EMBASE WORKSHOP - KCGG · INDEXING IN EMBASE Indexing in Embase = linkage with as many terms as...

EMBASE WORKSHOP:

COMPARISON WITH PUBMED AND SEARCH STRATEGY

Nele Pauwels (Information Specialist Knowledge Centre for Health Ghent)

VAKGROEP GE55 – KENNISCENTRUM VOOR DE GEZONDHEIDSZORG GENT

CONTENT

Access to Embase

Quick search in Embase

Searching in Embase: what can go wrong?

Embase vs. PubMed

Coverage

Why searching in both databases?

Indexing in Embase

Searching in Embase

How to increase specificity?

How to increase comprehension?

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ACCESS TO EMBASE

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EMBASE.COM

Accessible via the UGent /

UZ Ghent network

Outside UGhent / UZ Ghent:

via Athena

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TRAINING AND SUPPORT ON WWW.KCGG.BE

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QUICK SEARCH IN EMBASE

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Suggested Emtree term

Autocomplete

=> emtree en free text

Evaluate the ‘translation’ of your search query

Index term is not shown (compared with PubMed) in translation (i.e. ‘heart infarction’ is Emtree term, not ‘heart attack’)

SEARCHING IN EMBASE: WHAT CAN GO WRONG?

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EXAMPLE

Search query: aids

Translation: aids/exp OR aids

Results also contain records about visual aids, navigational aids, diabetes aids, aids for people with

disabilities

EXAMPLE

Search query: Parkinson

Translation: parkinson

Results also contain records published by an author named Parkinson

EXAMPLE

Search query: ‘chronic disease’ AND ‘quality of life’

Translation: ('chronic disease'/exp OR 'chronic disease') AND ('quality of life'/exp OR 'quality of life')

Results also contain records published by an author affiliated to an institute containing ‘chronic

disease’ (e.g. Centre for chronic disease prevention and health promotion)

WORKSHOP: 1.1-1.2

EMBASE VERSUS PUBMED

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EMBASE VERSUS PUBMED

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PubMed Embase

Owner National Library of Medicine (US) ELSEVIER (publisher)

Content Scientific articles; articles in press; e-books Scientific articles; conference proceedings (from 2009 onwards); articles in press

Assets - Free access to abstracts (for everybody)- MeSH terms are assigned based on the full text (on 2

levels)

- Contains more European and Pharmacological records- Indexing: fast an on 3 levels- Focus on drugs and devices

Minor points - American focus- Assigning MeSH terms takes time (everage 6 months)

Free access to full text? PubMed Central (PMC, a database integrated in PubMed) Yes

Unique records (compared to other biomedical databases)?

Yes Yes

Indexering/Thesaurus MeSH – updated annually Emtree – larger vocabulary and updated 3 times/year

Filter options Yes (but have limitations!) Before and during your screaning

Export to Reference Manager Software (e.g. EndNote)

Yes Yes

E-mail alerting/RSS Feed Yes Yes

Tools to find relevant search terms External: GoPubMed ; PubReMiner ; MeSHonDemand Internal: PICO search builder

COVERAGE AND FOCUS OF EMBASE

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WHY SEARCHING IN EMBASE AND PUBMED

Indexing is unique

Unique records

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Via PubMed.gov

Via embase.com

Embase MEDLINEPubMed

(not indexed)

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POSSIBILITY TO VIEW UNIQUE EMBASE CONTENT

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INDEXING IN EMBASE

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INDEXING IN EMBASEIndexing in Embase = linkage with as many terms as required to describe the content, with a special focus on drugs, devices and diseases

Manual indexing Full texts Performed by biomedical experts Based on full text Takes on average 5 days

Automatic indexing Conference proceedings (permanent), articles in press, articles in process (temporary) Immediate

=> Find relevant articles, no matter where a term is mentioned and what term is used

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Furolin

2 results

Furadantin

533 results

Ivadantin

3 results

Furolin

INDEXERING IN PUBMED

Publication

National Library of Medicine (NLM)

Indexing- MeSH / Major Topic- Subheadings

Elsevier (Publisher)

Indexing- MeSH / Major Topic- Subheadings- Triple linkage

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Yellow highlight: exact terms (Emtree / free tekst) from your queryGreen highlight: child terms of the Emtree terms from your query

WORKSHOP: 2.1-2.5

SEARCHING IN EMBASE

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SPECIFICITY VS. COMPREHENSION

EXAMPLE SEARCH STRATEGY Research question: is exercise therapy effective to treat osteoarthritis of the hip?

Search strategy:

‘hip osteoarthritis’/exp OR ((arthritis/de OR osteoarthritis/de) AND (hip/de OR ‘hip pain’/exp)) OR (((‘hip’ OR ‘cox’)

NEAR/2 (arthros* OR arthrit* OR artheros* OR osteoarthr*)) OR coxarth* OR ‘malum coxae senilis’):ti,ab,kw

AND

‘kinesiotherapy’/exp OR exercise/exp OR physiotherapy/exp OR ‘conservative treatment’/de 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 OR exercise) NEAR/5 (technique* OR therap* OR treat* OR isokinet* OR isomet* OR

management*)) OR kinesitherap* OR kinesiotherapy* OR gymnastic* OR ((muscle* OR muscul*) NEAR/3

train*)):ti,ab,kw

Index terms = Emtree terms

Free text words (in title, abstract and author keywords)

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PICO & PV (Pharmacovigilance) wizard:Increase comprehension

Drug, Disease en Device search: increase specificity

Article search & Authors search ≈ Single Citation Matcher in PubMed

SUBHEADING

Seabheadings are Emtree terms that are also used as concept qualifiers for drugs, diseases and

devices to refine their meaning, providing a very precise idea of what an article covers

Comprehension ↑ Specificity ↑

Start

WORKSHOP: 3.1-3.3

SEARCH STRATEGY IN EMBASE

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EXAMPLE 1Information about drug toxicity e.g. incidence of nephrotoxicity when using cisplatin

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Similar records: max 100 records, based on the number of common major terms (at least two).

Index miner: tool to identify possible relevant index terms for further searching

SEARCH TIPS AND OPERATORS IN PUBMEDPubMed Embase

Boolean operators

AND, OR and NOT (AND is the default setting)Example: hip AND (arthrosis OR arthritis)

Attitional tip: use round brackes to separate between different operators e.g. (xxx OR xxxx OR xx) AND xxxx

Truncation operators

* multiple characters will be automatically added at the end of a wordExample: Heart attack*

Pay attention: this operator can not be used in combination with dubble quotation marksPay attention: when > 600 combinations => PubMed will limit to the first 600 combinations (check Search details)

? (1 variable character); Example: behavio?r

* (multiple characters, at the end or in a search term)Example: Heart attack* ; sul*ur (retrieves sulfur and sulphur)

Proximity opertors

- NEXT/n (This requests terms which are within ‘n’ words of each other, in the order specified.)Example: Hip NEXT/3 prosthesis => “rheumatoid arthritis, joint surgery, hip or knee prosthesis”

NEAR/n (This requests terms which are within ‘n’ words of each other, in either direction.) Example: Cardiac NEAR/5 catheter => “patients undergoing catheterablation for cardiac arrhythmias”

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SEARCH TIPS AND OPERATORS IN PUBMEDPubMed Embase

To search for a particular combination of therms (Phrase searching)

Dubble quotation marksExample: “heart failure”!!!: Automatic Term Mapping is desactivated (= MeSH terms will not be automatically added. The ‘phrase’ will be searched in All Fields)

Or

Add field code such as [TIAB]

Single or double quotation marksExample: ‘heart failure’

Search in tite, abstract and author keywords

[TIAB]Example: “heart failure”[TIAB]

:ti,ab,kwExample: 'heart failure':ti,ab,kw

Search in the list of index terms

[Mesh]: Child terms will be included[Mesh:NoExp]: Child terms will not be includedExample: "Heart Failure"[MeSH]

/exp: Child terms will be included/de: Child terms will not be includedExample: ‘heart failure’/exp

Combinations of operators and field codes

Example: symptom*[TIAB] AND (headache*[TIAB] OR head ache*[TIAB]) Example: (symptom* NEAR/5 (headache* OR ‘head ache*’)):ti,ab,kw

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INCREASE SPECIFICITY OF YOUR SEARCH

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Limit your field to title and abstract for searching free text

words

Add limits (e.g. species, age groups, gender, article

language, date of publication, etc.)

Do not include child terms of an Emtree term (syntax ‘/de’)

Emtree term: major focus

Use subheadings

Use Triple linking (applicable for the key subheadings)

Ind

exin

g

Concept Key subheading

Drug Adverse drug reaction

Drug Drug combination

Drug Drug comparison

Drug Drug interaction

Drug Drug therapy

Device Adverse device effect

Device Device comparison

Disease Drug therapy

Disease Side effect

TRIPLE LINKING

Triple linkage is three level indexing of the full text of an article.

It consists of: ‒ Term (drug or device or disease) ‒ Key subheading (relationship) ‒ Linked terms

(drug or disease)

Has started for drugs in 2007, for diseases in 2009 and for devices in 2014

Syntax: 'cisplatin'/'adverse drug reaction'/‘nephrotoxicity‘

Records about the nephrotoxicity as adverse drug reaction of the drug cisplatin

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Cisplatin Adverse drug reaction Nephrotoxicity

TRIPLE LINKING: EXAMPLE

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WORKSHOP: 4.1-4.4

INCREASE COMPREHENSION OF YOUR SEARCH

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Include child terms of Emtree term (syntax /exp)

Add synonym(s) including subject terminology, singular/plural, used as noun/adjective and verb

conjugations, spelling variations (British and American spelling), Latin names, acronym(s), etc.

Use the PICO Wizard

WORKSHOP: 5.1-6.2

Nele PauwelsInformation Specialist

GE55 – KNOWLEDGE CENTRE FOR HEALTH GHENT (KCGG)

CAMPUS UZ GHENT - K3 GROUND FLOOR (ENTRANCE 42)

E nele.pauwels@ugent.be

T +32 9 332 24 43

www.kcgg.ugent.be/en

KCGG.UGent

@kcgg2

Ghent University