Post on 27-Jun-2020
PUBMED: BASIC AND ADVANCED SEARCHING
Nele Pauwels - Information specialist KCGG - nele.pauwels@ugent.be – 09/332.24.43
AIMS
PubMed: workshop basic and advanced searching
1. How does PubMed translates your search terms?
2. What is the difference between PubMed and MEDLINE?
3. MeSH terms: what are they, where can I find them, how and when can I use them?
4. How can I have ensure that I get more focused results?
5. How can I prepare a search strategy for a systematic review?
EXAMPLES
Research question: is physiotherapy
effective in the treatment of
osteoarthritis of the hip?
Search terms: osteoarthritis
PubMed translation:
"osteoarthritis"[MeSH Terms] OR
"osteoarthritis"[All Fields]
[MeSH Terms]
[All Fields]
EXAMPLES
Research question: is physiotherapy effective in the treatment of osteoarthritis of the hip?
Search terms: physiotherapy osteoarthritis
PubMed translation: ("osteoarthritis"[MeSHTerms] OR "osteoarthritis"[All Fields]) AND ("physical therapy modalities"[MeSH Terms] OR ("physical"[All Fields] AND "therapy"[All Fields] AND "modalities"[All Fields]) OR "physical therapy modalities"[All Fields] OR "physiotherapy"[All Fields])
[MeSH Terms]
[All Fields]
EXAMPLES
Research question: is physiotherapy effective in the treatment of osteoarthritis of the hip?
Search terms: physiotherapy osteoarthritis hip
PubMed translation: ("osteoarthritis"[MeSH Terms] OR "osteoarthritis"[All Fields]) AND ("physical therapy modalities"[MeSH Terms] OR ("physical"[All Fields] AND "therapy"[All Fields] AND "modalities"[All Fields]) OR "physical therapy modalities"[All Fields] OR "physiotherapy"[All Fields]) AND ("osteoarthritis, hip"[MeSH Terms] OR ("osteoarthritis"[All Fields] AND "hip"[All Fields]) OR "hip osteoarthritis"[All Fields] OR ("osteoarthritis"[All Fields] AND "hip"[All Fields]) OR "osteoarthritis hip"[All Fields])
[MeSH Terms]
[All Fields]
EXAMPLES
Search term: DCD
(referring to Developmental Coordination
Disorder)
PubMed translation:
"dicarboxydine"[Supplementary Concept] OR
"dicarboxydine"[All Fields] OR "dcd"[All Fields]
EXAMPLES
Search term: elderly
PubMed translation: "aged"[MeSH Terms] OR "aged"[All Fields] OR "elderly"[All Fields]
=> Results includes references with the description ‘xxx aged xxx years’
EXAMPLES
Search terms: self harm PubMed translation (± a year ago):
"dicarboxydine"[Supplementary Concept] OR "dicarboxydine"[All Fields] OR "dcd"[All Fields]
Current PubMed translation: "self-injurious behavior"[MeSHTerms] OR ("self-injurious"[All Fields] AND "behavior"[All Fields]) OR "self-injurious behavior"[All Fields] OR ("self"[All Fields] AND "harm"[All Fields]) OR "self harm"[All Fields]
EXAMPLES
Search terms: prophylactic intervention
PubMed translation: ("condoms"[MeSH Terms] OR "condoms"[All Fields] OR "prophylactic"[All
Fields]) AND ("methods"[MeSH Terms] OR "methods"[All Fields] OR "intervention"[All Fields])
EXAMPLES
Search term: AIDS
PubMed translation: "acquired immunodeficiency syndrome"[MeSH Terms] OR ("acquired"[All Fields]
AND "immunodeficiency"[All Fields] AND "syndrome"[All Fields]) OR "acquired immunodeficiency
syndrome"[All Fields] OR "aids"[All Fields]
=> Results include for example ‘handicapped aids’, ‘visual aids’ and ‘diabetes aids’
EXAMPLES
Search terms: Hypotension blood donation
PubMed translation: ("hypotension"[MeSH Terms] OR "hypotension"[All Fields]) AND ("blood
donors"[MeSH Terms] OR ("blood"[All Fields] AND "donors"[All Fields]) OR "blood donors"[All Fields]
OR ("blood"[All Fields] AND "donation"[All Fields]) OR "blood donation"[All Fields])
=> Results includes references describing ‘blood pressure’ and ‘liver donors’
EXAMPLES
Search term: Parkinson
Vertaling PubMed: parkinson[All Fields]
=> Results including Parkinson as author
EXAMPLES
Search terms: measurement instruments
PubMed translation: ("Measurement
(Lond)"[Journal] OR "measurement"[All Fields]
OR "Measurement ( Mahwah N J)"[Journal] OR
"measurement"[All Fields]) AND
("instrumentation"[Subheading] OR
"instrumentation"[All Fields] OR
"instruments"[All Fields])
APPROACH FOR STANDARD SEARCHES (≠ SYSTEMATIC REVIEW)
Enter Search term(s) in PubMed
Evaluate translated search strategy via Search Details (cf. Automatic Term Mapping)
Start screening / reading the results Correct the search strategy Fine-tune your search strategy
BOOLEAN OPERATORS: AND, OR, NOT / AND NOT
Boolean operators depend on the database
Examples
hip AND arthritis: this search would only retrieve results including both
the words hip and arthritis
osteoarthritis OR osteoarthrosis: this search would retrieve results with
osteoarthritis, with osteoarthrosis acid and with both terms
osteoarthritis NOT knee: this search would retrieve results with
osteoarthritis, and exclude those with knee
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WORKSHOP (1.1 – 1.4)
CONTENT
1. What is PubMed?
2. Access to PubMed (cf. SFX)
3. Indexing
4. Interesting functionalities in PubMed
5. Optimization of your search strategy (cf. sensitivity and specificity)
6. FAQs
Export to EndNote
myNCBI
1. WHAT IS PUBMED?
WHAT IS PUBMED?
PubMed = Public Access to MEDLINE
Content:
‘Indexed for MEDLINE’
‘PubMed - in process’: waiting to be indexed with MeSH-termen (MeSH = Medical Subject Heading)
‘PubMed - as supplied by publisher’: no indexing
Via PubMed.gov
MEDLINEPubMed (not
[yet] indexed for MEDLINE
Search via MeSH terms and free text words
PubMed
Owner National Library of Medicine (US)
Content Scientific articles; articles in press; e-books
Assets - Free access to abstracts (for everybody)- MeSH terms are assigned based on the full text (on 2 levels)
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)
Unique records (compared to other biomedical databases)? Yes
Indexering/Thesaurus MeSH – updated annually
Filter options Yes (but have limitations!)
Export to Reference Manager Software (e.g. EndNote) Yes
E-mail alerting/RSS Feed Yes
Tools to find relevant search terms External: GoPubMed ; PubReMiner ; MeSHonDemand
See FAQs
2. ACCESS TO PUBMED
ACCESS TO PUBMEDUGhent / UZ Ghent netwerk AND access via
www.kcgg.be or via lib.ugent.be
=> SFX button full tekst availability via Ghent
University
Access PubMed directly: https://www.ncbi.nlm.nih.gov/pubmed
Access PubMed via the KCGG website: https://www.ncbi.nlm.nih.gov/pubmed?otool=ibeuglib
ACCESS TO PUBMEDUGhent / UZ Ghent netwerk AND access via
www.kcgg.be or via lib.ugent.be
=> SFX button full tekst availability via Ghent
University
3. INDEXING
INDEXERING IN PUBMED
Publication
National Library of Medicine
Indexing- MeSH / Major Topic- Subheadings
INDEXING:EXAMPLE
* = MeSH Major TopicMeshterm/subheading
VOORBEELD MESH TERM EN SUBHEADINGS
MeSH term
Subheadings
Exclude Child Terms -> Specificity ↑
Restrict to Major Topic -> Specificity ↑
Synonyms -> Sensitivity ↑
Nitrofurantoin was added as MeSH term to this article But this term was not mentioned in the abstract
Without including the MeSH term, you would not have found the article...
Nitrofurantoin was neither added as MeSH term (althought the article has been indexed yet), neither mentioned as such in the abstract. The synonym ‘furadantin’ was mentioned in the abstract.
Without including synonyms, you would not have found the article...
WORKSHOP (2.1 – 2.4)
Based on predefined search filters e.g. to search for certain publication types (e.g. systematic reviews) or topics (e.g. AIDS).
Evaluate the Search Details when using thePubMed filters!
WORKSHOP (3.1 – 3.4)
5. OPTIMIZE YOUR SEARCH STRATEGY
SEARCH TIPS AND OPERATORS IN PUBMED
PubMedBoolean operators AND, OR and NOT (AND is the default setting)
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 word e.g. 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)
Proximity opertors -
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]
Search in tite, abstract and author keywords
[TIAB]
Search in the list of MeSH terms [Mesh]: Child terms will be included[Mesh:NoExp]: Child terms will not be included in the search
38
WORKSHOP (4.1 – 4.4)
SPECIFICITY VS. SENSITIVITY
SPECIFICITY OF YOUR SEARCH STRATEGY ↑
Use MeSH Major Topic (syntax [Majr])
Use subheadings
Restrict to MeSH term itself [parent term], without including the ‘child terms’
Add topic-specfic search blocks via the PubMed homepagina
Apply filters
E.g. article type
E.g. species, age groups, gender
E.g. date of publication (see ‘Results by Year’)
Via the MeSH database
By using the filter options on the left side of the results page(be carefull – see next slide !)
SEARCH FILTERS IN PUBMED: REASONS TO BE CRITICAL / CAREFULL
Article type e.g. Clinical trial => AND clinicaltrial[ptyp] But, a lot of publications don’t have a publication type assigned But, no consistency (e.g. Multicentre study)
Species e.g. Human => AND humans[MeSH] But, not all articles have been indexed (yet) It is better to use: NOT (animals[MeSH] NOT humans[MeSH])
Ages e.g. Birth – 18 years => AND ("infant"[MeSH Terms] OR "child"[MeSH Terms] OR "adolescent"[MeSH Terms])) But, not all articles have been indexed (yet) or a such (e.g. pediatric, boy, toddler, etc.) It is better to use a validated search filter for ‘Children’
Gender e.g. Female => AND female[MeSH] But, not all articles have been indexed (yet)
SENSITIVITY OF YOUR SEARCH STRATEGY ↑
Use MeSH term (syntax [MeSH]) instead of MeSH Major Topic
Do not use subheadings (unless as floating subheading e.g. rehabilitaton[subheading])
Included the MeSH term(s) as free textword(s) into your search strategy
Add synonyms as free text words into your search strategy
Source of inspiration in PubMed: Entry terms
External sources of inspriation who use PubMed content: GoPubMed ; PubReMiner ;
MeSHonDemand
Additional external source: synonymes and PICO search module in Embase
WORKSHOP (5.1 – 5.2)
6. FREQUENTLY ASKED QUESTIONS
IMPORT REFERENCES INTO ENDNOTE ≤ 200 references: Send to > Citation Manager
> 200 references
‒ Send to > File: select MEDLINE as format. A txt-file will be generated.
‒ In EndNote: Via Import > Select the txt-file and select
‒ ‘PubMed (NLM)’ as Import Option
46
MYNCBI & E-MAIL ALERT
To save searches
To save search strategies
To personalise home page (e.g. highlight your search terms in the results)
To receive an e-mail alert with new results - based on your search string - are available
=> Login required (free)
myNCBI
Best Match = sort by option
Results based on frequency count of search terms
MeSH terms are not taken into account
Number of results may change !
Intended goal: to screen the 1st resultspage
TAKE HOME MESSAGES
APPROACH FOR STANDARD SEARCHES
Search term(s) in PubMed
Evaluate translated search strategy via Search Details (cf. Automated Term Mapping)
Start screening / reading the results Correct the search strategy Fine-tune your search strategy
Take home message
Search for appropriate MeSH terms Select relevant fields codes (e.g. [TIAB]) for appropriate free text words
Add syntax (e.g. double quotation marks)
ONLINE SUPPORT
Information sheets of KCGG
Link to Tutorial provided by the supplier
Courseshttp://www.kcgg.ugent.be/events/
KCGG.UGent
@kcgg2
Ghent University
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