use it alone, always in combination with free text words

Mind this: articles about a certain publication type have the mesh
term … as topic


Practicum : syntax
--- continue with the synonyms provided by the workshop leader ---
7. Combine the synonyms the workshop leader found into correct PubMed syntax
a. Add field names.
- [mesh] or [mesh:noexp]
- [tiab]
- If necessary use [sh], [pa], [nm] or [pt] additionally
a. Use (phrase) truncation to reduce the number of synonyms necessary
mentioned
b. Can you search phrases as real phrases (remember you want to be
exhaustive, so you need to include all possible phrases) or is it wiser to split
some phrases into an AND combination? Don't you get too many noise?
c. Add parentheses around elements to group synonyms
d. Use boolean operators AND between elements and OR between synonyms
in an element (don’t use NOT)


6. Execute the query
- paste multiple lines in search details or advanced > edit
7. Analyse the results
- check for errors
- too much / too little results / are the results relevant?
- do you spot additional words/phrases you haven't included in your
search yet?
 optimization


Analyse the results: check for errors
How do you know an error occurred
Too often: NOT!
Sometimes: Too many or too little hits (than expected)
Check you query for mistakes
Go to Search details and use Ctrl-F to search
Frequent mistakes
Phrase unknown or 'all fields' Every instance is one too many
Field code missing
OR missing ' AND ' odd frequency is wrong
check if AND's are deliberate
Missing parentheses PubMed only checks the total number of
opening and closing parentheses. Split the
query in elements to check each
element.

Analyse the results: too much / too little
What is too much what is too little.
No clear borders!
Dependent on the time and effort you want to invest
Dependent on the goal of your research (systematic review or thesis or
more general)
Sometimes 50 is enough, sometimes 5000 is too little.

When can you stop?
If adding extra words or dropping elements doesn’t add any extra
relevant items.
What words should you add then? Those present in the already
retrieved articles that are synonyms of your elements.
 optimization

Basic optimization of your results
Always:
1. Pay close attention to mesh terms or free words/ phrases that
combine two elements in one.
2. Solve truncation problems if they appear (one by one!)
3. Scan the first relevant hits on synonyms you haven’t included in
your search
4. Per element: scan the abstracts of articles that have the MeSH
terms, but not the free text words already known.
5. Per element: Scan the MeSH terms of articles that have these
free text words, but not the MeSH terms already known.
6. Replace important specific elements with more general ones
7. Drop unimportant elements from your query and see what extra
articles you found.

Number of hits:
Elements : optimization
4091(+170%)
1236(+231%)
797 295
1913 (+55%)
(-53%)
specific general
important
broccoli
cruciferous vegetables cancer subset
cancer
in PubMed

Filter:
NOT ((animals[mh] OR
plants[mh]) NOT humans[mh])

prevention
unimportant

Practicum : optimization
--- continue with the syntax provided by the workshop leader ---

7. Try to solve the problems/ tips addressed by the workshop leader
8. Start optimizing your search yourself:
a. Solve any truncation problems that occur.
b. Can you find new relevant words in the first results?
c. What other synonyms can be found in articles have mesh terms for
an element, but not those free text words
d. And the other way around: what other mesh terms can you find?


1. What is it you want to know?
6. Execute the query
7. Analyse the results
8. Adapt the query to other databases
- change the syntax
- compare other keyword systems and synonyms
- check those results on relevancy and other words
9. Repeat until you are satisfied (but don't be satisfied to easily)


When are you done optimizing?
When you checked all of these methods and adding extra words does not add extra
relevant articles to your resultset
When all previously known items by you, or by other (systematic reviews on the same
topic) have been found
 You’ve reached a fair point of exhaustiveness

Never overestimate what you can do when searching! You will always miss articles,
because:
• Bad, short or missing abstract
• Published in smaller foreign journals (especially negative results)
• Unpublished works

So if you want to be exhaustive always use other methods:
• Hand search key journals
• Ask experts in the field (use Scopus)
• Check reference lists from key articles (use EndNote & Scopus)
How much searching is enough? Comprehensive versus optimal retrieval for
technology assessments Andrew Booth International Journal of Technology
Assessment in Health Care 26 (4) 431-5

Advanced tips en tricks
 Finding a specific article


Try to find this article in PubMed:

Fortes C, Mastroeni S, Melchi F, Pilla MA, Antonelli G,
Camaioni D, Alotto M, Pasquini P. A protective effect of the
Mediterranean diet for cutaneous melanoma. Int J Epidemiol.
2008 Oct;37(5):1018-29.

10
1
2
3
4
5
6
7
8
9


What is the PMID?


Try to find this article in PubMed:

Fortes C, Mastroeni S, Melchi F, Pilla MA, Antonelli G,
Camaioni D, Alotto M, Pasquini P. A protective effect of the
Mediterranean diet for cutaneous melanoma. Int J Epidemiol.
2008 Oct;37(5):1018-29.


What is the PMID?

Fortes 1018 : 18621803


Try to find this article:

Jones RB, O'Connor A, Brelsford J, Parsons N, Skirton H.
Costs and difficulties of recruiting patients to provide e-
health support: pilot study in one primary care trust. BMC
Med Inform Decis Mak. 2012 Mar 29;12:25.


What is the PMID?

jones 25 : 6492 hits


What else could we pick easily?



Try this!



What is the PMID?

jones 25 2012 : 712 hits

But:
jones[1au] 25[pg] 2012[dp] : 22458706


Advanced tips en tricks
 Finding a specific article

 Solving truncation problems

 Find free text words and mesh terms in relevant items or their
related references using pubreminer (and hubmed to collect
related articles)

 Find phrases not known to but present in pubmed using google


Disadvantages of PubMed
1. Limited truncation options (600 variants, no wildcard)
2. Strange behavior when truncating phrases (longer wordstem often
retrieves more results)
3. No proximity operators
If you want to be more precise every possible phrase should be written
out, but:
3. Not all phrases that are present in articles are known and searchable in
PubMed
4. No relevance ranking

 PubMed is not optimal for performing systematic searches.
We recommend searching other databases (as well)

Embase.com contains almost all PubMed articles, plus several others, can do
relevance ranking, better truncation and has real proximity operators


Summarized
1. Start your search in a MS Word Document
2. Divide your research question into elements
3. Open the MeSH database and try to find the best MeSH terms
for each element
4. For those MeSH terms use at least the entry terms as free text
searches and paste them in Word
5. Use one of the field names [mh] and [tiab] ([pa] [nm] [pt] [sh])
for all synonyms of all elements, use parenthesis and OR to
combine synonyms into elements, and combine all elements
with AND
6. Only after you translated all important elements this way, open
the PubMed database and search for articles
7. Optimize your search until you are satisfied (use the roadmap)
 If you really want to be exhaustive do the workshop on multiple
databases

Systematic Literature Retrieval in PubMed

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