EMBASE WORKSHOP - KCGG · INDEXING IN EMBASE Indexing in Embase = linkage with as many terms as...
Transcript of 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)
T +32 9 332 24 43
www.kcgg.ugent.be/en
KCGG.UGent
@kcgg2
Ghent University