systematic literature retrieval in pubmed

Workshop

Systematic Literature Retrieval in PubMed

Tuesday 11 April 2023

Wichor Bramer | Gerdien de Jonge

Information specialists Medical Library (Cf-232)

[email protected] | www.erasmusmc.nl/medbib

phone: 010-70 43785

@wichor | slideshare.net/wichor | nl.linkedin.com/in/wichor

Medische Bibliotheek Erasmus MC 2

Today’s scopeWhat 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


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!

Medische Bibliotheek Erasmus MC

PubMed (Medline)

Embase

Medline (OvidSP)

Cochrane Central

Scopus or Web-of-Science

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)

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What databases do we use?

SLR in PubMed (today)

SLR in other databases (next week)

Systematic Literature Retrieval uses at least these databases


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?

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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?

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Homework : results & feedback

We’d like to teach you better ways to get to better results

Systematic Literature Retrieval

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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 -


Homework : best practice

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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

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You Me Only I found Only you found

Relevant

Eva M 524 42 36 (86%) 518 (99%) 0/1Eva B 363 952 912 (96%) 322 (89%)

Geriolda 2431

Karen / Yannan

1709 296 257 (87%) 1670 (98%) 0/2

Mateus 1413 2930 1658 (57%) 141 (10%) 6/6Myrte 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


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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

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What is Systematic Literature Retrieval ?

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?

Sensitive search Specific searchGoal Finding as much relevant

articles as posible

Most of the found

articles are relevant

# of hits High Much lower

# of relevant

articles missed

Low Much higher


How to search systematically?

1. What is your research question?

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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



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

2. What elements (key concepts) does the question contain?

- are they specific or general and important or less important?

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Elements in your research question

Broccoli Prevention Cancer

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

• 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

meconium AND neonates

But sometimes less evident: a certain therapy only used in a specific disease:

Lichtenstein therapy AND inguinal hernias


Elements : on a gliding scale

generalspecific

important

unimportant

broccoli cancer

prevention

broccoli cancer prevention


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

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generalspecific

important

unimportant

Rianne : Relationship between falls and functional status in hospitalized adults

falls Functional status

hospitalization

adults


generalspecific

important

unimportant

burden

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

hospitalization

elderly

Informal care


generalspecific

important

unimportant

Methodologies

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

Health inequalities

Evaluation studies

Population-level policy

Intervention




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

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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 dropped by adding it can indeed be missed.

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)

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

Preferred standard filters to use

Subsets (aids, bioethics, cancer)

Sensitive Clinical Queries (therapy,

diagnosis, etiology etc)

Rather do not use

Limits in the left side of the PubMed

result screen (humans, children, RCTs)

Specific clinical queries


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).

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Practicum : feedbackGeriolda and Mateus:

Cardiovascular diseases / risk

Cardiovascular Diseases[mh]

Cardiovascular

Cardiac

Heart[mh]

Vascular

Blood Vessels[mh]

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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

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Boolean operators

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)

broccoli OR

brassica

broccoli AND

cancer

#2NOT

#1


TruncationWord 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

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5. Use the syntax of the chosen database

[tw] [tiab] [mesh]

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Practically Concurrent!

Interactive Demo : Red Blood Cells


Automatic Term Mapping

Based on Entry Terms query is

translated to [MeSH]

Combined with mesh term and

exact search words in [All Fields]

Field Names

Manually describe fields in which

words should be present between

quare brackets

Translation to MeSH sometime incorrect

Use of [All Fields] undesirable

No truncation

Query details much longer than

necessary

Exact translation to the desired MeSH term

Combined with exact phrasing in title and

abstract

Specific MeSH terms exploded or ignored

Truncation possible

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 namesKeywords:

[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

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Keyword

Seach for a specific concept

Independent of the autor's choice of

words

Search for related terms using the

explode function

Free text

All records contain text, but not all contain

MeSH terms (recent ones)

Are the additions correct?

Concepts not covered by mesh terms, or

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])

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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)

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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

b. Use (phrase) truncation to reduce the number of synonyms necessary

mentioned

c. 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?

d. Add parentheses around elements to group synonyms

e. Use boolean operators AND between elements and OR between synonyms

in an element (don’t use NOT)

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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

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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 mistakesGo 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 wrongcheck 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 resultsAlways:

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.


Elements : optimization

generalspecific

important

unimportant

broccoli cancer

prevention

cruciferous vegetables cancer subset in PubMed

Number of hits:

295

Number of hits:

797 (+170%)

Number of hits:

1236 (+55%)

Number of hits:

4091 (+231%)

Filter:

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

Number of hits:

1913 (-53%)


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?

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How to search systematically?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)

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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

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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.

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10987654321


What is the PMID?

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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.

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What is the PMID?

Fortes 1018 : 18621803

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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.

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What is the PMID?

jones 25 : 6492 hits

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What else could we pick easily?





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Try this!





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What is the PMID?

jones 25 2012 : 712 hits

But:

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

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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

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Disadvantages of PubMed 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


SummarizedSummarized 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

Education